Comprehensive molecular diagnosis of 179 Leber congenital amaurosis and juvenile retinitis pigmentosa patients by targeted next generation sequencing

Downloaded from jmg.bmj.com on November 2, 2013 - Published by group.bmj.com

Comprehensive molecular diagnosis of 179 Leber congenital amaurosis and juvenile retinitis pigmentosa patients by targeted next generation sequencing Xia Wang, Hui Wang, Vincent Sun, et al. J Med Genet 2013 50: 674-688 originally published online July 11, 2013

doi: 10.1136/jmedgenet-2013-101558

Updated information and services can be found at: http://jmg.bmj.com/content/50/10/674.full.html

These include:

Data Supplement

"Supplementary Data" http://jmg.bmj.com/content/suppl/2013/07/10/jmedgenet-2013-101558.DC1.html

References

This article cites 94 articles, 26 of which can be accessed free at: http://jmg.bmj.com/content/50/10/674.full.html#ref-list-1

Email alerting service

Topic Collections

Receive free email alerts when new articles cite this article. Sign up in the box at the top right corner of the online article.

Articles on similar topics can be found in the following collections Editor's choice (79 articles) Eye Diseases (270 articles) Clinical diagnostic tests (328 articles) Hereditary eye disease (87 articles) Molecular genetics (1135 articles) Genetic screening / counselling (766 articles)

Notes

To request permissions go to: http://group.bmj.com/group/rights-licensing/permissions

To order reprints go to: http://journals.bmj.com/cgi/reprintform

To subscribe to BMJ go to: http://group.bmj.com/subscribe/

Downloaded from jmg.bmj.com on November 2, 2013 - Published by group.bmj.com

Genotype-phenotype correlations

ORIGINAL ARTICLE

Editor’s choice Scan to access more free content

Comprehensive molecular diagnosis of 179 Leber congenital amaurosis and juvenile retinitis pigmentosa patients by targeted next generation sequencing Xia Wang,1,2 Hui Wang,1,2 Vincent Sun,3 Han-Fang Tuan,1 Vafa Keser,3 Keqing Wang,2 Huanan Ren,3 Irma Lopez,3 Jacques E Zaneveld,1,2 Sorath Siddiqui,3 Stephanie Bowles,1 Ayesha Khan,3 Jason Salvo,1,4 Samuel G Jacobson,5 Alessandro Iannaccone,6 Feng Wang,1,2 David Birch,7 John R Heckenlively,8 Gerald A Fishman,9 Elias I Traboulsi,10 Yumei Li,1,2 Dianna Wheaton,7 Robert K Koenekoop,3 Rui Chen1,2,4,11

For numbered affiliations see end of article. Correspondence to Dr Rui Chen, Human Genome Sequencing Center, One Baylor Plaza, Houston, Texas, US, 77054, [email protected] Dr Robert K Koenekoop, McGill Ocular Genetics Laboratory, Montreal Children’s Hospital, McGill University Health Centre, 2300 Tupper, Montreal, Quebec H3H 1P3 Canada, [email protected] XW and HW contributed equally to this study. Received 28 January 2013 Revised 20 May 2013 Accepted 13 June 2013 Published Online First 11 July 2013

ABSTRACT Background Leber congenital amaurosis (LCA) and juvenile retinitis pigmentosa (RP) are inherited retinal diseases that cause early onset severe visual impairment. An accurate molecular diagnosis can refine the clinical diagnosis and allow gene specific treatments. Methods We developed a capture panel that enriches the exonic DNA of 163 known retinal disease genes. Using this panel, we performed targeted next generation sequencing (NGS) for a large cohort of 179 unrelated and prescreened patients with the clinical diagnosis of LCA or juvenile RP. Systematic NGS data analysis, Sanger sequencing validation, and segregation analysis were utilised to identify the pathogenic mutations. Patients were revisited to examine the potential phenotypic ambiguity at the time of initial diagnosis. Results Pathogenic mutations for 72 patients (40%) were identified, including 45 novel mutations. Of these 72 patients, 58 carried mutations in known LCA or juvenile RP genes and exhibited corresponding phenotypes, while 14 carried mutations in retinal disease genes that were not consistent with their initial clinical diagnosis. We revisited patients in the latter case and found that homozygous mutations in PRPH2 can cause LCA/juvenile RP. Guided by the molecular diagnosis, we reclassified the clinical diagnosis in two patients. Conclusions We have identified a novel gene and a large number of novel mutations that are associated with LCA/juvenile RP. Our results highlight the importance of molecular diagnosis as an integral part of clinical diagnosis.

INTRODUCTION

To cite: Wang X, Wang H, Sun V, et al. J Med Genet 2013;50:674–688. 674

Leber congenital amaurosis (LCA) refers to a group of inherited retinal dystrophies that share the common feature of severe visual impairment within the first year of life. Clinically, LCA is defined by congenital blindness, congenital nystagmus, and lack of detectable signals on an electroretinogram (ERG).1 2 LCA affects 1 in every 50 000 individuals, but it accounts for 5% of all retinal dystrophies and 20% of blindness in school age

children.3 4 To date, mutations in 19 genes are reported to cause LCA.5–12 Despite the breadth of current knowledge, genetic defects in about 30% of LCA cases remain unknown.11 The clinical phenotypes and genetic causes of LCA and juvenile retinitis pigmentosa (RP) largely overlap. Both diseases belong to a spectrum of retinal diseases termed early onset retinal dystrophies (EORD). In fact, LCA was initially considered to be a congenital form of RP.2 Compared with LCA, juvenile RP tends to have milder phenotypes and a later onset. Juvenile RP patients appear to have better visual function at birth than those with LCA, and later develop night blindness, narrowed visual fields, and eventually severe vision impairment. Mutations in several known LCA genes, such as CRB1 and RDH12, are reported to cause juvenile RP.13 Interestingly, mutations in other retinal disease genes, such as IQCB1 and KCNJ13, are also known to be associated with LCA or ‘LCA-like’ phenotypes.10 11 These observations may be explained by a combination of allelic differences, genetic background, and environmental modifications. Also, it has been demonstrated that the clinical phenotypes of many retinal diseases overlap with that of LCA.11 It is likely that in some cases visual impairment is the most obvious phenotype in the initial evaluation, and that other syndromic features appear at a later time. Therefore, given the limited evaluation possible in infants and in early childhood, some patients initially diagnosed with LCA may actually have a different retinal disorder, such as Alström syndrome or Joubert syndrome.11 Despite these observations, systematic screening for mutations in all known retinal disease genes on a large LCA patient cohort has not yet been reported. Because of the genetic heterogeneity of LCA and other retinal diseases, an accurate molecular diagnosis can improve the clinical diagnosis, facilitate a more accurate description of prognosis, and allow gene specific treatment. One of the most common methods for molecular diagnosis of LCA is the

Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

Genotype-phenotype correlations Arrayed Primer Extension (APEX) chip (Asper Ophthalmics). It is a microarray based genotyping method that tests a subset of known mutations in known LCA genes, leading to molecular diagnosis in approximately 17–32% of LCA patients.14–16 With additional mutations added to the LCA APEX array, the estimated solving rate has been improved to about 50%.11 On the other hand, next generation sequencing (NGS) has been recently used for the molecular diagnosis of retinal diseases.17 18 Compared with the APEX chip, the NGS based approach is able to discover novel variants and genes. Recently, Coppieters and others described a workflow to screen the exons of known LCA genes, using amplicon PCR followed by NGS.19 However, this workflow was tested on a relatively small LCA patient cohort and did not cover other retinal disease genes. The goal of this study was to develop a comprehensive molecular diagnostic method for LCA and potentially for other retinal diseases. For this purpose, we developed a targeted NGS method that allows us to systematically screen the exons of most known retinal disease genes at low cost (163 genes at the time of design, online supplementary files 1 and 2). We first evaluated this method on a standard control sample, and then applied it to the molecular diagnosis of a large cohort of unrelated and prescreened patients with the clinical diagnosis of either LCA or juvenile RP (n=179). Pathogenic mutations for 72 patients were identified by systematic NGS data analysis, Sanger sequencing validation, and segregation analysis. These 72 patients were classified into different confidence groups based on the clinical significance of their mutations. Among the 72 patients, 58 carried mutations in known LCA or juvenile RP genes and exhibited corresponding phenotypes, while 14 carried mutations in retinal disease genes that were not consistent with their initial clinical diagnosis. Guided by the molecular diagnosis, we revisited 12 out of the 14 patients. We found that homozygous mutations in PRPH2 can cause LCA/juvenile RP. We also reclassified or refined the initial clinical diagnosis for 10 patients.

METHODS Study subjects We initially collected a cohort of 389 patients from around the world and with a variety of backgrounds. Using a combination of LCA APEX array, Sanger sequencing, homozygosity mapping, and phenotype directed genotyping methods (eg, preserved para-arteriolar retinal pigment epithelium in an LCA patient is associated with mutations in CRB1), we had previously identified the genetic causes for 210 patients (most of whom are LCA patients).13 20 The remaining 179 patients were included in this study. The available prescreening information for the 179 patients is listed in online supplementary table S5. The 179 patients were seen at McGill University (RKK), University of Pennsylvania (SGJ), The Lighthouse of Chicago (GAF), University of Tennessee Health Science Center (AI), and University of Michigan ( JRH), by ophthalmologists with expertise in retinal dystrophies. Informed consents and research protocols were approved by the respective institutional review boards or research ethics board and adhered to the tenets of the Declaration of Helsinki. Complete histories, pedigree analysis, and ophthalmic examinations were performed. Eye exams consisted of cycloplegic refractions, fixation testing, Snellen visual acuities (when possible), pupillary responses, slit lamp exams, dilated fundus exam by indirect ophthalmoscopy, retinal photography, and Goldmann visual field testing (when possible). In most cases, ERGs were done according to ISCEV (International Society for Clinical Electrophysiology of Vision) standards. LCA is defined by the phenotypes mentioned in the introduction and Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

the absence of overt systemic features. Juvenile RP represents a milder disease with later onset of signs and symptoms. In juvenile RP patients, vision can appear normal at birth, and the first symptom is progressive night blindness, with progressive visual loss at around age 2 years, with or without nystagmus. DNA was extracted from whole blood using the FlexiGene kit or the QIAamp DNA blood kit according to the manufacturer’s protocol. The quantity and quality of DNA were verified by using NanoDrop.

Target DNA capture and NGS experiments According to the manufacturer’s protocol, Illumina paired-end libraries were generated. Briefly, ∼1 mg of genomic DNA was sheared into fragments of approximately 300–500 bp. The DNA fragments were end-repaired and an extra ‘adenine’ base was added to the 30 end. Illumina Y-shape index adapters were ligated to the ends of the DNA fragments and eight cycles of PCR amplification were applied to each sample after ligation. The DNA libraries were quantified by the PicoGreen assay (Invitrogen). For each capture reaction, 24 to 48 libraries (3 mg of DNA in total) were pooled together. A design file (see online supplementary files 1 and 2) was submitted to Nimblegen for the design of the capture probe. NimbleGen SeqCap EZ Hybridisation and Wash Kits were used for the washing and recovery of captured DNA. Captured libraries were quantified and sequenced on the Illumina HiSeq 2000 as 100 bp paired-end reads, following the manufacturer’s protocols. Illumina sequencing was performed at the BCM-FGI core.

Evaluation of our method’s sensitivity to detect SNPs on the Hapmap sample Single nucleotide polymorphisms (SNPs) genotyping data of HapMap sample NA11831 were downloaded from 1000 Genome omni database (ftp://ftp-trace.ncbi.nih.gov/ 1000genomes/ftp/technical/working/20110527_bi_omni_1525_ v2_genotypes/). This sample had been genotyped using the Illumina OMNI2.5 SNP genotyping array. A total of 1190 genotyped single nucleotide polymorphisms (SNPs) in this sample are within our design region, including 919 homozygous reference SNPs, 107 homozygous alternative SNPs, and 164 heterozygous alternative SNPs. A total of 1184 SNPs were detected by our targeted NGS method. Among the detected SNPs, 1183 out of 1184 had the same genotype between the SNP array and NGS. The single disconcordant SNP rs3763073 was heterozygous C/T on the SNP array but homozygous C/C in targeted NGS. To resolve the conflict, we performed direct Sanger sequencing and confirmed that rs3763073 was indeed homozygous for the reference C, indicating that NGS detected the SNP correctly (data not shown).

Data analysis Sequencing reads were aligned to the human genome reference version hg19 using Burrows-Wheeler Aligner (BWA).21 Base quality recalibration and local realignment were performed using the Genome Analysis Toolkit (GATK).22 AtlasSNP was used for SNP calling and AtlasIndel2 was used for indel calling.23 The 1000 genome database, dbSNP, ESP5400, NIEHS95 exomes, and our internal database were used to filter out common SNPs and indels, with allele frequency cutoffs at 0.5% for recessive variants and at 0.1% for dominant variants (Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP), Seattle, Washington (http://evs.gs.washington.edu/EVS/), NIEHS Environmental Genome Project, Seattle, Washington (http://evs.gs.washington. edu/niehsExome/).24 25 Variant annotation was performed using 675

Genotype-phenotype correlations ANNOVAR.26 The Refseq gene sequences below were used for the mutation coordinates: AIPL1:NM_014336, ALMS1:NM_ 015120, BBS1:NM_024649, BBS7:NM_018190, CEP290:NM_ 025114, CERKL:NM_001160277, CLN3:NM_001042432, CRB1:NM_201253, GUCY2D:NM_000180, INPP5E:NM_ 019892, IQCB1:NM_001023570, LCA5:NM_181714, LRAT: NM_004744, NR2E3: NM_016346, OTX2:NM_172337, PDE6A:NM_000440, PRPF31:NM_015629, RDH12:NM_ 152443, RPE65:NM_000329, RPGR: NM_000328, RPGRIP1: NM_020366, SAG:NM_000541, SNRNP200:NM_014014, SPATA7:NM_018418, TULP1:NM_003322. The pathogenicity of novel missense mutations was predicted by dbNSFP, whose prediction score is derived from five algorithms (SIFT, Polyphen2, LRT, MutationTaster, and PhyloP).27–32

PCR and direct Sanger sequencing To validate the mutations detected by NGS, primers were designed (Primer3, http://biotools.umassmed.edu/bioapps/ primer3_www.cgi) to PCR-amplify the 400–500 bp region flanking the mutation. To ensure the high quality of Sanger sequencing, the amplicon was designed to have a boundary at least 50 bp away from the mutation. The amplicon was then Sanger sequenced on Applied BioSystems (ABI) 3730×l capillary sequencer. The Sanger sequencing results were analysed with Sequencher software. The intronic mutation c.2991+1655A>G in CEP290 was not initially included in the original design of our exonic capture panel. Sanger sequencing of this mutation was performed and the results were combined with the NGS data.

RESULTS A cohort of 179 patients clinically diagnosed with LCA or juvenile RP After prescreening for known mutations in LCA and juvenile RP genes using a combination of conventional genotyping methods, the genetic defects in 173 LCA and six juvenile RP patients remained unexplained (see online supplementary table S1 and Methods). We hypothesised that a portion of these cases were caused by mutations in known LCA and juvenile RP genes that were not included in the conventional screening methods, or caused by mutations in other retinal disease genes that had not been previously associated with LCA or juvenile RP. To Sanger-sequence all known retinal disease genes for such a large sample set would be prohibitively expensive and time consuming. Therefore, we utilised a targeted NGS based method for the comprehensive molecular diagnosis of these patients.

Targeted NGS of a standard control sample from HapMap project A capture panel was designed to enrich the target DNA, which consisted of 649 804 bp covering 2560 exons in 163 known retinal disease genes that had been reported and recorded in the RetNet at the time of design (see online supplementary files 1 and 2, https://sph.uth.tmc.edu/retnet/). The enriched DNA was then sent for NGS. We first evaluated the coverage of our targeted NGS method on NA11831, a standard control sample from the original HapMap Centre d’Etude du Polymorphisme Humain (CEPH) cohort.33 DNA from NA11831 was captured and sequenced at high coverage. A total of 8 240 805 mappable reads were obtained, 39% of which mapped to the target region and resulted in a 234× mean per base coverage. As shown in figure 1A and B, the vast majority of the targeted regions were well covered. Indeed, 97% of the bases in target region had coverage >10× and 92% of the bases had coverage >50× (figure 1A). 676

Also, 98% of the 2560 exons had mean coverage >5× (figure 1B). The low coverage exons were either within duplicate regions or those with a high GC content (see online supplementary tables S2 and S3). To systematically evaluate the accuracy of our method, we compared the genotyping data obtained from NGS to that from the SNP array. As part of the 1000 Genome project, sample NA11831 had been genotyped using the Illumina OMNI2.5 genotyping array. A total of 1190 genotyped SNPs in this sample were within our design region and were used as standards to test the accuracy of our method. As a result, 99.5% of SNPs (1184/ 1190) were detected by NGS (minimum coverage=3). The six undetected SNPs were within low coverage exons (data not shown). The genotypes of all 1184 NGS SNP calls were validated by either SNP array or Sanger sequencing (see Methods). Therefore, high quality SNP genotyping results were obtained by targeted NGS with a sensitivity of 99.5% (1184/1190) and a genotype concordance of 100% (1184/1184). To further explore the effect of coverage on the sensitivity of SNP detection, sequencing reads generated from NA11831 were randomly sampled in silico to achieve different levels of coverage from 3× to 234×. As shown in figure 1C, sensitivity increased sharply from 38% to 96% as the coverage increased from 2× to 12×, then gradually reached a sensitivity of 99% at around 23×. Based on this result, we chose to sequence patient samples at around 50× coverage to achieve nearly saturated sensitivity with a relatively low cost (cost is linear to the depth of coverage). At 50× coverage, up to 100 samples could be sequenced in one lane of Illumina HiSeq 2000. To develop a more cost effective method, we tested the robustness of sample multiplexing. We molecularly barcoded 12 replicates of NA11831 DNA and performed targeted NGS for these 12 replicates in one capture reaction. As shown in figure 1D, uniform and high coverage of these replicates was achieved.

Targeted NGS of 179 patients Using the capture panel described above, we applied targeted NGS to DNA obtained from a large cohort of 179 unrelated patients with the diagnosis of LCA or juvenile RP. The sequencing reads were processed by our bioinformatics pipeline that performed reads alignment, recalibration, realignment, variants calling, filtering, annotation, and quality control (see Methods). An average of 62× coverage was achieved for the 179 patient samples. Within the design region, 84% of bases had coverage >10× and 70% of bases had coverage >20×, indicating that sufficient coverage was achieved for high sensitivity of variants detection (table 1, figure 2A). For each individual, about 407 SNPs and small insertions/deletions (indels) were identified. Since LCA and juvenile RP are rare Mendelian diseases, common variants with a frequency >0.5% (for recessive variants) or >0.1% (for dominant variants) in any of the following databases were filtered out: the 1000 genome database, dbSNP135, the ESP5400 database, the NIEHS 95 exomes database, and our internal database (see Methods). As a result, an average of eight rare variants in retinal disease genes that lead to protein coding change were identified per sample (table 1). Furthermore, mutations known to cause retinal diseases in the Human Gene Mutation Database (HGMD) or the primary literature were identified.34 Finally, dbNSFP, a program that compiles prediction score from five well established prediction algorithms (PhyloP, SIFT, Polyphen2, LRT, and MutationTaster), was used to predict the pathogenicity of novel missense changes.27–32 In this study, we only reported novel missense variants that are predicted to be pathogenic by at least three of the Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

Genotype-phenotype correlations Figure 1 Systematic evaluation of targeted next generation sequencing method on a Hapmap sample NA11831. (A) The number of bases within different coverage groups. (B) The mean coverage of 2560 exons in the design region. (C) The sensitivity to detect single nucleotide polymorphisms versus the according mean coverage. (D) The high and uniform mean coverage for 12 multiplexed replicates. The blue dot line represents the average coverage for 12 replicates.

five algorithms (see online supplementary table S4). After all these stringent filtering steps, the remaining variants are likely to cause the disease in patients.

Identification of pathogenic mutations To identify the potential pathogenic mutations among several rare variants in each patient, we looked for variants that matched the reported inheritance pattern of the respective genes: Table 1 Target NGS statistics for 179 patients Per base coverage % Target bp covered ≥1× % Target bp covered ≥10× % Target bp covered ≥20× Total number of variants (SNPs and indels) Rare variants Rare variants that lead to protein coding change: Missense change Nonsense change Splicing site change Non-frameshift indels Frameshift indels

62 97 84 70 407 24 8.23 3.81 0.28 0.15 1.56 2.46

All the values are the mean number derived from 179 patients. NGS, next generation sequencing; SNPs, single nucleotide polymorphisms.

Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

1. Homozygous or compound heterozygous variants in recessive retinal disease genes, or 2. Reported heterozygous variants known to cause dominant retinal diseases, or 3. Novel heterozygous loss-of-function (LOF) variants in dominant retinal disease genes, if heterozygous LOF mutations in those genes are previously known to cause dominant retinal diseases. All potential pathogenic variants identified above were validated by Sanger sequencing. Segregation analysis was performed if DNA from family members was available. Through this procedure, we identified pathogenic mutations for 72 out of 179 patients (40%). Among the 72 patients, 58 patients carried mutations in known LCA or juvenile RP genes and exhibited corresponding phenotypes, while 14 harboured mutations in retinal disease genes that were not consistent with their initial clinical diagnosis (figure 2B). A total of 83 distinct pathogenic mutations were identified in the 72 patients, including a large number of novel mutations (n=45) (table 2). Most of these mutations were missense (39%) and nonsense (35%) mutations (figure 2C).

Molecular diagnosis of patients Patients carrying mutations in known LCA or juvenile RP genes In total, we identified 58 patients who carried mutations in known LCA or juvenile RP genes and exhibited corresponding 677

Genotype-phenotype correlations Figure 2 The targeted next generation sequencing statistics for 179 patients. (A) The percentage of bases in design region in each coverage group for 179 patients. (B) The percentage of 179 patients in different categories. (C) The percentage of different types of pathogenic mutations identified in the 72 patients. LCA, Leber congenital amaurosis.

phenotypes (tables 4–6). According to the American College of Medical Genetics standards to report sequence variants, mutations identified in our study can be classified into three categories with different clinical significance: (1) reported mutations that are known to cause retinal diseases; (2) novel LOF mutations that are expected to cause retinal diseases; (3) novel missense mutations that are predicted to be pathogenic by in silico prediction algorithms and may be causative of retinal diseases (see online supplementary table S4).35 To demonstrate the different confidence levels for different patients, we classified these patients into three groups based on the clinical significance of their mutations: patients in group 1 and 2 carried reported or novel LOF mutations with higher confidence, while patients in group 3 harboured one or more novel missense mutations with lower confidence (table 3). We identified 26 patients in group 1 who carried homozygous or compound heterozygous mutations that were known to cause recessive LCA or juvenile RP (tables 3 and 4, online supplementary table S1). For example, patient 3916 carried compound heterozygous reported nonsense mutations c.582C>G ( p.Y194X) and frameshift deletion c.805_809del (p. A269GfsX2) in RDH12 (table 4). The patient exhibited LCA phenotypes and the two mutations were previously known to cause LCA (see online supplementary figure S1, table S1).36 37

Table 2 Number of pathogenic mutations identified in this study

LCA and juvenile RP genes Retinal disease genes inconsistent with initial diagnosis Total

Reported

Novel

Total

30 8

38 7

68 15

38

45

83

LCA, Leber congenital amaurosis; RP, retinitis pigmentosa.

678

In this group of patients, AIPL1 was the most frequently mutated gene, which appeared in five patients. The nonsense mutation c.834G>A ( p.W278X) in AIPL1, the intronic mutation c.2991+1655A>G in CEP290, and the frameshift insertion c.805_809del ( p.A269GfsX2) in RDH12 were the most frequent mutations, all carried by three patients. We identified 22 patients in group 2 who carried novel LOF mutations in known LCA or juvenile RP genes (tables 3 and 5). First, 13 patients carried homozygous or compound heterozygous novel LOF mutations. For example, a novel homozygous frameshift deletion c.613_614del ( p.S205YfsX27) was identified in exon3 of LRAT in patient 4019. To our knowledge, this is the first reported disease allele outside LRAT exon2.48 51–53 The c.613_614del is predicted to change the 205–230 amino acids in the C terminus of LRAT protein, which is thought to be important for the LRAT protein enzymatic activity and its localisation to the endoplasmic reticulum membrane.54 55 Second, eight patients carried one reported mutation plus one novel LOF mutation. Third, patient 3561 carried a novel heterozygous frameshift insertion in OTX2. This insertion is likely to be pathogenic because a heterozygous protein truncating mutation in OTX2 was previously reported to cause ocular malformation and LCA.56 In this group of patients, CEP290 was the most frequently mutated gene, which appeared in seven patients. We identified 10 patients in group 3 who carried one or more novel missense mutations in known LCA or juvenile RP genes (table 6). Specifically, four patients carried homozygous or compound heterozygous novel missense mutations, three patients had a novel missense mutation plus a reported mutation, and three patients had a novel missense plus a novel LOF mutation (table 3). For example, patient 3319 carried a homozygous novel missense mutation (c.1439G>C, p.C480S) in CRB1 that changes a cysteine to a serine. The cysteine is conserved across mammals and this mutation is predicted to be damaging to protein function/structure by in silico Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

Genotype-phenotype correlations Table 3 Classification of patients according to clinical significance of mutations Mutated genes

Group

Allele 1

Allele 2

Homo

Compound hetero

LCA/juvenile RP genes

1 2

Reported Novel LOF Novel LOF Novel LOF Novel missense Novel missense Novel missense Reported Reported Novel LOF Novel missense

Reported Novel LOF Reported

15 8

11 5 8

Novel missense Reported Novel LOF Reported

2

2 3 3

Novel LOF Novel missense

1* 4 37

3

Retinal disease genes inconsistent with initial diagnosis

1 2 3

Hetero

1

7 1

Total

1 33

2

Total 26 13 8 1 4 3 3 7 1 2 4 72

The numbers in the four columns on the right represent the number of patients in each category. *This patient carried a hemizygous mutation. Compound hetero, compound heterozygous; Hetero, Heterozygous; Homo, homozygous; LCA, Leber congenital amaurosis; RP, retinitis pigmentosa.

prediction (see online supplementary table S4). Interestingly, similar missense mutations p.C480R and p.C480G at this residue were reported to cause LCA, further supporting the

Table 4

pathogenicity of p.C480S.43 In this group of patients, GUCY2D was the most frequently mutated gene, which appeared in four patients.

Twenty-six patients carrying two reported mutations in LCA or juvenile RP genes

Patient ID

Disease presentation

Gene

Type

Mutations

1473 3745

LCA LCA

AIPL1 AIPL1

Homozygous Compound Heterozygous

3746

LCA

AIPL1

Compound Heterozygous

393 3754

LCA LCA

AIPL1 AIPL1

Homozygous Compound Heterozygous

3638 3656

LCA LCA

CEP290 CEP290

Homozygous Compound Heterozygous

3661 3793 398 3738

LCA LCA LCA LCA

CEP290 CEP290 CRB1 CRB1

Homozygous Homozygous Homozygous Compound Heterozygous

1251 3722

LCA LCA

CRB1 GUCY2D

Homozygous Compound Heterozygous

3778 3750

LCA LCA

GUCY2D GUCY2D

Homozygous Compound Heterozygous

3577 54 622

LCA LCA LCA

LCA5 LRAT RDH12

Homozygous Homozygous Compound Heterozygous

1256

LCA

RDH12

Compound Heterozygous

1278 3916

Juvenile RP LCA

RDH12 RDH12

Homozygous Compound Heterozygous

3784

LCA

RPE65

Compound Heterozygous

1259 1303 3670 3671

LCA LCA LCA LCA

SPATA7 TULP1 TULP1 TULP1

Homozygous Homozygous Homozygous Homozygous

c.834G>A, p.W278X38 c.834G>A, p.W278X38 c.547G>T, p.G183X4 c.834G>A, p.W278X38 c.547G>T, p.G183X4 c.487C>T, p.Q163X39 c.265T>C, p.C89R15 c.214T>C, p.W72R4 c.2991+1655A>G40 c.5668G>T, p.G1890X41 c.2991+1655A>G40 c.2991+1655A>G40 c.4723A>T, p.K1575X42 c.610_616del, p.I205DfsX13343 c.1438T>C, p.C480R43 c.2945C>A, p.T982K4 c.3996C>A, p.C1332X43 c.1343C>A, p.S448X44 c.2598G>C, p.K866N45 c.1343C>A, p.S448X44 c.2302C>T, p.R768W46 c.3271C>T, p.R1091X4 c.835C>T, p.Q279X47 c.217_218del, p.M73DfsX4848 c.146C>T, p.T49M37 c.805_809del, p.A269GfsX237 c.146C>T, p.T49M37 c.805_809del, p.A269GfsX237 c.164C>T, p.T55M36 c.582C>G, p.Y194X36 c.805_809del, p.A269GfsX237 c.1205G>A, p.W402X4 c.1022T>C, p.L341S49 c.322C>T, p.R108X9 c.1381C>G, p.L461V13 c.901C>T, p.Q301X50 c.901C>T, p.Q301X50

LCA, Leber congenital amaurosis; RP, retinitis pigmentosa.

Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

679

Genotype-phenotype correlations Table 5

Twenty-two patients carrying novel LOF mutations in LCA or juvenile RP genes

Patient ID

Disease presentation

Gene

Type

Mutations

3739

LCA

CEP290

Compound Heterozygous

3640

LCA

CEP290

Compound Heterozygous

3645

LCA

CEP290

Compound Heterozygous

3650

LCA

CEP290

Compound Heterozygous

3653

LCA

CEP290

Compound Heterozygous

3666

LCA

CEP290

Compound Heterozygous

3741

LCA

CEP290

Compound Heterozygous

418 3557 1413 3796

LCA LCA LCA LCA

CRB1 CRB1 GUCY2D IQCB1

Homozygous Homozygous Homozygous Compound Heterozygous

3752

LCA

IQCB1

Compound Heterozygous

3737

LCA

IQCB1

Compound Heterozygous

4019 3561 1842 3676

LCA LCA Juvenile RP LCA

LRAT OTX2 PDE6A RPGRIP1

Homozygous Heterozygous Homozygous Compound Heterozygous

3677

LCA

RPGRIP1

Compound Heterozygous

1315 3679 3757

LCA LCA LCA

SPATA7 SPATA7 TULP1

Homozygous Homozygous Compound Heterozygous

1271

LCA

TULP1

Homozygous

c.5344C>T, p.R1782X c.1667_1668insA, p.I556NfsX20 c.1260_1264del, p.K421GfsX2 c.2991+1655A>G40 c.3811C>T, p.R1271X c.2991+1655A>G40 c.547_550del, p.Y183RfsX4 c.2991+1655A>G40 c.4882C>T, p.Q1628X c.2991+1655A>G40 c.1219_1220del, p.M407EfsX14 c.2991+1655A>G40 c.4723A>T, p.K1575X42 c.2052+1_2052+2del c.984G>A, p.W328X c.3687C>A, p.C1229X c.1116G>A, p.W372X c.1518_1519del, p.H506QfsX1357 c.1381C>T, p.R461X c.1518_1519del, p.H506QfsX1357 c.1465C>T, p.R489X c.1465C>T, p.R489X c.1381C>T, p.R461X c.613_614del, p.S205YfsX27 c.543_544insCTCA, p.Q181HfsX7 c.205C>T, p.Q69X c.1083_1084insGA, p.V364EfsX12 c.3749–1G>T c.1083_1084insGA, p.V364EfsX12 c.3749–1G>T c.1216–1G>A c.1373del, p.V458EfsX48 c.1376_1377del, p.I459RfsX12 c.725_728del, p.P242QfsX16 c.1113–2A>C

LCA, Leber congenital amaurosis; LOF, loss-of-function; RP, retinitis pigmentosa.

Table 6

Ten patients carrying one or more novel missense mutations in LCA or juvenile RP genes

Patient ID

Disease presentation

Gene

Type

Mutations

3319 3611 3799

LCA LCA LCA

CRB1 GUCY2D GUCY2D

Homozygous Homozygous Compound Heterozygous

3725

LCA

GUCY2D

Compound Heterozygous

1272

LCA

GUCY2D

Compound Heterozygous

1313

Juvenile RP

PDE6A

Compound Heterozygous

3740

LCA

RDH12

Compound Heterozygous

1268

LCA

TULP1

Compound Heterozygous

3771

LCA

TULP1

Compound Heterozygous

3681

LCA

TULP1

Compound Heterozygous

c.1439G>C, p.C480S c.2132C>T, p.P711L c.743C>G, p.S248W c.3224+1G>C c.1343C>A, p.S448X44 c.2678C>T, p.S893F c.1933T>C, p.S645P c.2207T>G, p.M736R c.2333A>T, p.D778V c.1363A>T, p.K455X c.692G>A, p.G231D c.823G>T, p.E275X c.1518C>A, p.F506L c.1277C>T, p.P426L c.1199G>A, p.R400Q58 c.961T>G, p.Y321D c.1102G>T, p.G368W59 c.1064A>T, p.D355V

LCA, Leber congenital amaurosis; RP, retinitis pigmentosa.

680

Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

Genotype-phenotype correlations Table 7

Eight patients carrying mutations known to cause other retinal diseases

Patient ID

Disease presentation

Gene

Previously reported disease

Type

Mutations

704 647 3748 617 3311 1318 3256 3425

Juvenile RP LCA LCA LCA Juvenile RP LCA LCA LCA

BBS1 CERKL CLN3 NR2E3 PRPF31 PRPH2 PRPH2 SAG

BBS Cone–rod dystrophy Batten disease Enhanced S-cone syndrome adRP adRP adRP Oguchi disease

Homozygous Homozygous Homozygous Homozygous Heterozygous Homozygous Homozygous Homozygous

c.1169T>G, p.M390R60 c.375C>G, p.C125W61 c.597C>A, p.Y199X62 c.119–2A>C63 c.220C>T, p.Q74X64 c.637T>C, p.C213R65 c.554T>C, p.L185P66 c.874C>T, p.R292X67

BBS, Bardet–Biedl syndrome; LCA, Leber congenital amaurosis; RP, retinitis pigmentosa.

Patients carrying mutations in other retinal disease genes We also identified 14 patients who carried mutations in retinal disease genes that were not consistent with their initial clinical diagnosis, representing 19% of the 72 diagnosed patients. Using the criteria mentioned above, we classified these 14 patients into three groups based on the clinical significance of their mutations. We identified eight patients in group 1 who carried reported mutations known to cause retinal disease genes that were not consistent with their initial clinical diagnosis (tables 3 and 7). Within this group, seven patients carried homozygous mutations. In addition, juvenile RP patient 3311 carried a heterozygous reported mutation known to cause autosomal dominant RP (adRP). We identified two LCA patients in group 2 who carried homozygous or compound heterozygous novel LOF mutations in other retinal disease genes (tables 3 and 8). For example, patient 3688 carried a hemizygous novel splice site mutation c.248–1G>T in RPGR. Previously reported splice site mutations in RPGR were known to cause X-linked RP, supporting that this mutation may cause the retinal defects in patient 3688. We identified four patients in group 3 who carried homozygous novel missense mutations in retinal diseases genes that were not consistent with their initial clinical diagnosis (tables 3 and 9). For example, patient 1327 carried a homozygous novel missense mutation c.728G>A ( p.C243Y) in Bardet–Biedl syndrome (BBS) gene BBS7. This mutation changes a cysteine residue that is conserved across vertebrates. It was predicted to be damaging by all of the five in silico prediction algorithms, supporting that this mutation is likely to be pathogenic (see online supplementary table S4).

Revisiting patients carrying mutations in other retinal disease genes In our study we observed that 14 patients carried mutations in genes that were not consistent with their initial clinical diagnosis. This observation may be explained by novel genotype– phenotype correlations, or by the difficulty assigning clinical diagnosis at the time of initial visit. In most cases, the first visit

of a blind or initial clinical most obvious test these two patients.

low vision infant occurs shortly after birth. The diagnosis may be difficult and influenced by the ophthalmic and visual findings at that time. To possibilities, we managed to revisit 12 of these 14

Homozygous mutations in PRPH2 cause EORD with LCA/juvenile RP phenotypes After revisiting, we confirmed the clinical diagnosis of LCA in patients 1318 and 3256 (figure 3, online supplementary table S1). Each patient carried a reported homozygous missense mutation in gene PRPH2: c.637T>C ( p.C213R) and c.554T>C (p.L185P), respectively (table 7). PRPH2 encodes peripherin, a membrane glycoprotein that is important for the stabilisation and compaction of photoreceptor outer segment discs.68 The p.C213R mutation is associated with autosomal dominant pattern dystrophy, and the p.L185P mutation, together with a null mutation in ROM1, has been reported to cause digenic RP.65 66 However, it has not been reported that homozygous mutations in PRPH2 cause severe EORD. To further validate this finding, we sequenced PRPH2 in another 135 unsolved LCA or juvenile RP patients and found the same homozygous missense mutation p.L185P in PRPH2 in a third juvenile RP patient, 741. These mutations were confirmed by Sanger sequencing and their segregations with the disease in the families were examined (figure 4). All the patients with homozygous mutations in PRPH2 exhibited LCA or juvenile RP phenotypes, including visual impairment within the first year of life, nystagmus in the two LCA patients (1318 and 3256), non-detectable or reduced ERGs, and a very similar form of maculopathies in the fundus (figure 3, online supplementary table S1). By contrast, family members who carried heterozygous mutations in PRPH2 were asymptomatic but showed detectable maculopathy phenotypes. For example, the 56-year-old father of patient 741 had macular pattern dystrophy and clear-cut foveal changes, but his visual acuity was essentially normal in both eyes (see online supplementary figure S2A–C, table S1). Similarly, the mother and the son of patient 1318 were both carriers of the mutation c.637T>C ( p.C213R) (figure 4). At 57 years of age, the mother

Table 8 Two patients carrying novel LOF mutations in other retinal disease genes Patient ID

Disease presentation

Gene

Previously reported disease

Type

Mutations

3494

LCA

ALMS1

Alström syndrome

Compound Heterozygous

3688

LCA

RPGR

X-linked RP

Hemizygous

c.2996C>G, p.S999X c.11410C>T, p.R3804X c.248–1G>T

LCA, Leber congenital amaurosis; LOF, loss-of-function; RP, retinitis pigmentosa.

Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

681

Genotype-phenotype correlations Table 9

four patients carrying homozygous novel missense mutations in other retinal disease genes

Patient ID

Disease presentation

Gene

Previously reported disease

Type

Mutations

3779 1327 3773 3795

LCA Juvenile RP LCA LCA

ALMS1 BBS7 INPP5E SNRNP200

Alström syndrome BBS Joubert syndrome adRP

Homozygous Homozygous Homozygous Homozygous

c.9764C>G, p.S3255C c.728G>A, p.C243Y c.1861C>T, p.R621W c.3133C>A, p.P1045T

BBS, Bardet–Biedl syndrome; LCA, Leber congenital amaurosis; adRP, autosomal dominant retinitis pigmentosa.

was asymptomatic with 20/20 visual acuity but had a florid butterfly-shaped macular pattern dystrophy and a number of other retinal flecks upon examination (see online supplementary figure S2D). The 7-year-old son had a significant refractive defect whereby visual acuity was reduced due to partial amblyopia. His fundus showed a miniature form of foveal butterflyshaped macular pattern dystrophy that was consistent with an early stage PRPH2 related phenotype (data not shown). The brother of patient 1318, who was homozygous wild-type for the mutation, had normal visual acuity (20/20) and no maculopathy (data not shown). To our knowledge, our study reported for the first time that homozygous mutations in PRPH2 cause EORD with LCA/juvenile RP phenotypes.

Revision of the initial clinical diagnosis in two patients After revisiting, two patients were reclassified to retinal diseases that were consistent with their molecular diagnosis (tables 7 and 8, online supplementary table S1). The clinical diagnosis of the first patient 3425 who carried a reported homozygous nonsense mutation in the known Oguchi disease gene SAG was revised to Oguchi disease, which presents as congenital stationary night blindness, fundus discolouration, and slowed dark adaptation.67 The second patient 3494 carried novel compound heterozygous nonsense mutations in the Alström syndrome gene ALMS1 (Otable 8). Both mutations segregated with the disease in the family (see online supplementary table S1). Patient 3494 was initially diagnosed with LCA at the age of 8; however, revisiting this patient at the age of 11 revealed other syndromic features including obesity, diabetes mellitus, and learning difficulties (see online supplementary table S1). Furthermore, the fundus examination showed an atrophic bull’s eye-like maculopathy, which was often seen in Alström syndrome patients (see online supplementary figure S3). These results indicate that molecular diagnosis can be a useful tool to revise or correct the initial clinical diagnosis.

The LCA-like or juvenile RP-like presentations in eight patients Guided by the molecular diagnosis, revisiting the phenotypes of an additional eight patients revealed their ‘LCA-like’ or ‘juvenile RP-like’ phenotypes that may represent spectrums of corresponding retinal diseases (see online supplementary table S1). For example, patient 3688 carried a novel hemizygous splicing site mutation in X-linked RP gene RPGR (table 8). This patient exhibited ‘LCA-like’ phenotypes including nystagmus at birth, which is typically absent in X-linked RP (see online supplementary table S1). However, it is already known that X-linked RP patients may lose central and peripheral vision more rapidly than average RP patients.69 Similarly, two patients (647, 617) carried reported mutations in cone–rod dystrophy gene CERKL and enhanced S-cone syndrome gene NR2E3, respectively (table 7). They exhibited ‘LCA-like’ phenotypes, including congenital visual impairment and nystagmus at birth (see online 682

supplementary table S1). However, based on the available clinical information, the phenotypes of the two patients may also represent severe spectrums of cone–rod dystrophy and S-cone syndrome, respectively. Patient 3311 carried a heterozygous mutation in PRPF31 that is known to cause RP with late onset and mild phenotypes.64 This patient exhibited early onset ‘juvenile RP-like’, possibly due to modifier effect from another gene (see online supplementary table S1, figure S4). In addition, four patients (704, 1327, 3748, and 3773) carried mutations in BBS1, BBS7, CLN3, and INPP5E, respectively (tables 7 and 9). Mutations in these genes were known to cause syndromes that are characterised by visual impairment and other systemic features.70–72 It was also reported in some cases that these genes were associated with ‘LCA-like’ or ‘RP-like’ phenotypes without defects in other organs.60 62 73 In our study, revisiting these patients confirmed their severe retinal degenerations without other syndromic features (see online supplementary table S1). For example, patient 704 carried a reported homozygous missense mutation in BBS gene BBS1 (table 7). This mutation segregated with disease within the family (see online supplementary table S1). Revisiting this patient at the age of 53 confirmed the ‘juvenile RP-like’ phenotypes without other syndromic features (see online supplementary table S1). However, the retinal features of this patient were consistent with those observed in other BBS patients with BBS1 mutations (see online supplementary figure S5).72 Due to these molecular findings and retinal features, we should still follow up the potential development of syndromic phenotypes in these patients. Collectively, these results suggest that the clinical manifestations of LCA/juvenile RP and related retinal diseases are overlapped, and that patients with ‘LCA-like’ or ‘juvenile RP-like’ phenotypes may actually carry mutations in non-canonical LCA/ juvenile RP genes.74 Therefore, molecular diagnosis should be used to refine the clinical diagnosis and get a better understanding of the disease. To achieve a more accurate diagnosis for these patients, it is essential to screen for mutations in a larger set of retinal disease genes.

DISCUSSION In this study, we developed a targeted NGS based method for the molecular diagnosis of LCA and most other retinal diseases. We systematically evaluated this method on a HapMap sample and then applied it to 179 unrelated and prescreened LCA or juvenile RP patients. To our knowledge, our sample set represents the largest cohort of unrelated patients diagnosed with LCA or juvenile RP that is systematically screened for all known LCA genes and most other known retinal disease genes. In-depth analysis of this dataset led to several important findings. A large number of novel mutations have been identified in our study, representing 54% (45/83) of the identified mutations in this patient cohort (table 2). Our observations are consistent Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

Genotype-phenotype correlations

Figure 3 The phenotypes of patients 1318, 3256, and 741 who carry homozygous mutations in PRPH2. (A) Fundus photograph of patient 1318 shows a prominent multilobulated central atrophic maculopathy surrounded by concentric rings of yellow deposits, with vessel narrowing and fine diffuse peripheral retinal changes. (B–D) Fundus photographs of patient 3256 show pigment deposits both peripherally and in the macular region, extensive disease with choroidal sclerosis, vessel narrowing, and optic disc pallor; a central extensive atrophic maculopathy is seen in C and D. (E) Optical coherence tomography images of patient 3256 confirm the extensive maculopathy and unusual globular lesions in the foveal region. (F) Fundus photograph of patient 741 shows the obvious diffuse retinal dystrophy with retinal vessel narrowing, retinal pigment epithelium mottling and loss, and a multilobulated maculopathy. (G) Fundus autofluorescence of patient 741 shows diffuse retinal abnormalities, perifoveal hyper-autofluorescence and a multilobulated foveal abnormality. (H) Optical coherence tomography images of patient 741 shows inner segment/ outer segment junction confined to the central macula, which explains well the fairly good visual acuity (20/40), and an unusual appearing deposit in the foveal regions. Note the similarity with the maculopathy shown in A, D, F, and G. The photographs of patients 1318, 3256, and 741 were taken at the age of 29, 66, and 30 years, respectively. with the 1000 genome project’s finding that every individual’s genome contains a large number of rare variants.25 Compared with common variants that arose earlier during the evolution, these recent rare variants may have greater impact on disease pathogenesis.75 Therefore, we expect that a significant number of novel mutations will continue to be discovered every time a Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

new patient is sequenced. Since NGS based molecular diagnosis can capture novel mutations, it is likely to achieve a high diagnosis rate. Among the 45 novel mutations that we identified, 29 were LOF mutations and 16 were missense mutations. All these novel mutations are likely to be pathogenic. First, these mutations are rare in large control databases. Collectively the 683

Genotype-phenotype correlations

Figure 4 Pathogenic mutations of PRPH2 identified in three patients. (A–C) Pedigree information of three patients and Sanger sequencing results for the two mutations in patients and controls. (A) The c.637T>C mutation is homozygous in patient 1318, heterozygous in both parents and the son, and homozygous wild-type in the brother. (B) The c.554T>C mutation is homozygous in patient 3256. (C) The c.554T>C mutation is homozygous in patient 741 and heterozygous in both parents. (D) Amino acid residues affected by the two missense mutations are conserved across different species. Solid symbols: affected; open symbols: unaffected; squares: male; circles: female; arrow: proband; asterisk: the DNA was not available for both parents of 3256; M1 and M2 represent the two mutations, respectively. databases used in our study contain more than 7400 control individuals. Second, all of these mutations match the reported inheritance pattern of the respective genes. In particular, the pathogenicity of all novel missense mutations reported in our study was supported by five well-established algorithms (see online supplementary table S4). Our study adds a significant 684

number of novel pathogenic mutations to our current knowledge of disease causing mutations. These mutations can serve as references and directly benefit the future molecular diagnosis of patients clinically diagnosed with LCA or juvenile RP. We identified the genetic defects in 40% of our patient cohort. This lower ratio is primarily due to the fact that our Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

Genotype-phenotype correlations patient cohort had been prescreened. Among the initial cohort of 389 patients, we had previously identified mutations in known LCA genes for 210 patients (see Methods). Among the remaining 179 patients included in this study, mutations in known LCA genes were identified in 56 patients. Therefore, about 68% ((210+56)/389) of our initial cohort can be explained by mutations in known LCA genes. This is concordant with the estimation that mutations in current known LCA genes explain about 70% of LCA cases.11 Among the 56 patients who carry mutations in known LCA genes, 24 patients have prescreening information available (see online supplementary table S5). We found that 16 patients had neither been screened by LCA APEX array nor been Sanger sequenced for the corresponding genes identified in this study. The remaining eight patients had been screened by LCA APEX array and/or Sanger sequencing for the corresponding genes identified in this study. Their mutations had not been identified in the prescreening because the mutations had not been covered by LCA APEX array and/or because Sanger sequencing only covered the frequently mutated exons of related genes.15 To our knowledge, our results demonstrate for the first time that homozygous mutations in PRPH2 cause EORD. The phenotypes of the three patients with homozygous mutations in PRPH2 were severe and quite consistent, especially with regard to the maculopathy phenotypes. By contrast, their family members who carried heterozygous mutations in PRPH2 had milder phenotypes. These results are consistent with the previous observations in PRPH2 mouse models. The rds/rds mouse that carried a homozygous null mutation in PRPH2 failed to develop photoreceptor outer segments and showed early onset and severe retinal degeneration, whereas the heterozygous rds/ +mouse displayed milder retinal degeneration and visual loss, suggesting that dose dependent phenotypic expression is an essential feature in the working of the PRPH2 gene.76 77 Until the discovery of these three patients homozygous for PRPH2 mutations, the full severity of the retinal degeneration seen in the rds/rds mouse had not yet been observed in humans. In our study, individuals with heterozygous mutations in PRPH2 were asymptomatic but had detectable macular flecks upon subsequent examination, exhibiting the clinical presentation of a macular pattern dystrophy, which is fully consistent with previously reported PRPH2 mediated phenotypes.65 By contrast, the severe early onset retinal defects in the three patients with homozygous mutations in PRPH2 are novel and likely due to dose dependent effect. It may be argued that the rds/rds mouse and our patients harboured different mutations and that individuals with the heterozygous p.L185P mutation in previously reported digenic RP families were originally reported as asymptomatic.78 However, the p.L185P mutation is now known to exert a measurable partial LOF effect. Work from Molday and co-workers established that this peripherin mutant is conditionally defective with respect to subunit assembly, and is capable of forming peripherin dimers but not tetramers.79 80 Furthermore, Kedzierski et al have shown that rds/+mice overexpressing L185P peripherin mutant indeed exhibited a mild phenotype. These mice had outer nuclear layer loss, partially disorganised outer segments, and reduced ERG responses. As observed in our patients homozygous for the p.L185P mutation, rds/rds mice overexpressing L185P peripherin mutant exhibited dramatically reduced levels of peripherin expression in their retinas, and a much more severe histological and electroretinographic retinal phenotype.81 Taken together, these findings suggest that, although asymptomatic, individuals harbouring the heterozygous p.L185P mutation Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

should be expected to exhibit a subclinical phenotype and it is possible that, as in our cases, later in life they may all consistently develop asymptomatic macular flecks or other minor yet measurable phenotypic manifestations. Interestingly, similar examples have been reported for many other genes.82 83 PITX3 is a gene that is usually mutated in dominant congenital cataracts and anterior segment dysgenesis. However, patients with two mutations in this gene exhibited microphthalmia and central nervous system (CNS) abnormalities.84 For another example, homozygous mutations in the low density lipoprotein (LDL) receptor gene were known to cause much more severe phenotypes of hypercholesterolaemia than heterozygous mutations.85 From a therapeutic standpoint, the implication for patients with retinal degenerations caused by homozygous mutations in PRPH2 is that their diseases can be modelled by the rds/rds mouse, which has been treated by gene augmentation therapy in proof-of-concept research.86 87 There is also a long history of investigation of the severe phenotype in this model, features of which can now be studied in the patients to determine how representative the model is in relation to the newly identified human condition. There are two main explanations for the 60% of our patients for whom we were unable to find pathogenic mutations in this study. First, mutations that were not covered by our method, including intronic mutations, synonymous mutations, large structural variations, and copy number variations, may account for diseases in these patients. Second, these unsolved cases may due to novel disease-causing genes. Indeed, whole exome sequencing (WES) of some of these unsolved cases has led to the identification of a novel LCA gene NMNAT1.6 Therefore, we expect that additional novel disease-causing genes will be identified by performing WES on these unsolved cases. Our results highlight the utility of molecular information in diagnosing clinically heterogeneous diseases. Assigning clinical diagnosis at the time of initial visit is difficult in some cases, and molecular diagnosis can guide the health care provider to reassess the phenotypes of their patients and achieve a more accurate diagnosis. Indeed, guided by their molecular diagnosis, two patients in our study were reclassified with other retinal diseases. Additionally, the clinical manifestations of different retinal diseases are sometimes overlapped, and molecular diagnosis can help us to better define the disease. In our report, eight patients exhibited ‘LCA-like’ or ‘juvenile RP-like’ presentations. Based on the available clinical information, the diagnosis of these patients may be either LCA/juvenile RP, or extreme spectrums of other related retinal diseases, due to the allelic differences or genetic background. Despite the phenotypic similarity between different clinical diagnoses, diseases can be well defined by the molecular diagnosis. Therefore, with the rapid drop of sequencing costs, comprehensive mutation screening that covers all known retinal disease genes should become an integral part of diagnosis in the near future. In addition to aiding the diagnosis, molecular information can directly contribute to better patient management. Recently, studies on gene therapy for LCA have made significant progress.88–91 An accurate molecular diagnosis is the first step toward realising the promise of gene therapy. Additionally, it can clarify the prognosis and change the focus of the clinical follow-up. Patients with different molecularly defined diseases may receive a different prognosis and clinical interventions. For example, patients who exhibit LCA phenotypes but carry mutations in syndromic retinal disease genes should be followed for the development of syndromic features and be given 685

Genotype-phenotype correlations corresponding clinical management. Finally, it can facilitate the genetic counselling and decision-making. Carrier tests or predictive tests for retinal diseases can inform prospective parents of their reproductive risk and possibly influence their decisions. The low coverage regions in our design either had a higher GC content or were within duplicate regions (see online supplementary tables S2 and S3). Indeed, the GC content bias of coverage in Illumina sequencing data has been previously reported and the bias could be potentially introduced in many steps during sequencing.92–94 It was recently recognised that PCR amplification before sequencing may be the major source of GC content bias; protocols to minimise such bias were proposed accordingly.95 96 In addition, low coverage in duplicated regions is likely due to the inability to map reads to a single unique position. The relatively shorts reads (90∼300 bp) generated by most currently available NGS platforms lack enough sequence specificity to be mapped to a single location among multiple duplicated regions. To uncover the genomic information of duplicated regions, long range PCR or NGS sequencer producing longer reads may be utilised. In summary, we were able to identify pathogenic mutations for 40% of this prescreened patient cohort. A total of 45 novel pathogenic mutations were found. Interestingly, we found that homozygous mutations in PRPH2 can cause LCA and juvenile RP. Our study highlighted the utility of comprehensive molecular information as an integral part of the diagnosis process to achieve more accurate diagnosis and potentially better disease treatment and management.

Competing interests None. Provenance and peer review Not commissioned; externally peer reviewed.

REFERENCES 1

2 3 4

5

6

7

8

Author affiliations 1 Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA 2 Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA 3 McGill Ocular Genetics Laboratory (MOGL), Departments of Paediatric Surgery, Human Genetics and Ophthalmology, Montreal Children’s Hospital, McGill University Health Center, Montreal, Quebec, Canada 4 Structural and Computational Biology & Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas, USA 5 Scheie Eye Institute, Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA 6 Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, Tennessee, USA 7 Retina Foundation of the Southwest and Department of Ophthalmology, University of Texas Southwestern Medical School, Dallas, Texas, USA 8 Department of Ophthalmology and Visual Sciences Center for Retinal and Macular Degeneration, University of Michigan, Ann Arbor, Michigan, USA 9 The Chicago Lighthouse for the Blind and Visually Impaired, Chicago, Illinois, USA 10 Ophthalmology, Cleveland Clinic, Cleveland, Ohio, USA 11 Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA Acknowledgements We sincerely thank all the patients and their families for their participation. We thank Ms Shirley Briand, Ms Alcira Vieiri and Ms Renee Pigeon for coordinating the blindness clinics at the McGill Ocular Genetics Laboratory. XW is supported by predoctoral fellowship: The Burroughs Wellcome Fund, The Houston Laboratory and Population Sciences Training Program in Gene Environment Interaction. HW is supported by NIH postdoctoral fellowship 5F32EY19430. JEZ is supported by NIH training grant T32 EY007102. RKK is supported by the Foundation Fighting Blindness Canada, the Canadian Institutes for Health Research, FRSQ, the Foundation for Retinal Research, and Reseau Vision. AI is supported by grant from Research to Prevent Blindness, Inc, New York, NY (unrestricted grant to UTHSC Department of Ophthalmology and a Physician Scientist Award to AI). This work is supported by grants from the Retinal Research Foundation and the National Eye Institute (R01EY018571 and R01EY020540) to RC. Contributors RC, XW and RKK designed the study. SGJ, AI, DB, JRH, GAF, EIT and DW performed the clinical study. XW, HW, VS, HFT, VK, KW, HR, IL, JEZ, SS, SB, AK, JS, FW and YL performed the molecular study. XW integrated the data and performed the analysis. XW, HFT, RC, RKK, JEZ, SGJ, AI wrote the manuscript. Funding Retinal Research Foundation and the National Eye Institute. 686

9

10

11

12

13

14

15

16

17

Franceschetti A, Dieterle P. [Diagnostic and prognostic importance of the electroretinogram in tapetoretinal degeneration with reduction of the visual field and hemeralopia]. Confin Neurol 1954;14:184–6. Leber T. Ueber Retinitis pigmentosa und angeborene Amaurose. Graefes Arch Clin Exp Ophthalmol 1869;15:1–25. Koenekoop RK. An overview of Leber congenital amaurosis: a model to understand human retinal development. Surv Ophthalmol 2004;49:379–98. Stone EM. Leber congenital amaurosis—a model for efficient genetic testing of heterogeneous disorders: LXIV Edward Jackson Memorial Lecture. Am J Ophthalmol 2007;144:791–811. Estrada-Cuzcano A, Koenekoop RK, Coppieters F, Kohl S, Lopez I, Collin RW, De Baere EB, Roeleveld D, Marek J, Bernd A, Rohrschneider K, van den Born LI, Meire F, Maumenee IH, Jacobson SG, Hoyng CB, Zrenner E, Cremers FP, den Hollander AI. IQCB1 mutations in patients with Leber congenital amaurosis. Invest Ophthalmol Vis Sci 2011;52:834–9. Koenekoop RK, Wang H, Majewski J, Wang X, Lopez I, Ren H, Chen Y, Li Y, Fishman GA, Genead M, Schwartzentruber J, Solanki N, Traboulsi EI, Cheng J, Logan CV, McKibbin M, Hayward BE, Parry DA, Johnson CA, Nageeb M, Poulter JA, Mohamed MD, Jafri H, Rashid Y, Taylor GR, Keser V, Mardon G, Xu H, Inglehearn CF, Fu Q, Toomes C, Chen R. Mutations in NMNAT1 cause Leber congenital amaurosis and identify a new disease pathway for retinal degeneration. Nat Genet 2012;44:1035–9. Falk MJ, Zhang Q, Nakamaru-Ogiso E, Kannabiran C, Fonseca-Kelly Z, Chakarova C, Audo I, Mackay DS, Zeitz C, Borman AD, Staniszewska M, Shukla R, Palavalli L, Mohand-Said S, Waseem NH, Jalali S, Perin JC, Place E, Ostrovsky J, Xiao R, Bhattacharya SS, Consugar M, Webster AR, Sahel JA, Moore AT, Berson EL, Liu Q, Gai X, Pierce EA. NMNAT1 mutations cause Leber congenital amaurosis. Nat Genet 2012;44:1040–5. Perrault I, Hanein S, Zanlonghi X, Serre V, Nicouleau M, Defoort-Delhemmes S, Delphin N, Fares-Taie L, Gerber S, Xerri O, Edelson C, Goldenberg A, Duncombe A, Le Meur G, Hamel C, Silva E, Nitschke P, Calvas P, Munnich A, Roche O, Dollfus H, Kaplan J, Rozet JM. Mutations in NMNAT1 cause Leber congenital amaurosis with early-onset severe macular and optic atrophy. Nat Genet 2012;44:975–7. Wang H, den Hollander AI, Moayedi Y, Abulimiti A, Li Y, Collin RW, Hoyng CB, Lopez I, Abboud EB, Al-Rajhi AA, Bray M, Lewis RA, Lupski JR, Mardon G, Koenekoop RK, Chen R. Mutations in SPATA7 cause Leber congenital amaurosis and juvenile retinitis pigmentosa. Am J Hum Genet 2009;84:380–7. Sergouniotis PI, Davidson AE, Mackay DS, Li Z, Yang X, Plagnol V, Moore AT, Webster AR. Recessive mutations in KCNJ13, encoding an inwardly rectifying potassium channel subunit, cause Leber congenital amaurosis. Am J Hum Genet 2011;89:183–90. den Hollander AI, Roepman R, Koenekoop RK, Cremers FP. Leber congenital amaurosis: genes, proteins and disease mechanisms. Prog Retin Eye Res 2008;27:391–419. Chiang PW, Wang J, Chen Y, Fu Q, Zhong J, Yi X, Wu R, Gan H, Shi Y, Barnett C, Wheaton D, Day M, Sutherland J, Heon E, Weleber RG, Gabriel LA, Cong P, Chuang K, Ye S, Sallum JM, Qi M. Exome sequencing identifies NMNAT1 mutations as a cause of Leber congenital amaurosis. Nat Genet 2012;44:972–4. den Hollander AI, Lopez I, Yzer S, Zonneveld MN, Janssen IM, Strom TM, Hehir-Kwa JY, Veltman JA, Arends ML, Meitinger T, Musarella MA, van den Born LI, Fishman GA, Maumenee IH, Rohrschneider K, Cremers FP, Koenekoop RK. Identification of novel mutations in patients with Leber congenital amaurosis and juvenile RP by genome-wide homozygosity mapping with SNP microarrays. Invest Ophthalmol Vis Sci 2007;48:5690–8. Yzer S, Leroy BP, De Baere E, de Ravel TJ, Zonneveld MN, Voesenek K, Kellner U, Ciriano JP, de Faber JT, Rohrschneider K, Roepman R, den Hollander AI, Cruysberg JR, Meire F, Casteels I, van Moll-Ramirez NG, Allikmets R, van den Born LI, Cremers FP. Microarray-based mutation detection and phenotypic characterization of patients with Leber congenital amaurosis. Invest Ophthalmol Vis Sci 2006;47:1167–76. Zernant J, Kulm M, Dharmaraj S, den Hollander AI, Perrault I, Preising MN, Lorenz B, Kaplan J, Cremers FP, Maumenee I, Koenekoop RK, Allikmets R. Genotyping microarray (disease chip) for Leber congenital amaurosis: detection of modifier alleles. Invest Ophthalmol Vis Sci 2005;46:3052–9. Henderson RH, Waseem N, Searle R, van der Spuy J, Russell-Eggitt I, Bhattacharya SS, Thompson DA, Holder GE, Cheetham ME, Webster AR, Moore AT. An assessment of the apex microarray technology in genotyping patients with Leber congenital amaurosis and early-onset severe retinal dystrophy. Invest Ophthalmol Vis Sci 2007;48:5684–9. Shanks ME, Downes SM, Copley RR, Lise S, Broxholme J, Hudspith KA, Kwasniewska A, Davies WI, Hankins MW, Packham ER, Clouston P, Seller A, Wilkie AO, Taylor JC, Ragoussis J, Nemeth AH. Next-generation sequencing (NGS)

Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

Genotype-phenotype correlations

18

19

20

21 22

23

24 25 26 27 28 29 30 31

32 33 34 35

36

37

38

39

40

41

as a diagnostic tool for retinal degeneration reveals a much higher detection rate in early-onset disease. Eur J Hum Genet 2012. Neveling K, Collin RW, Gilissen C, van Huet RA, Visser L, Kwint MP, Gijsen SJ, Zonneveld MN, Wieskamp N, de Ligt J, Siemiatkowska AM, Hoefsloot LH, Buckley MF, Kellner U, Branham KE, den Hollander AI, Hoischen A, Hoyng C, Klevering BJ, van den Born LI, Veltman JA, Cremers FP, Scheffer H. Next-generation genetic testing for retinitis pigmentosa. Hum Mutat 2012;33:963–72. Coppieters F, De Wilde B, Lefever S, De Meester E, De Rocker N, Van Cauwenbergh C, Pattyn F, Meire F, Leroy BP, Hellemans J, Vandesompele J, De Baere E. Massively parallel sequencing for early molecular diagnosis in Leber congenital amaurosis. Genet Med 2012;14:576–85. Galvin JA, Fishman GA, Stone EM, Koenekoop RK. Evaluation of genotype-phenotype associations in leber congenital amaurosis. Retina 2005;25:919–29. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754–60. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297–303. Challis D, Yu J, Evani US, Jackson AR, Paithankar S, Coarfa C, Milosavljevic A, Gibbs RA, Yu F. An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics 2012;13:8. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001;29:308–11. 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 2010;467:1061–73. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010;38:e164. Liu X, Jian X, Boerwinkle E. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat 2011;32:894–9. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009;4:1073–81. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 2010;20:110–21. Chun S, Fay JC. Identification of deleterious mutations within three human genomes. Genome Res 2009;19:1553–61. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods 2010;7:248–9. Schwarz JM, Rodelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods 2010;7:575–6. The International HapMap Consortium. The International HapMap Project. Nature 2003;426:789–96. Stenson PD, Mort M, Ball EV, Howells K, Phillips AD, Thomas NS, Cooper DN. The Human Gene Mutation Database: 2008 update. Genome Med 2009;1:13. Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE. ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007. Genet Med 2008;10:294–300. Thompson DA, Janecke AR, Lange J, Feathers KL, Hubner CA, McHenry CL, Stockton DW, Rammesmayer G, Lupski JR, Antinolo G, Ayuso C, Baiget M, Gouras P, Heckenlively JR, den Hollander A, Jacobson SG, Lewis RA, Sieving PA, Wissinger B, Yzer S, Zrenner E, Utermann G, Gal A. Retinal degeneration associated with RDH12 mutations results from decreased 11-cis retinal synthesis due to disruption of the visual cycle. Hum Mol Genet 2005;14:3865–75. Janecke AR, Thompson DA, Utermann G, Becker C, Hubner CA, Schmid E, McHenry CL, Nair AR, Ruschendorf F, Heckenlively J, Wissinger B, Nurnberg P, Gal A. Mutations in RDH12 encoding a photoreceptor cell retinol dehydrogenase cause childhood-onset severe retinal dystrophy. Nat Genet 2004;36:850–4. Sohocki MM, Bowne SJ, Sullivan LS, Blackshaw S, Cepko CL, Payne AM, Bhattacharya SS, Khaliq S, Qasim Mehdi S, Birch DG, Harrison WR, Elder FF, Heckenlively JR, Daiger SP. Mutations in a new photoreceptor-pineal gene on 17p cause Leber congenital amaurosis. Nat Genet 2000;24:79–83. Sohocki MM, Perrault I, Leroy BP, Payne AM, Dharmaraj S, Bhattacharya SS, Kaplan J, Maumenee IH, Koenekoop R, Meire FM, Birch DG, Heckenlively JR, Daiger SP. Prevalence of AIPL1 mutations in inherited retinal degenerative disease. Mol Genet Metab 2000;70:142–50. den Hollander AI, Koenekoop RK, Yzer S, Lopez I, Arends ML, Voesenek KE, Zonneveld MN, Strom TM, Meitinger T, Brunner HG, Hoyng CB, van den Born LI, Rohrschneider K, Cremers FP. Mutations in the CEP290 (NPHP6) gene are a frequent cause of Leber congenital amaurosis. Am J Hum Genet 2006;79:556–61. Sayer JA, Otto EA, O’Toole JF, Nurnberg G, Kennedy MA, Becker C, Hennies HC, Helou J, Attanasio M, Fausett BV, Utsch B, Khanna H, Liu Y, Drummond I, Kawakami I, Kusakabe T, Tsuda M, Ma L, Lee H, Larson RG, Allen SJ, Wilkinson CJ, Nigg EA, Shou C, Lillo C, Williams DS, Hoppe B, Kemper MJ, Neuhaus T, Parisi MA, Glass IA, Petry M, Kispert A, Gloy J, Ganner A, Walz G, Zhu X, Goldman D, Nurnberg P, Swaroop A, Leroux MR, Hildebrandt F. The centrosomal protein

Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

42

43

44

45

46

47

48

49

50

51

52

53

54 55 56

57

58

59

nephrocystin-6 is mutated in Joubert syndrome and activates transcription factor ATF4. Nat Genet 2006;38:674–81. Perrault I, Delphin N, Hanein S, Gerber S, Dufier JL, Roche O, Defoort-Dhellemmes S, Dollfus H, Fazzi E, Munnich A, Kaplan J, Rozet JM. Spectrum of NPHP6/CEP290 mutations in Leber congenital amaurosis and delineation of the associated phenotype. Hum Mutat 2007;28:416. Lotery AJ, Jacobson SG, Fishman GA, Weleber RG, Fulton AB, Namperumalsamy P, Heon E, Levin AV, Grover S, Rosenow JR, Kopp KK, Sheffield VC, Stone EM. Mutations in the CRB1 gene cause Leber congenital amaurosis. Arch Ophthalmol 2001;119:415–20. Perrault I, Rozet JM, Gerber S, Ghazi I, Ducroq D, Souied E, Leowski C, Bonnemaison M, Dufier JL, Munnich A, Kaplan J. Spectrum of retGC1 mutations in Leber’s congenital amaurosis. Eur J Hum Genet 2000;8:578–82. Coppieters F, Casteels I, Meire F, De Jaegere S, Hooghe S, van Regemorter N, Van Esch H, Matuleviciene A, Nunes L, Meersschaut V, Walraedt S, Standaert L, Coucke P, Hoeben H, Kroes HY, Vande Walle J, de Ravel T, Leroy BP, De Baere E. Genetic screening of LCA in Belgium: predominance of CEP290 and identification of potential modifier alleles in AHI1 of CEP290-related phenotypes. Hum Mutat 2010;31:E1709–66. Lotery AJ, Namperumalsamy P, Jacobson SG, Weleber RG, Fishman GA, Musarella MA, Hoyt CS, Heon E, Levin A, Jan J, Lam B, Carr RE, Franklin A, Radha S, Andorf JL, Sheffield VC, Stone EM. Mutation analysis of 3 genes in patients with Leber congenital amaurosis. Arch Ophthalmol 2000;118:538–43. den Hollander AI, Koenekoop RK, Mohamed MD, Arts HH, Boldt K, Towns KV, Sedmak T, Beer M, Nagel-Wolfrum K, McKibbin M, Dharmaraj S, Lopez I, Ivings L, Williams GA, Springell K, Woods CG, Jafri H, Rashid Y, Strom TM, van der Zwaag B, Gosens I, Kersten FF, van Wijk E, Veltman JA, Zonneveld MN, van Beersum SE, Maumenee IH, Wolfrum U, Cheetham ME, Ueffing M, Cremers FP, Inglehearn CF, Roepman R. Mutations in LCA5, encoding the ciliary protein lebercilin, cause Leber congenital amaurosis. Nat Genet 2007;39:889–95. Senechal A, Humbert G, Surget MO, Bazalgette C, Arnaud B, Arndt C, Laurent E, Brabet P, Hamel CP. Screening genes of the retinoid metabolism: novel LRAT mutation in leber congenital amaurosis. Am J Ophthalmol 2006;142:702–4. Morimura H, Fishman GA, Grover SA, Fulton AB, Berson EL, Dryja TP. Mutations in the RPE65 gene in patients with autosomal recessive retinitis pigmentosa or leber congenital amaurosis. Proc Natl Acad Sci U S A 1998;95:3088–93. Li Y, Wang H, Peng J, Gibbs RA, Lewis RA, Lupski JR, Mardon G, Chen R. Mutation survey of known LCA genes and loci in the Saudi Arabian population. Invest Ophthalmol Vis Sci 2009;50:1336–43. Thompson DA, Li Y, McHenry CL, Carlson TJ, Ding X, Sieving PA, Apfelstedt-Sylla E, Gal A. Mutations in the gene encoding lecithin retinol acyltransferase are associated with early-onset severe retinal dystrophy. Nat Genet 2001;28:123–4. Clark GR, Crowe P, Muszynska D, O’Prey D, O’Neill J, Alexander S, Willoughby CE, McKay GJ, Silvestri G, Simpson DA. Development of a diagnostic genetic test for simplex and autosomal recessive retinitis pigmentosa. Ophthalmology 2010;117:2169–77, e3. Collin RW, van den Born LI, Klevering BJ, de Castro-Miro M, Littink KW, Arimadyo K, Azam M, Yazar V, Zonneveld MN, Paun CC, Siemiatkowska AM, Strom TM, Hehir-Kwa JY, Kroes HY, de Faber JT, van Schooneveld MJ, Heckenlively JR, Hoyng CB, den Hollander AI, Cremers FP. High-resolution homozygosity mapping is a powerful tool to detect novel mutations causative of autosomal recessive RP in the Dutch population. Invest Ophthalmol Vis Sci 2011;52:2227–39. Moise AR, Golczak M, Imanishi Y, Palczewski K. Topology and membrane association of lecithin: retinol acyltransferase. J Biol Chem 2007;282:2081–90. Hu J, Ng PC. Predicting the effects of frameshifting indels. Genome Biol 2012; 13:R9. Henderson RH, Williamson KA, Kennedy JS, Webster AR, Holder GE, Robson AG, FitzPatrick DR, van Heyningen V, Moore AT. A rare de novo nonsense mutation in OTX2 causes early onset retinal dystrophy and pituitary dysfunction. Mol Vis 2009;15:2442–7. Otto EA, Loeys B, Khanna H, Hellemans J, Sudbrak R, Fan S, Muerb U, O’Toole JF, Helou J, Attanasio M, Utsch B, Sayer JA, Lillo C, Jimeno D, Coucke P, De Paepe A, Reinhardt R, Klages S, Tsuda M, Kawakami I, Kusakabe T, Omran H, Imm A, Tippens M, Raymond PA, Hill J, Beales P, He S, Kispert A, Margolis B, Williams DS, Swaroop A, Hildebrandt F. Nephrocystin-5, a ciliary IQ domain protein, is mutated in Senior-Loken syndrome and interacts with RPGR and calmodulin. Nat Genet 2005;37:282–8. Singh HP, Jalali S, Narayanan R, Kannabiran C. Genetic analysis of Indian families with autosomal recessive retinitis pigmentosa by homozygosity screening. Invest Ophthalmol Vis Sci 2009;50:4065–71. Hanein S, Perrault I, Gerber S, Tanguy G, Barbet F, Ducroq D, Calvas P, Dollfus H, Hamel C, Lopponen T, Munier F, Santos L, Shalev S, Zafeiriou D, Dufier JL, Munnich A, Rozet JM, Kaplan J. Leber congenital amaurosis: comprehensive survey of the genetic heterogeneity, refinement of the clinical definition, and genotype-phenotype correlations as a strategy for molecular diagnosis. Hum Mutat 2004;23:306–17.

687

Genotype-phenotype correlations 60

61

62

63

64

65

66

67

68 69 70

71 72

73

74

75 76 77

688

Estrada-Cuzcano A, Koenekoop RK, Senechal A, De Baere EB, de Ravel T, Banfi S, Kohl S, Ayuso C, Sharon D, Hoyng CB, Hamel CP, Leroy BP, Ziviello C, Lopez I, Bazinet A, Wissinger B, Sliesoraityte I, Avila-Fernandez A, Littink KW, Vingolo EM, Signorini S, Banin E, Mizrahi-Meissonnier L, Zrenner E, Kellner U, Collin RW, den Hollander AI, Cremers FP, Klevering BJ. BBS1 mutations in a wide spectrum of phenotypes ranging from nonsyndromic retinitis pigmentosa to Bardet-Biedl syndrome. Arch Ophthalmol 2012;130:1425–32. Littink KW, Koenekoop RK, van den Born LI, Collin RW, Moruz L, Veltman JA, Roosing S, Zonneveld MN, Omar A, Darvish M, Lopez I, Kroes HY, van Genderen MM, Hoyng CB, Rohrschneider K, van Schooneveld MJ, Cremers FP, den Hollander AI. Homozygosity mapping in patients with cone-rod dystrophy: novel mutations and clinical characterizations. Invest Ophthalmol Vis Sci 2010;51:5943–51. Sarpong A, Schottmann G, Ruther K, Stoltenburg G, Kohlschutter A, Hubner C, Schuelke M. Protracted course of juvenile ceroid lipofuscinosis associated with a novel CLN3 mutation ( p.Y199X). Clin Genet 2009;76:38–45. Haider NB, Jacobson SG, Cideciyan AV, Swiderski R, Streb LM, Searby C, Beck G, Hockey R, Hanna DB, Gorman S, Duhl D, Carmi R, Bennett J, Weleber RG, Fishman GA, Wright AF, Stone EM, Sheffield VC. Mutation of a nuclear receptor gene, NR2E3, causes enhanced S cone syndrome, a disorder of retinal cell fate. Nat Genet 2000;24:127–31. Sullivan LS, Bowne SJ, Birch DG, Hughbanks-Wheaton D, Heckenlively JR, Lewis RA, Garcia CA, Ruiz RS, Blanton SH, Northrup H, Gire AI, Seaman R, Duzkale H, Spellicy CJ, Zhu J, Shankar SP, Daiger SP. Prevalence of disease-causing mutations in families with autosomal dominant retinitis pigmentosa: a screen of known genes in 200 families. Invest Ophthalmol Vis Sci 2006;47:3052–64. Payne AM, Downes SM, Bessant DA, Bird AC, Bhattacharya SS. Founder effect, seen in the British population, of the 172 peripherin/RDS mutation-and further refinement of genetic positioning of the peripherin/RDS gene. Am J Hum Genet 1998;62:192–5. Kajiwara K, Hahn LB, Mukai S, Travis GH, Berson EL, Dryja TP. Mutations in the human retinal degeneration slow gene in autosomal dominant retinitis pigmentosa. Nature 1991;354:480–3. Nakamura M, Yamamoto S, Okada M, Ito S, Tano Y, Miyake Y. Novel mutations in the arrestin gene and associated clinical features in Japanese patients with Oguchi’s disease. Ophthalmology 2004;111:1410–14. Travis GH, Sutcliffe JG, Bok D. The retinal degeneration slow (rds) gene product is a photoreceptor disc membrane-associated glycoprotein. Neuron 1991;6:61–70. Iannaccone A. The genetics of hereditary retinopathies and optic neuropathies. Compr Ophthalmol Update 2005;6:39–62. Badano JL, Ansley SJ, Leitch CC, Lewis RA, Lupski JR, Katsanis N. Identification of a novel Bardet-Biedl syndrome protein, BBS7, that shares structural features with BBS1 and BBS2. Am J Hum Genet 2003;72:650–8. The International Batten Disease Consortium. Isolation of a novel gene underlying Batten disease, CLN3. Cell 1995;82:949–57. Bielas SL, Silhavy JL, Brancati F, Kisseleva MV, Al-Gazali L, Sztriha L, Bayoumi RA, Zaki MS, Abdel-Aleem A, Rosti RO, Kayserili H, Swistun D, Scott LC, Bertini E, Boltshauser E, Fazzi E, Travaglini L, Field SJ, Gayral S, Jacoby M, Schurmans S, Dallapiccola B, Majerus PW, Valente EM, Gleeson JG. Mutations in INPP5E, encoding inositol polyphosphate-5-phosphatase E, link phosphatidyl inositol signaling to the ciliopathies. Nat Genet 2009;41:1032–6. Cox KF, Kerr NC, Kedrov M, Nishimura D, Jennings BJ, Stone EM, Sheffield VC, Iannaccone A. Phenotypic expression of Bardet-Biedl syndrome in patients homozygous for the common M390R mutation in the BBS1 gene. Vision Res 2012;75:77–87. Wang X, Wang H, Cao M, Li Z, Chen X, Patenia C, Gore A, Abboud EB, Al-Rajhi AA, Lewis RA, Lupski JR, Mardon G, Zhang K, Muzny D, Gibbs RA, Chen R. Whole-exome sequencing identifies ALMS1, IQCB1, CNGA3, and MYO7A mutations in patients with Leber congenital amaurosis. Hum Mutat 2011;32:1450–9. Lupski JR, Belmont JW, Boerwinkle E, Gibbs RA. Clan genomics and the complex architecture of human disease. Cell 2011;147:32–43. van Nie R, Ivanyi D, Demant P. A new H-2-linked mutation, rds, causing retinal degeneration in the mouse. Tissue Antigens 1978;12:106–8. Hawkins RK, Jansen HG, Sanyal S. Development and degeneration of retina in rds mutant mice: photoreceptor abnormalities in the heterozygotes. Exp Eye Res 1985;41:701–20.

78 79

80

81

82

83

84

85 86

87

88

89

90

91

92 93

94 95

96

Kajiwara K, Berson EL, Dryja TP. Digenic retinitis pigmentosa due to mutations at the unlinked peripherin/RDS and ROM1 loci. Science 1994;264:1604–8. Goldberg AF, Molday RS. Defective subunit assembly underlies a digenic form of retinitis pigmentosa linked to mutations in peripherin/rds and rom-1. Proc Natl Acad Sci U S A 1996;93:13726–30. Loewen CJ, Moritz OL, Molday RS. Molecular characterization of peripherin-2 and rom-1 mutants responsible for digenic retinitis pigmentosa. J Biol Chem 2001;276:22388–96. Kedzierski W, Nusinowitz S, Birch D, Clarke G, McInnes RR, Bok D, Travis GH. Deficiency of rds/peripherin causes photoreceptor death in mouse models of digenic and dominant retinitis pigmentosa. Proc Natl Acad Sci USA 2001;98:7718–23. Wittstrom E, Ekvall S, Schatz P, Bondeson ML, Ponjavic V, Andreasson S. Morphological and functional changes in multifocal vitelliform retinopathy and biallelic mutations in BEST1. Ophthalmic Genet 2011;32:83–96. Burgess R, Millar ID, Leroy BP, Urquhart JE, Fearon IM, De Baere E, Brown PD, Robson AG, Wright GA, Kestelyn P, Holder GE, Webster AR, Manson FD, Black GC. Biallelic mutation of BEST1 causes a distinct retinopathy in humans. Am J Hum Genet 2008;82:19–31. Bidinost C, Matsumoto M, Chung D, Salem N, Zhang K, Stockton DW, Khoury A, Megarbane A, Bejjani BA, Traboulsi EI. Heterozygous and homozygous mutations in PITX3 in a large Lebanese family with posterior polar cataracts and neurodevelopmental abnormalities. Invest Ophthalmol Vis Sci 2006;47:1274–80. Naoumova RP, Thompson GR, Soutar AK. Current management of severe homozygous hypercholesterolaemias. Curr Opin Lipidol 2004;15:413–22. Ali RR, Sarra GM, Stephens C, Alwis MD, Bainbridge JW, Munro PM, Fauser S, Reichel MB, Kinnon C, Hunt DM, Bhattacharya SS, Thrasher AJ. Restoration of photoreceptor ultrastructure and function in retinal degeneration slow mice by gene therapy. Nat Genet 2000;25:306–10. Schlichtenbrede FC, da Cruz L, Stephens C, Smith AJ, Georgiadis A, Thrasher AJ, Bainbridge JW, Seeliger MW, Ali RR. Long-term evaluation of retinal function in Prph2Rd2/Rd2 mice following AAV-mediated gene replacement therapy. J Gene Med 2003;5:757–64. Bennett J, Ashtari M, Wellman J, Marshall KA, Cyckowski LL, Chung DC, McCague S, Pierce EA, Chen Y, Bennicelli JL, Zhu X, Ying GS, Sun J, Wright JF, Auricchio A, Simonelli F, Shindler KS, Mingozzi F, High KA, Maguire AM. AAV2 gene therapy readministration in three adults with congenital blindness. Sci Transl Med 2012;4:120ra15. Maguire AM, Simonelli F, Pierce EA, Pugh EN Jr., Mingozzi F, Bennicelli J, Banfi S, Marshall KA, Testa F, Surace EM, Rossi S, Lyubarsky A, Arruda VR, Konkle B, Stone E, Sun J, Jacobs J, Dell’Osso L, Hertle R, Ma JX, Redmond TM, Zhu X, Hauck B, Zelenaia O, Shindler KS, Maguire MG, Wright JF, Volpe NJ, McDonnell JW, Auricchio A, High KA, Bennett J. Safety and efficacy of gene transfer for Leber’s congenital amaurosis. N Engl J Med 2008;358:2240–8. Bainbridge JW, Smith AJ, Barker SS, Robbie S, Henderson R, Balaggan K, Viswanathan A, Holder GE, Stockman A, Tyler N, Petersen-Jones S, Bhattacharya SS, Thrasher AJ, Fitzke FW, Carter BJ, Rubin GS, Moore AT, Ali RR. Effect of gene therapy on visual function in Leber’s congenital amaurosis. N Engl J Med 2008;358:2231–9. Jacobson SG, Cideciyan AV, Ratnakaram R, Heon E, Schwartz SB, Roman AJ, Peden MC, Aleman TS, Boye SL, Sumaroka A, Conlon TJ, Calcedo R, Pang JJ, Erger KE, Olivares MB, Mullins CL, Swider M, Kaushal S, Feuer WJ, Iannaccone A, Fishman GA, Stone EM, Byrne BJ, Hauswirth WW. Gene therapy for Leber congenital amaurosis caused by RPE65 mutations: safety and efficacy in 15 children and adults followed up to 3 years. Arch Ophthalmol 2011;130:9–24. Hansen KD, Brenner SE, Dudoit S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 2010;38:e131. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ. A large genome center’s improvements to the Illumina sequencing system. Nat Methods 2008;5:1005–10. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008;36:e105. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 2009;6:291–5. Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 2011;12:R18.

Wang X, et al. J Med Genet 2013;50:674–688. doi:10.1136/jmedgenet-2013-101558

# UCSC hg19 coordinate Chromosome Start chr1 94458393 chr1 94461664 chr1 94463416 chr1 94466391 chr1 94466557 chr1 94467413 chr1 94470996 chr1 94473189 chr1 94473790 chr1 94474306 chr1 94476355 chr1 94476817 chr1 94480098 chr1 94481294 chr1 94485137 chr1 94486795 chr1 94487195 chr1 94487401 chr1 94488941 chr1 94490509 chr1 94495000 chr1 94495983 chr1 94496551 chr1 94497333 chr1 94502295 chr1 94502700 chr1 94505598 chr1 94506764 chr1 94508316 chr1 94508891 chr1 94510168 chr1 94512474 chr1 94514423 chr1 94517188 chr1 94520666 chr1 94522156 chr1 94526092 chr1 94528132 chr1 94528667 chr1 94543245 chr1 94544145 chr1 94544877 chr1 94546033 chr1 94548907 chr1 94564349

End 94458798 94461751 94463666 94466484 94466661 94467548 94471138 94473296 94473853 94474427 94476485 94476941 94480246 94481410 94485315 94486965 94487270 94487507 94488974 94490604 94495187 94496082 94496676 94497599 94502344 94502906 94505683 94506958 94508454 94509031 94510300 94512649 94514513 94517254 94520871 94522378 94526315 94528309 94528873 94543443 94544262 94545017 94546274 94548997 94564547

Gene ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCA4

chr1 chr1 chr1 chr1 chr1 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8

94568570 94574132 94576993 94578528 94586535 16243421 16244434 16248484 16248729 16251519 16253338 16255294 16256849 16259479 16263502 16267140 16269767 16271308 16272654 16276268 16276660 16278815 16280980 16282687 16284020 16286686 16291877 16295857 16297266 16302584 16306041 16308180 16313410 16313678 16315505 16317255 38854504 38865404 38869176 38871483 38873636 38874737 38876371 38879161 38880674 38883321 38884195

94568698 94574272 94577135 94578622 94586705 16244098 16244629 16248651 16248888 16251666 16253440 16255421 16257049 16259790 16263710 16267261 16269843 16271483 16272822 16276445 16276787 16278891 16281068 16282831 16284224 16286779 16292039 16296035 16297470 16302716 16306103 16308306 16313539 16313804 16315688 16317328 38854679 38865502 38869235 38871562 38873713 38874933 38876437 38879233 38880844 38883403 38884329

ABCA4 ABCA4 ABCA4 ABCA4 ABCA4 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ABCC6 ADAM9 ADAM9 ADAM9 ADAM9 ADAM9 ADAM9 ADAM9 ADAM9 ADAM9 ADAM9 ADAM9

chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr17 chr17 chr17 chr17 chr17 chr17 chr2 chr2 chr2 chr2

38899464 38911999 38913095 38928816 38934746 38947565 38948777 38959381 38961125 135605111 135611560 135621637 135639656 135644299 135679269 135715913 135726088 135732485 135748304 135749766 135751019 135752345 135754164 135759512 135763719 135768145 135769427 135774478 135776871 135778631 135784262 135786951 135788718 135811760 135813365 135818325 135818720 6327058 6329934 6330200 6331637 6337238 6338328 73612885 73635749 73646250 73649984

38899636 38912092 38913291 38928922 38934930 38947707 38948865 38959449 38962777 135606785 135611663 135621696 135639754 135644462 135679325 135716034 135726115 135732682 135748445 135749897 135751138 135752452 135754394 135759636 135763852 135768298 135769613 135774574 135777064 135778851 135784444 135787511 135788772 135811885 135813429 135818387 135818903 6329150 6330076 6330377 6331826 6337418 6338519 73613320 73635875 73646446 73650102

ADAM9 ADAM9 ADAM9 ADAM9 ADAM9 ADAM9 ADAM9 ADAM9 ADAM9 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AHI1 AIPL1 AIPL1 AIPL1 AIPL1 AIPL1 AIPL1 ALMS1 ALMS1 ALMS1 ALMS1

chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr10 chr10 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11

73651557 73653580 73659325 73675089 73682288 73716760 73746901 73761950 73777393 73784346 73786098 73799388 73826527 73827804 73828321 73829311 73830367 73835601 73836694 97483594 97484834 97486924 97499002 97499458 97503798 97506833 97510614 97516867 124214178 124216422 63953419 63965590 63967861 63968614 63973734 63975851 63976413 63981180 63985125 66278118 66278483 66278675 66281876 66283010 66283163 66283331 66287087

73652030 73653681 73659419 73681194 73682422 73718625 73747143 73762076 73777564 73784481 73786269 73800551 73826648 73828008 73828563 73829495 73830431 73835701 73837046 97483821 97484933 97487074 97499064 97499527 97503893 97506963 97510670 97517373 124214540 124216868 63953651 63965843 63968121 63968697 63974000 63976050 63976535 63982159 63989134 66278177 66278560 66278710 66282149 66283057 66283202 66283404 66287219

ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ALMS1 ARL6 ARL6 ARL6 ARL6 ARL6 ARL6 ARL6 ARL6 ARL6 ARMS2 ARMS2 ATXN7 ATXN7 ATXN7 ATXN7 ATXN7 ATXN7 ATXN7 ATXN7 ATXN7 BBS1 BBS1 BBS1 BBS1 BBS1 BBS1 BBS1 BBS1

chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr12 chr12 chr4 chr4 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr2

66288740 66290926 66291194 66293593 66294119 66297289 66298364 66299126 66299421 76738265 76741941 123653856 123663037 56518258 56519501 56530878 56531654 56532348 56533689 56534765 56535264 56536228 56536584 56539861 56540031 56543868 56544770 56545070 56548364 56553657 72978525 72987517 73002040 73004584 73007631 73009118 73015134 73016868 73020280 73021956 73023645 73023895 73027453 73028165 73029102 73029818 170336005

66288847 66291047 66291353 66293663 66294278 66297423 66298499 66299213 66301084 76741567 76742222 123654039 123666098 56518779 56519650 56530991 56531792 56532480 56533819 56534937 56535409 56536368 56536720 56539948 56540136 56543946 56544833 56545196 56548592 56554008 72978592 72987569 73002120 73004648 73007743 73009191 73015188 73016996 73020335 73022025 73023798 73024067 73027523 73028307 73029304 73030816 170336122

BBS1 BBS1 BBS1 BBS1 BBS1 BBS1 BBS1 BBS1 BBS1 BBS10 BBS10 BBS12 BBS12 BBS2 BBS2 BBS2 BBS2 BBS2 BBS2 BBS2 BBS2 BBS2 BBS2 BBS2 BBS2 BBS2 BBS2 BBS2 BBS2 BBS2 BBS4 BBS4 BBS4 BBS4 BBS4 BBS4 BBS4 BBS4 BBS4 BBS4 BBS4 BBS4 BBS4 BBS4 BBS4 BBS4 BBS5

chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7

170338760 170343578 170344315 170344496 170349383 170350250 170354136 170355995 170359604 170360812 170360990 122745634 122749300 122749556 122749773 122754385 122756298 122760785 122765081 122766658 122768558 122769998 122774110 122775858 122776643 122780146 122782658 122784371 122789135 122791432 33169151 33185853 33192312 33195249 33217089 33296847 33303901 33312623 33313438 33376052 33380508 33384192 33388679 33390830 33392470 33397466 33407378

170338843 170343644 170344365 170344624 170349519 170350346 170354199 170356130 170359688 170360836 170363165 122747148 122749424 122749660 122749883 122754550 122756438 122760851 122765156 122766851 122768661 122770083 122774241 122775975 122776716 122780333 122782834 122784434 122789201 122791642 33169653 33185976 33192463 33195314 33217203 33297022 33303986 33312807 33313568 33376234 33380585 33384246 33388782 33390935 33392485 33397607 33407474

BBS5 BBS5 BBS5 BBS5 BBS5 BBS5 BBS5 BBS5 BBS5 BBS5 BBS5 BBS7 BBS7 BBS7 BBS7 BBS7 BBS7 BBS7 BBS7 BBS7 BBS7 BBS7 BBS7 BBS7 BBS7 BBS7 BBS7 BBS7 BBS7 BBS7 BBS9 BBS9 BBS9 BBS9 BBS9 BBS9 BBS9 BBS9 BBS9 BBS9 BBS9 BBS9 BBS9 BBS9 BBS9 BBS9 BBS9

chr7 chr7 chr7 chr7 chr7 chr7 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr2 chr2 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19

33423277 33427603 33545074 33573565 33644476 33644806 61717355 61719242 61722578 61723189 61724315 61724858 61725617 61726969 61727363 61729726 61731575 31895265 31895731 31896508 31901386 31901643 31901942 31903699 31905095 31907007 31910735 31911001 31911192 31911420 31911693 31911911 31912503 31912756 31912954 29284557 29293459 6677845 6678162 6678382 6679135 6679417 6680168 6681951 6682152 6684398 6684570

33423450 33427756 33545257 33573788 33644587 33645680 61717899 61719430 61722673 61723423 61724470 61724936 61725770 61727050 61727515 61730365 61731939 31895575 31895941 31896694 31901560 31901742 31902076 31903838 31905236 31907097 31910876 31911096 31911304 31911586 31911770 31912003 31912630 31912806 31913448 29287933 29297127 6678034 6678298 6678466 6679219 6679507 6680274 6682041 6682240 6684450 6684661

BBS9 BBS9 BBS9 BBS9 BBS9 BBS9 BEST1 BEST1 BEST1 BEST1 BEST1 BEST1 BEST1 BEST1 BEST1 BEST1 BEST1 C2 C2 C2 C2 C2 C2 C2 C2 C2 C2 C2 C2 C2 C2 C2 C2 C2 C2 C2ORF71 C2ORF71 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3

chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr11 chr11 chr11 chr11 chr11 chr11 chrX chrX

6684785 6684998 6686134 6686756 6690639 6692934 6693422 6694441 6696389 6696603 6697354 6697662 6702137 6702481 6707086 6707476 6707810 6709694 6710649 6710997 6712267 6712518 6713199 6713417 6714002 6714176 6714362 6718104 6718257 6719221 6720526 58227301 58232674 58233920 58234787 58235050 58235421 58235643 58236590 67222817 67223658 67223769 67225043 67225841 67226101 49061522 49062075

6684845 6685157 6686298 6686913 6690738 6693094 6693498 6694645 6696476 6696670 6697567 6697805 6702223 6702590 6707284 6707548 6707940 6709853 6710856 6711207 6712417 6712634 6713326 6713520 6714093 6714259 6714457 6718175 6718423 6719414 6720662 58227453 58232728 58234076 58234933 58235149 58235488 58235807 58236906 67223260 67223689 67223913 67225153 67225989 67229243 49061827 49062273

C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 C3 CA4 CA4 CA4 CA4 CA4 CA4 CA4 CA4 CABP4 CABP4 CABP4 CABP4 CABP4 CABP4 CACNA1F CACNA1F

chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chr12

49062971 49063188 49063465 49064974 49065721 49066088 49066400 49066760 49067049 49067424 49067781 49068357 49068702 49069126 49069433 49070278 49070618 49071545 49071801 49072841 49074213 49074356 49074913 49075087 49075340 49075779 49076092 49076931 49077493 49078980 49079176 49079387 49081222 49082370 49082678 49082870 49083071 49083398 49084497 49084712 49086681 49086928 49087311 49087663 49088139 49089746 1901122

49063084 49063316 49063573 49065144 49065853 49066219 49066502 49066863 49067146 49067552 49067941 49068449 49068768 49069255 49069454 49070362 49070729 49071704 49072003 49072988 49074266 49074464 49075001 49075194 49075400 49075909 49076249 49076983 49077539 49079062 49079297 49079595 49081448 49082531 49082705 49082964 49083164 49083589 49084601 49084909 49086834 49087071 49087451 49087769 49088389 49089833 1902925

CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA1F CACNA2D4

chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4

1904464 1904831 1906583 1908840 1909165 1909551 1910208 1910739 1919443 1919708 1920827 1949904 1953567 1955759 1963116 1965177 1965349 1967742 1969310 1983769 1984416 1987480 1988121 1988969 1992032 1993408 1993933 1994152 1995130 1995388 1996174 2016605 2017040 2019071 2022188 2024019 2027412 15471488 15474845 15477538 15480346 15482327 15504051 15504444 15511761 15512869 15516329

1904545 1904946 1906701 1908861 1909218 1909604 1910284 1910810 1919506 1919753 1920889 1949985 1953695 1955855 1963210 1965275 1965395 1967810 1969372 1983841 1984503 1987555 1988202 1989047 1992166 1993487 1994047 1994242 1995205 1995539 1996235 2016737 2017203 2019131 2022305 2024101 2027870 15471681 15474879 15477595 15480430 15482451 15504140 15504546 15511863 15513046 15516492

CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CACNA2D4 CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A

chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10

15517490 15518247 15529069 15530242 15534815 15538542 15539521 15542459 15552446 15554780 15556694 15558926 15560787 15562153 15564977 15568999 15569299 15570915 15572020 15575772 15581590 15587779 15589438 15591167 15597707 15599029 15601151 15602859 73555527 73556860 73558110 73558867 73559248 73560392 73562654 73562965 73565562 73565924 73567033 73567272 73567602 73569576 73570228 73571071 73571267 73571469 73571711

15517627 15518379 15529279 15530349 15534956 15538699 15539760 15542637 15552603 15554928 15556833 15559130 15560880 15562245 15565145 15569105 15569409 15571012 15572119 15575949 15581794 15587869 15589552 15591302 15597830 15599088 15601329 15603180 73555836 73556977 73558335 73559037 73559386 73560512 73562832 73563177 73565754 73566038 73567163 73567524 73567764 73569833 73570326 73571192 73571347 73571510 73571772

CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CC2D2A CDH23 CDH23 CDH23 CDH23 CDH23 CDH23 CDH23 CDH23 CDH23 CDH23 CDH23 CDH23 CDH23 CDH23 CDH23 CDH23 CDH23 CDH23 CDH23

chr10 chr10 chr10 chr10 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12

73572236 73572524 73573000 73574708 68678150 68679538 68710287 68712036 68712403 68712664 68713701 68714870 68716204 68718485 68719107 68721414 68725622 68729157 68729679 68732093 85954411 85955249 85956260 85957541 85958787 85960356 85961562 85962735 85964282 85965582 85967929 85968484 85970756 85971403 85971934 85972846 85978834 88442789 88444130 88447428 88448116 88449352 88452624 88453674 88454606 88456468 88457757

73572366 73572647 73573105 73575702 68679327 68679653 68710373 68712180 68712559 68712809 68713877 68714999 68716390 68718727 68719253 68721639 68725829 68729288 68729826 68732957 85954571 85955345 85956406 85957592 85958877 85960443 85961676 85962879 85964361 85965683 85968133 85968637 85970921 85971471 85972163 85973104 85979374 88443191 88444210 88447523 88448190 88449494 88452797 88453797 88454771 88456555 88457892

CDH23 CDH23 CDH23 CDH23 CDH3 CDH3 CDH3 CDH3 CDH3 CDH3 CDH3 CDH3 CDH3 CDH3 CDH3 CDH3 CDH3 CDH3 CDH3 CDH3 CDHR1 CDHR1 CDHR1 CDHR1 CDHR1 CDHR1 CDHR1 CDHR1 CDHR1 CDHR1 CDHR1 CDHR1 CDHR1 CDHR1 CDHR1 CDHR1 CDHR1 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290

chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr2 chr2 chr2

88462298 88465070 88465557 88470998 88471473 88472868 88473958 88476807 88477623 88478362 88479815 88480167 88481556 88482808 88484504 88486457 88487546 88490664 88496614 88500451 88500772 88502842 88504978 88505470 88508196 88508874 88510809 88512259 88512419 88513890 88514773 88519022 88520092 88522722 88523470 88524044 88524321 88524941 88530419 88532921 88533271 88534732 88534982 88535676 182401402 182403818 182409426

88462422 88465226 88465703 88471121 88471695 88473006 88474172 88477007 88477731 88478629 88479950 88480275 88481721 88483264 88484616 88486609 88487752 88490776 88496788 88500682 88500875 88502958 88505128 88505635 88508339 88508959 88510922 88512347 88512520 88514053 88514943 88519146 88520215 88522812 88523653 88524197 88524342 88524995 88530563 88532968 88533341 88534810 88535111 88535993 182402971 182403991 182409523

CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CEP290 CERKL CERKL CERKL

chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1

182412344 182412548 182413271 182413406 182414360 182423292 182468563 182521495 31913720 31914149 31914783 31915124 31915518 31915721 31916150 31916606 31917019 31917196 31917826 31918062 31918395 31918644 31918920 31919117 31919331 31919651 196621007 196642107 196642986 196645118 196646605 196648752 196654193 196658549 196659192 196682864 196684722 196694250 196695599 196695890 196697475 196705953 196706604 196709748 196711004 196712581 196714946

182412453 182412574 182413331 182413584 182414435 182423435 182468806 182521834 31914062 31914383 31914969 31915298 31915620 31915858 31916289 31916738 31917121 31917334 31917924 31918180 31918549 31918721 31919021 31919250 31919381 31919861 196621305 196642293 196643092 196645195 196646797 196648923 196654367 196658744 196659369 196683047 196684899 196694427 196695782 196696070 196697652 196706136 196706790 196709922 196711181 196712758 196715129

CERKL CERKL CERKL CERKL CERKL CERKL CERKL CERKL CFB CFB CFB CFB CFB CFB CFB CFB CFB CFB CFB CFB CFB CFB CFB CFB CFB CFB CFH CFH CFH CFH CFH CFH CFH CFH CFH CFH CFH CFH CFH CFH CFH CFH CFH CFH CFH CFH CFH

chr1 chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr3 chr3 chr3 chr3 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr2

196716240 85116184 85128056 85133969 85149192 85155650 85156088 85166265 85211157 85212859 85213865 85218669 85233770 85236740 85282494 85302487 28488599 28489057 28493425 28493647 28493797 28493946 28495326 28497667 28497898 28498776 28498982 28499911 28500610 28502802 28503034 28503340 150643949 150645851 150659368 150661606 47937993 47942779 47944057 47945197 47945387 47951849 47953369 47954599 47972912 47983409 98962617

196716634 85119826 85128217 85134068 85149289 85155714 85156193 85166343 85211383 85212980 85213982 85219057 85233895 85236813 85282561 85302566 28488956 28489198 28493519 28493703 28493866 28493993 28495439 28497811 28497971 28498862 28499062 28499983 28500707 28502881 28503156 28503623 150644659 150645988 150659548 150662023 47939846 47942886 47944165 47945305 47945429 47951912 47953486 47954720 47973117 47983550 98962997

CFH CHM CHM CHM CHM CHM CHM CHM CHM CHM CHM CHM CHM CHM CHM CHM CLN3 CLN3 CLN3 CLN3 CLN3 CLN3 CLN3 CLN3 CLN3 CLN3 CLN3 CLN3 CLN3 CLN3 CLN3 CLN3 CLRN1 CLRN1 CLRN1 CLRN1 CNGA1 CNGA1 CNGA1 CNGA1 CNGA1 CNGA1 CNGA1 CNGA1 CNGA1 CNGA1 CNGA3

chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr8 chr8 chr8 chr8 chr8 chr8 chr8

98986401 98994149 98996637 98999850 99006120 99008326 99012306 57916243 57921758 57931300 57931699 57935255 57935431 57937725 57938637 57945656 57946833 57949152 57950032 57951171 57953002 57954290 57957176 57965619 57973333 57974137 57983256 57984284 57991244 57992313 57993791 57994385 57994743 57996468 57996745 57996877 57998033 57998390 58001031 58004963 87586163 87590916 87591333 87616320 87623815 87638210 87641146

98986539 98994263 98996817 98999904 99006237 99008433 99015064 57918361 57921978 57931447 57931818 57935339 57935529 57937885 57938779 57945779 57946898 57949239 57950083 57951380 57953158 57954448 57957284 57965782 57973496 57974225 57983343 57984444 57991281 57992389 57993969 57994434 57994819 57996514 57996776 57996968 57998106 57998448 58001198 58005020 87588358 87591091 87591480 87616439 87623899 87638308 87641306

CNGA3 CNGA3 CNGA3 CNGA3 CNGA3 CNGA3 CNGA3 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB1 CNGB3 CNGB3 CNGB3 CNGB3 CNGB3 CNGB3 CNGB3

chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1

87644979 87655978 87656849 87660028 87666239 87679152 87680246 87683171 87738758 87751882 87755726 97426638 97462748 97463249 97464793 97465288 97474297 97475056 103342022 103345238 103347252 103348754 103352362 103354132 103354278 103354421 103355010 103356006 103363680 103364221 103364496 103377714 103379192 103379907 103380259 103381186 103385866 103387073 103388891 103400004 103400615 103404590 103405882 103412404 103427421 103427731 103428208

87645121 87656101 87656914 87660115 87666290 87679361 87680396 87683326 87738885 87751964 87755903 97428138 97462892 97463384 97464963 97465385 97474479 97477628 103343721 103345472 103347321 103348867 103352612 103354186 103354314 103354475 103355118 103356060 103363734 103364329 103364550 103377768 103379246 103379961 103380367 103381240 103385920 103387127 103388945 103400112 103400669 103404644 103405990 103412512 103427475 103427821 103428316

CNGB3 CNGB3 CNGB3 CNGB3 CNGB3 CNGB3 CNGB3 CNGB3 CNGB3 CNGB3 CNGB3 CNNM4 CNNM4 CNNM4 CNNM4 CNNM4 CNNM4 CNNM4 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1

chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12

103431042 103435774 103440385 103444263 103444415 103444615 103444937 103449693 103453188 103455073 103461419 103461544 103462635 103463865 103467480 103467983 103468302 103468770 103469999 103470163 103471393 103471623 103471817 103474018 103477968 103480066 103481223 103483375 103484373 103487262 103488297 103491076 103491355 103496671 103540173 103544213 103548360 103573628 48366747 48367871 48368457 48369099 48369745 48370296 48370594 48370884 48371102

103431096 103435828 103440439 103444308 103444469 103444660 103444991 103449747 103453296 103455127 103461464 103461598 103462680 103463919 103467525 103468037 103468347 103468824 103470044 103470217 103471447 103471677 103471871 103474072 103478025 103480150 103481298 103483438 103484415 103487325 103488552 103491169 103491508 103496800 103540336 103544427 103548528 103574052 48367336 48368114 48368645 48369388 48369853 48370350 48370702 48370938 48371210

COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL11A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1

chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr6 chr6 chr6

48371382 48371792 48372073 48372379 48373293 48373791 48374336 48374697 48375125 48375558 48375889 48376284 48376630 48376875 48377167 48377465 48377869 48378328 48378777 48379316 48379510 48379694 48380118 48380617 48380860 48381051 48381393 48383010 48383543 48386660 48387240 48387591 48387776 48388206 48389037 48389492 48389657 48390330 48391388 48391653 48391814 48391951 48392197 48398019 70925742 70935634 70942285

48371436 48371900 48372181 48372541 48373347 48373845 48374444 48374751 48375179 48375612 48375943 48376392 48376729 48376920 48377221 48377519 48377923 48378382 48378876 48379370 48379609 48379748 48380226 48380671 48380959 48381096 48381492 48383064 48383588 48386714 48387285 48387645 48387830 48388260 48389091 48389546 48389702 48390408 48391490 48391707 48391847 48391984 48392214 48398285 70926784 70935712 70942474

COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL2A1 COL9A1 COL9A1 COL9A1

chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr19 chr19 chr19 chr19 chr4 chr4

70944241 70944496 70948956 70950391 70951121 70951666 70952364 70961822 70961964 70963087 70964178 70964665 70964852 70965039 70966470 70970359 70972946 70976419 70978506 70979335 70980016 70981357 70981767 70983749 70984421 70990514 70990706 70991092 70992683 197237333 197297551 197313410 197316469 197325960 197390129 197396583 197398578 197403835 197407676 197411295 197446793 48325098 48337665 48339499 48342576 187112673 187115653

70944296 70944643 70948989 70950436 70951157 70951738 70952418 70961876 70962018 70963132 70964232 70964719 70964906 70965093 70966524 70970413 70973000 70976473 70978563 70979368 70980070 70981411 70981791 70983785 70984475 70990577 70990742 70991167 70992911 197237612 197298133 197313606 197316609 197326143 197391086 197397131 197398744 197404742 197407805 197411422 197447584 48325267 48337800 48339651 48346586 187113191 187115766

COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 COL9A1 CRB1 CRB1 CRB1 CRB1 CRB1 CRB1 CRB1 CRB1 CRB1 CRB1 CRB1 CRB1 CRX CRX CRX CRX CYP4V2 CYP4V2

chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2

187117156 187118093 187118686 187120110 187122310 187126353 187130018 187130246 187131622 117164360 117165496 117166175 117168634 117170226 117185593 117186613 117187267 117188490 117228546 117240832 117265386 31137344 31144758 31152218 31164407 31165391 31187559 31190464 31191655 31196785 31198486 31200854 31222077 31224698 31227614 31241163 31279071 31284926 56093101 56097854 56098134 56102080 56103757 56104880 56108746 56144799 56145353

187117242 187118284 187118756 187120237 187122496 187126456 187130153 187130426 187134617 117165216 117165619 117166357 117169172 117170298 117185803 117186826 117187304 117188693 117228672 117241051 117265495 31140047 31144790 31152311 31164531 31165635 31187718 31190530 31191721 31196922 31198598 31201021 31222235 31224784 31227816 31241238 31279133 31285024 56094369 56098050 56098258 56102200 56103877 56105000 56108869 56145186 56145402

CYP4V2 CYP4V2 CYP4V2 CYP4V2 CYP4V2 CYP4V2 CYP4V2 CYP4V2 CYP4V2 DFNB31 DFNB31 DFNB31 DFNB31 DFNB31 DFNB31 DFNB31 DFNB31 DFNB31 DFNB31 DFNB31 DFNB31 DMD DMD DMD DMD DMD DMD DMD DMD DMD DMD DMD DMD DMD DMD DMD DMD DMD EFEMP1 EFEMP1 EFEMP1 EFEMP1 EFEMP1 EFEMP1 EFEMP1 EFEMP1 EFEMP1

chr2 chr2 chr6 chr6 chr6 chr6 chr6 chr6 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr14 chr14 chr14 chr14 chr14 chr14

56149494 56150845 80624528 80629136 80631341 80634668 80635910 80656896 50664490 50668418 50669397 50678227 50679020 50680421 50680954 50681522 50682072 50684260 50686399 50690732 50691391 50701162 50708583 50713929 50732078 50736462 50738765 50740588 50747007 66039170 66044872 66053930 66063350 66094278 66112370 66115066 66200486 66204555 66205751 66349670 66417027 92335754 92343830 92347635 92349297 92353536 92357564

56149582 56150932 80626600 80629264 80631513 80634749 80636098 80657315 50667280 50668497 50669602 50678935 50679166 50680516 50681074 50681633 50682288 50684356 50686516 50690909 50691562 50701298 50708742 50714058 50732823 50736571 50738886 50741024 50747147 66042310 66045039 66054070 66063510 66094393 66112498 66115260 66200600 66205500 66205886 66349785 66417118 92336729 92344026 92347762 92349420 92353656 92357681

EFEMP1 EFEMP1 ELOVL4 ELOVL4 ELOVL4 ELOVL4 ELOVL4 ELOVL4 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 ERCC6 EYS EYS EYS EYS EYS EYS EYS EYS EYS EYS EYS EYS FBLN5 FBLN5 FBLN5 FBLN5 FBLN5 FBLN5

chr14 chr14 chr14 chr14 chr14 chr17 chr17 chr17 chr17 chr11 chr11 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5

92361293 92403290 92406908 92409250 92413556 79495416 79503171 79503575 79503900 86656720 86665842 50229042 50230565 50230697 50230938 50231185 50231524 50231933 50232197 50232700 110145888 110146572 110148591 110148929 110151252 110152661 110153086 110155374 89854616 89910651 89913620 89914902 89918413 89920946 89923027 89924378 89925026 89930930 89933541 89938452 89938672 89939619 89940522 89941784 89943314 89947420 89948162

92361416 92403545 92406960 92409305 92414046 79496384 79503293 79503815 79504155 86663512 86666433 50229264 50230608 50230839 50231096 50231314 50231654 50232087 50232389 50235129 110146166 110146726 110148721 110149058 110151410 110152803 110153129 110155705 89854734 89910836 89913770 89914998 89918518 89921060 89923593 89924649 89925356 89931107 89933765 89938579 89938858 89939800 89940686 89941908 89943581 89947547 89948380

FBLN5 FBLN5 FBLN5 FBLN5 FBLN5 FSCN2 FSCN2 FSCN2 FSCN2 FZD4 FZD4 GNAT1 GNAT1 GNAT1 GNAT1 GNAT1 GNAT1 GNAT1 GNAT1 GNAT1 GNAT2 GNAT2 GNAT2 GNAT2 GNAT2 GNAT2 GNAT2 GNAT2 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98

chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5

89949025 89953721 89968362 89969870 89971059 89971896 89975365 89977131 89979402 89981596 89985677 89986613 89988421 89989706 89992753 89999481 90000205 90001216 90002047 90004632 90006797 90007000 90008103 90012283 90015864 90016751 90020648 90020902 90021365 90024485 90025458 90040862 90041407 90046367 90049390 90050799 90052270 90052795 90055225 90059121 90070002 90072269 90073721 90074243 90074681 90077246 90078940

89949769 89954095 89968539 89970051 89971262 89972026 89975446 89977271 89980012 89981812 89985893 89986858 89988603 89990518 89992963 89999612 90000305 90001396 90002211 90004726 90006876 90007139 90008245 90012546 90016040 90016876 90020806 90021049 90021473 90024750 90025581 90041082 90041612 90046514 90049646 90051002 90052447 90052978 90055405 90059286 90070120 90072393 90073860 90074426 90074914 90077395 90079142

GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98

chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr13 chr13 chr13 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6

90079654 90083887 90085518 90086689 90098555 90101100 90103418 90106049 90111435 90119241 90124760 90136394 90144453 90149100 90149878 90151557 90159573 90261231 90281160 90368263 90398035 90445846 90449037 90459598 114321596 114324001 114325813 178405329 178409910 178413130 178413838 178415935 178416265 178417592 178418424 178418867 178421441 42123143 42130657 42141070 42146017 42146539 42146980 42151022 42153417 42156319 42162351

90079874 90084127 90085668 90087163 90098699 90101275 90103554 90107155 90111553 90119413 90125003 90136802 90144638 90149350 90150018 90151718 90159674 90261348 90281339 90368421 90398157 90446038 90449215 90460033 114322400 114324129 114325972 178408855 178410222 178413754 178413984 178416136 178416406 178417747 178418560 178419084 178422124 42123331 42130833 42141552 42146167 42146633 42147792 42152680 42153535 42156469 42162694

GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GPR98 GRK1 GRK1 GRK1 GRM6 GRM6 GRM6 GRM6 GRM6 GRM6 GRM6 GRM6 GRM6 GRM6 GUCA1A GUCA1A GUCA1A GUCA1A GUCA1A GUCA1A GUCA1B GUCA1B GUCA1B GUCA1B

chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1

7905987 7906356 7907169 7909680 7910377 7910743 7911248 7912823 7915461 7915767 7916420 7917197 7917918 7918176 7918645 7919060 7919244 7919522 7919760 7923445 185703682 185815157 185833601 185834872 185878468 185880805 185891510 185892521 185894178 185897677 185902680 185931649 185932899 185934933 185939466 185946918 185950109 185951393 185953300 185956563 185958619 185959406 185962313 185963946 185966560 185969176 185970429

7906052 7907086 7907474 7910032 7910462 7910846 7911350 7912904 7915668 7915924 7916570 7917346 7918082 7918369 7918820 7919159 7919339 7919608 7919872 7923658 185704179 185815228 185833760 185834995 185878640 185880912 185891631 185892785 185894323 185897799 185902956 185931791 185933027 185935047 185939625 185947113 185950205 185951521 185953445 185956676 185958779 185959575 185962441 185964219 185966656 185969371 185970560

GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D GUCY2D HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1

chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1

185970725 185972849 185976259 185984290 185985089 185986094 185987314 185988672 185992161 186007065 186007960 186008859 186010144 186014819 186017874 186022083 186022956 186024524 186026365 186030982 186031645 186034369 186036965 186038794 186039743 186043872 186045559 186047238 186050338 186051996 186055377 186056348 186056574 186057063 186057276 186057737 186059889 186062265 186062617 186063407 186064374 186072603 186076015 186077592 186081943 186083110 186083950

185970873 185972976 185976414 185984569 185985371 185986203 185987484 185988827 185992285 186007167 186008137 186009011 186010268 186014995 186017971 186022206 186023118 186024806 186026533 186031096 186031732 186034561 186037139 186038908 186039889 186044023 186045754 186047352 186050526 186052093 186055539 186056462 186056777 186057145 186057408 186057887 186060049 186062390 186062801 186063505 186064653 186072800 186076097 186077729 186082085 186083255 186084078

HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1

chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr20 chr20 chr20 chr20 chr20

186084389 186086125 186086590 186088322 186088876 186089142 186092082 186094735 186097209 186099097 186099638 186101459 186105799 186106629 186106933 186113304 186113664 186114534 186114884 186120331 186120737 186121881 186122881 186134242 186135315 186135939 186140468 186141137 186143645 186147547 186151299 186157014 186158643 124221040 124248417 124248937 124266206 124266885 124268171 124269611 124271485 124273706 2639040 2640170 2640344 2640675 2640908

186084546 186086247 186086755 186088430 186089014 186089277 186092352 186094926 186097423 186099232 186099829 186101541 186106069 186106800 186107104 186113475 186113835 186114705 186115055 186120481 186120875 186122003 186123119 186134305 186135435 186136074 186140582 186141263 186143774 186147898 186151419 186157141 186160085 124221640 124248517 124249142 124266401 124266918 124268286 124269669 124271581 124274424 2639483 2640231 2640439 2640822 2641011

HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HMCN1 HTRA1 HTRA1 HTRA1 HTRA1 HTRA1 HTRA1 HTRA1 HTRA1 HTRA1 IDH3B IDH3B IDH3B IDH3B IDH3B

chr20 chr20 chr20 chr20 chr20 chr20 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9

2641102 2641554 2644091 2644305 2644570 2644798 128032331 128034331 128034509 128034942 128035184 128036653 128036985 128038467 128040148 128040386 128040870 128041068 128043759 128045820 139323071 139324728 139325453 139326275 139326930 139327407 139327606 139328488 139329191 139333059 102861510 102866779 102888664 102988343 102991941 103002341 103004851 103008897 103014564 103015188 103027103 103035145 103046601 103054607 103059198 103060217 103062849

2641475 2641615 2644212 2644404 2644651 2644843 128033082 128034415 128034653 128035087 128035328 128036749 128037076 128038667 128040236 128040593 128040945 128041170 128043808 128046024 139324259 139324865 139325569 139326437 139327038 139327527 139327731 139328586 139329315 139334256 102861698 102866909 102888831 102988517 102992109 103002522 103004961 103009069 103014720 103015418 103027210 103035358 103046885 103055325 103059428 103060292 103063426

IDH3B IDH3B IDH3B IDH3B IDH3B IDH3B IMPDH1 IMPDH1 IMPDH1 IMPDH1 IMPDH1 IMPDH1 IMPDH1 IMPDH1 IMPDH1 IMPDH1 IMPDH1 IMPDH1 IMPDH1 IMPDH1 INPP5E INPP5E INPP5E INPP5E INPP5E INPP5E INPP5E INPP5E INPP5E INPP5E INVS INVS INVS INVS INVS INVS INVS INVS INVS INVS INVS INVS INVS INVS INVS INVS INVS

chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr2 chr2 chr2 chr9 chr9 chr7 chr7 chr7 chr7

121488609 121491403 121500589 121507130 121508919 121526190 121527762 121544897 121547316 121547707 121553237 121553812 10618331 10621430 10621760 10622107 10622430 10623135 10624425 10625004 10625510 10625790 10626003 10626618 10627586 10628607 10629196 10629708 10630169 10630894 10632228 10632778 10633115 10637045 10639115 10644610 10653348 10654097 233630511 233635612 233641154 2717525 2729445 23145916 23163395 23164306 23164666

121489421 121491560 121500721 121507279 121509062 121526290 121527856 121545027 121547479 121547819 121553326 121553926 10620603 10621581 10621892 10622341 10622540 10623249 10624511 10625032 10625627 10625904 10626117 10626732 10627751 10628758 10629370 10629755 10630283 10631008 10632342 10632898 10633246 10637106 10639370 10644662 10653654 10654694 233633523 233636088 233641275 2719095 2729757 23146413 23163498 23164400 23164791

IQCB1 IQCB1 IQCB1 IQCB1 IQCB1 IQCB1 IQCB1 IQCB1 IQCB1 IQCB1 IQCB1 IQCB1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 JAG1 KCNJ13 KCNJ13 KCNJ13 KCNV2 KCNV2 KLHL7 KLHL7 KLHL7 KLHL7

chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr4 chr4 chr4 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr2 chr2 chr2 chr2 chr2

23180387 23183469 23191685 23205316 23207454 23212566 23213633 80194708 80198800 80201304 80202267 80203329 80222928 80228421 80234880 80246832 155665162 155665477 155670135 68080107 68115314 68125117 68131214 68133038 68153783 68157348 68170950 68173991 68177381 68178903 68181156 68183795 68190956 68192569 68193445 68197042 68201069 68204356 68205913 68207244 68213903 68216276 112656190 112686696 112702536 112704970 112722767

23180563 23183644 23191828 23205557 23207656 23212664 23215036 80197583 80198933 80201447 80202364 80203467 80223458 80228802 80234986 80247147 155665374 155666018 155674270 68080273 68115711 68125315 68131411 68133170 68154180 68157520 68171167 68174281 68177608 68179088 68181480 68183995 68191165 68192760 68193655 68197168 68201306 68204467 68206150 68207384 68214001 68216743 112656373 112687117 112702637 112705144 112722854

KLHL7 KLHL7 KLHL7 KLHL7 KLHL7 KLHL7 KLHL7 LCA5 LCA5 LCA5 LCA5 LCA5 LCA5 LCA5 LCA5 LCA5 LRAT LRAT LRAT LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 LRP5 MERTK MERTK MERTK MERTK MERTK

chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr20 chr20 chr20 chr20 chr20 chr20 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4

112725713 112732865 112740418 112751827 112754899 112758777 112760668 112761480 112765959 112767524 112776989 112778998 112779834 112785927 119209651 119210893 119211404 119212566 119213305 119213582 119214525 119215024 119215341 119215583 119216129 119216482 119216755 119216981 119217169 10385832 10388263 10389275 10393177 10401175 10414755 100485239 100495965 100503061 100504530 100510799 100512391 100512807 100515889 100518223 100521721 100522763 100527904

112725829 112733049 112740570 112751981 112755053 112758863 112760764 112761561 112766052 112767643 112777099 112779158 112779971 112786945 119210558 119211150 119212482 119212694 119213437 119213713 119214674 119215101 119215467 119215714 119216343 119216638 119216869 119217084 119217383 10386335 10388374 10389451 10394579 10401406 10414866 100485394 100496127 100503249 100504674 100510907 100512508 100512947 100516040 100518381 100521890 100522871 100528117

MERTK MERTK MERTK MERTK MERTK MERTK MERTK MERTK MERTK MERTK MERTK MERTK MERTK MERTK MFRP:C1QTNF5 MFRP:C1QTNF5 MFRP:C1QTNF5 MFRP:C1QTNF5 MFRP:C1QTNF5 MFRP:C1QTNF5 MFRP:C1QTNF5 MFRP:C1QTNF5 MFRP:C1QTNF5 MFRP:C1QTNF5 MFRP:C1QTNF5 MFRP:C1QTNF5 MFRP:C1QTNF5 MFRP:C1QTNF5 MFRP:C1QTNF5 MKKS MKKS MKKS MKKS MKKS MKKS MTTP MTTP MTTP MTTP MTTP MTTP MTTP MTTP MTTP MTTP MTTP MTTP

chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11

100529922 100532299 100532488 100534069 100540130 100542217 100543833 76839309 76841634 76853754 76858843 76866952 76867705 76867907 76868324 76869322 76870492 76871208 76872018 76873165 76873898 76877101 76883793 76885801 76886417 76888594 76890090 76890780 76891419 76892425 76892996 76893468 76894112 76895632 76900388 76901064 76901741 76903095 76905398 76908525 76909539 76910579 76912492 76913344 76914104 76915120 76916506

100530134 100532397 100532610 100534297 100540255 100542388 100545154 76839535 76841698 76853868 76858996 76867137 76867827 76868050 76868438 76869476 76870569 76871328 76872161 76873376 76874034 76877208 76883931 76885960 76886510 76888689 76890175 76890999 76891527 76892635 76893200 76893645 76894202 76895760 76900515 76901184 76901915 76903323 76905569 76908643 76909666 76910863 76912683 76913469 76914262 76915274 76916662

MTTP MTTP MTTP MTTP MTTP MTTP MTTP MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A

chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chrX chrX chrX chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3

76917141 76918333 76919474 76919741 76922196 76922865 76923996 76924904 76925651 43808024 43817717 43832549 110880913 110883213 110886762 110889255 110901118 110902069 110904329 110905492 110907758 110917703 110919179 110920624 110922096 110922628 110926028 110927382 110935999 110937200 110958997 110962476 132399453 132401546 132402242 132403397 132405103 132405994 132407493 132407917 132409371 132410035 132411497 132413670 132415574 132416103 132418196

76917247 76918447 76919562 76919848 76922382 76922982 76924080 76925024 76926286 43809272 43818098 43832921 110881640 110883258 110886836 110889368 110901218 110902146 110904412 110905603 110907833 110917832 110919274 110920712 110922307 110922732 110926130 110927575 110936124 110937261 110959071 110962639 132400934 132401662 132402368 132403638 132405231 132406070 132407735 132408107 132409494 132410130 132411662 132413809 132415657 132416206 132418294

MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A MYO7A NDP NDP NDP NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP1 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3

chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr15 chr15 chr15 chr15 chr15

132418761 132419177 132420273 132423041 132424583 132426944 132431969 132433928 132435600 132437837 132438548 132440806 5922869 5923949 5924397 5925161 5926432 5927089 5927799 5933311 5934530 5934933 5937152 5940173 5947345 5950927 5964676 5965351 5965691 5967174 5969211 5987708 5993206 6007163 6008129 6012759 6021853 6027358 6029146 6038329 6046214 6052303 72102893 72103822 72104105 72104294 72104675

132418905 132419292 132420377 132423215 132424658 132427101 132432130 132434062 132435753 132437988 132438674 132441276 5923465 5924093 5924577 5925333 5926518 5927175 5927956 5933395 5934717 5935160 5937358 5940299 5947526 5951088 5964864 5965543 5965843 5967282 5969273 5987847 5993389 6007290 6008311 6012896 6022009 6027423 6029319 6038473 6046387 6052531 72103201 72103949 72104209 72104516 72104851

NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP3 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NPHP4 NR2E3 NR2E3 NR2E3 NR2E3 NR2E3

chr15 chr15 chr14 chr14 chr14 chrX chrX chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chr3 chr3 chr3 chr3 chr3 chr3 chr3

72105728 72106352 24549315 24551676 24553728 41306712 41332743 126085871 126089408 126090294 126091495 126092366 126094004 126097110 126097309 126100541 126107441 13752831 13753366 13754596 13756964 13757120 13762533 13764437 13764898 13767545 13769367 13771486 13773269 13774696 13775778 13776455 13778233 13779203 13780462 13781863 13785245 13786172 13786836 13787184 193310932 193332511 193333462 193336657 193349400 193353206 193354983

72105976 72107270 24550777 24552084 24553832 41307179 41334905 126086671 126089553 126090408 126091624 126092489 126094132 126097206 126097534 126100769 126107545 13753202 13753465 13754797 13757033 13757151 13762638 13764574 13765072 13767652 13769487 13771560 13773361 13774886 13775909 13776567 13778839 13779330 13780563 13781974 13785403 13786343 13786904 13787480 193311198 193332830 193333559 193336725 193349454 193353311 193355070

NR2E3 NR2E3 NRL NRL NRL NYX NYX OAT OAT OAT OAT OAT OAT OAT OAT OAT OAT OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OFD1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1

chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr19 chr19 chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chr7 chr7 chr7 chr7 chr7 chr14

193355740 193360553 193360763 193361161 193361316 193361763 193363341 193363516 193364853 193365858 193366583 193372650 193374868 193376675 193377270 193380610 193382668 193384084 193384958 193409851 193412394 46049540 46087880 153409724 153416127 153418412 153420048 153421768 153424290 153448084 153453258 153455542 153457178 153458898 153461420 153485202 153490376 153492660 153494296 153496016 153498538 128412542 128413702 128414551 128415039 128415492 57267424

193355854 193360634 193360838 193361233 193361416 193361894 193363414 193363589 193364969 193365923 193366660 193372816 193375021 193376784 193377350 193380751 193382785 193384178 193385069 193409921 193415599 46057169 46088122 153409869 153416424 153418581 153420214 153422008 153424507 153448278 153453555 153455711 153457344 153459138 153462351 153485396 153490673 153492829 153494462 153496256 153499469 128412713 128413942 128414717 128415208 128415844 57269073

OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA1 OPA3 OPA3 OPN1LW OPN1LW OPN1LW OPN1LW OPN1LW OPN1LW OPN1MW OPN1MW OPN1MW OPN1MW OPN1MW OPN1MW OPN1MW OPN1MW OPN1MW OPN1MW OPN1MW OPN1MW OPN1SW OPN1SW OPN1SW OPN1SW OPN1SW OTX2

chr14 chr14 chr14 chr14 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10

57270905 57272077 57276876 57277093 3869741 3888572 3891223 3893104 3897573 3899317 3903890 102505467 102509502 102510450 102539254 102541002 102546699 102566186 102568866 102584404 102586765 102587299 55568452 55570315 55587148 55588324 55591074 55600079 55616934 55626401 55663002 55698574 55700625 55719491 55721511 55755408 55779951 55782651 55826516 55839090 55849743 55892634 55912859 55943203 55944893 55949123 55955442

57271081 57272293 57276940 57277184 3870375 3888925 3891477 3893281 3897697 3899443 3904502 102506060 102509671 102510648 102539340 102541122 102546768 102566362 102568993 102584506 102586852 102589698 55569306 55570426 55587308 55588333 55591293 55600256 55617023 55626617 55663130 55698715 55700735 55719604 55721652 55755525 55780176 55782957 55826645 55839184 55849823 55892767 55913053 55943353 55945028 55949144 55955649

OTX2 OTX2 OTX2 OTX2 PANK2 PANK2 PANK2 PANK2 PANK2 PANK2 PANK2 PAX2 PAX2 PAX2 PAX2 PAX2 PAX2 PAX2 PAX2 PAX2 PAX2 PAX2 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15

chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4

55973695 55996582 56077030 56089355 56106124 56128879 56138541 56287571 56288147 56423931 56560684 149237518 149242681 149245732 149247287 149247657 149262991 149264041 149264342 149265827 149274745 149275918 149276273 149277925 149278937 149283210 149286874 149294505 149301197 149310590 149313492 149314128 149323762 619362 628465 629668 647640 647868 648612 649728 650033 650662 651139 652740 654255 655922 656297

55973808 55996691 56077201 56089466 56106244 56129035 56138702 56287637 56288162 56424050 56561051 149240534 149242829 149245816 149247362 149247721 149263099 149264142 149264430 149265937 149274853 149276065 149276339 149278069 149279087 149283258 149286941 149294570 149301272 149310731 149313582 149314281 149324356 619883 628618 629758 647781 647943 648677 649795 650081 650812 651283 652806 654402 656030 656407

PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PCDH15 PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6A PDE6B PDE6B PDE6B PDE6B PDE6B PDE6B PDE6B PDE6B PDE6B PDE6B PDE6B PDE6B PDE6B PDE6B

chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr7 chr7 chr7 chr7 chr7 chr7 chr7

656888 657558 657902 658669 659043 660319 661644 663834 95372344 95380388 95380647 95381688 95385331 95386396 95386561 95389014 95394514 95395253 95396751 95399826 95400206 95400676 95405716 95415516 95418657 95418860 95421815 95422316 95422784 95425116 102777088 102777855 102778578 102780374 102781554 102781965 102783192 102783684 102789750 102790829 92116336 92118606 92119027 92120585 92122266 92123606 92123800

656976 657659 658010 658733 659118 660403 661795 664680 95372962 95380541 95380737 95381829 95385406 95386461 95386628 95389062 95394664 95395397 95396820 95399973 95400314 95400786 95405804 95415617 95418765 95418924 95421890 95422400 95422935 95425429 102777372 102778053 102778974 102780435 102781702 102782142 102783367 102783825 102790141 102790879 92116855 92118737 92119225 92120816 92122443 92123710 92123943

PDE6B PDE6B PDE6B PDE6B PDE6B PDE6B PDE6B PDE6B PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDE6C PDZD7 PDZD7 PDZD7 PDZD7 PDZD7 PDZD7 PDZD7 PDZD7 PDZD7 PDZD7 PEX1 PEX1 PEX1 PEX1 PEX1 PEX1 PEX1

chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr8 chr8 chr8 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chr10 chr10 chr10 chr10 chr10 chr10

92126026 92129017 92130820 92131203 92132354 92134045 92135561 92136307 92138642 92140257 92140893 92143161 92146589 92147454 92148308 92151415 92157620 77892495 77912225 77913118 137143701 137146351 137147456 137166752 137167210 137187764 137191027 137193335 137219279 137234595 77359665 77365363 77369240 77369512 77372808 77373547 77378331 77378691 77380370 77380823 77381286 13319795 13322975 13325689 13330359 13333830 13336427

92126091 92129152 92130987 92131393 92132509 92134216 92135658 92136440 92138725 92140361 92141017 92143281 92147356 92147569 92148392 92151559 92157845 77896431 77912368 77913280 137143933 137146409 137147607 137166830 137167319 137187871 137191141 137193391 137219379 137235071 77359902 77365414 77369396 77369657 77372912 77373667 77378446 77378871 77380548 77380922 77382324 13320354 13323110 13325839 13330541 13333912 13336596

PEX1 PEX1 PEX1 PEX1 PEX1 PEX1 PEX1 PEX1 PEX1 PEX1 PEX1 PEX1 PEX1 PEX1 PEX1 PEX1 PEX1 PEX2 PEX2 PEX2 PEX7 PEX7 PEX7 PEX7 PEX7 PEX7 PEX7 PEX7 PEX7 PEX7 PGK1 PGK1 PGK1 PGK1 PGK1 PGK1 PGK1 PGK1 PGK1 PGK1 PGK1 PHYH PHYH PHYH PHYH PHYH PHYH

chr10 chr10 chr10 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4

13337495 13340186 13341967 6354583 6360913 6364692 6367051 6367489 6367974 6371544 6373579 6374480 6375976 6377751 6380348 6381294 6381866 6386836 6387535 6406846 6441306 6459704 74536120 74536586 74538634 74539110 74539884 15969848 15972665 15981017 15981503 15982044 15985885 15987382 15987579 15989285 15991354 15992844 15993870 15995609 16000007 16002118 16008160 16010571 16014897 16017788 16019945

13337606 13340245 13342130 6358963 6361042 6364876 6367201 6367638 6368091 6371661 6373728 6374675 6376147 6377924 6380533 6381417 6382056 6387072 6387612 6406894 6441402 6459877 74536297 74536655 74538715 74539203 74541458 15970991 15972705 15981086 15981527 15982160 15985978 15987451 15987660 15989339 15991447 15992916 15994014 15995694 16000111 16002242 16008313 16010731 16014961 16017863 16020163

PHYH PHYH PHYH PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PITPNM3 PRCD PRCD PRCD PRCD PRCD PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1

chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17

16024948 16025917 16026814 16034926 16037357 16040568 16077309 150293927 150297352 150298208 150300778 150305154 150305449 150307405 150310635 150312873 150315784 150316637 150316909 150318493 150318883 150321632 150325308 54618789 54621650 54621952 54625238 54625875 54626832 54627127 54627877 54629902 54631447 54631679 54632431 54632646 54634737 1553922 1554401 1554707 1554941 1556835 1557070 1558643 1559685 1559941 1561546

16025038 16025981 16026935 16035132 16037384 16040624 16077741 150294041 150297545 150298339 150300925 150305238 150305670 150307712 150310802 150312953 150315928 150316737 150317023 150318612 150318967 150321694 150325704 54619177 54621835 54622013 54625322 54625973 54626939 54627297 54628035 54629992 54631575 54631752 54632560 54632745 54635150 1554250 1554604 1554847 1555082 1556977 1557310 1558837 1559859 1560055 1561675

PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PROM1 PRPF3 PRPF3 PRPF3 PRPF3 PRPF3 PRPF3 PRPF3 PRPF3 PRPF3 PRPF3 PRPF3 PRPF3 PRPF3 PRPF3 PRPF3 PRPF3 PRPF31 PRPF31 PRPF31 PRPF31 PRPF31 PRPF31 PRPF31 PRPF31 PRPF31 PRPF31 PRPF31 PRPF31 PRPF31 PRPF31 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8

chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr6 chr6 chr6 chr19 chr19 chr19 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13

1561819 1562650 1563134 1563725 1563991 1564286 1564564 1564904 1565199 1576374 1576650 1577039 1577735 1578445 1578913 1579221 1579500 1579798 1580269 1580858 1581811 1582055 1582310 1582584 1582902 1584019 1584222 1584771 1585113 1585422 1586826 1587765 1588073 42664332 42672102 42689491 3769088 3771524 3772160 48877882 48881415 48916734 48919215 48921960 48923091 48934152 48936950

1562057 1562842 1563295 1563872 1564121 1564456 1564700 1565084 1565447 1576491 1576861 1577186 1577974 1578633 1579106 1579348 1579664 1580005 1580466 1580988 1581946 1582175 1582500 1582704 1583093 1584125 1584348 1584984 1585332 1585587 1586995 1587876 1588176 42666245 42672349 42690358 3770957 3771749 3772219 48878185 48881542 48916850 48919335 48921999 48923159 48934263 48937093

PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPF8 PRPH2 PRPH2 PRPH2 RAX2 RAX2 RAX2 RB1 RB1 RB1 RB1 RB1 RB1 RB1 RB1

chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr1 chr1 chr1 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr12 chr12 chr12 chr12 chr12 chr10

48939029 48941629 48942662 48947540 48951053 48953729 48954188 48954300 48955382 49027128 49030339 49033823 49037866 49039133 49039340 49047495 49050836 49051490 49054133 48381486 48383843 48385846 48387823 95351592 95353579 95360149 95360423 95360674 95360927 211649863 211654461 211665109 68168602 68187564 68189140 68191189 68191815 68192767 68193697 68195907 68200462 56114150 56114936 56115472 56117669 56118105 86004808

48939107 48941739 48942740 48947628 48951170 48953786 48954220 48954377 48955579 49027247 49030485 49033969 49037971 49039247 49039504 49047526 49050979 49051540 49056026 48382260 48383986 48386037 48390991 95351869 95353792 95360256 95360560 95360803 95360993 211652669 211654771 211666259 68168652 68187619 68189427 68191308 68191971 68192872 68193907 68196097 68201168 56114301 56115278 56115731 56117833 56118525 86004925

RB1 RB1 RB1 RB1 RB1 RB1 RB1 RB1 RB1 RB1 RB1 RB1 RB1 RB1 RB1 RB1 RB1 RB1 RB1 RBP3 RBP3 RBP3 RBP3 RBP4 RBP4 RBP4 RBP4 RBP4 RBP4 RD3 RD3 RD3 RDH12 RDH12 RDH12 RDH12 RDH12 RDH12 RDH12 RDH12 RDH12 RDH5 RDH5 RDH5 RDH5 RDH5 RGR

chr10 chr10 chr10 chr10 chr10 chr10 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr17 chr19 chr3 chr3 chr3 chr3 chr3 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6

86007346 86008665 86012612 86014081 86017648 86018263 63133455 63149539 63154412 63156350 63156653 63156968 63159130 63164317 63173849 63185403 63186292 63189660 63193243 63198110 63200280 63204039 63206605 63221119 63223392 33166312 129247481 129249718 129251093 129251375 129252450 72596649 72678685 72806651 72809677 72889277 72891986 72943475 72945320 72947525 72952016 72955517 72957717 72960032 72960623 72960917 72962463

86007503 86008799 86012766 86014199 86017762 86018944 63133715 63149636 63154463 63156457 63156705 63157027 63159207 63164399 63173921 63185433 63186354 63189774 63193359 63198198 63200419 63204125 63206723 63221604 63223819 33169206 129247937 129249887 129251259 129251615 129254187 72596890 72678766 72806865 72809689 72889618 72892852 72943543 72945431 72947625 72952140 72955564 72957830 72960163 72960795 72961071 72962535

RGR RGR RGR RGR RGR RGR RGS9 RGS9 RGS9 RGS9 RGS9 RGS9 RGS9 RGS9 RGS9 RGS9 RGS9 RGS9 RGS9 RGS9 RGS9 RGS9 RGS9 RGS9 RGS9 RGS9BP RHO RHO RHO RHO RHO RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1

chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr11 chr11 chr11 chr8 chr8 chr8 chr8 chrX chrX chrX chrX chrX chr7 chr7 chr7 chr7 chr7 chr7 chr1 chr1

72967827 72968688 72970407 72974677 72975092 72975662 72984051 72993749 73000381 73001636 73016960 73023208 73043302 73100299 73102399 73107950 73108656 73110197 89753097 89753929 89754973 89758290 89760350 89761795 89762194 89762967 89764765 62380212 62381729 62382092 55528626 55533514 55534676 55537229 46696346 46712910 46719422 46736939 46739120 33134409 33136104 33136882 33138918 33140142 33148832 68894506 68896747

72967984 72968814 72970470 72974755 72975206 72975752 72984135 72993821 73000564 73001749 73017073 73023375 73043538 73100438 73102512 73108052 73108796 73112845 89753674 89754040 89755132 89758469 89760555 89761924 89762306 89763090 89764922 62381343 62381976 62382590 55528762 55534141 55534848 55543394 46696637 46713576 46719537 46737025 46741791 33135044 33136166 33136974 33139048 33140173 33149002 68895610 68896859

RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RIMS1 RLBP1 RLBP1 RLBP1 RLBP1 RLBP1 RLBP1 RLBP1 RLBP1 RLBP1 ROM1 ROM1 ROM1 RP1 RP1 RP1 RP1 RP2 RP2 RP2 RP2 RP2 RP9 RP9 RP9 RP9 RP9 RP9 RPE65 RPE65

chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chrX chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14

68896964 68897153 68903869 68904624 68904873 68905243 68906535 68910213 68910458 68912392 68914306 68915577 38143701 38147113 38150211 38150645 38156536 38158208 38160499 38163887 38169867 38176568 38178081 38180279 38182105 38182651 38186592 21756135 21762835 21769124 21770646 21771489 21775889 21778742 21779982 21780591 21785854 21788175 21789417 21790012 21792776 21793390 21793989 21795781 21796582 21798407 21802763

68897059 68897268 68903999 68904764 68905006 68905325 68906683 68910355 68910566 68912543 68914389 68915642 38146498 38147294 38150277 38150737 38156705 38158394 38160624 38164043 38170026 38176718 38178240 38180342 38182198 38182777 38186788 21756220 21762968 21769396 21770743 21771702 21775995 21778766 21780129 21780665 21786009 21788336 21789561 21790163 21793229 21793542 21794332 21795966 21796786 21798546 21802864

RPE65 RPE65 RPE65 RPE65 RPE65 RPE65 RPE65 RPE65 RPE65 RPE65 RPE65 RPE65 RPGR RPGR RPGR RPGR RPGR RPGR RPGR RPGR RPGR RPGR RPGR RPGR RPGR RPGR RPGR RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1

chr14 chr14 chr14 chr14 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chr16 chrX chrX chrX chrX chrX chrX chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2

21811194 21813271 21816330 21819262 53633817 53639392 53644878 53652936 53656130 53670350 53671606 53672221 53674944 53675196 53679536 53682875 53686446 53690383 53691364 53692325 53692683 53698781 53705421 53706781 53708928 53720344 53721774 53725977 53730062 53734550 53737714 18657809 18662549 18665310 18674772 18675759 18690136 234216308 234217807 234224720 234227396 234229275 234231591 234235766 234237123 234238138 234240285

21811387 21813356 21816461 21819460 53636100 53639526 53644963 53653120 53656268 53670424 53671766 53672323 53675028 53675387 53679915 53683027 53686899 53690501 53691544 53692376 53692790 53698921 53705495 53706928 53709034 53720488 53721877 53726276 53730207 53734642 53737771 18660276 18662745 18665452 18674878 18675785 18690223 234216668 234217910 234224781 234227441 234229469 234231651 234235843 234237259 234238223 234240358

RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1 RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RPGRIP1L RS1 RS1 RS1 RS1 RS1 RS1 SAG SAG SAG SAG SAG SAG SAG SAG SAG SAG

chr2 chr2 chr2 chr2 chr2 chr2 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2

234243607 234247321 234249100 234250916 234255048 234255452 156123321 156124340 156126204 156127860 156128178 156128509 156130233 156130695 156131136 156132734 156142616 156144612 156144876 156145346 156146195 96940074 96940994 96942641 96942818 96943276 96943544 96943974 96944284 96944546 96945188 96947551 96948938 96949272 96949550 96950095 96950917 96952048 96952425 96952743 96953176 96953600 96954400 96954774 96954964 96955536 96956063

234243745 234247399 234249124 234250972 234255058 234255701 156123555 156124508 156126365 156127923 156128277 156128615 156130350 156130820 156131309 156132885 156142797 156144731 156145034 156145447 156147541 96940893 96941087 96942723 96942979 96943453 96943688 96944096 96944449 96944736 96945297 96947660 96949090 96949451 96949742 96950323 96951078 96952222 96952615 96952898 96953295 96953707 96954484 96954855 96955117 96955734 96956252

SAG SAG SAG SAG SAG SAG SEMA4A SEMA4A SEMA4A SEMA4A SEMA4A SEMA4A SEMA4A SEMA4A SEMA4A SEMA4A SEMA4A SEMA4A SEMA4A SEMA4A SEMA4A SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200

chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chrX chrX chr22

96956421 96957129 96957488 96958709 96959053 96961225 96962273 96962670 96963100 96963374 96964021 96964340 96964552 96965066 96966735 96967261 96968896 96970442 96971130 88851987 88857724 88859736 88862499 88883054 88892575 88893973 88895691 88897515 88899478 88903886 88904181 12695968 12696955 12785725 12883796 12886384 12901254 12902551 12903442 12904547 12923486 12946458 12951720 12958655 100603026 100603520 33196801

96956553 96957240 96957638 96958833 96959247 96961396 96962429 96962808 96963274 96963458 96964158 96964440 96964705 96965165 96966791 96967454 96969068 96970606 96971297 88852181 88857799 88859832 88862547 88883188 88893048 88894040 88895807 88897569 88899556 88903941 88904802 12696381 12697108 12785981 12883861 12886447 12901389 12902598 12903504 12904672 12923660 12946599 12951873 12966283 100603389 100603708 33198108

SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SNRNP200 SPATA7 SPATA7 SPATA7 SPATA7 SPATA7 SPATA7 SPATA7 SPATA7 SPATA7 SPATA7 SPATA7 SPATA7 TEAD1 TEAD1 TEAD1 TEAD1 TEAD1 TEAD1 TEAD1 TEAD1 TEAD1 TEAD1 TEAD1 TEAD1 TEAD1 TIMM8A TIMM8A TIMP3

chr22 chr22 chr22 chr22 chr4 chr4 chr4 chr4 chr4 chr9 chr9 chr11 chr11 chr11 chr11 chr11 chr9 chr9 chr9 chr3 chr9 chr9 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15

33245438 33253235 33254003 33255166 186990308 186997766 186999993 187003473 187005798 120466459 120474666 85358962 85361292 85365106 85366637 85367352 32540542 32550771 32552431 48507228 119449580 119459940 31293550 31318341 31319117 31320534 31321573 31323185 31324891 31327748 31329913 31330246 31332320 31334153 31338406 31339313 31340091 31341577 31342611 31352746 31353644 31354781 31355320 31358278 31359265 31360081 31362233

33245521 33253347 33254125 33259028 186990402 186998214 187000185 187005326 187006252 120466843 120479764 85359133 85361385 85365300 85366752 85367596 32544324 32550966 32552622 48509044 119449660 119463579 31295273 31318474 31319320 31320679 31321594 31323360 31325143 31327877 31330045 31330369 31332549 31334446 31338436 31339454 31340142 31341712 31342785 31352847 31353717 31354905 31355495 31358450 31359390 31360295 31362429

TIMP3 TIMP3 TIMP3 TIMP3 TLR3 TLR3 TLR3 TLR3 TLR3 TLR4 TLR4 TMEM126A TMEM126A TMEM126A TMEM126A TMEM126A TOPORS TOPORS TOPORS TREX1 TRIM32 TRIM32 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1 TRPM1

chr15 chr15 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr8 chr8 chr8 chr8 chr8 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr17 chr17

31369107 31393859 120427373 120446602 120450516 120455782 120478830 120480080 120496751 120497873 89290977 89300036 89305795 89307208 89307380 89307768 89310149 89319314 89323533 89327565 89336402 89337892 89338673 89341369 89343637 63972049 63976764 63978462 63985493 63998376 35465650 35467757 35471335 35471513 35473517 35473779 35474050 35476985 35477410 35477603 35478637 35479424 35479956 35480415 35480588 26873724 26874694

31369187 31393924 120428951 120446746 120450624 120455857 120478966 120480163 120496887 120498177 89291165 89300066 89305916 89307272 89307540 89307858 89310194 89319400 89323621 89327676 89336542 89338067 89338796 89341453 89344335 63973984 63976875 63978656 63985647 63998612 35466237 35467929 35471434 35471625 35473630 35473950 35474056 35477089 35477527 35477705 35478787 35479583 35480047 35480467 35480647 26874427 26874867

TRPM1 TRPM1 TSPAN12 TSPAN12 TSPAN12 TSPAN12 TSPAN12 TSPAN12 TSPAN12 TSPAN12 TTC8 TTC8 TTC8 TTC8 TTC8 TTC8 TTC8 TTC8 TTC8 TTC8 TTC8 TTC8 TTC8 TTC8 TTC8 TTPA TTPA TTPA TTPA TTPA TULP1 TULP1 TULP1 TULP1 TULP1 TULP1 TULP1 TULP1 TULP1 TULP1 TULP1 TULP1 TULP1 TULP1 TULP1 UNC119 UNC119

chr17 chr17 chr17 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr17 chr17 chr17 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1

26875016 26875609 26879355 17515442 17518304 17519708 17522597 17523028 17523485 17538947 17542416 17542892 17544330 17544757 17544965 17545997 17547893 17548299 17548562 17548769 17552700 17552945 17554801 17565818 72912175 72915548 72919004 216347293 216363564 216369894 216371656 216372968 216380614 216390728 216405294 216419926 216424244 216462621 216465516 216495224 216496815 216497509 216498646 216500932 216538294 216591855 216595193

26875119 26875723 26879646 17515923 17518360 17519818 17522697 17523082 17523527 17539021 17542541 17542958 17544473 17544814 17545025 17546082 17547988 17548357 17548587 17548878 17552839 17553089 17554869 17565963 72914171 72916766 72919351 216348824 216363709 216370064 216371926 216373463 216380773 216390892 216405478 216420568 216424440 216462752 216465712 216495318 216497037 216497694 216498941 216500996 216538427 216592021 216595882

UNC119 UNC119 UNC119 USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1C USH1G USH1G USH1G USH2A USH2A USH2A USH2A USH2A USH2A USH2A USH2A USH2A USH2A USH2A USH2A USH2A USH2A USH2A USH2A USH2A USH2A USH2A USH2A

chr1 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4

216596555 82767492 82779331 82785916 82789364 82789622 82807921 82815167 82832825 82841355 82843789 82849182 82850774 82868234 82875798 82876125 6271576 6279177 6288819 6290713 6292923 6293643 6296767 6302383

216596738 82767842 82779407 82786291 82789539 82789750 82808215 82818128 82838087 82841469 82843903 82849341 82850857 82868379 82875981 82878122 6271741 6279414 6288902 6290858 6293094 6293724 6296916 6304991

USH2A VCAN VCAN VCAN VCAN VCAN VCAN VCAN VCAN VCAN VCAN VCAN VCAN VCAN VCAN VCAN WFS1 WFS1 WFS1 WFS1 WFS1 WFS1 WFS1 WFS1

ABCA4 ABCC6 ADAM9 AHI1 AIPL1 ALMS1 ARL6 ARMS2 ATXN7 BBS1 BBS10 BBS12 BBS2 BBS4 BBS5 BBS7 BBS9 BEST1 C2 C2ORF71 C3 CA4 CABP4 CACNA1F CACNA2D4 CC2D2A CDH23 CDH3 CDHR1 CEP290 CERKL CFB CFH CHM CLN3 CLRN1 CNGA1 CNGA3 CNGB1 CNGB3 CNNM4 COL11A1 COL2A1 COL9A1 CRB1 CRX CYP4V2

DFNB31 DMD EFEMP1 ELOVL4 ERCC6 EYS FBLN5 FSCN2 FZD4 GNAT1 GNAT2 GPR98 GRK1 GRM6 GUCA1A GUCA1B GUCY2D HMCN1 HTRA1 IDH3B IMPDH1 INPP5E INVS IQCB1 JAG1 KCNJ13 KCNV2 KLHL7 LCA5 LRAT LRP5 MERTK MFRP:C1QTNF5 MKKS MTTP MYO7A NDP NPHP1 NPHP3 NPHP4 NR2E3 NRL NYX OAT OFD1 OPA1 OPA3

OPN1LW OPN1MW OPN1SW OTX2 PANK2 PAX2 PCDH15 PDE6A PDE6B PDE6C PDZD7 PEX1 PEX2 PEX7 PGK1 PHYH PITPNM3 PRCD PROM1 PRPF3 PRPF31 PRPF8 PRPH2 RAX2 RB1 RBP3 RBP4 RD3 RDH12 RDH5 RGR RGS9 RGS9BP RHO RIMS1 RLBP1 ROM1 RP1 RP2 RP9 RPE65 RPGR RPGRIP1 RPGRIP1L RS1 SAG SEMA4A

SNRNP200 SPATA7 TEAD1 TIMM8A TIMP3 TLR3 TLR4 TMEM126A TOPORS TREX1 TRIM32 TRPM1 TSPAN12 TTC8 TTPA TULP1 UNC119 USH1C USH1G USH2A VCAN WFS1

Table S1. The clinical features of patients carrying pathogenic mutations

Patient Initial Molecular ID Diagnosis Diagnosis

617

622

647

704

LCA

LCA

LCA

NR2E3

RDH12

CERKL

Mutations segregate Diagnosis with after re- disease in visit family Comments

LCA-like

N/A

LCA-like

Yes

N/A

N/A

Juv RP

BBS1

741

Juv AR RP

PRPH2 (homozygo us mutations) Juv ARRP

741a 1278 1303

asymptom atic carrier father of 741 Juv RP LCA

PRPH2 (heterozygo us mutation) RDH12 TULP1

mild Pattern dystrophy N/A Yes LCA N/A

1313

Juv RP

PDE6A

Juv RP

1318

1327

1413

1842

LCA

Juv RP

LCA

Juv RP

Juv RP-like Yes

PRPH2(hom ozygous mutations) LCA

BBS7

GUCY2D

PDE6A

LCA-like

N/A

Juv RP

N/A

N/A

N/A

Yes

Yes

Age Age (last (onset) visit)

2

Birth

Birth

9

PRPH2 mutations are known cause of adRP, maculopathy, pattern macular dystrophy, but not known to cause LCA or ARRP. 9 mo Although the father of 741 is asymptomatic, he clearly showed a maculopathy on retinal exam, OCT and FAF (Fig S2). N/A 5 3.5

6

PRPH2 mutations are known cause of adRP, maculopathy, pattern macular dystrophy, but now known to cause LCA or ARRP. 8mo

16

N/A

3

3256

LCA

PRPH2(hom ozygous mutations) LCA

N/A

PRPH2 mutations are known cause of adRP, maculopathy, pattern macular dystrophy, but not known to cause LCA or ARRP. Birth

3311

Juv RP

PRPF31

N/A

Birth

3425

LCA

SAG

3494

LCA

ALMS1

Juv RP Oguchi disease

29

26

11

53

Gender

F

M

F

Visual Acuity (VA)

Refraction error

VA1 (OD)

Hyperopia (H) or Myopia (M) VF1 (OD)

N/A

N/A

VA2 VA1 (OS) (OD)

N/A

N/A

10/160 10/160

20/100

20/80

20/300

10°

10°

N/A

5° + peripheral island

5° + peripheral island

Y

Y

N

Grossly Normal (Y/N) CME

Y

N

Y

N

N

Maculopathy

N

Y

Sees best at night

Y

N/A

N/A

N/A

N/A

N/A No central vision, small peripheral island

N

Y

N

Maculopathy

N

Peripheral Retina

N

Band of BMC, fine bone spicules, choroidal sclerosis Right exotropia

N

Hypotension

N

Attenuated vessels, bone spicules, salt and pepper appearance

N

N

N/A

N

N

N/A

Other

ERG

N

Obese

Scotopic small but recordable, photopic decreased to 25% of normal value + timing delayed

N

N

N

Cone 3/5 uV, photopic ERG almost flat, scotopic ERG flat

N/A

N/A

N/A

N/A

46.6µV, 100.0msec, 0.4µV, 46.4msec (OS)

N

HTN

N

N

Irregular periods since 15 yo, slightly overweight Non detectable

N

N

N

N

N

Non detectablerod and cone ERGs

No vessel attenuation, no RPE or choroidal abnormalities N Diffuse loss of RPE Right esotropia No pigment clumping N

N N N

N N N

N N N

N N N

N N N

Essentially normal ERG N/A Non detectable

Equatorial mottling, with early bone-spicule like deposits. PPRPE like vessel pattern present at equator OU on FA N

N

N

N

Headaches

N

Non recordable (rods), reduced (cones)

Salt & pepper appearance, disseminated microfleked, crystal-like deposits 360-deg OU

Y (hearing loss)

N

N

N

Thyroid nodule (hypothyroid)

Reduced

N

N

N

N

2 peg shaped incisors, shorter pinky finger Non detectable

20/40

H

I4e: 5° V4e: 50° with large temporal scotoma

N

Y

N

Clear

Clear

severe atrophic multilobulated maculopathy Severe attenuationof retinal (Fig 3) vessels, RPE atrophy

20/25 N/A N/A

20/20 N/A N/A

N/A H M

N/A 7 ° IV4e N/A

N/A 10° N/A

N/A N/A N/A

N/A N/A N/A

N Y Y

N Y Y

N N Y

Clear Y Y

Peripheral cortical opacities N N

Mild pattern maculopathy N N

20/20

N/A

N/A

M

65 °

60°

N/A

N/A

N

Y

N

N

N

20/70

20/70

20/70

M

Constricted

Constricted

N/A

N/A

Y

Y

N

N

N

N

Diffuse atrophy and granular changes

F

58 N/A 5

M M M

N/A N/A 20/160 20/60 10/180 10/160

N/A

F

20/20

29

F

20/70

10/250

NLP

HM

NLP

LP

15/400

NLP

M

H

temporal 5 ° 5 °

N/A

temporal 5 °

temporal 5 ° Y

Y

Bone spicules, waxy pallor, attenuated vessels, Elevated pigmented area nasal to disc in OD

Y

Diffuse RPE atrophy, mottling with granular changes

N

Vitreous full of cells. No progression. Left exotropia

N/A

I4e: 5° V4e: 70° with several scotomatous islands

LP

Other Ocular

Strabismus

ENT involvement Heart

Kidney/ Urinary System

Atrophic

I4e: 7° V4e: 75° with moderate temporal scotoma

30

NLP

N/A

N/A

Nystagmus Nyctalopia Photosensitivity

severe constriction of !4e: I4e: 7° V4e: 75°

20/40(15 y) 20/50

M

N/A

N/A

VF2 (OS)

N/A

20/40 (15y)

9.5

20/300

H

N/A

VF2 (OD)

N/A

HM

HM

20/200

H

VF1 (OS)

Systemic Features

N/A

HM

M

20/70

Macula

No central vision, small peripheral island

F

28

VA2 (OS)

Visual Field (VF)

CNS

N/A

N/A

Y

N

N

Y

N

Attenuated vessels, pale discs, optic atrophy

Enophthalmos

N

N

N

N

Austistic (severe, global handicapped development, no language), partially deaf (right ear), brachycephaly, widow's peak, midline posterior hair whorl. Non detectable

N

Y

N

Mild Bull's eye

N

Beaten metal appearance, attenuated vessels, fine bone spicules, hypopigmented spots

Punctate opacities

N

N

N

N

N

N

Mild ON pallor, attenuated vessels, bone spicules,

N

N/A

21

F

N/A

N/A

20/40

20/40

M

N/A

N/A

20° 20° (progressive (progressive loss noted) loss noted)

66

F

N/A

N/A

20/400

20/400

N/A

N/A

N/A

10°

10°

Y

Y

N

Foveal atrophy

35

F

20/20

20/40 (25 yo) 20/20

20/40

M

N/A

N/A

Normal

Normal

N

Y

N

OS minimal macular edema

11

M

N/A

N/A

8/400

H

N/A

N/A

15°

40°

Y

N

Y

Fovea pooly developed

Non detectable

N

N

N

N

Diabetes Mellitus x 10 years Non detectable

Single bone spicule OD, LASIK in 2000 attenuated vessels, normal discs (myopia)

N

N

N

N

N

Decreased

N

Attenuated vessels

N

N

N

N

N

Non detectable

N/A

Alström syndrome Yes

ALMS1 mutations are a well known cause of Alström syndrome. On revisit at age 11 he had slowly developed obesity, learnng difficulties, acanthosis nigricans and diabetes mellitus. 8

10/400

N

3557

LCA

CRB1

N/A

Yes

2mo

M

N/A

LP

LP

H

N/A

N/A

N/A

N/A

Y

N

N

Macular coloboma

N

Attenuated vessels, scattered spots of RPE atrophy

N

N

N

N

N

Epilectic activity/seizure noted at 3mo Non detectable

3561

LCA

OTX2

N/A

N/A

Infancy 47

F

20/200 20/200

10/120

LP

H

20°