Supplemental Table 1. List of 96 target IDs with 1791 regions (329.914-kb) using in the targeted exome sequencing

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Target ID Regions Coverage High coverage Low coverage

(≥90%) (<90%)

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ABCA4 50 100.0 % 50 0

AHI1 27 100.0 % 27 0

ALMS1 23 100.0 % 23 0

ARL13B 10 100.0 % 10 0

ARL4D 1 100.0 % 1 0

ARL6 7 100.0 % 7 0

ATXN10 12 100.0 % 12 0

B9D1 8 100.0 % 8 0

B9D2 3 100.0 % 3 0

BBS1 17 100.0 % 17 0

BBS10 2 100.0 % 2 0

BBS12 1 100.0 % 1 0

BBS2 17 100.0 % 17 0

BBS4 16 100.0 % 16 0

BBS5 12 100.0 % 12 0

BBS7 19 100.0 % 19 0

BBS9 22 100.0 % 22 0

C5ORF42 51 100.0 % 51 0

CC2D2A 38 98.12651 % 37 1

CCDC149 13 95.66126 % 12 1

CCDC28B 5 100.0 % 5 0

CEP164 31 100.0 % 31 0

CEP290 53 100.0 % 53 0

CEP41 11 100.0 % 11 0

CNGB3 18 100.0 % 18 0

CRB1 13 100.0 % 13 0

DNAAF1 12 100.0 % 12 0

DYNC2H1 90 100.0 % 90 0

ELOVL4 6 100.0 % 6 0

EYA1 17 100.0 % 17 0

EYS 41 100.0 % 41 0

FAN1 13 100.0 % 13 0

GATA3 5 100.0 % 5 0

GLIS2 6 100.0 % 6 0

HNF1B 9 100.0 % 9 0

IFNG 4 100.0 % 4 0

IFT140 29 100.0 % 29 0

IFT80 19 100.0 % 19 0

INPP5E 10 100.0 % 10 0

INVS 16 100.0 % 16 0

IQCB1 13 100.0 % 13 0

KIF7 18 100.0 % 18 0

KIFC1 11 100.0 % 11 0

LCA5 7 100.0 % 7 0

LZTFL1 10 100.0 % 10 0

MKKS 4 100.0 % 4 0

MKS1 19 100.0 % 19 0

MRE11A 19 96.17072 % 18 1

MYO9A 41 100.0 % 41 0

NEK1 34 100.0 % 34 0

NEK8 15 100.0 % 15 0

NPHP1 20 100.0 % 20 0

NPHP3 27 100.0 % 27 0

NPHP4 29 100.0 % 29 0

OFD1 23 100.0 % 23 0

PAX2 12 100.0 % 12 0

PDE6D 5 100.0 % 5 0

PKD1 46 100.0 % 46 0

PKD2 15 100.0 % 15 0

PKHD1 67 100.0 % 67 0

PLLP 4 100.0 % 4 0

PLXDC2 14 100.0 % 14 0

PROM1 26 100.0 % 26 0

RAB11A 5 100.0 % 5 0

RCN2 7 100.0 % 7 0

RPGRIP1L 26 96.46374 % 25 1

SDCCAG8 18 100.0 % 18 0

SIX1 2 100.0 % 2 0

SIX5 3 96.666664 % 3 0

SLCO2A1 14 100.0 % 14 0

TCTN1 15 99.487656 % 14 1

TCTN2 18 100.0 % 18 0

TCTN3 14 100.0 % 14 0

TMEM138 4 100.0 % 4 0

TMEM216 5 100.0 % 5 0

TMEM231 6 100.0 % 6 0

TMEM237 14 100.0 % 14 0

TMEM67 29 100.0 % 29 0

TNK2 16 100.0 % 16 0

TRIM32 1 100.0 % 1 0

TRIM37 25 100.0 % 25 0

TSC1 21 100.0 % 21 0

TSC2 41 100.0 % 41 0

TTC21B 29 100.0 % 29 0

TTC8 15 100.0 % 15 0

UMOD 10 100.0 % 10 0

USH2A 71 100.0 % 71 0

VHL 3 100.0 % 3 0

WDPCP 18 100.0 % 18 0

WDR19 36 100.0 % 36 0

WDR35 28 100.0 % 28 0

XAB2 19 100.0 % 19 0

XPNPEP3 10 100.0 % 10 0

ZDHHC12 5 100.0 % 5 0

ZNF423 8 100.0 % 8 0

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Supplemental Table 2. Other gene variations detected by targeted exome sequencing and in silico tools for prediction.

Patient / Gene / Exonic Function / Genbank ID / Exon / Nt change / AA change / dbSNP / SIFT / PP2 / MT / GERP++ / Phylop / LRT
I-2 / WDR19 / nonsynonymous SNV / NM_025132 / 32 / c.3533G>A / p.R1178Q / rs79436363 / 0.24 / 0.948 / 1 / 5.53 / 2.597 / 1
WDR19 / nonsynonymous SNV / NM_025132 / 33 / c.3703G>A / p.E1235K / - / 0.02 / 0.999 / 1 / 5.77 / 2.712 / 1
CRB1 / in-frame deletion / NM_201253 / 5 / c.1109_1111del / p.371delS / - / - / - / - / - / - / -
SLCO2A1 / nonsynonymous SNV / NM_005630 / 13 / c.1703C>A / p.S568Y / - / 0 / 0.815 / 1 / 5.4 / 2.802 / 1
CEP164 / nonsynonymous SNV / NM_014956 / 13 / c.1484C>G / p.P498R / rs59763167 / 0.04 / 0.648 / 0 / -1.37 / -0.254 / 0.467
PKD1 / nonsynonymous SNV / NM_001009944 / 2 / c.242C>T / p.A81V / - / 0.02 / 0.32 / 0 / 1.18 / 0.109 / 0.749
II-1 / WDR19 / nonsynonymous SNV / NM_025132 / 15 / c.1483G>T / p.G495C / - / 0.03 / 1 / 1 / 5.97 / 2.833 / 1
WDR19 / nonsynonymous SNV / NM_025132 / 32 / c.3533G>A / p.R1178Q / rs79436363 / 0.24 / 0.948 / 1 / 5.53 / 2.597 / 1
ABCA4 / nonsynonymous SNV / NM_000350 / 6 / c.575C>T / p.A192V / rs185729337 / 0.74 / 0.353 / 1 / 4.92 / 1.458 / 1
CRB1 / nonsynonymous SNV / NM_201253 / 8 / c.2714G>A / p.R905Q / rs114052315 / 0.68 / 0.076 / 0 / 3.25 / 0.392 / -
ARL13B / nonsynonymous SNV / NM_182896 / 5 / c.568A>G / p.I190V / rs193219215 / 0.12 / 0.971 / 1 / 5.67 / 2.158 / 1
EYS / nonsynonymous SNV / NM_001142800 / 38 / c.7454G>A / p.G2485D / - / 0.41 / 0.998 / 1 / 4.95 / 2.296 / 1
EYS / nonsynonymous SNV / NM_001142800 / 26 / c.4469C>T / p.S1490L / - / 0.01 / 0.245 / 0.996 / 4.03 / 0.797 / 1
EYA1 / nonsynonymous SNV / NM_000503 / 9 / c.724A>G / p.S242G / rs191838840 / 0.18 / 0.079 / 1 / 3.97 / 2.06 / 1
PAX2 / nonsynonymous SNV / NM_003987 / 10 / c.1127A>C / p.Q376P / rs201021899 / 0.03 / 0.21 / 0.442 / 4.2 / 1.523 / 0.999
MYO9A / nonsynonymous SNV / NM_006901 / 25 / c.4579C>T / p.R1527C / - / 0.01 / 0.998 / 1 / 5.88 / 2.796 / -
PKD1 / nonsynonymous SNV / NM_001009944 / 11 / c.2371C>T / p.R791W / - / 0.08 / 0.701 / 0 / 4.43 / 1.238 / 0.89
RPGRIP1L / nonsynonymous SNV / NM_015272 / 21 / c.3116A>G / p.Q1039R / rs181022346 / 0.57 / 0.101 / 0 / 4.37 / 0.891 / 0.999
III-1 / WDR19 / nonsynonymous SNV / NM_025132 / 17 / c.1853T>C / p.L618P / - / 0.01 / 0.978 / 1 / 5.48 / 2.21 / 1
WDR19 / nonsynonymous SNV / NM_025132 / 32 / c.3533G>A / p.R1178Q / rs79436363 / 0.24 / 0.948 / 1 / 5.53 / 2.597 / 1
CEP164 / nonsynonymous SNV / NM_014956 / 30 / c.3931A>C / p.T1311P / - / 0.22 / 0.189 / 0 / -2.4 / -0.488 / 0.013
MYO9A / in-frame deletion / NM_006901 / 28 / c.5309_5311del / p.1770delK / - / - / - / - / - / - / -
B9D1 / nonsynonymous SNV / NM_001243473 / 6 / c.767A>G / p.Y256C / rs7221577 / - / - / - / - / - / -

All of the variations in this table were heterozygous.

Nt, nucleotide; AA, amino acid; PP2, PolyPhen2; MT, mutation taster; LRT, likelihood-ration test

Supplemental Table 3. In silico tools for functional prediction of the genetic variations.

Tools / Website / References
SIFT / http://sift.jcvi.org/ / 1
PolyPhen2 / http://genetics.bwh.harvard.edu/pph2/dokuwiki/about / 2
Mutation Taster / http://www.mutationtaster.org/ / 3
GERP++ / http://mendel.stanford.edu/SidowLab/downloads/gerp/ / 4
Phylop / ftp://ccg.vital-it.ch/mga/hg19/phylop/phylop.html / 5
LRT / N/A / 6

More details of these tools are available on http://www.openbioinformatics.org/annovar/annovar_filter.html.

References

1. Kumar P1, Henikoff S, Ng PC (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4:1073-1081

2. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR (2010) A method and server for predicting damaging missense mutations. Nat Methods 7:248-249

3. Schwarz JM, Rödelsperger C, Schuelke M, Seelow D (2010) MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods 7:575-576

4. Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S (2010) Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol 6:e1001025

5. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A (2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 20:110-121

6. Chun S, Fay JC (2009) Identification of deleterious mutations within three human genomes. Genome Res 19:1553-1561