Toward the Mutational Landscape of Autosomal ...

Supplementary Table S1. Subpanel of 74 genes associated with retinitis pigmentosa, choroideremia, macular dystrophy, cone-rod dystrophy, Leber congenital amaurosis, congenital stationary night blindness, and Usher syndrome. In bold: 24 out of 28 genes associated with adRP (RetNet) that were screened by NGS.

ABCA4 ABHD12 ADAMTS18 AIPL1 BBS1 BEST1 C1QTNF5 C2orf71 C8orf37 CA4 CABP4 CEP290 CERKL CHM CLRN1 CNGA1

CNGB1 CRB1 CRX CYP4V2 DHDDS EYS FAM161A FSCN2 GUCA1B GUCY2D HK1 IDH3B IMPDH1 IMPG2 IQCB1 KCNJ13

KLHL7 LCA5 LRAT MAK MERTK NMNAT1 NR2E3 NRL OFD1 PDE6A PDE6B PDE6G PRCD PROM1 PRPF3 PRPF31

PRPF6 PRPF8 PRPH2 RBP3 RD3 RDH5 RDH12 RGR RHO RLBP1 ROM1 RP1 RP2 RP9 RPE65 RPGR

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RPGRIP1 SAG SEMA4A SNRNP200 SPATA7 TOPORS TTC8 TULP1 USH2A ZNF513

Supplementary Table S2. Most frequent pathogenic variants found in our population. Gene RHO NR2E3 RHO C1QTNF5 PRPF3 RHO RHO Total

Exon 5 2 2 15 11 2 3

Nucleotide change c.1040C>T c.166G>A c.403C>T c.489C>A c.1481C>T c.491C>A c.544G>A

Protein change p.(Pro347Leu) p.(Gly56Arg) p.(Arg135Trp) p.(Ser163Arg) p.(Thr494Met) p.(Ala164Glu) p.(Gly182Ser)

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No. Families (%) 10 (3.9) 7 (2.7) 5 (1.9) 4 (1.6) 3 (1.2) 3 (1.2) 3 (1.2) 35 (13.6)

Supplementary Figure S1. Pedigrees of the reclassified families. Cosegregation in available family members are shown. m: mutated allele. wt: wild-type allele.

LORD: late-onset retinal degeneration

RP-2760

I:1

I:2

II:5

II:2

m: C1QTNF5 Ex.15 c.489C>A p.(Ser163Arg)

RP-0488 II:1

II:3

II:4

III:1

III:2

I:1

I:2

? III:3

II:1

II:2

II:3

II:4

m/wt

RP-2409

III:1

III:2

III:3

III:4

? I:1

I:2

? II:6

II:1

II:2

II:3

II:4

IV:1

II:5

II:7

IV:2

IV:3

m/wt

m/wt ?

V:1

III:1

III:2

III:3

III:4

III:5

III:6

III:7

III:8

III:9

III:10

III:11

V:2

III:12

wt/m

?

?

I:1

I:2

VI:1

VI:2

RP-0911

? II:6

III:1 5

II:1

III:1

II:7

III:1 6

III:2

III:3

III:4

II:2

III:5

II:8

III:1 7

III:7

II:3

III:6

wt/m

IV :5

IV :7

IV :8

IV :6

IV :1 3

IV :9

wt/m

IV :1 4

IV :1 0

IV :1 5

IV :1 1

wt/m

wt/m

?

?

?

V :1

V :2

V :3

V :4

V :5

V :6

V :7

V :8

V :9

IV :1 2

IV :1 6

wt/m

V :1 0

wt/wt wt/wt


IV :1 7

wt/wt

V :1 1

3

IV :1 8

IV :1 9

m/wt

IV :1

IV :2

IV :3 IV :4

II:9

III:8

II:4

III:9

III:1 0

III:1 1

II:5

II:1 0

III:1 2

III:1 3

III:1 4

RP-0858

II:1

X-linked genes

II:2

m: RPGR Ex.6 c.485_486del p.(Phe162Tyrfs*4)

III:4

III:1

III:3

III:2

wt

IV:5

IV:8

IV:9

wt

V:1

V:2

wt

wt/wt

V:5

IV:6

IV:10

m/wt

wt

V:3

V:4

V:6

wt/wt

wt

m

IV:7

V:10

V:7

m/wt

VI:2

VI:3

m

m/wt

IV:12

IV:2

IV:13

IV:15

wt

V:8

m/wt

VI:1

IV:1

m/wt

V:9

V:11

m/wt

wt/wt

V:12

wt/wt

V:13

V:14

wt

wt

V:15

V:16

V:18

IV:11

IV:14

wt/wt

wt

V:17

V:19

wt

wt

IV:16

V:20

wt/wt

RP-2646 m: RPGR Ex.15 c.2296_2299del p.(Gly766Asnfs*48)

RP-0615 m: RPGR Ex.15 c.2405_2406del p.(Glu802Glyfs*32) I:1

I:1

RP-2683

I:2

m: RPGR Ex.8 c.888_889del p.(Ile297Lysfs*48)

I:2

? II:3

II:5

II:1

II:2

II:3

II:6

II:7

III:2

III:3

III:6

III:4

wt

m/wt

III:5

III:7

III:9

m IV:2

IV:3

IV:4

wt/wt

wt

wt/wt

m

IV:5

IV:6

II:2

I:1

I:2

III:1

III:2

III:3 II:1

II:3

III:1

III:2

II:2

II:4

III:8

IV:1 IV:1

II:4

II:4

III:4

III:1

II:1

IV:7


4

IV:2 III:3

m/wt

RP-1313

RP-1682

m: RP2 Ex.1 c.1A>G p.(Met1?)

m: RP2 Ex.1 c.14_16del p.(Phe5del) I:1

I:2

I:1

II:4

II:1

II:5

II:2

I:2

II:3

wt/m

II:1

II:2

II:3

II:4

II:5

II:6

wt/wt III:1

III:2

III:3

III:4

III:5

m

?

III:1

III:2

III:3

III:4

III:7

wt

III:5

III:8

III:6

m/wt

?

IV:1

RP-2518 m: CHM Ex.5 c.340G>T p.(Glu114*)

I:1

II:1

II:2

I:1

I:2

II:5

II:2

I:2

II:4 II:3

II:4

II:1

5


II:3

m/wt

II:5

m

III:1

IV:3

IV:4

wt/wt

m: CHM Ex.6 c.757C>T p.(Arg253*)

RP-2204

IV:2

III:2

III:3

III:4

autosomal recessive RP genes

RP-1446 RP-1123

m1: USH2A Ex.13 c.2299del p.(Glu767Serfs*21) m2: USH2A Ex.62 c.12094G>A p.(Gly4032Arg)

m1: RDH5 Ex.4 c.625C>T p.(Arg209*) m2: RDH5 Ex.5 c.776C>T p.(Pro259Leu) I:1

II:1

m1: ABCA4 Ex.19 c.2888del p.(Gly963Alafs*14) m2: ABCA4 Ex.48 c.6688del p.(Leu2230Serfs*17) m3: ABCA4 Ex.8 c.950del p.(Gly317Alafs*57)

I:2

I:1

II:4

RP-1455

II:2

I:2

I:2

II:1

II:2

II:3

II:1

II:2

II:3

m1/m2 III:1

I:1

II:3

wt/m2 m1/m2

III:2

m1/m2

RP-1217

III:1

m: EYS IVS28 c.5928-2A>G

RP-0038 m1: CNGA1 Ex.5 c.94C>T p.(Arg32*) m2: CNGA1 Ex.6 c.131delA p.(Glu44Glyfs*49)

I:1

m2/m3 I:1

I:2

m/wt

I:2

II:3

II:1

II:2

m/m II:1

II:2

II:3

wt/m2

m1/wt III:1

III:4

m/m III:1

wt/m2

III:2

III:3

III:6

III:4

wt/wt

III:2

III:5

m/m

III:5

m1/m2 ?

IV:1

IV:2

IV:3

IV:1

IV:4

m/wt

6


III:3

m/wt

IV:2

IV:3

IV:4

m/wt

m/wt

m/wt

Supplementary Figure S2. Haplotype analysis using 3 microsatellite markers with high heterozygosity (D19S606, D19S596, and D19S879) flanking 1.5 Mb around the CRX gene and an intragenic polymorphic marker (D19S902) in RP-1092 and RP-1192 families with the deletion of exons 3 to 4 in the gene. Haplotype analysis suggests a recurrent mutation. m: mutated allele (deletion of exons 3 to 4 of the CRX gene). wt: wild-type allele.

CRX: chr19:4832509748346586

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Markers

Start (Mb)

D19S606 D19S902

47.97 48.33

Del E3-4 D19S596

48.34 49.25

D19S879

49.52

1.5Mb

Supplementary Table S3. Percentage of characterization and prevalence of the RHO, PRPF31, PRPH2, and RP1 mutations in different adRP populations. Char.: characterization. No.: number. * Various techniques, including NGS.

Population % Char. Spanish 60.5 American 78.5 Belgian 56 French Canadian 40 Japanese 35.1 Italian 27 Chinese 15 South African 6.7 Indian 2

No. adRP No. genes cases screened Technique 258 Various * 270 Various * 86 Various * 60 9 Sanger 77 193 NGS 43 12 Sanger 60 RHO Sanger 60 RHO SSCP 53 4 Sanger

%RHO 20.9 30.7 14 18.3 9 16 15 6.7 -

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%PRPF31 8.1 8.9 10.5 3.3 3.9 2

%RP1 4.3 4.8 10.5 3.9 5 -

%PRPH2 3.9 7 4.7 5 5.2 -

Reference Present study Daiger et al., 20141 Van Cauwenbergh et al., 20172 Coussa et al., 20153 Oishi et al., 20144 Ziviello et al., 20055 Yang et al., 20146 Roberts et al., 20007 Gandra et al., 20088

References: 1. Daiger SP, Bowne SJ, Sullivan LS. Genes and Mutations Causing Autosomal Dominant Retinitis Pigmentosa. Cold Spring Harb Perspect Med 2014;5. 2. Van Cauwenbergh C, Coppieters F, Roels D, et al. Mutations in Splicing Factor Genes Are a Major Cause of Autosomal Dominant Retinitis Pigmentosa in Belgian Families. PLoS One 2017;12:e0170038. 3. Coussa RG, Chakarova C, Ajlan R, et al. Genotype and Phenotype Studies in Autosomal Dominant Retinitis Pigmentosa (adRP) of the French Canadian Founder Population. Invest Ophthalmol Vis Sci 2015;56:8297-8305. 4. Oishi M, Oishi A, Gotoh N, et al. Comprehensive molecular diagnosis of a large cohort of Japanese retinitis pigmentosa and Usher syndrome patients by next-generation sequencing. Invest Ophthalmol Vis Sci 2014;55:7369-7375. 5. Ziviello C, Simonelli F, Testa F, et al. Molecular genetics of autosomal dominant retinitis pigmentosa (ADRP): a comprehensive study of 43 Italian families. J Med Genet 2005;42:e47. 6. Yang G, Xie S, Feng N, Yuan Z, Zhang M, Zhao J. Spectrum of rhodopsin gene mutations in Chinese patients with retinitis pigmentosa. Mol Vis 2014;20:1132-1136. 7. Roberts L, Ramesar R, Greenberg J. Low frequency of rhodopsin mutations in South African patients with autosomal dominant retinitis pigmentosa. Clin Genet 2000;58:77-78. 8. Gandra M, Anandula V, Authiappan V, et al. Retinitis pigmentosa: mutation analysis of RHO, PRPF31, RP1, and IMPDH1 genes in patients from India. Mol Vis 2008;14:1105-1113.

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