Whole-exome Sequencing Analysis Identifies Mutations in the EYS Gene
in Retinitis Pigmentosa in the Indian Population
Yanan Di1,2,3,7*, Lulin Huang2,3,7*, Periasamy Sundaresan4*, Shujin Li2,6,7, Ramasamy
Kim5, Bibhuti Ballav Saikia4, Chao Qu2,7, Xiong Zhu2,3,7, Yu Zhou2,3,7, Zhilin Jiang2,7, Lin
Zhang2,6,7, Ying Lin2,7, Dingding Zhang2,7, Yuanfen Li2,7, Houbin Zhang2,3,7, Yibing Yin1,
Fang Lu2,3,7, Xianjun Zhu2,3,6,7#, Zhenglin Yang1,2,3,6,7#
*
These authors contributed equally to this study.
Supplementary information file
Supplementary information file includes three Tables (Table S1, S2，S3 and S4).
Table S1 The primer pairs used for mutations identification by Sanger Sequence
Mutations
c.8422G>A
Primer name
EYS-8422
c.7868G>A
EYS-7868
c.4606C>G
EYS-4606,5038
c.5038A>G
EYS-4606,5038
c.9059T>C
EYS-9059
c.1418G>T
EYS-1418
c.2971C>T
EYS-2971
c.8455delA
EYS-8455
c.8388C>A
EYS-8388
c.7187C>G
EYS-7187
c.2259+1 G>A
EYS-splicing
c.3024C>A
EYS-3024
F
R
F
R
F
R
F
R
F
R
F
R
F
R
F
R
F
R
F
R
F
R
F
R
Primer pairs 5’-3’
CTGGCAAACATCTGCAAGAA
ATCCAACTTGGCCAGAAACA
ATGGCATAAATGCTGTGCTG
TTCTCTGCGCATTTCTGTATTC
GCCTCCATAAGTGCAACTCC
CACTTGGGTGAAGTTTGAACAG
GCCTCCATAAGTGCAACTCC
CACTTGGGTGAAGTTTGAACAG
TGCAGAAATGGAGGTGAATG
CCATATTCAAAGCCCCCTAGA
TCACTGTGGTTTTAAAAATTAGCTG
CCATTAACCACTCCCTTCCA
TGGTTTCCAGCTTCATCCAT
ATTTTTGCCCTGTTTGCATC
TCCGTTCAACTTCGCTACAA
TCACCTCCATTTCTGCATGT
TCCGTTCAACTTCGCTACAA
TCACCTCCATTTCTGCATGT
GCATATGTGTTCATGCATGTGT
CCTGCTTGGTGATCAGTCTC
TGTTTTTTCCAGTGGTTGATG
AAACCAACCTGTATAGAGTGGAGA
GAGGGTCTTCATTTCTTGGTGATG
TCAACTTTCCCTTGATGTTAAGTC
Table S2 Overview of data production
Items
ARRP 49-II:5
ARRP 206-IV:1
RP:S-2
RP:S-10
RP:S-14
Total reads
Total yield (bp)
Average throughput depth of target region
Mapped to human genome
De-duplicated by Picard tools
Uniquely mapped to human genome
Mapped to target regions
% Coverage of target regions ≥1X
% Coverage of target regions ≥10 X
Mean read depth of target regions
49,8119,518
5,031,771,318
99.9
49,563,492
48,277,967
46,960,891
35,099,450
98.1%
94%
58.3
48,389,056
4,887,294,656
97.0
48,211,940
47,041,876
45,862,952
35,466,449
98.2%
94.9%
58.7
43,538,982
4,397,437,182
87.3
43,388,304
41,323,899
40,264,663
33,097,880
97.6%
91.4%
55.5
44,372,220
4,481,594,220
88.9
44,242,436
42,827,662
41,770,934
33,955,987
98.0%
93.2%
56.3
48,018,436
4,849,862,036
96.2
47,877,526
45,442,035
44,292,449
35,627,912
98.2%
94,2%
58.8
Number of SNPs
Number of coding SNPs
Number of synonymous SNPs
Number of nonsynonymous SNPs
Number of Indels
Number of coding Indels
66,992
20,370
10,557
9,336
5,541
413
67,419
20,510
10,703
9,325
5,621
427
60,462
19,310
10,027
8,805
4,526
381
63,932
19,869
10,299
9,102
5.001
411
65,656
20,126
10,525
9,096
5,151
397
Table S2 Overview of data production (continued)
Items
RP:S-18
RP:S-22
RP:S-34
RP:S-40
RP:S-48
Total reads
52,316,262
Total yield (bp)
5,283,942,462
Average throughput depth of target region 104.9
49,518,246
5,001,342,846
99.3
46,810,310
4,727,841,310
93.8
41,988,552
4,240,843,752
84.2
48,627,488
4,911,376,288
97.5
Mapped to human genome
De-duplicated by Picard tools
Uniquely mapped to human genome
Mapped to target regions
% Coverage of target regions ≥1X
% Coverage of target regions ≥10 X
Mean read depth of target regions
Number of SNPs
Number of coding SNPs
Number of synonymous SNPs
Number of nonsynonymous SNPs
Number of Indels
Number of coding Indels
49,363,126
47,303,076
46,128,933
37,029,371
98.0%
93.4%
61,1
64,050
19,841
10,291
9,045
4,906
413
46,629,684
44,118,412
42,999,222
35,063,689
97.7%
91.8%
58.7
63,228
19,843
10,419
8,951
4,526
389
41,854,296
40,213,737
39,173,334
31,423,908
98.0%
92.6%
52.4
62,018
19,218
9,964
8,740
4,945
414
48,474,470
46,857,500
45,702,299
35,869,218
98.0%
93.9%
59.5
64,465
19,624
10,244
8,935
5,193
440
52,138,722
49,538,198
48,283,596
39,579,744
97.9%
93.2%
66.2
64,689
20,273
10,552
9,248
4,898
4
Table S3. The SNP quality and depth by NGS of each identified mutation
Patient ID
ARRP-49
ARRP-49
ARRP-206
RP:S-2
RP:S-10
RP:S-10
RP:S-14
RP:S-18
RP:S-18
RP:S-22
RP:S-34
RP:S-40
RP:S-48
Mutations
c.8422G>A
c.G7868A
c.1871G>A
c.8455delA
c.4606C>G
c.5038A>G
c.9059T>C
c.1418G>T
c.2971C>T
c.8388C>A
c. 7187 G>C
c.2259+1 G>A
c. 3024 C>A
SNP Quality
179
97
157
214
124
194
173
201
167
191
196
222
222
Total depth
45
56
101
99
78
101
106
86
57
138
62
75
98
Alternate depth
24
21
101
99
38
50
106
43
28
136
62
75
98
Table S4 The genotype of family ARRP-49 members
Family member
I:1
I:2
II:1
II:2
II:5
II:6
II:7
II:8
III:1
III:2
III:4
III:5
Sex
M
F
M
F
M
F
F
M
F
F
M
M
Mutations
+/MU2
MU1/+
MU1/MU2
+/+
MU1/MU2
+/+
MU1/MU2
+/+
+/MU2
MU1/+
+/MU2
MU1/+
III:6
III:7
M
M
MU1/+
MU1/+
*M: male; F: female；MU1：c.7868G>A, p.2623G>E; MU2: c.8422G>A, p.2808A>T; MU3: c.1871G>A, p.624S>L.