IROme, a New High-Throughput Molecular Tool for the Diagnosis of Inherited Retinal Dystrophies
Table 3
Synopsis of molecular diagnostic on RP patients by IROme.
Pat number
Total seq Mb
Read length bp
Median fold cvg
Total seq var
cds seq var
filt. seq var
prio. seq var
Test/val seq var
Potential mutation
cvg pot mut
mut reads %
Cosegregate family
1
47
453
21.3
1206
114
51
8
2/2
p.C2ORF71-R571_P576del p.FSCN2-P231S
38 25
55.3 44
M het norm F het norm
2
47.6
433
20.9
1217
98
44
7
2/2
p.PDE6B-H337R p.OTX2-G222R
21 52
100 48
? ?
3
42.2
416
17.0
1085
78
39
6
1/1
p.CLRN1-P134L
19
68.4
?
4
44.6
395
21.6
1173
95
42
5
3/3
p.RHO-Y191C
39
38.5
yes
5
24.4
429
13.8
894
104
45
1
1/1
p.TULP1-F529_A530dup
6
100
yes
6
31.7
422
16.2
1039
85
47
1
1/1
p.RHO-R252P
22
54.5
?
7
20.1
281
13.3
789
77
38
4
2/2
p.SAG-E11K p.IMPG2-G684R
30 34
56.7 38.2
no no
8
13.9
445
9.1
736
70
33
2
1/1
p.RP2-D161Y
22
45.5
yes
9
29
297
17.3
832
80
39
9
1/1
g.ABCA4-ex45-47del
0
0
yes
10
37.3
443
16.7
1247
93
46
3
3/3
p.PROM1-R373C
32
50
yes
11
50.2
440
21.5
1151
92
46
2
1/1
p.RP2-E20X
28
67.8
yes
12
49.1
394
23.8
1116
94
39
9
4/4
p.CNGB1-R765C
30
100
yes
13
33
436
14.6
1017
85
33
3
2/2
p.GUCY2D-V887G
18
94.4
yes
14
32.6
443
15.3
1205
93
42
3
1/1
p.CRX-Q105X
17
58.8
M het norm
15
32.7
442
14.2
1026
86
40
3
1/1
p.USH2A-P2630R
25
40
no
16
69.4
434
28.4
1246
87
41
1
1/1
p.PRPF31-E183_ins33bp
74
40
yes
17
16.7
452
9.8
861
82
43
2
2/2
p.PRPH2-L39P
18
50
yes
18
39.6
429
17.2
1826
85
35
3
1/1
19
66.5
449
26.4
1298
103
45
5
2/2
p.PRPH2-S217_dup16bp
71
39.4
yes
20
47.1
358
19.8
1171
91
47
3
2/1
p.C2ORF71-L889P
23
39.1
?
21
47
363
17.3
1197
102
48
3
1/0
22
36.6
354
14.7
1072
86
45
2
2/1
p.EYS-D2930G
38
60.5
?
23
53.3
393
22.4
1164
92
40
7
5/5
p.PRPF8-E2331X
38
44.7
yes
For each patient, the total number of Mb (106 bp) sequenced on the Roche 454 GS Junior (total seq Mb) and the average read length (read length bp) are indicated. The median fold coverage (cvg) was extracted from the unique depth information. From all the sequence variants (total seq var), first only the sequence variants located in coding sequences were analyzed (cds seq var), with filtering (filt seq var) and prioritizing (prio seq var) according to Figure 2. The sequence variants eventually tested and validated by Sanger sequencing (test/val seq var) are also indicated. For each potential mutation, the coverage (cvg pot mut) and the percentage of sequence reads reporting the potential mutation (mut reads %) are indicated. For cosegregation analysis, “?” indicates absence of available family members and/or simplex cases. For patients 1 and 14, the mother (M) and/or the father (F) are healthy heterozygous carriers (het norm).