Table 3.
Identification of the causative gene for PKD from three patients by exome sequencing
| Filter | Sample II: 4 (Family A) | Sample II: 2 (Family B) | Sample II: 4 (Family B) | Shared genes |
|---|---|---|---|---|
| Total number of variants | 98 581 | 90 317 | 101 037 | 9083 |
| Number of NS/SS/ Indel | 10 811 | 10 530 | 10 927 | 2840 |
| Number of NS/SS/ Indel after Filter 1 | 1603 | 1572 | 1607 | 265 |
| Number of NS/SS/ Indel after Filter 2 | 1122 | 1098 | 1162 | 187 |
| Number of NS/SS/ Indel after Filter 3 | 562 | 539 | 736 | 135 |
| SULT1A2(K258N) | CD19(V217M) | AC138894.2-1(N44S) | ||
| NS/SS/indel in 16p12.1-q12.1 | FAM57B(P27A) | LAT(V163M) | PRRT2(Q163*) | |
| ITGAX(Q856H) | PRRT2(Q163*) | CORO1A(V229L) | PRRT2 | |
| PRRT2 (P217fsX7) | ZNF646(G1793E) | |||
| ZNF720 (Indel) | AC136932.2 (Indel) |
‘Shared genes’ indicates the gene mutations occurred in all three samples. In the step of Filter 1, we first removed the NS/SS/Indel variants reported in the dbSNP129. Then, the NS/SS/Indel variants reported in the eight previously exome-sequenced HapMap samples (‘HapMap 8’) were further removed in Filter 2. Consequently, the NS/SS/Indel variants reported in the 1000 Genome Project were removed in Filter 3; * = stop codon.