Table 1.
Application of TMC-SNPdb across cancer types to filter germline variants in Indian population
| S.No. | Cancer type | Total variants | Number of samples | Number and percentage (along row) of novel variants |
Overall reduction by TMC-SNPdb post dbSNP depletion | |
|---|---|---|---|---|---|---|
| Post dbSNP depletion | Post TMC-SNPdb depletion | |||||
| 1 | Tongue cancer | 613 055 | 24 | 84 001 (13.7%) | 48 182 (7.8%) | 42.6% |
| 2 | Cervical cancer | 923 547 | 34 | 99 032 (10.7%) | 71 594 (7.7%) | 27.7% |
| 3 | Gall-bladder | 328 245 | 17 | 26 530 (8%) | 17 682 (5.3%) | 33.3% |
Total number of variants observed for each cancer types and reduction in number and percent variants post dbSNP and post TMC-SNPdb subtraction is tabulated for three cancer types. Number of samples analysed across tumor is also denoted.