Table 1. All called SNVs and indels.
| Cancer cell line | HCC1143 | HCC1187 | HCC1395 | HCC1937 | HCC1954 | HCC38 | Average | Total |
|---|---|---|---|---|---|---|---|---|
| Matched normal cell line | HCC1143BL | HCC1187BL | HCC1395BL | HCC1937BL | HCC1954BL | HCC38BL | ||
| # of SNPs called (passing variant call filter in GATK) | 5302 | 5426 | 5740 | 5517 | 5557 | 5421 | 5494 | 32963 |
| # of Indels called (passing variant call filter in GATK) | 572 | 673 | 685 | 621 | 664 | 644 | 643 | 3859 |
| # of SNPs and indels (passing variant call filter in GATK) | 5874 | 6099 | 6425 | 6138 | 6221 | 6065 | 6137 | 36822 |
| # of somatic heterozygous variants ("high confidence" variants in GATK) | 51 | 49 | 198 | 87 | 54 | 51 | 82 | 490 |
| # of somatic homozygous variants ("high confidence" variants in GATK) | 10 | 23 | 88 | 31 | 4 | 12 | 28 | 168 |
| In dbSNP138 (SNPs >1% minor allele frequency (MAF), non-clinically associated, passing variant call filter in GATK) | 5670 | 5845 | 6061 | 5912 | 5904 | 5830 | 5870 | 35222 |
| Total # of somatic variants ("high confidence" variants in GATK)* | 61 (21) | 72 (18) | 286 (155) | 118 (77) | 58 (19) | 63 (25) | 110 | 658 (315) |
| Exonic* | 46 (6) | 62 (8) | 170 (49) | 69 (31) | 41 (3) | 49 (13) | 73 | 437 (110) |
| frameshift deletion* | 1 (1) | 1 (0) | 1 (1) | 0 | 1 (0) | 2 (1) | 1 | 6 (3) |
| frameshift insertion* | 0 | 4 (2) | 0 | 0 | 1 (0) | 0 | 1 | 5 (2) |
| nonframeshift deletion* | 0 | 2 (0) | 0 | 0 | 0 | 0 | 0 | 2 (0) |
| nonsynonymous SNV* | 37 (2) | 46 (3) | 133 (26) | 46 (16) | 33 (0) | 38 (9) | 56 | 333 (56) |
| stopgain SNV* | 3 (0) | 5 (0) | 6 (0) | 5 (1) | 1 (0) | 1 (0) | 4 | 21 (1) |
| stoploss SNV* | 0 | 0 | 0 | 0 | 0 | 1 (0) | 0 | 1 (0) |
| synonymous SNV* | 5 (3) | 4 (3) | 29 (21) | 18 (14) | 5 (3) | 7 (3) | 11 | 68 (47) |
| Unknown* | 0 | 0 | 1 (1) | 0 | 0 | 0 | 0 | 1 (1) |
| Splicing* | 0 | 0 | 6 (0) | 2 (1) | 1 (0) | 1 (0) | 2 | 10 (1) |
| UTR3* | 5 (5) | 4 (4) | 26 (26) | 18 (18) | 3 (3) | 3 (3) | 10 | 59 (59) |
| UTR5* | 1 (1) | 0 (0) | 8 (8) | 4 (4) | 2 (2) | 2 (2) | 3 | 17 (17) |
| Others (intronic, upstream, downstream, intergenic, ncRNA)* | 9 (9) | 6 (5) | 76 (72) | 25 (23) | 11 (11) | 8 (7) | 23 | 135 (128) |
| # of somatic variants, non-silent ("high confidence" variant calls in GATK)* | 41 (3) | 58 (5) | 146 (27) | 53 (18) | 37 (0) | 43 (10) | 63 | 378 (63) |
*Novel variants in parenthesis