Table 2.
Validation. Targeted sequencing confirmed that 89.6% (optimal filtering pipeline) and 86.3% (permissive filtering pipeline) of single nucleotide variants identified using our algorithm. Excluding MUC6 and low input amounts of DNA we validated 94.7% (O) or 93.2% (P) of variants. We found that the 14.2% (O) or 12% (P) of the confirmed variants are also present in the control samples with a frequency >10%. These variants may be SNPs
| Optimal filter (O) | Variants | Common (A and B) | Private (A or B) | Variants in controls (>10%) |
|---|---|---|---|---|
| Total number of SNVs | 154 | 146 (94.8%) | 8 (5.2%) | 33 (21.4%) |
| Validated variants | 138 (89.6%) | 133 (91.1%) | 5 (62.5%) | 32 (97%) |
| Nonvalidated variants | 16 (10.4%) | 13 (8.9%) | 3 (37.5%) | 1 (3%) |
| MUC6-excluded, DNA ≧ 40 ng SNVs | 113 | 110 (97.3%) | 3 (2.7%) | 16 (14.2%) |
| Validated variants | 107 (94.7%) | 105 (95.5%) | 2 (66.7%) | 15 (93.8%) |
| Nonvalidated variants | 6 (5.3%) | 5 (4.5%) | 1 (33.3%) | 1 (6.3%) |
| Permissive filter (P) | Variants | Common (A and B) | Private (A or B) | Variants in controls (>10%) |
| Total number of SNVs | 182 | 170 (93.4%) | 12 (6.6%) | 34 (18.7%) |
| Validated variants | 157 (86.3%) | 152 (89.4%) | 5 (41.7%) | 33 (97.1%) |
| Nonvalidated variants | 25 (13.7%) | 18 (10.6%) | 7 (10.6%) | 1 (2.9%) |
| MUC6-excluded, DNA ≧ 40 ng SNVs | 133 | 130 (97.7%) | 3 (2.3%) | 16 (12%) |
| Validated variants | 124 (93.2%) | 122 (93.8%) | 2 (66.7%) | 15 (93.8%) |
| Nonvalidated variants | 9 (6.8%) | 8 (6.2%) | 1 (33.3%) | 1 (6.3%) |