Table 2.
The overlap of somatic variants (both SNVs and short indels) called in tumour using either blood or normal breast tissue as the germline reference using exome sequencing and targeted Ampliseq validation
| Exome sequencing | ||||
|---|---|---|---|---|
| Sample no. | Total variants versus normal breast tissue | Total variants versus blood | Shared variants | Percentage of variants shared using normal breast or blood as reference (%) |
| 1 | 29 | 30 | 27 | 84.38 |
| 2 | 321 | 341 | 320 | 93.57 |
| 3 | 12 | 11 | 10 | 76.92 |
| 4 | 85 | 90 | 84 | 92.31 |
| 5 | 55 | 59 | 55 | 93.22 |
| Targeted Ampliseq validation | ||||
|---|---|---|---|---|
| Sample no. | No of variants with results | Variant present in exome sequencing using blood as reference | Variant present in exome sequencing using normal breast as reference | Percentage of shared exome sequencing variants validated by Ampliseq panel (%) |
| 1 | 15 | 15 | 14 | 93.3 |
| 2 | 57 | 57 | 41 | 71.9 |
| 3 | 2 | 2 | 2 | 100.0 |
| 4 | 28 | 28 | 27 | 96.4 |
| 5 | 8 | 8 | 7 | 87.5 |
| Total | 110 | 110 | 91 | |
SNV single nucleotide variation