Table 1 Viral sequences detected in the samples with the use of several computational methods
From: No significant viral transcription detected in whole breast cancer transcriptomes
Sample | Age | Raw Reads | Pipeline1 viral reads | Pipeline 2 viral reads | Pipeline 3 viral contigs | Pipeline 4 viral reads | Pipeline 5 viral reads | Virus Name | EBV IHC | HPV PCR |
|---|---|---|---|---|---|---|---|---|---|---|
Test Set | NA | 424484976 | 46821 | 50681 | 2 | 45071 | 43466 | HBV | ||
HER2-13 | 46 | 64893130 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
HER2-14 | 49 | 50499646 | 0 | 0 | 0 | 0 | 0 | negative | positive high risk | |
HER2-15 | 45 | 61599108 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
HER2-16 | 58 | 61491812 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
HER2-18 | 38 | 67873006 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
HER2-19 | 60 | 67894004 | 22 (27) | 25 (27) | 0 (0) | 17 (27) | 26 | HHV6 | negative | negative |
HER2-2 | 83 | 59452650 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
HER2-20 | 66 | 85761124 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
HER2-21 | 46 | 93380848 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
HER2-22 | 39 | 50262908 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
HER2-23 | 55 | 68452272 | 0 | 0 | 0 | 0 | 0 | failure | negative | |
HER2-24 | 49 | 45799400 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
HER2-3 | 35 | 59739682 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LA-18 | 63 | 50984238 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LA-19 | 37 | 83958354 | 0 | 0 | 0 | 0 | 0 | negative | positive hpv16 | |
LA-20 | 50 | 32869722 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LA-21 | 51 | 76552678 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LA-22 | 62 | 60308476 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LA-23 | 73 | 42225858 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LA-24 | 63 | 39585066 | 0 | 0 | 0 | 0 | 0 | negative | NA | |
LA-25 | 58 | 49913768 | 0 | 0 | 0 | 0 | 0 | negative | NA | |
LA-26 | 66 | 72421722 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LA-27 | 62 | 66523668 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LA-28 | 64 | 64969514 | 0 | 0 | 0 | 0 | 0 | negative | NA | |
LA-29 | 51 | 23434748 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LA-31 | 85 | 79158278 | 0 | 0 | 0 | 0 | 0 | negative | NA | |
LA-32 | 58 | 68369496 | 0 | 0 | 0 | 0 | 0 | negative | NA | |
LA-33 | 68 | 75436316 | 0 | 0 | 0 | 0 | 0 | NA | negative | |
LA-4 | 61 | 64916390 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LB-1 | 42 | 70818118 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LB-3 | 53 | 44475406 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LB-5 | 42 | 58896182 | 0 | 0 | 0 | 0 | 0 | NA | NA | |
LB-15 | 79 | 37855250 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LB-17 | 57 | 71008672 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LB-18 | 61 | 56839562 | 0 | 0 | 0 | 0 | 0 | negative | NA | |
LB-19 | 34 | 66451162 | 2 (4) | 2 (4) | 0 (0) | 2 (4) | 2 | EBV | negative | negative |
LB-20 | 45 | 114639766 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LB-21 | 51 | 64647066 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LB-22 | 53 | 79028228 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
LB-23 | 55 | 116825666 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
TN-1 | 41 | 75308960 | 3 (0) | 3 (0) | 0 (0) | 2(0) | 3 | Merkel cell polyomavirus | negative | negative |
TN-2 | 47 | 107171302 | 0 | 0 | 0 | 0 | 0 | NA | NA | |
TN-3 | 59 | 34339412 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
TN-5 | 39 | 44460594 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
TN-15 | 35 | 56793532 | 0 | 0 | 0 | 0 | 0 | NA | NA | |
TN-16 | 52 | 71331804 | 0 | 0 | 0 | 0 | 0 | failure | negative | |
TN-17 | 34 | 81351348 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
TN-18 | 62 | 84104974 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
TN-19 | 50 | 19621240 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
TN-20 | 51 | 80751454 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
TN-21 | 56 | 65225662 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
TN-22 | 39 | 63983318 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
TN-23 | 65 | 50443546 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
TN-24 | 63 | 70061346 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
TN-25 | 79 | 43789446 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
TN-26 | 81 | 56344394 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
TN-27 | 57 | 64691190 | 0 | 0 | 0 | 0 | 0 | negative | negative | |
TN-28 | 54 | 46437934 | 0 | 0 | 0 | 0 | 0 | negative | negative |