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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
  1. The numbers in the parenthesis indicate the number of sequences detected in exome-seq analysis. Viral hits are highlighted in bold.