A method to reduce ancestry related germline false positives in tumor only somatic variant calling

BMC Medical Genomics

Table 1 Samples and sequencing statistics

Sample name	Cancer type	Self reported ancestry	Reads (Millions)	Mean target coverage	% Covered at 100X
GBM6-HA	Glioblastoma	Hispanic	897	553X	95.7
GBM1-EA	Glioblastoma	Caucasian	2768	2101X	98.3
TNBC3-AA	Breast	African American	905	599X	96.1
TNBC4-AA	Breast	African American	906	546X	95.4
TNBC6-AA	Breast	African American	1040	658X	95.4
TNBC7-AA	Breast	African American	899	588X	95.6
TNBC11-EA	Breast	Caucasian	1066	645X	95.8
TNBC14-EA	Breast	Caucasian	875	454X	94.5
TNBC15-GH	Breast	Ghanian	598	1012X	97.4

Description of the patient samples and sequencing metrics of the patients used in the evaluation dataset. Note that GBM1-EA was sequenced to higher mean target coverage for in-silico dilution and down-sampling experiments. Blood samples from each patient were also sequenced to establish true variant classification

ISSN: 1755-8794