GSA: an independent development algorithm for calling copy number and detecting homologous recombination deficiency (HRD) from target capture sequencing

Table 2 The HRD Score and BRCA1/2 mutations and methylation of 17 OC and BC cell lines

Cell line	Cancer type	LOH	TAI	LST	ploidy	HRD score	BRCA1/2 mutation	BRCA1-methylation (%)
HCC38	BRCA	30	24	71	3.34	73.21	WT	74.33
HCC1806	BRCA	34	23	42	2.29	63.47	WT	1.41
NCI/ADR-RES	OV	32	19	47	2.32	61.99	WT	64.64
HCC1143	BRCA	28	20	67	3.59	59.35	WT	1.26
HCC70	BRCA	29	23	57	3.22	59.13	WT	0.28
MX-1	BRCA	30	21	50	2.72	58.90	BRCA1 c.2679_2682delGAAA p.K893Nfs*106 frameshift 99.84%	2.40
OVCAR4	OV	29	19	55	3.12	54.67	WT	47.56
HCC1428	BRCA	17	17	53	3.62	30.82	WT	0.31
ZR-75-1	BRCA	9	15	40	3.20	14.42	WT	0.17
MDA-MB-453	BRCA	11	16	48	4.17	10.42	WT	0.45
MDA-MB-231	BRCA	11	11	30	2.78	8.90	WT	0.19
MDA-MB-361	BRCA	6	13	46	3.67	8.18	WT	1.91
MDA-MB-415	BRCA	9	13	34	3.09	8.10	WT	0.09
ZR-75-30	BRCA	7	13	41	3.67	4.10	WT	3.77
HS-578T	BRCA	10	7	16	2.47	− 5.33	WT	0.22
IGR-OV1	OV	7	0	7	1.85	− 14.73	BRCA1 c.1961delA p.K654Sfs*47 frameshift 50.07%	0.15
A2780	OV	3	3	4	2.01	− 21.19	WT	0.69

ISSN: 1471-2105