Whole genome sequencing of 51 breast cancers reveals that tumors are devoid of bovine leukemia virus DNA

Gillet, Nicolas A.; Willems, Luc

doi:10.1186/s12977-016-0308-3

Retrovirology

Table 1 Absence of BLV DNA in 51 whole genomes of breast tumors

From: Whole genome sequencing of 51 breast cancers reveals that tumors are devoid of bovine leukemia virus DNA

Subject ID	Country	Age	Diagnosis	Sample type	Grade	HER2 status	ER status	PR status	Total no of reads	No. of reads that align on
Subject ID	Country	Age	Diagnosis	Sample type	Grade	HER2 status	ER status	PR status	Total no of reads	Control DNA (nuclear)	Control DNA (mitochondrial)	BLV_AF033818	BLV_AF257515	BLV_D00647	BLV_K02021	BLV_LC080667
MEX-BR-106	Mexico	42	IDC	Tumor	II	−	+	+	583,906,975	669	396,239	0	0	0	0	0
MEX-BR-116	Mexico	92	IDC	Tumor	III	−	+	−	577,618,196	796	1,166,916	0	0	0	0	0
MEX-BR-15	Mexico	45	IDC	Tumor	II	+	−	+	571,043,227	652	1,167,672	0	0	0	0	0
MEX-BR-154	Mexico	52	IDC	Tumor	III	−	+	+	700,630,351	811	400,383	0	0	0	0	0
MEX-BR-165	Mexico	42	IDC	Tumor	II	−	+	+	757,323,566	737	742,646	0	0	0	0	0
MEX-BR-198	Mexico	44	IDC	Tumor	II	−	+	+	745,509,529	1019	1,264,555	0	0	0	0	0
MEX-BR-50	Mexico	47	IDC	Tumor	II	−	+	+	605,198,587	653	958,812	0	0	0	0	0
MEX-BR-82	Mexico	59	IDC	Tumor	II	−	+	−	681,881,066	687	547,863	0	0	0	0	0
BRC12	USA	81	IDC	Tumor	II	−	U	U	548,255,169	745	1,113,306	0	0	0	0	0
BRC13	USA	51	IDC	Tumor	III	−	7	U	587,461,482	686	1,106,780	0	0	0	0	0
BRC14	USA	86	IDC	Tumor	III	−	7	U	755,094,207	899	1,469,976	0	0	0	0	0
BRC15	USA	83	IDC	Tumor	II	−	7	U	758,784,262	934	2,327,824	0	0	0	0	0
BRC16	USA	61	IDC	Tumor	III	−	7	U	821,134,040	1287	2,084,782	0	0	0	0	0
BRC18	USA	85	IDC	Tumor	I	−	8	U	568,355,455	677	1,395,823	0	0	0	0	0
BRC19	USA	75	IDC	Tumor	II	−	8	U	596,337,842	747	1,648,870	0	0	0	0	0
BRC20	USA	61	IDC	Tumor	III	−	4	U	507,651,900	570	1,026,830	0	0	0	0	0
BRC21	USA	73	IDC	Tumor	I	−	7	U	719,742,122	817	1,710,010	0	0	0	0	0
BRC22	USA	64	ILC	Tumor	I	−	6	U	608,469,920	708	953,100	0	0	0	0	0
BRC23	USA	68	IDC	Tumor	I	−	7	U	613,481,215	687	1,272,519	0	0	0	0	0
BRC24	USA	51	IDC	Tumor	II	−	7	U	656,115,800	721	1,980,030	0	0	0	0	0
BRC25	USA	52	IDC	Tumor	II	−	5	U	583,560,227	712	580,203	0	0	0	0	0
BRC28	USA	52	IDC	Tumor	I	−	7	U	664,667,777	781	973,990	0	0	0	0	0
BRC29	USA	74	IDC	Tumor	III	−	6	U	785,019,563	596	2,085,482	0	0	0	0	0
BRC3	USA	62	IDC	Tumor	II	−	8	U	695,174,967	1026	3,134,341	0	0	0	0	0
BRC30	USA	60	ILC	Tumor	II	−	5	U	663,769,744	794	1,442,014	0	0	0	0	0
BRC31	USA	66	IDC	Tumor	II	−	6	U	734,384,352	1028	1,415,996	0	0	0	0	0
BRC32	USA	54	IDC	Tumor	I	−	7	U	643,884,178	703	1,404,436	0	0	0	0	0
BRC33	USA	83	IDC	Tumor	II	−	8	U	660,668,877	819	1,284,599	0	0	0	0	0
BRC34	USA	79	IDC	Tumor	I	−	7	U	572,861,930	704	1,499,414	0	0	0	0	0
BRC35	USA	76	IDC	Tumor	II	−	6	U	543,480,474	697	1,709,943	0	0	0	0	0
BRC36	USA	68	IDC	Tumor	II	−	7	U	706,448,348	804	1,501,763	0	0	0	0	0
BRC40	USA	66	IDC	Tumor	I	−	8	U	600,847,516	690	1,686,112	0	0	0	0	0
BRC41	USA	55	IDC	Tumor	II	−	8	U	689,312,217	812	3,735,591	0	0	0	0	0
BRC42	USA	74	IDC	Tumor	II	−	U	U	684,312,302	685	1,308,948	0	0	0	0	0
BRC44	USA	64	IDC	Tumor	II	−	7	U	717,390,251	891	1,430,064	0	0	0	0	0
BRC47	USA	54	IDC	Tumor	III	−	5	U	580,674,755	865	960,944	0	0	0	0	0
BRC48	USA	66	IDC	Tumor	II	−	6	U	782,262,353	783	1,236,102	0	0	0	0	0
BRC49	USA	56	IDC	Tumor	II	−	8	U	577,656,003	559	881,804	0	0	0	0	0
BRC5	USA	72	IDC	Tumor	II	−	7	U	762,026,860	1155	2,462,819	0	0	0	0	0
BRC50	USA	78	ILC	Tumor	I	−	4	U	661,525,693	792	357,915	0	0	0	0	0
BRC7	USA	78	IDC	Tumor	II	−	8	U	455,727,994	795	580,484	0	0	0	0	0
BRC8	USA	87	IDC	Tumor	I	−	8	U	518,548,285	628	1,394,439	0	0	0	0	0
BRC9	USA	65	ILC	Tumor	II	−	8	U	516,702,802	697	1,759,444	0	0	0	0	0
9DDA1	Vietnam	60	IDC	Tumor	III	U	U	U	706,450,950	759	1,109,340	0	0	0	0	0
9P4X9	Vietnam	54	IDC	Tumor	III	U	U	U	610,913,537	778	619,066	0	0	0	0	0
9YBUF	Vietnam	52	IDC	Tumor	III	U	U	U	595,959,881	616	788,058	0	0	0	0	0
CI5PD	Vietnam	51	IDC	Tumor	III	U	U	U	572,612,309	626	786,787	0	0	0	0	0
FYGW6	Vietnam	38	IDC	Tumor	III	U	U	U	238,201,059	282	221,942	0	0	0	0	0
GT33 V	Vietnam	52	IDC	Tumor	III	U	U	U	548,640,325	604	766,320	0	0	0	0	0
SX1A2	Vietnam	53	IDC	Tumor	III	U	+	+	598,405,143	693	1,002,577	0	0	0	0	0
UQWDS	Vietnam	35	IDC	Tumor	III	U	−	−	596,126,825	665	1,285,884	0	0	0	0	0
9DDA1	Vietnam	60	IDC	Normal	III	U	U	U	691,060,649	797	1,122,133	0	0	0	0	0
9P4X9	Vietnam	54	IDC	Normal	III	U	U	U	601,815,791	664	694,153	0	0	0	0	0
9YBUF	Vietnam	52	IDC	Normal	III	U	U	U	593,968,922	646	1,202,175	0	0	0	0	0
CI5PD	Vietnam	51	IDC	Normal	III	U	U	U	566,065,567	595	911,133	0	0	0	0	0
FYGW6	Vietnam	38	IDC	Normal	III	U	U	U	337,274,647	386	361,063	0	0	0	0	0
GT33 V	Vietnam	52	IDC	Normal	III	U	U	U	581,403,783	652	1,189,003	0	0	0	0	0
SX1A2	Vietnam	53	IDC	Normal	III	U	+	+	608,739,604	700	878,362	0	0	0	0	0
UQWDS	Vietnam	35	IDC	Normal	III	U	−	−	590,387,671	685	829,847	0	0	0	0	0
MEX-BR-106	Mexico	42	IDC	Normal	II	−	+	+	539,137,287	526	351,034	0	0	0	0	0
MEX-BR-116	Mexico	92	IDC	Normal	III	−	+	−	513,833,151	520	258,287	0	0	0	0	0
MEX-BR-123	Mexico	71	IDC	Normal	III	−	+	U	668,026,494	761	515,501	0	0	0	0	0
MEX-BR-15	Mexico	45	IDC	Normal	II	+	−	+	592,958,041	670	756,778	0	0	0	0	0
MEX-BR-154	Mexico	52	IDC	Normal	III	−	+	+	670,289,201	929	817,446	0	0	0	0	0
MEX-BR-165	Mexico	42	IDC	Normal	II	−	+	+	712,308,425	706	537,516	0	0	0	0	0
MEX-BR-198	Mexico	44	IDC	Normal	II	−	+	+	726,225,752	831	216,109	0	0	0	0	0
MEX-BR-200	Mexico	42	IDC	Normal	II	−	+	+	767,097,542	1197	279,031	0	0	0	0	0
MEX-BR-28	Mexico	79	MC	Normal	II	−	+	+	588,561,634	607	215,022	0	0	0	0	0
MEX-BR-50	Mexico	47	IDC	Normal	II	−	+	+	551,537,695	618	394,842	0	0	0	0	0
MEX-BR-82	Mexico	59	IDC	Normal	II	−	+	−	608,849,308	719	385,789	0	0	0	0	0

Whole genome sequencing data from 51 breast tumors and 19 normal adjacent breast tissues were downloaded from the NCBI dbGaP. Hundreds of millions of paired-reads per sample were probed for alignment on different BLV strains and on nuclear and mitochondrial human control sequences
IDC infiltrating ductal carcinoma, ILC infiltrating lobular carcinoma, MC mixed carcinoma, U unknown

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ISSN: 1742-4690

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