Genome sequencing analysis of blood cells identifies germline haplotypes strongly associated with drug resistance in osteosarcoma patients

Bhuvaneshwar, Krithika; Harris, Michael; Gusev, Yuriy; Madhavan, Subha; Iyer, Ramaswamy; Vilboux, Thierry; Deeken, John; Yang, Elizabeth; Shankar, Sadhna

doi:10.1186/s12885-019-5474-y

Table 5 Most frequent haplotypes in the TARGET and INOVA datasets

From: Genome sequencing analysis of blood cells identifies germline haplotypes strongly associated with drug resistance in osteosarcoma patients

		TARGET _NSNP	TARGENHAP	TARGET_CHR	TARGET_BP1	TARGET_BP2	TARGET_Haplo	TARGET_Region	TARGET_Genes	TARGET_F	INOVA_NSNP	INOVA_NHAP	INOVA_CHR	INOVA_BP1	INOVA_BP2	INOVA_Haplo	Inova_Region	Inova_Genes	Inova_F
Haplotype#1	Most frequent in Target	3	2	23	153,056,311	153,084,802	222	intronic, exonic	IDH3G, PDZD4	0.699	5	5	23	153,073,319	153,075,655	22,222	intronic	PDZD4	0.167
Haplotype#4	Most frequent in Target	8	5	22	18,878,593	18,879,911	22,222,122	intergenic	DQ786190, DGCR6	0.506	8	8	22	18,877,869	18,878,859	22,122,121	intergenic	DQ786190, DGCR6	0.106
Haplotype#12	Most frequent in Target	7	6	22	18,878,593	18,879,898	2,222,212	intergenic	DQ786190, DGCR6	0.487	8	8	22	18,877,869	18,878,859	22,122,121	intergenic	DQ786190, DGCR6	0.106
Haplotype#20	Most frequent in Target	8	4	22	18,878,349	18,878,632	11,222,221	intergenic	DQ786190, DGCR6	0.478	8	8	22	18,877,869	18,878,859	22,122,121	intergenic	DQ786190, DGCR6	0.106
Haplotype#31	Most frequent in Target	2	3	17	26,816,365	26,817,537	11	intronic, exonic	SLC13A2	0.353	8	9	17	26,816,365	26,822,518	11,121,221	intronic, exonic	SLC13A2	0.0839
Haplotype#32	Most frequent in Target	3	4	17	26,816,365	26,818,676	112	intronic, exonic	SLC13A2	0.341	8	9	17	26,816,365	26,822,518	11,121,221	intronic, exonic	SLC13A2	0.0839
Haplotype#61	Most frequent in Inova	3	6	19	55,614,923	55,624,113	111	intronic, exonic	PPP1R12C	0.125	7	7	19	55,619,303	55,622,518	2,222,222	intronic	PPP1R12C	0.71
Haplotype#74	Most frequent in Inova	3	6	19	55,614,923	55,624,113	111	intronic, exonic	PPP1R12C	0.125	8	8	19	55,618,992	55,622,518	22,222,222	intronic	PPP1R12C	0.675
Haplotype#126	Most frequent in Inova	5	16	5	67,513,481	67,554,172	11,121	intronic	PIK3R1	0.0625	5	9	5	67,548,442	67,549,836	22,222	intronic	PIK3R1	0.448
Haplotype#160	Most frequent in Inova	7	12	10	19,620,439	19,641,239	1,221,212	intergenic	DQ600701, C10orf112 (MALRD1)	0.0409	7	9	10	19,621,103	19,624,121	2,222,221	intergenic	DQ600701, C10orf112 (MALRD1)	0.267

NSNP: Number of SNPs in the haplotype, NHAP: Number of common haplotypes, CHR: Chromosome, BP1: Position of left most SNP, BP2: Position of right most SNP, Haplo: Indicates the haplotype that was formed. The numbers 1 and 2 represent the genotypes. F: Sample frequency

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ISSN: 1471-2407

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