Loss of heterozygosity: what is it good for?

BMC Medical Genomics

Table 2 Ovarian cancer GWAS SNPs and LOH

SNP^a	Risk Allele^b	Locus	het^c	hom	AA	BB	NC	N	CHI sq	Direction	% LOH^d	N LOH	Affy SNP	Rsquared
rs1243180	NA	10p12
rs1243188	minor/A	10p12	112	183	22	6	41	364	0.0025	yes	0.20	28	SNP_A-2024177	0.881
rs7098100	minor/B	10p12	132	181	1	9	41	364	0.0114	yes	0.07	10	SNP_A-8636193	0.781
rs757210	NA	17q12
rs11658063	minor/B	17q12	23	148	44	44	105	364	1.0000	.	0.79	88	SNP_A-8714923	0.704
rs9303542	NA	17q21
rs4451990	minor/B	17q21	20	197	49	61	37	364	0.2526	.	0.85	110	SNP_A-2282117	1
rs12944592	minor/B	17q21	24	198	54	60	28	364	0.5741	.	0.83	114	SNP_A-1836563	1
rs12452212	minor/A	17q21	19	196	74	53	22	364	0.0624	yes	0.87	127	SNP_A-2128564	1
rs9894812	minor/A	17q21	20	198	70	48	28	364	0.0428	yes	0.86	118	SNP_A-2209606	1
rs8170	NA	19p13
rs34084277	minor/B	19p13	80	260	9	8	7	364	0.8084	.	0.18	17	SNP_A-1788674	1
rs2072590	NA	2q31
rs711830	minor/B	2q31	77	160	8	14	105	364	0.2008	.	0.22	22	SNP_A-8652216	0.965
rs7651446	NA	3q25
rs344008	minor/A	3q25	58	297	2	3	4	364	0.6547	.	0.08	5	SNP_A-8543714	0.85
rs2292336	minor/B	3q25	48	299	2	5	10	364	0.2568	.	0.13	7	SNP_A-8587822	0.85
rs17380639	minor/A	3q25	28	320	11	3	2	364	0.0325	yes	0.33	14	SNP_A-2078455	0.85
rs11782652	minor/B	8q21	38	291	8	7	20	364	0.7963	.	0.28	15	SNP_A-8702651	.
rs10088218	major/A	8q24	47	280	11	11	15	364	1.0000	.	0.32	22	SNP_A-1801410	.
rs1516974	major/A	8q24	45	291	4	15	9	364	0.0116	no	0.30	19	SNP_A-2088878	1
rs3814113	NA	9p22
rs7032221	major/B	9p22	123	201	6	11	23	364	0.2253	yes	0.12	17	SNP_A-8603886	1
rs10738467	major/B	9p22	111	206	5	11	31	364	0.1336	yes	0.13	16	SNP_A-8328297	0.892
rs10962668	major/B	9p22	103	177	7	22	55	364	0.0053	yes	0.22	29	SNP_A-4198891	0.794

^a SNPs in bold are those named in the GWAS iCOG publication [29] All others are linked as indicated by the R-squared value of >0.7. If the minor allele is the risk allele named, it is assumed that this will also be the case for the linked SNP
^b Minor = risk allele is the less frequent allele in the population. A, B = risk allele corresponds to the “A” or “B” allele respectively in the Affymetrix array nomenclature. NA = not on Affymetrix SNP6 array
^c Het = Number of cases where germline and tumour are heterozygous, hom = cases where germline is heterozygous, AA, BB = germline is heterozygous, tumour is homozygous for A or B respectively, NC = no call in either tumour or germline. N = total number
^d % LOH is the number of individuals with loss of one allele divided by the total number of heterozygous individuals as measured at that SNP, i.e. not the overall % of LOH that could be determined from all cases using a wider genetic window. This may therefore include regions of extreme allelic imbalance (e.g. likely for 8q24)

ISSN: 1755-8794