Evaluating outlier loci and their effect on the identification of pedigree errors

BMC Genomic Data

Table 3 Pedigree errors identified in the COGA data

				With outlier loci						Without outlier loci
Ped^a	ID in error^b	ID of relative^c	Description	SNPs (Illumina)		SNPs (Affymetrix)		Microsatellite		SNPs (Illumina)		SNPs (Affymetrix)		Microsatellite
				P0^d	AIBS^e	P0	AIBS	P0	AIBS	P0	AIBS	P0	AIBS	P0	AIBS
2	1540	530	Avuncular of 530	0.411	0.390	0.225	0	0.423	0.142	0.435	0.605	0.224	0	0.450	0.179
9	832	1459	full sib of 1459	0.738	0^h	0.741	0	0.244	0.409	0.700	0	0.718	0	0.202	0.383
10	397	887	full sib of 887	0.997	0	0.593	0	0.842	0	1	0	0.583	0	0.872	0
34	1272	616^f	half sib of 616	0.327	0.663	0.184	0	0.255	0.002	0.297	0.471	0.227	0	0.252	0.004
50	1406	313	Avuncular of 313	0.293	0.894	0.505	0.292	0.308	0	0.407	0.941	0.549	0.239	0.323	0
52	515	1246	first cousin of 1246	0.197	0	0.161	0	0.248	0	0.179	0	0.178	0	0.278	0
59	1062	1375	full sib of 1375	0.98	0	0.964	0	0.298	0.130	0.992	0	0.950	0	0.282	0.177
81	418	1060	full sib of 1060	0.497	0	0.321	0.003	0.334	0.114	0.509	0	0.364	0.007	0.318	0.176
81	285	708	parent-offspring relationship of 708	NA^g	NA	0	0	0	0	NA	NA	0	0	0	0
126	259	505	half sib of 505	0.196	0	0.118	0	0.865	0.00008	0.153	0	0.117	0	0.857	0.00013

^a Ped = pedigree id
^b ID in error = id of individual which has problematic genetic relationships with other individuals within the pedigree
^c ID of relative = id of individuals which are relatives to id in error
^d P0 = the probability of sharing 0 alleles IBD
^e AIBS = two-sided p-value for the adjusted IBS test
^f individual 616 is genotyped for only 163 microsatellite markers.
^g NA = 708 has no genotype data
^h 0 refers to p-values smaller than 0.00001

ISSN: 2730-6844