Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

Table 2 Genotyping concordance rates across HapMap and 1000 Genomes Panel samples genotyped on the TxArray

SNPs	Reference panel	Ancestry	Number of samples	Total overlapping SNPs post-QC*	Total SNPs concordant	Concordance (%)
All	HM2	ALL	85	22,944,075	22,843,908	99.56
All	HM2	EUR	48	13,058,670	12,986,021	99.44
All	HM2	ASN	24	6,414,064	6,396,803	99.73
All	HM2	AFR	13	3,471,341	3,461,084	99.70
Chr X	HM2	ALL	85	515,791	514,641	99.78
MHC**	HM2	ALL	85	619,108	615,244	99.38
All	1KGP	ALL	55	36,430,433	36,241,576	99.48
All	1KGP	EUR	27	17,830,297	17,716,762	99.36
All	1KGP	ASN	21	13,953,847	13,905,332	99.65
All	1KGP	AFR	7	4,646,289	4,619,482	99.42
Chr X	1KGP	ALL	55	937,853	933,799	99.57
MHC**	1KGP	ALL	55	232,410	230,458	99.16

*Total number of SNPs tested such that each SNP that is non-missing for all samples is counted 85 times
**Defined as between chr6:25.5Mb and chr6:34Mb (hg19)
HM2, International HapMap 2 dataset; 1KGP, 1000 Genomes Project reference dataset

ISSN: 1756-994X