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

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

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