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. Author manuscript; available in PMC: 2014 Mar 1.
Published in final edited form as: Pancreas. 2013 Mar;42(2):209–215. doi: 10.1097/MPA.0b013e318264cea5

Table 3.

Genotype concordance rates for SNPs on chromosomes 5p15.33, 1q32.1 and 13q22.1 with publicly available datasets

Population HapMap HapMap HapMap PanScan PanScan
Ethnicity CEU CHB YRI CEU CEU
Locus Chr5 Chr5 Chr5 Chr1 Chr13
The 1000 Genomes
 # of samples 26 47 34 - -
 # of SNPs 485 403 727 - -
 Concordance rate 0.962 (0.095–1) 0.979 (0.116–1) 0.971 (0.176–1) - -
Omni chip
 # of samples 37 52 44 - -
 # of SNPs 151 131 168 - -
 Concordance rate 0.946 (0.833–1) 1 (0.940–1) 0.977 (0.795–1) - -
HapMap data
 # of samples 49 54 55 - -
 # of SNPs 96 86 93 - -
 Concordance rate 0.947 (0.048–1) 0.981 (0.038–1) 0.981 (0.592–1) - -
PanScan GWAS
 # of samples - - - 88 94
 # of SNPs - - - 42 26
 Concordance rate - - - 0.989 (0.784–1) 1 (0.915–1)

Genotype concordance rates between the current dataset and the 1000 Genomes (October 2011 release), GATK Omni 2.5M chip, HapMap (Release 28) and PanScan GWAS datasets for SNPs observed on chromosomes 5p.15.33, 1q32.1 and 13q22.1.