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T-test comparison to data from untreated panel release rates on day 60 showed no significant difference between the sets of panels.
In each study, we performed an association analysis of up to 2 543 888 SNPs, including genotypes that were imputed with reference to the International HapMap Project CEU panel release 22.
IMPUTE2 was used to phase the observed genotypes and impute unobserved genotypes [ 28, 29] using the 1000 Genomes phase 1 reference panel (release June 2011, b37) [ 30] separately by ancestry.
Using the Phase II CEU HapMap individuals as a reference panel (release 22, build 36), genotypes were imputed for each study (MICROS, popgen and KORA-F3) for the entire set of polymorphic HapMap SNPs (>2.5 million SNPs), using a hidden Markov model as implemented in the MACH software version 1.0.15/16 (33) (http://www.sph.umich.edu/csg/abecasis/MACH/).edu/csg/abecasis/MACH/
Genotypes were imputed for all polymorphic SNPs (minor allele frequency >0.01) using either the MACH (36) or the IMPUTE (37) software, based upon phased autosomal chromosomes of the HapMap CEU Phase II panel (release 22, build 36), orientated on the positive strand.
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