. Author manuscript; available in PMC: 2013 Aug 1.

Published in final edited form as: Nat Genet. 2012 Jul 22;44(8):955–959. doi: 10.1038/ng.2354

Table 2.

Accuracy of different imputation methods and 1000 Genomes reference panels applied to various GWAS datasets.

GWAS dataset	Imputation method^a	Reference panel^b	Imputation Accuracy (mean R²)^c
GWAS dataset	Imputation method^a	Reference panel^b	MAF 1–3%	MAF 3–5%	MAF >5%
GAIN Psoriasis (European-American; N = 2,759)	MaCH/minimac	60 CEU	0.67	0.76	0.91
			0.69	0.77	0.91
		283 EUR	0.73	0.78	0.92
		381 EUR	0.83	0.85	0.94
WTCCC2 (United Kingdom; N = 2,490)	IMPUTE2 (sampling/pre-phasing)	60 CEU	0.66	0.78	0.88
			0.65	0.77	0.87
		283 EUR	0.77	0.82	0.89
			0.75	0.81	0.88
		381 EUR	0.84	0.88	0.92
			0.82	0.86	0.91
WHI (African-American; N = 8,421)	MaCH/minimac	60 CEU + 59 YRI	0.51	0.73	0.83
			0.49	0.70	0.80
		283 EUR + 172 AFR	0.55	0.72	0.81
		381 EUR + 174 AFR	0.61	0.75	0.83
1000 Genomes EUR (European ancestry; N = 381)	IMPUTE2 (sampling/pre-phasing)	380 EUR (WTCCC2 SNPs)	0.82	0.86	0.92
			0.81	0.85	0.91
		380 EUR (sequence SNPs)	0.66	0.79	0.91
			0.64	0.78	0.90

We imputed each GWAS dataset with an existing imputation method (plain text) and its pre-phasing counterpart (bold text).

Reference panels used to impute each GWAS dataset, in order: 1000 Genomes low-coverage pilot (June 2010); 1000 Genomes interim release (Aug 2010); 1000 Genomes interim Phase I release (Nov 2010).

Each cell shows the mean R² between true genotypes and imputed dosages for the specified MAF band and reference panel. For a given GWAS dataset, all accuracy values within an MAF band were calculated on the same set of SNPs; the corresponding SNP counts are shown in Figure S1. Accuracy values from pre-phasing are shown in bold (some analyses were performed only with pre-phasing).