A new strategy for enhancing imputation quality of rare variants from next-generation sequencing data via combining SNP and exome chip data

Table 4 Relative increase in mean estimated r ² by using combination of reference panel and combined approach (MAFs 0.5–1 %)

	R300-C	R500-C	R700-C	R848-C
R300-G	10.88 %	19.95 %	25.30 %	27.49 %
R500-G	1.47 %	9.77 %	14.67 %	16.67 %
R700-G	−3.27 %	4.64 %	9.31 %	11.21 %
R848-G	−5.25 %	2.50 %	7.07 %	8.94 %

The names of panels were abbreviated as follows: R (reference panel), G (the genotype panel of SNP chip only), and C (the genotype panel of combined data). R300, R500, R700, and R848 indicates sample sizes of 300, 500, 700, and 848 for reference panel, respectively. R(sample size) -G represents combination of R(sample size) reference panel and G genotype panel. R(sample size)-C represents the combination of R(sample size) reference panel and C genotype panel

ISSN: 1471-2164