Chunk #20 — Results — Evaluation of Imputation Accuracy with Dosage R2

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In search of rare variants: preliminary results from whole genome sequencing of 1,325 individuals with psychophysiological endophenotypes.

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For 333 common variants (MAF > 5%), imputation accuracy was comparable between 1000 Genomes and MCTFR sequences (dosage R2 = .905 and .952, respectively). For less common variants, with MAF ≤ 5%, imputation using the MCTFR sequences performed noticeably better, resulting in increases of .2–.3 in the dosage R2 value for SNPs with MAF < 1%. The results are displayed in Figure 3, where one notices that MCTFR outperforms 1000 Genomes for each minor allele frequency bin.