University Of Tasmania

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Haplotype reference consortium panel: Practical implications of imputations with large reference panels

journal contribution
posted on 2023-05-19, 15:59 authored by Iglesias, AI, van der Lee, SJ, Bonnemaijer, PWM, Hohn, R, Nag, A, Gharahkhani, P, Khawaja, AP, Broer, L, Foster, PJ, Hammond, CJ, Hysi, PG, van Leeuwen, EM, MacGregor, S, David MackeyDavid Mackey, Mazur, J, Nickels, S, Uitterlinden, AG, Klaver, CCW, Amin, N, van Duijn, CM
Recently, the Haplotype Reference Consortium (HRC) released a large imputation panel that allows more accurate imputation of genetic variants. In this study, we compared a set of directly assayed common and rare variants from an exome array to imputed genotypes, that is, 1000 genomes project (1000GP) and HRC. We showed that imputation using the HRC panel improved the concordance between assayed and imputed genotypes at common, and especially, low‐frequency variants. Furthermore, we performed a genome‐wide association meta‐analysis of vertical cup‐disc ratio, a highly heritable endophenotype of glaucoma, in four cohorts using 1000GP and HRC imputations. We compared the results of the meta‐analysis using 1000GP to the meta‐analysis results using HRC. Overall, we found that using HRC imputation significantly improved P values (= 3.07 × 10−61), particularly for suggestive variants. Both meta‐analyses were performed in the same sample size, yet we found eight genome‐wide significant loci in the HRC‐based meta‐analysis versus seven genome‐wide significant loci in the 1000GP‐based meta‐analysis. This study provides supporting evidence of the new avenues for gene discovery and fine mapping that the HRC imputation panel offers.


Publication title

Human Mutation










Tasmanian School of Medicine



Place of publication

Div John Wiley & Sons Inc, 605 Third Ave, New York, USA, Ny, 10158-0012

Rights statement

Copyright 2017 The Authors

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  • Restricted

Socio-economic Objectives

Clinical health not elsewhere classified