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This article is part of a special issue on exome sequencing.

Open Access Method

Reducing the exome search space for Mendelian diseases using genetic linkage analysis of exome genotypes

Katherine R Smith1*, Catherine J Bromhead1, Michael S Hildebrand2, A Eliot Shearer23, Paul J Lockhart45, Hossein Najmabadi6, Richard J Leventer478, George McGillivray4, David J Amor47, Richard J Smith239 and Melanie Bahlo110

Author Affiliations

1 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia

2 Department of Otolaryngology-Head and Neck Surgery, University of Iowa, Iowa City, Iowa 52242, USA

3 Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA

4 Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia

5 Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia

6 Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran 19834, Iran

7 Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria 3052, Australia

8 Children's Neuroscience Centre, Royal Children's Hospital, Parkville, Victoria 3052, Australia

9 Interdepartmental PhD Program in Genetics, University of Iowa, Iowa City, Iowa 52242, USA

10 Department of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia

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Genome Biology 2011, 12:R85  doi:10.1186/gb-2011-12-9-r85

Published: 14 September 2011

Abstract

Many exome sequencing studies of Mendelian disorders fail to optimally exploit family information. Classical genetic linkage analysis is an effective method for eliminating a large fraction of the candidate causal variants discovered, even in small families that lack a unique linkage peak. We demonstrate that accurate genetic linkage mapping can be performed using SNP genotypes extracted from exome data, removing the need for separate array-based genotyping. We provide software to facilitate such analyses.