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Combinatorial Conflicting Homozygosity (CCH) analysis enables the rapid identification of shared genomic regions in the presence of multiple phenocopies.


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Authors

Levine, AP 
Connor, TM 
Oygar, DD 
Neild, GH 
Segal, AW 

Abstract

The ability to identify regions of the genome inherited with a dominant trait in one or more families has become increasingly valuable with the wide availability of high throughput sequencing technology. While a number of methods exist for mapping of homozygous variants segregating with recessive traits in consanguineous families, dominant conditions are conventionally analysed by linkage analysis, which requires computationally demanding haplotype reconstruction from marker genotypes and, even using advanced parallel approximation implementations, can take substantial time, particularly for large pedigrees. In addition, linkage analysis lacks sensitivity in the presence of phenocopies (individuals sharing the trait but not the genetic variant responsible). Combinatorial Conflicting Homozygosity (CCH) analysis uses high density biallelic single nucleotide polymorphism (SNP) marker genotypes to identify genetic loci within which consecutive markers are not homozygous for different alleles. This allows inference of identical by descent (IBD) inheritance of a haplotype among a set or subsets of related or unrelated individuals.

Description

Keywords

Linkage, Identical by descent, Phenocopy, Haplotype, Pedigree

Journal Title

BMC Genomics

Conference Name

Journal ISSN

1471-2164
1471-2164

Volume Title

Publisher

Springer Science and Business Media LLC
Sponsorship
Wellcome Trust (096956/Z/11/Z)
Department of Health (via National Institute for Health Research (NIHR)) (NF-SI-0514-10122)
Wellcome Trust (100140/Z/12/Z)