A unique genome-wide association analysis in extended Utah high-risk pedigrees identifies a novel melanoma risk variant on chromosome arm 10q

Craig Teerlink, James Farnham, Kristina Allen-Brady, Nicola J. Camp, Alun Thomas, Sancy Leachman, Lisa Cannon-Albright

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

Only two genome-wide association (GWA) screens have been published for melanoma (Nat Genet 47:920-925, 2009; Nat Genet 40:838-840, 2008). Using a unique approach, we performed a genome-wide association study in 156 related melanoma cases from 34 high-risk Utah pedigrees. Genome-wide association analysis was performed on nearly 500,000 markers; we compared cases to 2,150 genotypically matched samples from Illumina's iControls database. We performed genome-wide association with EMMAX software, which is designed to account for population structure, including relatedness between cases. Three SNPs exceeded a genome-wide significance threshold of p <5 × 10 -8 on chromosome arm 10q25.1 (rs17119434, rs17119461, and rs17119490), where the most extreme p value was 7.21 × 10 -12. This study represents a new and unique approach to predisposition gene identification; and it is the first genome-wide association study performed in related cases in high-risk pedigrees. Our approach illustrates an example of using high-risk pedigrees for the identification of new melanoma predisposition variants.

Original languageEnglish (US)
Pages (from-to)77-85
Number of pages9
JournalHuman Genetics
Volume131
Issue number1
DOIs
StatePublished - Jan 2012
Externally publishedYes

Fingerprint

Genome-Wide Association Study
Pedigree
Viverridae
Melanoma
Chromosomes
Genome
Chromosomes, Human, Pair 8
Single Nucleotide Polymorphism
Software
Databases
Population
Genes

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics

Cite this

A unique genome-wide association analysis in extended Utah high-risk pedigrees identifies a novel melanoma risk variant on chromosome arm 10q. / Teerlink, Craig; Farnham, James; Allen-Brady, Kristina; Camp, Nicola J.; Thomas, Alun; Leachman, Sancy; Cannon-Albright, Lisa.

In: Human Genetics, Vol. 131, No. 1, 01.2012, p. 77-85.

Research output: Contribution to journalArticle

Teerlink, Craig ; Farnham, James ; Allen-Brady, Kristina ; Camp, Nicola J. ; Thomas, Alun ; Leachman, Sancy ; Cannon-Albright, Lisa. / A unique genome-wide association analysis in extended Utah high-risk pedigrees identifies a novel melanoma risk variant on chromosome arm 10q. In: Human Genetics. 2012 ; Vol. 131, No. 1. pp. 77-85.
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