Human Genetics

, Volume 131, Issue 1, pp 77–85

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
Original Investigation

DOI: 10.1007/s00439-011-1048-z

Cite this article as:
Teerlink, C., Farnham, J., Allen-Brady, K. et al. Hum Genet (2012) 131: 77. doi:10.1007/s00439-011-1048-z

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.

Supplementary material

439_2011_1048_MOESM1_ESM.docx (14 kb)
Supplementary material 1 (DOCX 13 kb)

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Craig Teerlink
    • 1
  • James Farnham
    • 1
  • Kristina Allen-Brady
    • 1
  • Nicola J. Camp
    • 1
  • Alun Thomas
    • 1
  • Sancy Leachman
    • 2
  • Lisa Cannon-Albright
    • 1
    • 3
  1. 1.Division of Genetic Epidemiology, Department of Internal MedicineUniversity of Utah School of MedicineSalt Lake CityUSA
  2. 2.Department of DermatologyUniversity of Utah School of MedicineSalt Lake CityUSA
  3. 3.George E. Wahlen Department of Veterans Affairs Medical CenterSalt Lake CityUSA