title: Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus.
abstract: The findings from genome-wide association studies hold enormous potential for novel insight into disease mechanisms. A major challenge in the field is to map these low-risk association signals to their underlying functional sequence variants (FSV). Simple sequence study designs are insufficient, as the vast numbers of statistically comparable variants and a limited knowledge of noncoding regulatory elements complicate prioritization. Furthermore, large sample sizes are typically required for adequate power to identify the initial association signals. One important question is whether similar sample sizes need to be sequenced to identify the FSVs. Here, we present a proof-of-principle example of an extreme discordant design to map FSVs within the 2q33 low-risk breast cancer locus. Our approach employed DNA sequencing of a small number of discordant haplotypes to efficiently identify candidate FSVs. Our results were consistent with those from a 2,000-fold larger, traditional imputation-based fine-mapping study. To prioritize further, we used expression-quantitative trait locus analysis of RNA sequencing from breast tissues, gene regulation annotations from the ENCODE consortium, and functional assays for differential enhancer activities. Notably, we implicate three regulatory variants at 2q33 that target CASP8 (rs3769823, rs3769821 in CASP8, and rs10197246 in ALS2CR12) as functionally relevant. We conclude that nested discordant haplotype sequencing is a promising approach to aid mapping of low-risk association loci. The ability to include more efficient sequencing designs into mapping efforts presents an opportunity for the field to capitalize on the potential of association loci and accelerate translation of association signals to their underlying FSVs. Cancer Res; 76(7); 1916-25. ©2016 AACR.
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah. nicola.camp@hci.utah.edu.
authors.forename: Nicola J
authors.initials: NJ
authors.lastname: Camp
authors.affiliation: Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom.
authors.forename: Wei-Yu
authors.initials: WY
authors.lastname: Lin
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah. University of Utah School of Computing, Salt Lake City, Utah.
authors.forename: Alex
authors.initials: A
authors.lastname: Bigelow
authors.affiliation: Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom.
authors.forename: George J
authors.initials: GJ
authors.lastname: Burghel
authors.affiliation: Bioinformatics Shared Resource, University of Utah, Salt Lake City, Utah.
authors.forename: Timothy L
authors.initials: TL
authors.lastname: Mosbruger
authors.affiliation: Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom.
authors.forename: Marina A
authors.initials: MA
authors.lastname: Parry
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Rosalie G
authors.initials: RG
authors.lastname: Waller
authors.affiliation: Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom.
authors.forename: Sushilaben H
authors.initials: SH
authors.lastname: Rigas
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Pei-Yi
authors.initials: PY
authors.lastname: Tai
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Kristofer
authors.initials: K
authors.lastname: Berrett
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Venkatesh
authors.initials: V
authors.lastname: Rajamanickam
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Rachel
authors.initials: R
authors.lastname: Cosby
authors.affiliation: Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom.
authors.forename: Ian W
authors.initials: IW
authors.lastname: Brock
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Brandt
authors.initials: B
authors.lastname: Jones
authors.affiliation: Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom.
authors.forename: Dan
authors.initials: D
authors.lastname: Connley
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Robert
authors.initials: R
authors.lastname: Sargent
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Guoying
authors.initials: G
authors.lastname: Wang
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Rachel E
authors.initials: RE
authors.lastname: Factor
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Philip S
authors.initials: PS
authors.lastname: Bernard
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Lisa
authors.initials: L
authors.lastname: Cannon-Albright
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Stacey
authors.initials: S
authors.lastname: Knight
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Ryan
authors.initials: R
authors.lastname: Abo
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Theresa L
authors.initials: TL
authors.lastname: Werner
authors.affiliation: Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom.
authors.forename: Malcolm W R
authors.initials: MW
authors.lastname: Reed
authors.affiliation: University of Utah School of Medicine, Salt Lake City, Utah.
authors.forename: Jason
authors.initials: J
authors.lastname: Gertz
authors.affiliation: Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom.
authors.forename: Angela
authors.initials: A
authors.lastname: Cox
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D005260:Female; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation / Q000235:genetics*; D006239:Haplotypes; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D012306:Risk