Fine mapping of chromosome 5p15.33 based on a targeted deep sequencing and high density genotyping identifies novel lung cancer susceptibility loci

L Kachuri; CI Amos; JD McKay; M Johansson; P Vineis; HB Bueno-de-Mesquita; MC Boutron-Ruault; M Johansson; JR Quirós; S Sieri; RC Travis; E Weiderpass; L Le Marchand; BE Henderson; L Wilkens; GE Goodman; C Chen; JA Doherty; DC Christiani; Y Wei; L Su; S Tworoger; X Zhang; P Kraft; D Zaridze; JK Field; MW Marcus; MPA Davies; R Hyde; NE Caporaso; MT Landi; G Severi; GG Giles; G Liu; JR McLaughlin; Y Li; X Xiao; G Fehringer; X Zong; RE Denroche; PC Zuzarte; JD McPherson; P Brennan; RJ Hung

Journal article

Fine mapping of chromosome 5p15.33 based on a targeted deep sequencing and high density genotyping identifies novel lung cancer susceptibility loci

L Kachuri, CI Amos, JD McKay, M Johansson, P Vineis, HB Bueno-de-Mesquita, MC Boutron-Ruault, M Johansson, JR Quirós, S Sieri, RC Travis, E Weiderpass, L Le Marchand, BE Henderson, L Wilkens, GE Goodman, C Chen, JA Doherty, DC Christiani, Y Wei Show all

Carcinogenesis | Published : 2016

DOI: 10.1093/carcin/bgv165

Abstract

Chromosome 5p15.33 has been identified as a lung cancer susceptibility locus, however the underlying causal mechanisms were not fully elucidated. Previous fine-mapping studies of this locus have relied on imputation or investigated a small number of known, common variants. This study represents a significant advance over previous research by investigating a large number of novel, rare variants, as well as their underlying mechanisms through telomere length. Variants for this fine-mapping study were identified through a targeted deep sequencing (average depth of coverage greater than 4000×) of 576 individuals. Subsequently, 4652 SNPs, including 1108 novel SNPs, were genotyped in 5164 cases an..

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University of Melbourne Researchers

Graham Giles Author

Grants

Awarded by National Institutes of Health

Funding Acknowledgements

This work was supported by: the National Institutes of Health grant U19CA148127 (PI: Amos), the data harmonization was supported by Cancer Care Ontario Research Chair of Population Studies to Rayjean J. Hung. The MSH-PMH study was supported by Canadian Cancer Society Research Institute (no. 020214, PI: Hung). The Harvard Lung Cancer Study was funded by the National Institutes of Health grants: CA092824, CA074386, CA090578 (PI: Christiani). The Multiethnic Cohort Study was supported by the National Institutes of Health grant UM1 CA164973. Linda Kachuri is a trainee in the Canadian Institutes of Health Research (CIHR) Strategic Training for Advanced Genetic Epidemiology (STAGE) Program, and is supported by the CIHR Research Doctoral Award-Frederick Banting and Charles Best Canada Graduate Scholarships.