Oncotarget

Research Papers:

Two-stage genome-wide association study identifies a novel susceptibility locus associated with melanoma

Katherine J. Ransohoff, Wenting Wu, Hyunje G. Cho, Harvind C. Chahal, Yuan Lin, Hong-Ji Dai, Christopher I. Amos, Jeffrey E. Lee, Jean Y. Tang, David A. Hinds, Jiali Han, Qingyi Wei, Kavita Y. Sarin _

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Oncotarget. 2017; 8:17586-17592. doi: 10.18632/oncotarget.15230

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Abstract

Katherine J. Ransohoff1,*, Wenting Wu2,*, Hyunje G. Cho1, Harvind C. Chahal1, Yuan Lin2, Hong-Ji Dai2,3, Christopher I. Amos4, Jeffrey E. Lee5, Jean Y. Tang1, David A. Hinds6, Jiali Han2,7,#, Qingyi Wei8,#, Kavita Y. Sarin1,#

1Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA

2Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA

3Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Hospital and Institute, National Clinical Research Center for Cancer, Tianjin and Key Laboratory of Cancer Prevention and Therapy, Tianjin, China

4Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA

5Department of Surgical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA

623andMe Inc., Mountain View, CA, USA

7Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA

8Duke Cancer Institute, Department of Medicine, Duke University, Durham, NC, USA

*Co-first author

#Co-senior author

Correspondence to:

Kavita Y. Sarin, email: ksarin@stanford.edu

Keywords: melanoma, genome-wide association study, single nucleotide polymorphism, susceptibility loci, BASP1

Received: December 02, 2016     Accepted: January 27, 2017     Published: February 09, 2017

ABSTRACT

Genome-wide association studies have identified 21 susceptibility loci associated with melanoma. These loci implicate genes affecting pigmentation, nevus count, telomere maintenance, and DNA repair in melanoma risk. Here, we report the results of a two-stage genome-wide association study of melanoma. The stage 1 discovery phase consisted of 4,842 self-reported melanoma cases and 286,565 controls of European ancestry from the 23andMe research cohort and the stage 2 replication phase consisted of 1,804 melanoma cases and 1,026 controls from the University of Texas M.D. Anderson Cancer Center. We performed a combined meta-analysis totaling 6,628 melanoma cases and 287,591 controls. Our study replicates 20 of 21 previously known melanoma-loci and confirms the association of the telomerase reverse transcriptase, TERT, with melanoma susceptibility at genome-wide significance. In addition, we uncover a novel polymorphism, rs187843643 (OR = 1.96; 95% CI = [1.54, 2.48]; P = 3.53 x 10–8), associated with melanoma. The SNP rs187842643 lies within a noncoding RNA 177kb downstream of BASP1 (brain associated protein-1). We find that BASP1 expression is suppressed in melanoma as compared with benign nevi, providing additional evidence for a putative role in melanoma pathogenesis.

Author Information

Katherine J. Ransohoff

Wenting Wu

Hyunje G. Cho

Harvind C. Chahal

Yuan Lin

Hong-Ji Dai

Christopher I. Amos

Jeffrey E. Lee

Jean Y. Tang

David A. Hinds

Jiali Han

Qingyi Wei

Kavita Y. Sarin
Primary Contact  _


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