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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Genome-wide association study of esophageal squamous cell cancer identifies shared and distinct risk variants in African and Chinese populations
American Journal of Human Genetics, Volume 110, No. 10, Year 2023
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Description
Esophageal squamous cell carcinoma (ESCC) has a high disease burden in sub-Saharan Africa and has a very poor prognosis. Genome-wide association studies (GWASs) of ESCC in predominantly East Asian populations indicate a substantial genetic contribution to its etiology, but no genome-wide studies have been done in populations of African ancestry. Here, we report a GWAS in 1,686 African individuals with ESCC and 3,217 population-matched control individuals to investigate its genetic etiology. We identified a genome-wide-significant risk locus on chromosome 9 upstream of FAM120A (rs12379660, p = 4.58 × 10−8, odds ratio = 1.28, 95% confidence interval = 1.22–1.34), as well as a potential African-specific risk locus on chromosome 2 (rs142741123, p = 5.49 × 10−8) within MYO1B. FAM120A is a component of oxidative stress-induced survival signals, and the associated variants at the FAM120A locus co-localized with highly significant cis-eQTLs in FAM120AOS in both esophageal mucosa and esophageal muscularis tissue. A trans-ethnic meta-analysis was then performed with the African ESCC study and a Chinese ESCC study in a combined total of 3,699 ESCC-affected individuals and 5,918 control individuals, which identified three genome-wide-significant loci on chromosome 9 at FAM120A (rs12379660, pmeta = 9.36 × 10−10), chromosome 10 at PLCE1 (rs7099485, pmeta = 1.48 × 10−8), and chromosome 22 at CHEK2 (rs1033667, pmeta = 1.47 × 10−9). This indicates the existence of both shared and distinct genetic risk loci for ESCC in African and Asian populations. Our GWAS of ESCC conducted in a population of African ancestry indicates a substantial genetic contribution to ESCC risk in Africa. © 2023 American Society of Human Genetics
Authors & Co-Authors
Chen, Wenlong Carl
South Africa, Johannesburg
National Health Laboratory Service
South Africa, Johannesburg
University of the Witwatersrand
Brandenburg, Jean Tristan
South Africa, Johannesburg
University of the Witwatersrand
Choudhury, Ananyo
South Africa, Johannesburg
University of the Witwatersrand
Hayat, Mahtaab
South Africa, Johannesburg
University of the Witwatersrand
Sengupta, Dhriti
South Africa, Johannesburg
University of the Witwatersrand
Babb de Villiers, Chantal
South Africa, Johannesburg
University of the Witwatersrand
Ferndale, Lucien C.
South Africa, Pietermaritzburg
Grey's Hospital Pietermaritzburg
South Africa, Durban
University of Kwazulu-natal
Aldous, Colleen Michelle
South Africa, Durban
University of Kwazulu-natal
Soo, Cassandra Claire
South Africa, Johannesburg
University of the Witwatersrand
Curtis, Charles J.C.
United Kingdom, London
King's College London
United Kingdom, London
Nihr Maudsley Biomedical Research Centre
Newton, Robert A.
Uganda, Entebbe
Mrc/uvri and Lshtm Uganda Research Unit
United Kingdom, York
University of York
Waterboer, Tim
Germany, Heidelberg
German Cancer Research Center
Sitas, F.
South Africa, Tygerberg
South African Medical Research Council
Australia, Sydney
Unsw Sydney
Australia, Sydney
The University of Sydney
Bradshaw, Debbie Young
South Africa, Tygerberg
South African Medical Research Council
Abnet, Christian C.
United States, Rockville
National Cancer Institute Nci
Ramsay, Michèle
South Africa, Johannesburg
University of the Witwatersrand
Iqbal Parker, Mohammed
South Africa, Cape Town
University of Cape Town
Singh, Elvira
South Africa, Johannesburg
National Health Laboratory Service
South Africa, Johannesburg
University of the Witwatersrand Faculty of Health Sciences
Lewis, Cathryn M.
United Kingdom, London
King's College London
Mathew, Christopher George
South Africa, Johannesburg
University of the Witwatersrand
United Kingdom, London
King's College London
Statistics
Authors: 20
Affiliations: 15
Identifiers
Doi:
10.1016/j.ajhg.2023.08.007
ISSN:
00029297
Research Areas
Cancer
Genetics And Genomics
Study Design
Cross Sectional Study
Case-Control Study
Study Approach
Systematic review