Genomic regions associated with susceptibility to Barrett's esophagus and esophageal adenocarcinoma in African Americans: The cross BETRNet admixture study

PloS One
Xiangqing SunAmitabh Chak

Abstract

Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) are far more prevalent in European Americans than in African Americans. Hypothesizing that this racial disparity in prevalence might represent a genetic susceptibility, we used an admixture mapping approach to interrogate disease association with genomic differences between European and African ancestry. Formalin fixed paraffin embedded samples were identified from 54 African Americans with BE or EAC through review of surgical pathology databases at participating Barrett's Esophagus Translational Research Network (BETRNet) institutions. DNA was extracted from normal tissue, and genotyped on the Illumina OmniQuad SNP chip. Case-only admixture mapping analysis was performed on the data from both all 54 cases and also on a subset of 28 cases with high genotyping quality. Haplotype phases were inferred with Beagle 3.3.2, and local African and European ancestries were inferred with SABER plus. Disease association was tested by estimating and testing excess European ancestry and contrasting it to excess African ancestry. Both datasets, the 54 cases and the 28 cases, identified two admixture regions. An association of excess European ancestry on chromosome 11p reached a 5% g...Continue Reading

References

Nov 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·A L GashlerV P Sukhatme
Oct 1, 1992·Gastroenterology·A J Cameron, C T Lomboy
Jan 1, 1990·Seminars in Surgical Oncology·N K Altorki, D B Skinner
Dec 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·R Chakraborty, K M Weiss
May 18, 2001·Digestive Diseases·K R DeVault
May 23, 2002·Gastroenterology·Gary W Falk
Apr 17, 2004·American Journal of Human Genetics·C J HoggartP M McKeigue
Sep 24, 2004·American Journal of Human Genetics·Giovanni Montana, Jonathan K Pritchard
Jan 20, 2005·Journal of the National Cancer Institute·Heiko Pohl, H Gilbert Welch
Jan 25, 2005·Nature Genetics·Xiaofeng ZhuAlan Weder
Sep 2, 2006·Proceedings of the National Academy of Sciences of the United States of America·Matthew L FreedmanDavid Reich
Sep 21, 2006·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Amitabh ChakCharis Eng
Dec 23, 2006·Seminars in Radiation Oncology·Rebecca S Holmes, Thomas L Vaughan
Apr 3, 2007·Nature Genetics·Meredith YeagerGilles Thomas
Apr 6, 2007·Cancer Research·Fredrick R SchumacherDavid J Hunter
Apr 28, 2007·World Journal of Gastroenterology : WJG·Lesley A AndersonLiam J Murray
Mar 25, 2008·Advances in Genetics·Xiaofeng ZhuNeil Risch
Aug 13, 2008·Journal of the National Cancer Institute·Linda Morris BrownWong-Ho Chow
Sep 17, 2008·Nature Genetics·Jeffrey B KoppCheryl A Winkler
Nov 27, 2008·The American Journal of Gastroenterology·Prateek SharmaFrank Hamilton
Apr 16, 2009·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Kathryn L PenneyMatthew L Freedman
Jun 9, 2009·Surgical Oncology Clinics of North America·Gary W Falk
Jun 25, 2009·Cancer Research·Mark M PomerantzMatthew L Freedman
Sep 22, 2009·Nature Genetics·Meredith YeagerStephen J Chanock
Dec 23, 2009·Genome Biology·Fouad ZakhariaHua Tang
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jose SoteloXiaolin Wu
May 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·Nasim AhmadiyehMatthew L Freedman
Jun 4, 2011·Genome Biology·Daniel ShrinerCharles N Rotimi
Dec 24, 2011·PLoS Genetics·Nicholas A JohnsonHua Tang
Aug 24, 2012·Journal of Hypertension·Priya B ShettyUNKNOWN Candidate Gene Association Resource (CARe) Consortium
Jan 15, 2013·Current Protocols in Human Genetics·Daniel Shriner
Mar 5, 2013·Digestive and Liver Disease : Official Journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver·Côme LepageJean Faivre
Dec 23, 2014·American Journal of Human Genetics·Katarzyna BrycJoanna L Mountain
Oct 4, 2015·Nature·UNKNOWN 1000 Genomes Project ConsortiumGonçalo R Abecasis
Jan 30, 2016·Journal of the National Cancer Institute·Ying HanChristopher A Haiman

❮ Previous
Next ❯

Citations

Mar 5, 2020·Diseases of the Esophagus : Official Journal of the International Society for Diseases of the Esophagus·W M WestraK K Krishnadath
May 28, 2019·Nature Reviews. Disease Primers·Yonne PetersPeter D Siersema
Jul 17, 2021·Annals of Surgical Oncology·Wasay NizamFabian M Johnston

❮ Previous
Next ❯

Methods Mentioned

BETA
biopsies
chip
genotyping

Software Mentioned

Beagle
SABER

Related Concepts

Related Feeds

Barrett Esophagus

Barrett’s esophagus if a serious complication of gastroesophageal reflux disease during which the normal esophageal lining changes to tissue that resembles intestinal lining. Here is the latest research.

Cancer Genomics (Keystone)

Cancer genomics approaches employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Discover the latest research using such technologies in this feed.