Wang, Xiaoyu ORCID: 0000-0002-4504-7799, Gharahkhani, Puya ORCID: 0000-0002-4203-5952, Levine, David M., Fitzgerald, Rebecca C., Gockel, Ines, Corley, Douglas A., Risch, Harvey A., Bernstein, Leslie ORCID: 0000-0002-7692-6518, Chow, Wong-Ho, Onstad, Lynn, Shaheen, Nicholas J., Lagergren, Jesper, Hardie, Laura J., Wu, Anna H., Pharoah, Paul D. P., Liu, Geoffrey, Anderson, Lesley A., Iyer, Prasad G., Gammon, Marilie D., Caldas, Carlos ORCID: 0000-0003-3547-1489, Ye, Weimin, Barr, Hugh, Moayyedi, Paul, Harrison, Rebecca, Watson, R. G. Peter, Attwood, Stephen, Chegwidden, Laura, Love, Sharon B., MacDonald, David, DeCaestecker, John, Prenen, Hans ORCID: 0000-0001-8802-7352, Ott, Katja, Moebus, Susanne, Venerito, Marino, Lang, Hauke, Mayershofer, Rupert, Knapp, Michael, Veits, Lothar, Gerges, Christian, Weismueller, Josef, Reeh, Matthias, Noethen, Markus M., Izbicki, Jakob R., Manner, Hendrik, Neuhaus, Horst, Roesch, Thomas, Boehmer, Anne C., Hoelscher, Arnulf H., Anders, Mario, Pech, Oliver, Schumacher, Brigitte, Schmidt, Claudia, Schmidt, Thomas, Noder, Tania, Lorenz, Dietmar, Vieth, Michael, May, Andrea, Hess, Timo, Kreuser, Nicole, Becker, Jessica, Ell, Christian, Tomlinson, Ian, Palles, Claire, Jankowski, Janusz A., Whiteman, David C., MacGregor, Stuart, Schumacher, Johannes, Vaughan, Thomas L., Buas, Matthew F. and Dai, James Y. (2022). eQTL Set-Based Association Analysis Identifies Novel Susceptibility Loci for Barrett Esophagus and Esophageal Adenocarcinoma. Cancer Epidemiol. Biomarkers Prev., 31 (9). S. 1735 - 1746. PHILADELPHIA: AMER ASSOC CANCER RESEARCH. ISSN 1538-7755

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Abstract

Background: Over 20 susceptibility single-nucleotide poly-morphisms (SNP) have been identified for esophageal adenocarcinoma (EAC) and its precursor, Barrett esophagus (BE), explaining a small portion of heritability.Methods: Using genetic data from 4,323 BE and 4,116 EAC patients aggregated by international consortia including the Barrett's and Esophageal Adenocarcinoma Consortium (BEACON), we conducted a comprehensive transcriptome-wide association study (TWAS) for BE/EAC, leveraging Genotype Tissue Expression (GTEx) gene-expression data from six tissue types of plausible relevance to EAC etiology: mucosa and muscularis from the esophagus, gastroesophageal (GE) junction, stomach, whole blood, and visceral adipose. Two analytical approaches were taken: standard TWAS using the predicted gene expression from local expression quantitative trait loci (eQTL), and set-based SKAT association using selected eQTLs that predict the gene expression. Results: Although the standard approach did not identify significant signals, the eQTL set-based approach identified eight novel associations, three of which were validated in independent external data (eQTL SNP sets for EXOC3, ZNF641, and HSP90AA1). Conclusions: This study identified novel genetic susceptibility loci for EAC and BE using an eQTL set-based genetic association approach.Impact: This study expanded the pool of genetic susceptibility loci for EAC and BE, suggesting the potential of the eQTL set-based genetic association approach as an alternative method for TWAS analysis.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Wang, XiaoyuUNSPECIFIEDorcid.org/0000-0002-4504-7799UNSPECIFIED
Gharahkhani, PuyaUNSPECIFIEDorcid.org/0000-0002-4203-5952UNSPECIFIED
Levine, David M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Fitzgerald, Rebecca C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gockel, InesUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Corley, Douglas A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Risch, Harvey A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Bernstein, LeslieUNSPECIFIEDorcid.org/0000-0002-7692-6518UNSPECIFIED
Chow, Wong-HoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Onstad, LynnUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Shaheen, Nicholas J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lagergren, JesperUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hardie, Laura J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wu, Anna H.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pharoah, Paul D. P.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Liu, GeoffreyUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Anderson, Lesley A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Iyer, Prasad G.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gammon, Marilie D.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Caldas, CarlosUNSPECIFIEDorcid.org/0000-0003-3547-1489UNSPECIFIED
Ye, WeiminUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Barr, HughUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Moayyedi, PaulUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Harrison, RebeccaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Watson, R. G. PeterUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Attwood, StephenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Chegwidden, LauraUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Love, Sharon B.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
MacDonald, DavidUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
DeCaestecker, JohnUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Prenen, HansUNSPECIFIEDorcid.org/0000-0001-8802-7352UNSPECIFIED
Ott, KatjaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Moebus, SusanneUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Venerito, MarinoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lang, HaukeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Mayershofer, RupertUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Knapp, MichaelUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Veits, LotharUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gerges, ChristianUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Weismueller, JosefUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Reeh, MatthiasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Noethen, Markus M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Izbicki, Jakob R.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Manner, HendrikUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Neuhaus, HorstUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Roesch, ThomasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Boehmer, Anne C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hoelscher, Arnulf H.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Anders, MarioUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pech, OliverUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schumacher, BrigitteUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schmidt, ClaudiaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schmidt, ThomasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Noder, TaniaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lorenz, DietmarUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Vieth, MichaelUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
May, AndreaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hess, TimoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kreuser, NicoleUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Becker, JessicaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ell, ChristianUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tomlinson, IanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Palles, ClaireUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Jankowski, Janusz A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Whiteman, David C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
MacGregor, StuartUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schumacher, JohannesUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Vaughan, Thomas L.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Buas, Matthew F.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Dai, James Y.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-699192
DOI: 10.1158/1055-9965.EPI-22-0096
Journal or Publication Title: Cancer Epidemiol. Biomarkers Prev.
Volume: 31
Number: 9
Page Range: S. 1735 - 1746
Date: 2022
Publisher: AMER ASSOC CANCER RESEARCH
Place of Publication: PHILADELPHIA
ISSN: 1538-7755
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
GENOME-WIDE ASSOCIATION; POPULATION ATTRIBUTABLE RISKS; BODY-MASS INDEX; GASTROESOPHAGEAL-REFLUX; POOLED ANALYSIS; ESOPHAGOGASTRIC JUNCTION; CIGARETTE-SMOKING; GENE-EXPRESSION; CANCER SURVIVAL; INCREASES RISKMultiple languages
Oncology; Public, Environmental & Occupational HealthMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/69919

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