Genome-wide association studies in oesophageal adenocarcinoma and Barrett's oesophagus: a large-scale meta-analysis
Creators: name: Nöthen, Markus M
name: Chow, Wong-Ho
name: Mayershofer, Rupert
name: Hölscher, Arnulf H
name: Bernstein, Leslie
name: Moayyedi, Paul
name: Gammon, Marilie D
name: Neuhaus, Horst
name: MacGregor, Stuart
name: Becker, Jessica
name: Jankowski, Janusz
name: Rösch, Thomas
name: Iyer, Prasad G
name: Vashist, Yogesh
name: Barr, Hugh
name: Schumacher, Brigitte
name: Love, Sharon B
name: Schmidt, Thomas
name: Wu, Anna H
name: Prenen, Hans
name: Gerges, Christian
name: Ye, Weimin
name: Harrison, Rebecca
name: Tomlinson, Ian
name: Bird, Nigel C
name: Venerito, Marino
name: Peters, Wilbert H M
name: MacDonald, David
name: Ott, Katja
name: Liu, Geoffrey
name: Schmidt, Claudia
name: de Caestecker, John
name: Hackelsberger, Andreas
name: Hess, Timo
name: Izbicki, Jakob R
name: Gharahkhani, Puya
name: Moebus, Susanne
name: Fitzgerald, Rebecca C
name: Pech, Oliver
name: Hardie, Laura J
name: Vieth, Michael
name: Corley, Douglas A
name: May, Andrea
name: Noder, Tania
name: Weismüller, Josef
name: Buas, Matthew F
name: Veits, Lothar
name: Ell, Christian
name: Lorenz, Dietmar
name: Manner, Hendrik
name: Vaughan, Thomas L
name: Whiteman, David C
name: Pharoah, Paul
name: Attwood, Stephen
name: Schumacher, Johannes
name: Caldas, Carlos
name: Chegwidden, Laura
name: Palles, Claire
name: Risch, Harvey A
name: Gockel, Ines
name: Watson, R G Peter
name: Shaheen, Nicholas J
name: Anders, Mario
name: Lang, Hauke
name: Böhmer, Anne C
name: Anderson, Lesley A
name: Knapp, Michael
name: Lagergren, Jesper
name: Kreuser, Nicole
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: BACKGROUND: Oesophageal adenocarcinoma represents one of the fastest rising cancers in high-income countries. Barrett's oesophagus is the premalignant precursor of oesophageal adenocarcinoma. However, only a few patients with Barrett's oesophagus develop adenocarcinoma, which complicates clinical management in the absence of valid predictors. Within an international consortium investigating the genetics of Barrett's oesophagus and oesophageal adenocarcinoma, we aimed to identify novel genetic risk variants for the development of Barrett's oesophagus and oesophageal adenocarcinoma.

METHODS: We did a meta-analysis of all genome-wide association studies of Barrett's oesophagus and oesophageal adenocarcinoma available in PubMed up to Feb 29, 2016; all patients were of European ancestry and disease was confirmed histopathologically. All participants were from four separate studies within Europe, North America, and Australia and were genotyped on high-density single nucleotide polymorphism (SNP) arrays. Meta-analysis was done with a fixed-effects inverse variance-weighting approach and with a standard genome-wide significance threshold (p<5 × 10-8). We also did an association analysis after reweighting of loci with an approach that investigates annotation enrichment among genome-wide significant loci. Furthermore, the entire dataset was analysed with bioinformatics approaches-including functional annotation databases and gene-based and pathway-based methods-to identify pathophysiologically relevant cellular mechanisms.

FINDINGS: Our sample comprised 6167 patients with Barrett's oesophagus and 4112 individuals with oesophageal adenocarcinoma, in addition to 17 159 representative controls from four genome-wide association studies in Europe, North America, and Australia. We identified eight new risk loci associated with either Barrett's oesophagus or oesophageal adenocarcinoma, within or near the genes CFTR (rs17451754; p=4·8 × 10-10), MSRA (rs17749155; p=5·2 × 10-10), LINC00208 and BLK (rs10108511; p=2·1 × 10-9), KHDRBS2 (rs62423175; p=3·0 × 10-9), TPPP and CEP72 (rs9918259; p=3·2 × 10-9), TMOD1 (rs7852462; p=1·5 × 10-8), SATB2 (rs139606545; p=2·0 × 10-8), and HTR3C and ABCC5 (rs9823696; p=1·6 × 10-8). The locus identified near HTR3C and ABCC5 (rs9823696) was associated specifically with oesophageal adenocarcinoma (p=1·6 × 10-8) and was independent of Barrett's oesophagus development (p=0·45). A ninth novel risk locus was identified within the gene LPA (rs12207195; posterior probability 0·925) after reweighting with significantly enriched annotations. The strongest disease pathways identified (p<10-6) belonged to muscle cell differentiation and to mesenchyme development and differentiation.

INTERPRETATION: Our meta-analysis of genome-wide association studies doubled the number of known risk loci for Barrett's oesophagus and oesophageal adenocarcinoma and revealed new insights into causes of these diseases. Furthermore, the specific association between oesophageal adenocarcinoma and the locus near HTR3C and ABCC5 might constitute a novel genetic marker for prediction of the transition from Barrett's oesophagus to oesophageal adenocarcinoma. Fine-mapping and functional studies of new risk loci could lead to identification of key molecules in the development of Barrett's oesophagus and oesophageal adenocarcinoma, which might encourage development of advanced prevention and intervention strategies.

FUNDING: US National Cancer Institute, US National Institutes of Health, National Health and Medical Research Council of Australia, Swedish Cancer Society, Medical Research Council UK, Cambridge NIHR Biomedical Research Centre, Cambridge Experimental Cancer Medicine Centre, Else Kröner Fresenius Stiftung, Wellcome Trust, Cancer Research UK, AstraZeneca UK, University Hospitals of Leicester, University of Oxford, Australian Research Council.