BEACON heritability paper published in JNCI

The second of two papers based on the BEACON GWAS was published in JNCI. Also see this Science Spotlight article from the Fred Hutchinson Cancer Research Center.

JNCI 2013 [Epub ahead of print] doi:10.1093/jnci/djt303

Germline Genetic Contributions to Risk for Esophageal Adenocarcinoma, Barrett’s Esophagus, and Gastroesophageal Reflux

Weronica E. Ek,  David M. Levine,  Mauro D’Amato,  Nancy L. Pedersen,  Patrik K. E. Magnusson,  Francesca Bresso,  Lynn E. Onstad,  Peter T. Schmidt,  Hans Törnblom,  Helena Nordenstedt,  Yvonne Romero,  (on behalf of the Mayo Clinic Esophageal Adenocarcinoma and Barrett’s Esophagus Registry Consortium),  Wong-Ho Chow,  Liam J. Murray,  Marilie D. Gammon,  Geoffrey Liu,  Leslie Bernstein,  Alan G. Casson,  Harvey A. Risch,  Nicholas J. Shaheen,  Nigel C. Bird,  Brian J. Reid,  Douglas A. Corley,  Laura J. Hardie,  Weimin Ye,  Anna H. Wu,  Marco Zucchelli,  Tim D. Spector,  Pirro Hysi,  Thomas L. Vaughan,  David C. Whiteman,  Stuart MacGregor,  on behalf of the BEACON study investigators


Background: Esophageal adenocarcinoma (EA) is an increasingly common cancer with poor survival. Barrett’s esophagus (BE) is the main precursor to EA, and every year 0.12% to 0.5% of BE patients progress to EA. BE typically arises on a background of chronic gastroesophageal reflux (GERD), one of the risk factors for EA.

Methods:  We used genome-wide association data to investigate the genetic architecture underlying GERD, BE, and EA. We applied a method to estimate the variance explained (array heritability, h2 g) and the genetic correlation (rg) between GERD, BE, and EA by considering all single nucleotide polymorphisms (SNPs) simultaneously. We also estimated the polygenic overlap between GERD, BE, and EA using a prediction approach. All tests were two-sided, except in the case of variance-explained estimation where one-sided tests were used.

Results:  We estimated a statistically significant genetic variance explained for BE (h2 g = 35%; standard error [SE] = 6%; one-sided P = 1 × 10?9) and for EA (h2 g = 25 %; SE = 5%; one-sided P = 2 × 10?7). The genetic correlation between BE and EA was found to be high (rg = 1.0; SE = 0.37). We also estimated a statistically significant polygenic overlap between BE and EA (one-sided P = 1 × 10?6), which suggests, together with the high genetic correlation, that shared genes underlie the development of BE and EoverlapA. Conversely, no statistically significant results were obtained for GERD.

Conclusions: We have demonstrated that risk to BE and EA is influenced by many germline genetic variants of small effect and that shared polygenic effects contribute to risk of these two diseases.

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