Genome-wide association study of Hirschsprung disease detects a novel low-frequency variant at the RET locus View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2018-04

AUTHORS

João Fadista, Marie Lund, Line Skotte, Frank Geller, Priyanka Nandakumar, Sumantra Chatterjee, Hans Matsson, Anna Löf Granström, Tomas Wester, Perttu Salo, Valtter Virtanen, Lisbeth Carstensen, Jonas Bybjerg-Grauholm, David Michael Hougaard, Mikko Pakarinen, Markus Perola, Agneta Nordenskjöld, Aravinda Chakravarti, Mads Melbye, Bjarke Feenstra

ABSTRACT

Hirschsprung disease (HSCR) is a congenital disorder with a population incidence of ~1/5000 live births, defined by an absence of enteric ganglia along variable lengths of the colon. HSCR genome-wide association studies (GWAS) have found common associated variants at RET, SEMA3, and NRG1, but they still fail to explain all of its heritability. To enhance gene discovery, we performed a GWAS of 170 cases identified from the Danish nationwide pathology registry with 4717 controls, based on 6.2 million variants imputed from the haplotype reference consortium panel. We found a novel low-frequency variant (rs144432435), which, when conditioning on the lead RET single-nucleotide polymorphism (SNP), was of genome-wide significance in the discovery analysis. This conditional association signal was replicated in a Swedish HSCR cohort with discovery plus replication meta-analysis conditional odds ratio of 6.6 (P = 7.7 × 10-10; 322 cases and 4893 controls). The conditional signal was, however, not replicated in two HSCR cohorts from USA and Finland, leading to the hypothesis that rs144432435 tags a rare haplotype present in Denmark and Sweden. Using the genome-wide complex trait analysis method, we estimated the SNP heritability of HSCR to be 88%, close to estimates based on classical family studies. Moreover, by using Lasso (least absolute shrinkage and selection operator) regression we were able to construct a genetic HSCR predictor with a area under the receiver operator characteristics curve of 76% in an independent validation set. In conclusion, we combined the largest collection of sporadic Hirschsprung cases to date (586 cases) to further elucidate HSCR's genetic architecture. More... »

PAGES

561-569

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41431-017-0053-7

DOI

http://dx.doi.org/10.1038/s41431-017-0053-7

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1100690080

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/29379196


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