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

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

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1-9
Number of pages9
JournalEuropean Journal of Human Genetics
DOIs
StateAccepted/In press - Jan 29 2018

Fingerprint

Hirschsprung Disease
Genome-Wide Association Study
Haplotypes
Single Nucleotide Polymorphism
Genome
Congenital, Hereditary, and Neonatal Diseases and Abnormalities
Inborn Genetic Diseases
Live Birth
Genetic Association Studies
Denmark
Finland
Sweden
Ganglia
Registries
Meta-Analysis
Colon
Odds Ratio
Pathology
Incidence
Population

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Fadista, J., Lund, M., Skotte, L., Geller, F., Nandakumar, P., Chatterjee, S., ... Feenstra, B. (Accepted/In press). Genome-wide association study of Hirschsprung disease detects a novel low-frequency variant at the RET locus. European Journal of Human Genetics, 1-9. https://doi.org/10.1038/s41431-017-0053-7

Genome-wide association study of Hirschsprung disease detects a novel low-frequency variant at the RET locus. / Fadista, João; Lund, Marie; Skotte, Line; Geller, Frank; Nandakumar, Priyanka; Chatterjee, Sumantra; Matsson, Hans; Granström, Anna Löf; Wester, Tomas; Salo, Perttu; Virtanen, Valtter; Carstensen, Lisbeth; Bybjerg-Grauholm, Jonas; Hougaard, David Michael; Pakarinen, Mikko; Perola, Markus; Nordenskjöld, Agneta; Chakravarti, Aravinda; Melbye, Mads; Feenstra, Bjarke.

In: European Journal of Human Genetics, 29.01.2018, p. 1-9.

Research output: Contribution to journalArticle

Fadista, J, Lund, M, Skotte, L, Geller, F, Nandakumar, P, Chatterjee, S, Matsson, H, Granström, AL, Wester, T, Salo, P, Virtanen, V, Carstensen, L, Bybjerg-Grauholm, J, Hougaard, DM, Pakarinen, M, Perola, M, Nordenskjöld, A, Chakravarti, A, Melbye, M & Feenstra, B 2018, 'Genome-wide association study of Hirschsprung disease detects a novel low-frequency variant at the RET locus', European Journal of Human Genetics, pp. 1-9. https://doi.org/10.1038/s41431-017-0053-7
Fadista, João ; Lund, Marie ; Skotte, Line ; Geller, Frank ; Nandakumar, Priyanka ; Chatterjee, Sumantra ; Matsson, Hans ; Granström, Anna Löf ; Wester, Tomas ; Salo, Perttu ; Virtanen, Valtter ; Carstensen, Lisbeth ; Bybjerg-Grauholm, Jonas ; Hougaard, David Michael ; Pakarinen, Mikko ; Perola, Markus ; Nordenskjöld, Agneta ; Chakravarti, Aravinda ; Melbye, Mads ; Feenstra, Bjarke. / Genome-wide association study of Hirschsprung disease detects a novel low-frequency variant at the RET locus. In: European Journal of Human Genetics. 2018 ; pp. 1-9.
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AU - Nandakumar, Priyanka

AU - Chatterjee, Sumantra

AU - Matsson, Hans

AU - Granström, Anna Löf

AU - Wester, Tomas

AU - Salo, Perttu

AU - Virtanen, Valtter

AU - Carstensen, Lisbeth

AU - Bybjerg-Grauholm, Jonas

AU - Hougaard, David Michael

AU - Pakarinen, Mikko

AU - Perola, Markus

AU - Nordenskjöld, Agneta

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AU - Melbye, Mads

AU - Feenstra, Bjarke

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