TY - JOUR
T1 - Exome chip association study excluded the involvement of rare coding variants with large effect sizes in the etiology of anorectal malformations
AU - van de Putte, Romy
AU - Wijers, Charlotte H. W.
AU - Reutter, Heiko
AU - Vermeulen, Sita H.
AU - Marcelis, Carlo L. M.
AU - Brosens, Erwin
AU - Broens, Paul M. A.
AU - Homberg, Markus
AU - Ludwig, Michael
AU - Jenetzky, Ekkehart
AU - Zwink, Nadine
AU - Sloots, Cornelius E. J.
AU - de Klein, Annelies
AU - Brooke, Alice S.
AU - Hofstra, Robert M. W.
AU - Holsink, Sophie A. C.
AU - van Der Zanden, Loes F. M.
AU - Galesloot, Tessel E.
AU - Tam, Paul Kwong-Hang
AU - Steehouwer, Marloes
AU - Acuna-Hidalgo, Rocio
AU - van de Vorst, Maartje
AU - Kiemeney, Lambertus A.
AU - Garcia-Barcelo, Maria-Merce
AU - de Blaauw, Ivo
AU - Brunner, Han G.
AU - Roeleveld, Nel
AU - van Rooij, Iris A. L. M.
N1 - Funding Information:
Funding:TheworkofRvdPandCWwas supportedbyapersonalresearchgrantfromthe Radbouduniversitymedicalcenter,Nijmegen,The Netherlands.CURE-Netwassupportedbya researchgrantfromtheGermanFederalMinistry of Educationand Research (Bundesministeriumfu ¨r BildungundForschung,BMBF),funding-sign 01GM08107(2009-2012)andisnowsupportedby theGermanResearchFoundation(Deutsche Forschungsgemeinschaft,DFG)underthefunding signJE681/3-1(2013-2015).EBwassupportedby agrant(SSWOS13-9)oftheSophiafoundations. Partofthefundingforthisprojectwasprovidedby theNetherlandsOrganizationforScientific Researchunderawardnumber184021007,dated July9,2009andmadeavailableasaRainbow ProjectoftheBiobankingandBiomolecular ResearchInfrastructureNetherlands(BBMRI-NL). Thefundershadnoroleinstudydesign,data collectionandanalysis,decisiontopublish,or preparationofthemanuscript.
Funding Information:
The work of RvdP and CW was supported by a personal research grant from the Radboud university medical center, Nijmegen, The Netherlands. CURE-Net was supported by a research grant from the German Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF), funding-sign 01GM08107 (2009-2012) and is now supported by the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) under the funding sign JE681/3-1 (2013-2015). EB was supported by a grant (SSWO S13-9) of the Sophia foundations. Part of the funding for this project was provided by the Netherlands Organization for Scientific Research under award number 184021007, dated July 9, 2009 and made available as a Rainbow Project of the Biobanking and Biomolecular Research Infrastructure Netherlands (BBMRI-NL)
Publisher Copyright:
© 2019 van de Putte et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2019/5/28
Y1 - 2019/5/28
N2 - IntroductionAnorectal malformations (ARM) are rare congenital malformations, resulting from disturbed hindgut development. A genetic etiology has been suggested, but evidence for the involvement of specific genes is scarce. We evaluated the contribution of rare and low-frequency coding variants in ARM etiology, assuming a multifactorial model.MethodsWe analyzed 568 Caucasian ARM patients and 1,860 population-based controls using the Illumina Human Exome Beadchip array, which contains >240,000 rare and low-frequency coding variants. GenomeStudio clustering and calling was followed by re-calling of 'no-calls' using zCall for patients and controls simultaneously. Single variant and gene-based analyses were performed to identify statistically significant associations, applying Bonferroni correction. Following an extra quality control step, candidate variants were selected for validation using Sanger sequencing.ResultsWhen we applied a MAF of >= 1.0%, no variants or genes showed statistically significant associations with ARM. Using a MAF cut-off at 0.4%, 13 variants initially reached statistical significance, but had to be discarded upon further inspection: ten variants represented calling errors of the software, while the minor alleles of the remaining three variants were not confirmed by Sanger sequencing.ConclusionOur results show that rare and low-frequency coding variants with large effect sizes, present on the exome chip do not contribute to ARM etiology.
AB - IntroductionAnorectal malformations (ARM) are rare congenital malformations, resulting from disturbed hindgut development. A genetic etiology has been suggested, but evidence for the involvement of specific genes is scarce. We evaluated the contribution of rare and low-frequency coding variants in ARM etiology, assuming a multifactorial model.MethodsWe analyzed 568 Caucasian ARM patients and 1,860 population-based controls using the Illumina Human Exome Beadchip array, which contains >240,000 rare and low-frequency coding variants. GenomeStudio clustering and calling was followed by re-calling of 'no-calls' using zCall for patients and controls simultaneously. Single variant and gene-based analyses were performed to identify statistically significant associations, applying Bonferroni correction. Following an extra quality control step, candidate variants were selected for validation using Sanger sequencing.ResultsWhen we applied a MAF of >= 1.0%, no variants or genes showed statistically significant associations with ARM. Using a MAF cut-off at 0.4%, 13 variants initially reached statistical significance, but had to be discarded upon further inspection: ten variants represented calling errors of the software, while the minor alleles of the remaining three variants were not confirmed by Sanger sequencing.ConclusionOur results show that rare and low-frequency coding variants with large effect sizes, present on the exome chip do not contribute to ARM etiology.
KW - BIRTH-DEFECTS
KW - CANDIDATE GENE
KW - RISK
KW - ANOMALIES
KW - EXCLUSION
KW - REGISTRY
KW - OBESITY
KW - FGF10
U2 - 10.1371/journal.pone.0217477
DO - 10.1371/journal.pone.0217477
M3 - Article
C2 - 31136621
SN - 1932-6203
VL - 14
JO - PLOS ONE
JF - PLOS ONE
IS - 5
M1 - 0217477
ER -