Exome chip association study excluded the involvement of rare coding variants with large effect sizes in the etiology of anorectal malformations

• Published in: PloS one Vol. 14; no. 5; p. e0217477
• Main Authors: van de Putte, Romy, Wijers, Charlotte H. W., Reutter, Heiko, Vermeulen, Sita H., Marcelis, Carlo L. M., Brosens, Erwin, Broens, Paul M. A., Homberg, Markus, Ludwig, Michael, Jenetzky, Ekkehart, Zwink, Nadine, Sloots, Cornelius E. J., de Klein, Annelies, Brooks, Alice S., Hofstra, Robert M. W., Holsink, Sophie A. C., van der Zanden, Loes F. M., Galesloot, Tessel E., Tam, Paul Kwong-Hang, Steehouwer, Marloes, Acuna-Hidalgo, Rocio, Vorst, Maartje van de, Kiemeney, Lambertus A., Garcia-Barceló, Maria-Mercè, de Blaauw, Ivo, Brunner, Han G., Roeleveld, Nel, van Rooij, Iris A. L. M.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 28.05.2019; Public Library of Science (PLoS)
• Subjects: Adult; Alleles; Anorectal; Anorectal Malformations - genetics; Biology and Life Sciences; Birth defects; Care and treatment; Child & adolescent psychiatry; Clustering; Congenital defects; Development and progression; DNA sequencing; EDTA; Engineering and Technology; Etiology; Etiology (Medicine); Exome; Exome sequencing; Female; Genes; Genetic disorders; Genetic Variation; Genomes; Health sciences; Hindgut; Hospitals; Humans; Inspection; Life sciences; Male; Medical research; Medicine and Health Sciences; Oligonucleotide Array Sequence Analysis; Pediatrics; Population (statistical); Psychotherapy; Quality control; Research and analysis methods; Significance; Statistical analysis; Statistical significance; Surgery; Hong Kong China; Netherlands; China; Germany
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0217477

Anorectal 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. We analyzed 568 Caucasian ARM patients and 1,860 population-based controls using the Illumina HumanExome 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. When 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. Our results show that rare and low-frequency coding variants with large effect sizes, present on the exome chip do not contribute to ARM etiology.