1. Extending the allelic spectrum at noncoding risk loci of orofacial clefting
- Author
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Bert Braumann, Khalid Aldhorae, Carlo Maj, Elisabeth Mangold, Kerstin U. Ludwig, Peter Krawitz, Alexander Hoischen, Andreas Jäger, Frederic Thieme, Nigel L. Hammond, Christian Gilissen, Michael J. Dixon, Angelika Biedermann, John Bowes, Hanna K. Zieger, Jonas Hausen, Antony Adamson, Leonie Henschel, Andreas Buness, Thomas Kreusch, Teresa Kruse, Nina Ishorst, Lina Gölz, and Augusto Rojas-Martinez
- Subjects
Cleft Lip ,In silico ,lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4] ,Genomics ,Genome-wide association study ,Biology ,Molecular Inversion Probe ,Polymorphism, Single Nucleotide ,developmental biology ,03 medical and health sciences ,genomics ,Genetics ,Humans ,SNP ,genetics ,Genetic Predisposition to Disease ,ddc:610 ,Epigenetics ,Allele ,Genetics (clinical) ,030304 developmental biology ,Genetic association ,cleft palate ,craniofacial anomalies ,0303 health sciences ,030305 genetics & heredity ,Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6] ,Cleft Palate ,orofacial cleft(s) ,connective tissue biology ,craniofacial biology/genetics ,epidemiology ,Genome-Wide Association Study - Abstract
Contains fulltext : 237830.pdf (Publisher’s version ) (Open Access) Genome-wide association studies (GWAS) have generated unprecedented insights into the genetic etiology of orofacial clefting (OFC). The moderate effect sizes of associated noncoding risk variants and limited access to disease-relevant tissue represent considerable challenges for biological interpretation of genetic findings. As rare variants with stronger effect sizes are likely to also contribute to OFC, an alternative approach to delineate pathogenic mechanisms is to identify private mutations and/or an increased burden of rare variants in associated regions. This report describes a framework for targeted resequencing at selected noncoding risk loci contributing to nonsyndromic cleft lip with/without cleft palate (nsCL/P), the most frequent OFC subtype. Based on GWAS data, we selected three risk loci and identified candidate regulatory regions (CRRs) through the integration of credible SNP information, epigenetic data from relevant cells/tissues, and conservation scores. The CRRs (total 57 kb) were resequenced in a multiethnic study population (1061 patients; 1591 controls), using single-molecule molecular inversion probe technology. Combining evidence from in silico variant annotation, pedigree- and burden analyses, we identified 16 likely deleterious rare variants that represent new candidates for functional studies in nsCL/P. Our framework is scalable and represents a promising approach to the investigation of additional congenital malformations with multifactorial etiology.
- Published
- 2021