Genotyping of a tri-allelic polymorphism by a novel melting curve assay in MTHFD1L: an association study of nonsyndromic Cleft in Ireland

BMC Medical Genetics

Technical Advance

Kirke Peadar¹  James Troendle²  James Mills²  Lawrence Brody³  Faith Pangilinan³  Anne Parle-McDermott⁴  Stefano Minguzzi⁴  John M Scott⁵  Anne M Molloy⁶ 

[1] Child Health Epidemiology Unit, Health Research Board, Dublin, Ireland;Department of Health and Human Services, Eunice Kennedy Shriver National Institute of Health, Bethesda, MD, USA;Molecular Pathogenesis Section, Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD, USA;Nutritional Genomics Group, School of Biotechnology, Dublin City University, Dublin, Ireland;School of Immunology & Biochemistry, Trinity College Dublin, Dublin 2, Ireland;School of Medicine, Trinity College Dublin, Dublin 2, Ireland;

关键词: Cleft Palate;    Linkage Disequilibrium Block;    Transmission Disequilibrium Test;    Buccal Swab;    Anchor Probe;   

DOI  :  10.1186/1471-2350-13-29

 received in 2011-12-19, accepted in 2012-04-20,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundPolymorphisms within the MTHFD1L gene were previously associated with risk of neural tube defects in Ireland. We sought to test the most significant MTHFD1L polymorphisms for an association with risk of cleft in an Irish cohort. This required the development of a new melting curve assay to genotype the technically challenging MTHFD1L triallelic deletion/insertion polymorphism (rs3832406).MethodsMelting curve analysis was used to genotype the MTHFD1L triallelic deletion/insertion polymorphism (rs3832406) and a Single Nucleotide Polymorphism rs17080476 in an Irish cohort consisting of 981 Irish case-parent trios and 1,008 controls. Tests for association with nonsyndromic cleft lip with or without cleft palate and cleft palate included case/control analysis, mother/control analysis and Transmission Disequilibrium Tests of case-parent trios.ResultsA successful melting curve genotyping assay was developed for the deletion/insertion polymorphism (rs3832406). The TDT analysis initially showed that the rs3832406 polymorphism was associated with isolated cleft lip with or without cleft palate. However, corrected p-values indicated that this association was not significant.ConclusionsMelting Curve Analysis can be employed to successfully genotype challenging polymorphisms such as the MTHFD1L triallelic deletion/insertion polymorphism (DIP) reported here (rs3832406) and is a viable alternative to capillary electrophoresis. Corrected p-values indicate no association between MTHFD1L and risk of cleft in an Irish cohort.

【 授权许可】

Unknown   
© Minguzzi et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.