title: Genotyping of a tri-allelic polymorphism by a novel melting curve assay in MTHFD1L: an association study of nonsyndromic Cleft in Ireland.
abstract: BACKGROUND
  Polymorphisms 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).
  
  
  METHODS
  Melting 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.
  
  
  RESULTS
  A 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.
  
  
  CONCLUSIONS
  Melting 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.
authors.affiliation: Nutritional Genomics Group, School of Biotechnology, Dublin City University, Dublin, Ireland.
authors.forename: Stefano
authors.initials: S
authors.lastname: Minguzzi
authors.forename: Anne M
authors.initials: AM
authors.lastname: Molloy
authors.forename: Kirke
authors.initials: K
authors.lastname: Peadar
authors.forename: James
authors.initials: J
authors.lastname: Mills
authors.forename: John M
authors.initials: JM
authors.lastname: Scott
authors.forename: James
authors.initials: J
authors.lastname: Troendle
authors.forename: Faith
authors.initials: F
authors.lastname: Pangilinan
authors.forename: Lawrence
authors.initials: L
authors.lastname: Brody
authors.forename: Anne
authors.initials: A
authors.lastname: Parle-McDermott
mesh_terms: D000328:Adult; D000483:Alleles; D000619:Aminohydrolases / Q000235:genetics*; D016022:Case-Control Studies; D002648:Child; D002971:Cleft Lip / Q000235:genetics*; D015331:Cohort Studies; D019075:Electrophoresis, Capillary; D005260:Female; D005574:Formate-Tetrahydrofolate Ligase / Q000235:genetics*; D005838:Genotype; D006801:Humans; D007494:Ireland; D015810:Linkage Disequilibrium; D008297:Male; D008754:Methylenetetrahydrofolate Dehydrogenase (NADP) / Q000235:genetics*; D009097:Multienzyme Complexes / Q000235:genetics*; D016017:Odds Ratio; D044367:Phase Transition; D020641:Polymorphism, Single Nucleotide; D012307:Risk Factors; D044366:Transition Temperature
chemical_list: D009097:Multienzyme Complexes; C021836:formyl-methenyl-methylenetetrahydrofolate synthetase; D008754:Methylenetetrahydrofolate Dehydrogenase (NADP); D000619:Aminohydrolases; D005574:Formate-Tetrahydrofolate Ligase