DESCRIPTION:

List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Cleft lip. The EFO term cleft lip was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.

LABEL:

GWAS: cleft lip

SCORE TYPE:

P-Value

DATE ADDED:

2017-05-02

DATE UPDATED:

2024-04-25

SPECIES:

AUTHORS:

TH Beaty, JC Murray, ML Marazita, RG Munger, I Ruczinski, JB Hetmanski, KY Liang, T Wu, T Murray, MD Fallin, RA Redett, G Raymond, H Schwender, SC Jin, ME Cooper, M Dunnwald, MA Mansilla, E Leslie, S Bullard, AC Lidral, LM Moreno, R Menezes, AR Vieira, A Petrin, AJ Wilcox, RT Lie, EW Jabs, YH Wu-Chou, PK Chen, H Wang, X Ye, S Huang, V Yeow, SS Chong, SH Jee, B Shi, K Christensen, M Melbye, KF Doheny, EW Pugh, H Ling, EE Castilla, AE Czeizel, L Ma, LL Field, L Brody, F Pangilinan, JL Mills, AM Molloy, PN Kirke, JM Scott, JM Scott, M Arcos-Burgos, AF Scott

TITLE:

A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4.

JOURNAL:

Nature genetics Jun 2010, Vol 42, pp. 525-9

ABSTRACT:

Case-parent trios were used in a genome-wide association study of cleft lip with and without cleft palate. SNPs near two genes not previously associated with cleft lip with and without cleft palate (MAFB, most significant SNP rs13041247, with odds ratio (OR) per minor allele = 0.704, 95% CI 0.635-0.778, P = 1.44 x 10(-11); and ABCA4, most significant SNP rs560426, with OR = 1.432, 95% CI 1.292-1.587, P = 5.01 x 10(-12)) and two previously identified regions (at chromosome 8q24 and IRF6) attained genome-wide significance. Stratifying trios into European and Asian ancestry groups revealed differences in statistical significance, although estimated effect sizes remained similar. Replication studies from several populations showed confirming evidence, with families of European ancestry giving stronger evidence for markers in 8q24, whereas Asian families showed stronger evidence for association with MAFB and ABCA4. Expression studies support a role for MAFB in palatal development. PUBMED: 20436469
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