During the initial period of R01-DE-014581 (2003-2008), we successfully conducted a multi-center, international study on the genetic etiology of oral clefts (including cleft lip, CL;cleft lip and palate, CLP;and cleft palate, CP) by recruiting cases from 5 sites (Maryland, Singapore, Taiwan, and 2 sites in China). We have assembled 1497 case-parent trios, and successfully genotyped 5412 single nucleotide polymorphic (SNP) markers in candidate genes and candidate pathways on subsets of trios. Several genes have been identified as influencing risk to oral clefts (including some recognized candidate genes and some novel ones), and some genes show distinct parent-of-origin effects and potential interaction with common environmental risk factors. This competitive renewal application will extend and build upon our previous studies plus a genome wide association study (GWAS) from a consortium of our Hopkins group and 4 other groups. We propose 4 specific aims: 1) To compare our GWAS findings using case-parent trios with those of a German case-control study through combined analysis followed by fine mapping of new case-parent trios from the US, Asia, Germany and Ireland. 2) To consider models for assessing gene-environment (GxE) interactions with common maternal exposures (maternal smoking, alcohol consumption and vitamin supplementation) by analyzing the entire genome wide SNP array using our GWAS case-parent trios and the German cases. We will also collaborate with Dr. Munger of Utah State University (long time consultant to this project) to measure levels of vitamin B12 and methylmalonic acid in serum samples from mothers of cleft cases to evaluate biological models relevant to one carbon metabolism and DNA methylation. 3) To further investigate genes showing evidence of parent- of-origin effects (which may reflect genetic imprinting) by extending case families to include grandparents in 3 populations (Maryland, Taiwan and Singapore). We will also test for differential methylation patterns in selected genes identified during this study. 4) We will conduct deep resequencing studies of genes showing evidence of acting alone, only in the presence of environmental exposures or only when transmitted through one parent to identify all variants in genes and their cis-regulatory regions, especially rare variants, that may control risk to oral clefts.
This project will combine data from two genome wide studies of non-syndromic oral clefts (cleft lip, cleft lip &palate, and cleft palate) to identify genes that may act alone in controlling risk, genes that may interact with common maternal exposures (maternal smoking, alcohol consumption and vitamin use), and genes that show evidence of different transmission from mothers and fathers which may reflect imprinting.
|Wu, Tao; Schwender, Holger; Ruczinski, Ingo et al. (2014) Evidence of gene-environment interaction for two genes on chromosome 4 and environmental tobacco smoke in controlling the risk of nonsyndromic cleft palate. PLoS One 9:e88088|
|Bureau, Alexandre; Younkin, Samuel G; Parker, Margaret M et al. (2014) Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives. Bioinformatics 30:2189-96|
|Schwender, Holger; Li, Qing; Neumann, Christoph et al. (2014) Detecting disease variants in case-parent trio studies using the bioconductor software package trio. Genet Epidemiol 38:516-22|
|Younkin, Samuel G; Scharpf, Robert B; Schwender, Holger et al. (2014) A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk. BMC Genet 15:24|
|Chen, Qianqian; Wang, Hong; Schwender, Holger et al. (2014) Joint testing of genotypic and gene-environment interaction identified novel association for BMP4 with non-syndromic CL/P in an Asian population using data from an International Cleft Consortium. PLoS One 9:e109038|
|Beaty, T H; Taub, M A; Scott, A F et al. (2013) Confirming genes influencing risk to cleft lip with/without cleft palate in a case-parent trio study. Hum Genet 132:771-81|
|Baugher, Joseph D; Baugher, Benjamin D; Shirley, Matthew D et al. (2013) Sensitive and specific detection of mosaic chromosomal abnormalities using the Parent-of-Origin-based Detection (POD) method. BMC Genomics 14:367|
|Omoumi, Ardeshir; Wang, Zihua; Yeow, Vincent et al. (2013) Fetal polymorphisms at the ABCB1-transporter gene locus are associated with susceptibility to non-syndromic oral cleft malformations. Eur J Hum Genet 21:1436-41|
|Patel, Poorav J; Beaty, Terri H; Ruczinski, Ingo et al. (2013) X-linked markers in the Duchenne muscular dystrophy gene associated with oral clefts. Eur J Oral Sci 121:63-8|
|Wang, Hong; Hetmanski, Jacqueline B; Ruczinski, Ingo et al. (2012) ROR2 gene is associated with risk of non-syndromic cleft palate in an Asian population. Chin Med J (Engl) 125:476-80|
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