Genome-wide association study of multiethnic non-syndromic orofacial cleft families identifies novel loci specific to family and phenotypic subtypes

Orofacial clefts (OFCs) are among the most common craniofacial birth defects and constitute a high public health burden around the world. OFCs are phenotypically heterogeneous, affecting only the lip, only the palate, or involving both the lip and palate. Cleft palate alone is demonstrably a genetically distinct abnormality from OFCs that involve the lip, therefore, it is common to study cleft lip (CL) in combination with cleft lip plus cleft palate (CLP) as a phenotypic group (i.e. cleft lip with or without cleft palate, CL/P), usually considering CLP to be a clinically more severe form of CL. However, even within CL/P, important genetic differences among subtypes may be present. The Pittsburgh Orofacial Cleft (Pitt-OFC) multiethnic study is a rich resource for the study of non-syndromic OFC, comprising a large number of families (~12,000 individuals) from multiple populations worldwide: US and Europe (whites), Central and South America (mixed Native American, European and African), Asia, and Africa. In this study we focused on the CL/P families from this resource grouped into three non-overlapping family types: those with only CL affected members, only CLP affected members, or both CL and CLP. In all, seven total subtypes besides the combined CL/P phenotype, were defined based on the cleft type(s) that were present within pedigree members. The full sample for these analyses includes 2,218 CL and CLP cases along with 4,537 unaffected relatives, as well as 2,673 pure controls with no family history of OFC. Genome-wide association analyses were conducted within each subset, as well as the combined sample. Five novel genome-wide significant associations were observed: 3q29 (rs62284390, p=2.70E-08), 5p13.2 (rs609659, p= 4.57E-08), 7q22.1 (rs6465810, p= 1.25E-08), 19p13.3 (rs628271, p=1.90E-08) and 20q13.33 (rs2427238, p=1.51E-09). In addition, five significant and four suggestive associations confirmed regions previously published as OFC risk loci - PAX7 , IRF6 , FAM49A , DCAF4L2 , 8q24.21, ARID3B, NTN1 , TANC2 and the WNT9B:WNT3 gene cluster. At each of these loci, we compared effect sizes of associated SNPs observed across subtypes and the full sample, and found that certain loci were associated with a specific cleft type, and/or specific family types. Our findings indicate that risk factors differ between cleft and family types, but each cleft type also exhibits some degree of genetic heterogeneity.

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Genome-wide Association Study of Non-syndromic Orofacial Clefts in a Multiethnic Sample of Families and Controls Identifies Novel Regions

10.1101/2020.10.27.20220574 ◽

2020 ◽

Author(s):

Nandita Mukhopadhyay ◽

Eleanor Feingold ◽

Lina Moreno-Uribe ◽

George Wehby ◽

Luz Consuelo Valencia-Ramirez ◽

...

Keyword(s):

Native American ◽

Cleft Lip ◽

Genome Wide Association Study ◽

Population Level ◽

Allele Frequencies ◽

Genome Wide Association ◽

South American ◽

Orofacial Clefts ◽

Public Health Burden ◽

Genome Wide

AbstractOrofacial clefts (OFCs) are among the most prevalent craniofacial birth defects worldwide and create a significant public health burden. The majority of OFCs are non-syndromic and vary in prevalence by ethnicity. Africans have the lowest prevalence of OFCs (∼ 1/2,500), Asians have the highest prevalence (∼1/500), European and Latin Americans lie somewhere in the middle (∼1/800 and 1/900 respectively). Thus, ethnicity appears to be a major determinant of the risk of developing OFC. The Pittsburgh Orofacial Clefts Multiethnic study was designed to explore this ethnic variance, comprising a large number of families and individuals (∼12,000 individuals) from multiple populations worldwide: US and Europe, Asians, mixed Native American/Caucasians, and Africans. In this current study, we analyzed 2,915 OFC cases, 6,044 unaffected individuals related to the OFC cases, and 2,685 controls with no personal or family history of OFC. Participants were grouped by their ancestry into African, Asian, European, and Central and South American subsets, and genome-wide association run on the combined sample as well as the four ancestry-based groups. We observed 22 associations to cleft lip with or without cleft palate at 18 distinct loci with p-values < 1e-06, including 10 with genome-wide significance (< 5e-08), in the combined sample and within ancestry groups. Three loci - 2p12 (rs62164740, p=6.27e-07), 10q22.2 (rs150952246, p=3.14e-07), and 10q24.32 (rs118107597, p=8.21e-07) are novel. Nine were in or near known OFC loci - PAX7, IRF6, FAM49A, DCAF4L2, 8q24.21, NTN1, WNT3-WNT9B, TANC2, and RHPN2. The majority of the associations were observed only in the combined sample, European, and Central and South American groups. We investigated whether the observed differences in association strength were a) purely due to sample sizes, b) due to systematic allele frequency difference at the population level, or (c) due to the fact certain OFC-causing variants confer different amounts of risk depending on ancestral origin, by comparing effect sizes to observed allele frequencies of the effect allele in our ancestry-based groups. While some of the associations differ due to systematic differences in allele frequencies between groups, others show variation in effect size despite similar frequencies across ancestry groups.

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Genome-Wide Association Study of Non-syndromic Orofacial Clefts in a Multiethnic Sample of Families and Controls Identifies Novel Regions

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.621482 ◽

2021 ◽

Vol 9 ◽

Author(s):

Nandita Mukhopadhyay ◽

Eleanor Feingold ◽

Lina Moreno-Uribe ◽

George Wehby ◽

Luz Consuelo Valencia-Ramirez ◽

...

Keyword(s):

Native American ◽

Cleft Lip ◽

Genome Wide Association Study ◽

Population Level ◽

Allele Frequencies ◽

Genome Wide Association ◽

South American ◽

Orofacial Clefts ◽

Public Health Burden ◽

Genome Wide

Orofacial clefts (OFCs) are among the most prevalent craniofacial birth defects worldwide and create a significant public health burden. The majority of OFCs are non-syndromic and vary in prevalence by ethnicity. Africans have the lowest prevalence of OFCs (~ 1/2,500), Asians have the highest prevalence (~1/500), Europeans and Latin Americans lie somewhere in the middle (~1/800 and 1/900, respectively). Thus, ethnicity appears to be a major determinant of the risk of developing OFC. The Pittsburgh Orofacial Clefts Multiethnic study was designed to explore this ethnic variance, comprising a large number of families and individuals (~12,000 individuals) from multiple populations worldwide: US and Europe, Asians, mixed Native American/Caucasians, and Africans. In this current study, we analyzed 2,915 OFC cases, 6,044 unaffected individuals related to the OFC cases, and 2,685 controls with no personal or family history of OFC. Participants were grouped by their ancestry into African, Asian, European, and Central and South American subsets, and genome-wide association run on the combined sample as well as the four ancestry-based groups. We observed 22 associations to cleft lip with or without cleft palate at 18 distinct loci with p-values < 1e-06, including 10 with genome-wide significance (<5e-08), in the combined sample and within ancestry groups. Three loci - 2p12 (rs62164740, p = 6.27e-07), 10q22.2 (rs150952246, p = 3.14e-07), and 10q24.32 (rs118107597, p = 8.21e-07) are novel. Nine were in or near known OFC loci - PAX7, IRF6, FAM49A, DCAF4L2, 8q24.21, NTN1, WNT3-WNT9B, TANC2, and RHPN2. The majority of the associations were observed only in the combined sample, European, and Central and South American groups. We investigated whether the observed differences in association strength were (a) purely due to sample sizes, (b) due to systematic allele frequency difference at the population level, or (c) due to the fact certain OFC-causing variants confer different amounts of risk depending on ancestral origin, by comparing effect sizes to observed allele frequencies of the effect allele in our ancestry-based groups. While some of the associations differ due to systematic differences in allele frequencies between groups, others show variation in effect size despite similar frequencies across ancestry groups.

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Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate

Nature Genetics ◽

10.1038/ng.506 ◽

2009 ◽

Vol 42 (1) ◽

pp. 24-26 ◽

Cited By ~ 266

Author(s):

Elisabeth Mangold ◽

Kerstin U Ludwig ◽

Stefanie Birnbaum ◽

Carlotta Baluardo ◽

Melissa Ferrian ◽

...

Keyword(s):

Cleft Palate ◽

Association Study ◽

Cleft Lip ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Susceptibility Loci ◽

Genome Wide

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Genome-wide association study identifies a new susceptibility locus for cleft lip with or without a cleft palate

Nature Communications ◽

10.1038/ncomms7414 ◽

2015 ◽

Vol 6 (1) ◽

Cited By ~ 98

Author(s):

Yimin Sun ◽

Yongqing Huang ◽

Aihua Yin ◽

Yongchu Pan ◽

Yirui Wang ◽

...

Keyword(s):

Cleft Palate ◽

Association Study ◽

Cleft Lip ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Susceptibility Locus ◽

Genome Wide

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

Nature Genetics ◽

10.1038/ng0810-727 ◽

2010 ◽

Vol 42 (8) ◽

pp. 727-727 ◽

Cited By ~ 3

Author(s):

Terri H Beaty ◽

Jeffrey C Murray ◽

Mary L Marazita ◽

Ronald G Munger ◽

Ingo Ruczinski Jacqueline B Hetmanski ◽

...

Keyword(s):

Cleft Palate ◽

Association Study ◽

Cleft Lip ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Risk Variants ◽

Genome Wide ◽

A Genome

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Investigation of dominant and recessive inheritance models in genome-wide association studies data of nonsyndromic cleft lip with or without cleft palate

Birth Defects Research ◽

10.1002/bdr2.1144 ◽

2017 ◽

Vol 110 (4) ◽

pp. 336-341 ◽

Cited By ~ 3

Author(s):

Anne C. Böhmer ◽

Lina Gölz ◽

Thomas Kreusch ◽

Franz-Josef Kramer ◽

Bernd Pötzsch ◽

...

Keyword(s):

Cleft Palate ◽

Cleft Lip ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Recessive Inheritance ◽

Genome Wide

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A multi-ethnic genome-wide association study identifies novel loci for non-syndromic cleft lip with or without cleft palate on 2p24.2, 17q23 and 19q13

Human Molecular Genetics ◽

10.1093/hmg/ddw104 ◽

2016 ◽

pp. ddw104 ◽

Cited By ~ 31

Author(s):

Elizabeth J. Leslie ◽

Jenna C. Carlson ◽

John R. Shaffer ◽

Eleanor Feingold ◽

George Wehby ◽

...

Keyword(s):

Cleft Palate ◽

Association Study ◽

Cleft Lip ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide

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Expression and mutation analyses implicate ARHGAP29 as the etiologic gene for the cleft lip with or without cleft palate locus identified by genome-wide association on chromosome 1p22

Birth Defects Research Part A Clinical and Molecular Teratology ◽

10.1002/bdra.23076 ◽

2012 ◽

Vol 94 (11) ◽

pp. 934-942 ◽

Cited By ~ 59

Author(s):

Elizabeth J. Leslie ◽

M. Adela Mansilla ◽

Leah C. Biggs ◽

Kristi Schuette ◽

Steve Bullard ◽

...

Keyword(s):

Cleft Palate ◽

Cleft Lip ◽

Genome Wide Association ◽

Genome Wide ◽

Mutation Analyses

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Non-Syndromic Cleft Lip with or without Cleft Palate: Genome-Wide Association Study in Europeans Identifies a Suggestive Risk Locus at 16p12.1 and Supports SH3PXD2A as a Clefting Susceptibility Gene

Genes ◽

10.3390/genes10121023 ◽

2019 ◽

Vol 10 (12) ◽

pp. 1023 ◽

Cited By ~ 3

Author(s):

Iris ALM van Rooij ◽

Kerstin U Ludwig ◽

Julia Welzenbach ◽

Nina Ishorst ◽

Michelle Thonissen ◽

...

Keyword(s):

Cleft Palate ◽

Association Study ◽

Cleft Lip ◽

Genome Wide Association Study ◽

Susceptibility Gene ◽

Small Sample ◽

Genome Wide Association ◽

P Value ◽

Genome Wide ◽

A Genome

Non-syndromic cleft lip with or without cleft palate (nsCL/P) ranks among the most common human congenital malformations, and has a multifactorial background in which both exogenous and genetic risk factors act in concert. The present report describes a genome-wide association study (GWAS) involving a total of 285 nsCL/P patients and 1212 controls from the Netherlands and Belgium. Twenty of the 40 previously reported nsC/LP susceptibility loci were replicated, which underlined the validity of this sample. SNV-based analysis of the data identified an as yet unreported suggestive locus at chromosome 16p12.1 (p-value of the lead SNV: 4.17 × 10−7). This association was replicated in two of three patient/control replication series (Central European and Yemeni). Gene analysis of the GWAS data prioritized SH3PXD2A at chromosome 10q24.33 as a candidate gene for nsCL/P. To date, support for this gene as a cleft gene has been restricted to data from zebrafish and a knockout mouse model. The present GWAS was the first to implicate SH3PXD2A in non-syndromic cleft formation in humans. In summary, although performed in a relatively small sample, the present GWAS generated novel insights into nsCL/P etiology.

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