1
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Awotoye W, Comnick C, Pendleton C, Zeng E, Alade A, Mossey PA, Gowans LJJ, Eshete MA, Adeyemo WL, Naicker T, Adeleke C, Busch T, Li M, Petrin A, Olotu J, Hassan M, Pape J, Miller SE, Donkor P, Anand D, Lachke SA, Marazita ML, Adeyemo AA, Murray JC, Albokhari D, Sobreira N, Butali A. Genome-wide Gene-by-Sex Interaction Studies Identify Novel Nonsyndromic Orofacial Clefts Risk Locus. J Dent Res 2021; 101:465-472. [PMID: 34689653 DOI: 10.1177/00220345211046614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Risk loci identified through genome-wide association studies have explained about 25% of the phenotypic variations in nonsyndromic orofacial clefts (nsOFCs) on the liability scale. Despite the notable sex differences in the incidences of the different cleft types, investigation of loci for sex-specific effects has been understudied. To explore the sex-specific effects in genetic etiology of nsOFCs, we conducted a genome-wide gene × sex (GxSex) interaction study in a sub-Saharan African orofacial cleft cohort. The sample included 1,019 nonsyndromic orofacial cleft cases (814 cleft lip with or without cleft palate and 205 cleft palate only) and 2,159 controls recruited from 3 sites (Ethiopia, Ghana, and Nigeria). An additive logistic model was used to examine the joint effects of the genotype and GxSex interaction. Furthermore, we examined loci with suggestive significance (P < 1E-5) in the additive model for the effect of the GxSex interaction only. We identified a novel risk locus on chromosome 8p22 with genome-wide significant joint and GxSex interaction effects (rs2720555, p2df = 1.16E-08, pGxSex = 1.49E-09, odds ratio [OR] = 0.44, 95% CI = 0.34 to 0.57). For males, the risk of cleft lip with or without cleft palate at this locus decreases with additional copies of the minor allele (p < 0.0001, OR = 0.60, 95% CI = 0.48 to 0.74), but the effect is reversed for females (p = 0.0004, OR = 1.36, 95% CI = 1.15 to 1.60). We replicated the female-specific effect of this locus in an independent cohort (p = 0.037, OR = 1.30, 95% CI = 1.02 to 1.65), but no significant effect was found for the males (p = 0.29, OR = 0.86, 95% CI = 0.65 to 1.14). This locus is in topologically associating domain with craniofacially expressed and enriched genes during embryonic development. Rare coding mutations of some of these genes were identified in nsOFC cohorts through whole exome sequencing analysis. Our study is additional proof that genome-wide GxSex interaction analysis provides an opportunity for novel findings of loci and genes that contribute to the risk of nsOFCs.
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Affiliation(s)
- W Awotoye
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - C Comnick
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - C Pendleton
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - E Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - A Alade
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA.,Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - P A Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - L J J Gowans
- Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - M A Eshete
- Department of Surgery, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - W L Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - T Naicker
- Department of Pediatrics, University of KwaZulu-Natal, Durban, South Africa
| | - C Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - T Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - M Li
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - A Petrin
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - J Olotu
- Department of Anatomy, University of Port Harcourt, Choba, Nigeria
| | - M Hassan
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - J Pape
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - S E Miller
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - P Donkor
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - D Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - S A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - M L Marazita
- Center for Craniofacial and Dental Genetics, Departments of Oral Biology and Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - A A Adeyemo
- National Human Genomic Research Institute, Bethesda, MD, USA
| | - J C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - D Albokhari
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - N Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - A Butali
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA.,Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
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2
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Carlson JC, Nidey NL, Butali A, Buxo CJ, Christensen K, Deleyiannis FWD, Hecht JT, Field LL, Moreno-Uribe LM, Orioli IM, Poletta FA, Padilla C, Vieira AR, Weinberg SM, Wehby GL, Feingold E, Murray JC, Marazita ML, Leslie EJ. Genome-wide interaction studies identify sex-specific risk alleles for nonsyndromic orofacial clefts. Genet Epidemiol 2018; 42:664-672. [PMID: 30277614 PMCID: PMC6185762 DOI: 10.1002/gepi.22158] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/17/2018] [Accepted: 07/28/2018] [Indexed: 01/11/2023]
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common craniofacial birth defect in humans and is notable for its apparent sexual dimorphism where approximately twice as many males are affected as females. The sources of this disparity are largely unknown, but interactions between genetic and sex effects are likely contributors. We examined gene-by-sex (G × S) interactions in a worldwide sample of 2,142 NSCL/P cases and 1,700 controls recruited from 13 countries. First, we performed genome-wide joint tests of the genetic (G) and G × S effects genome-wide using logistic regression assuming an additive genetic model and adjusting for 18 principal components of ancestry. We further interrogated loci with suggestive results from the joint test ( p < 1.00 × 10 -5 ) by examining the G × S effects from the same model. Out of the 133 loci with suggestive results ( p < 1.00 × 10 -5 ) for the joint test, we observed one genome-wide significant G × S effect in the 10q21 locus (rs72804706; p = 6.69 × 10 -9 ; OR = 2.62 CI [1.89, 3.62]) and 16 suggestive G × S effects. At the intergenic 10q21 locus, the risk of NSCL/P is estimated to increase with additional copies of the minor allele for females, but the opposite effect for males. Our observation that the impact of genetic variants on NSCL/P risk differs for males and females may further our understanding of the genetic architecture of NSCL/P and the sex differences underlying clefts and other birth defects.
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Affiliation(s)
- Jenna C. Carlson
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Nichole L. Nidey
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA 52246
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, Dows Institute for Dental Research, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Carmen J. Buxo
- Dental and Craniofacial Genomics Core, School of Dental Medicine, University of Puerto Rico, San Juan, 00936, Puerto Rico
| | - Kaare Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, DK-5230, Denmark
| | - Frederic W-D Deleyiannis
- Department of Surgery, Plastic and Reconstructive Surgery, University of Colorado School of Medicine, Denver, CO, 80045, USA
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry UT Health at Houston, Houston, TX, 77030, USA
| | - L. Leigh Field
- Department of Medical Genetics, University of British Columbia, Vancouver, V6H 3N1, Canada
| | - Lina M. Moreno-Uribe
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Ieda M. Orioli
- ECLAMC (Latin American Collaborative Study of Congenital Malformations) at INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro, Brazil
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil
| | - Fernando A. Poletta
- ECLAMC (Latin American Collaborative Study of Congenital Malformations) at INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro, Brazil
- CEMIC-CONICET: Center for Medical Education and Clinical Research “Norberto Quirno”, Buenos Aires, 1431, Argentina
| | - Carmencita Padilla
- Department of Pediatrics, College of Medicine, University of the Philippines Manila, 1000 and the Philippine Genome Center, University of the Philippines System 1101, The Philippines
| | - Alexandre R. Vieira
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - George L. Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, 52242, USA
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa,52242, USA
| | - Mary L. Marazita
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University School of Medicine, Emory University, Atlanta, GA, 30322, USA
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Skare Ø, Lie RT, Haaland ØA, Gjerdevik M, Romanowska J, Gjessing HK, Jugessur A. Analysis of Parent-of-Origin Effects on the X Chromosome in Asian and European Orofacial Cleft Triads Identifies Associations with DMD, FGF13, EGFL6, and Additional Loci at Xp22.2. Front Genet 2018. [PMID: 29520293 PMCID: PMC5827165 DOI: 10.3389/fgene.2018.00025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background: Although both the mother's and father's alleles are present in the offspring, they may not operate at the same level. These parent-of-origin (PoO) effects have not yet been explored on the X chromosome, which motivated us to develop new methods for detecting such effects. Orofacial clefts (OFCs) exhibit sex-specific differences in prevalence and are examples of traits where a search for various types of effects on the X chromosome might be relevant. Materials and Methods: We upgraded our R-package Haplin to enable genome-wide analyses of PoO effects, as well as power simulations for different statistical models. 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European case-parent triads of isolated OFCs were available from a previous GWAS. For each ethnicity, cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO) were analyzed separately using two X-inactivation models and a sliding-window approach to haplotype analysis. In addition, we performed analyses restricted to female offspring. Results: Associations were identified in "Dystrophin" (DMD, Xp21.2-p21.1), "Fibroblast growth factor 13" (FGF13, Xq26.3-q27.1) and "EGF-like domain multiple 6" (EGFL6, Xp22.2), with biologically plausible links to OFCs. Unlike EGFL6, the other associations on chromosomal region Xp22.2 had no apparent connections to OFCs. However, the Xp22.2 region itself is of potential interest because it contains genes for clefting syndromes [for example, "Oral-facial-digital syndrome 1" (OFD1) and "Midline 1" (MID1)]. Overall, the identified associations were highly specific for ethnicity, cleft subtype and X-inactivation model, except for DMD in which associations were identified in both CPO and CL/P, in the model with X-inactivation and in Europeans only. Discussion/Conclusion: The specificity of the associations for ethnicity, cleft subtype and X-inactivation model underscores the utility of conducting subanalyses, despite the ensuing need to adjust for additional multiple testing. Further investigations are needed to confirm the associations with DMD, EGF16, and FGF13. Furthermore, chromosomal region Xp22.2 appears to be a hotspot for genes implicated in clefting syndromes and thus constitutes an exciting direction to pursue in future OFCs research. More generally, the new methods presented here are readily adaptable to the study of X-linked PoO effects in other outcomes that use a family-based design.
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Affiliation(s)
- Øivind Skare
- Department of Occupational Medicine and Epidemiology, National Institute of Occupational Health, Oslo, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
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4
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A new approach to chromosome-wide analysis of X-linked markers identifies new associations in Asian and European case-parent triads of orofacial clefts. PLoS One 2017; 12:e0183772. [PMID: 28877219 PMCID: PMC5587310 DOI: 10.1371/journal.pone.0183772] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/10/2017] [Indexed: 11/19/2022] Open
Abstract
Background GWAS discoveries on the X-chromosome are underrepresented in the literature primarily because the analytical tools that have been applied were originally designed for autosomal markers. Our objective here is to employ a new robust and flexible tool for chromosome-wide analysis of X-linked markers in complex traits. Orofacial clefts are good candidates for such analysis because of the consistently observed excess of females with cleft palate only (CPO) and excess of males with cleft lip with or without cleft palate (CL/P). Methods Genotypes for 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European isolated cleft triads were available from a previously published GWAS. The R-package HAPLIN enables genome-wide–level analyses as well as statistical power simulations for a range of biologic scenarios. We analyzed isolated CL/P and isolated CPO for each ethnicity in HAPLIN, using a sliding-window approach to haplotype analysis and two different statistical models, with and without X-inactivation in females. Results There was a larger number of associations in the Asian versus the European sample, and similar to previous reports that have analyzed the same GWAS dataset using different methods, we identified associations with EFNB1/PJA1 and DMD. In addition, new associations were detected with several other genes, among which KLHL4, TBX22, CPXCR1 and BCOR were noteworthy because of their roles in clefting syndromes. A few of the associations were only detected by one particular X-inactivation model, whereas a few others were only detected in one sex. Discussion/Conclusion We found new support for the involvement of X-linked variants in isolated clefts. The associations were specific for ethnicity, sex and model parameterization, highlighting the need for flexible tools that are capable of detecting and estimating such effects. Further efforts are needed to verify and elucidate the potential roles of EFNB1/PJA1, KLHL4, TBX22, CPXCR1 and BCOR in isolated clefts.
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Vieira-Machado CD, de Carvalho FM, Santana da Silva LC, Dos Santos SE, Martins C, Poletta FA, Mereb JC, Vieira AR, Castilla EE, Orioli IM. Analysis of the genetic ancestry of patients with oral clefts from South American admixed populations. Eur J Oral Sci 2016; 124:406-11. [PMID: 27105611 DOI: 10.1111/eos.12275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2016] [Indexed: 12/30/2022]
Abstract
Increased susceptibility to cleft lip, with or without cleft palate (CL±P) has been observed in South America, as related to Amerindian ancestry, using epidemiological data, uniparental markers, and blood groups. In this study, it was evaluated whether this increased risk remains when Amerindian ancestry is estimated using autosomal markers and considered in the predictive model. Ancestry was estimated through genotyping 62 insertion and deletion (INDEL) markers in sample sets of patients with CL±P, patients with cleft palate (CP), and controls, from Patagonia in southern Argentina and Belém in northern Brazil. The Amerindian ancestry in patients from Patagonia with CL±P was greater than in controls although it did not reach statistical significance. The European ancestry in patients with CL±P from Belém and in patients with CP from Belém and Patagonia was higher than in controls and statistically significant for patients with CP who were from Belém. This high contribution of European genetic ancestry among patients with CP who were from Belém has not been previously observed in American populations. Our results do not corroborate the currently accepted risks for CL±P and CP estimated by epidemiological studies in the North American populations and probably reflect the higher admixture found in South American ethnic groups when compared with the same ethnic groups from the North American populations.
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Affiliation(s)
- Camilla D Vieira-Machado
- ECLAMC at Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro.,INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro
| | - Flavia M de Carvalho
- INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro.,ECLAMC at LEMC (Laboratory of Congenital Malformations Epidemiology), Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro
| | - Luiz C Santana da Silva
- INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro.,Institute of Biological Sciences, Federal University of Pará, Belém, Pará
| | | | - Claudia Martins
- Speech Therapy Division, Ophir Loyola Hospital, Belém, Pará, Brazil
| | - Fernando A Poletta
- INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro.,ECLAMC at CEMIC (Center for Medical Education and Clinical Research) and CONICET (National Council for Scientific and Technical Investigation), Buenos Aires
| | - Juan C Mereb
- (In memoriam) ECLAMC at Hospital Zonal El Bolsón, El Bolsón, Argentina
| | - Alexandre R Vieira
- Department of Oral Biology and Pediatric Dentistry, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA.,Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eduardo E Castilla
- INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro.,ECLAMC at LEMC (Laboratory of Congenital Malformations Epidemiology), Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro.,ECLAMC at CEMIC (Center for Medical Education and Clinical Research) and CONICET (National Council for Scientific and Technical Investigation), Buenos Aires
| | - Iêda M Orioli
- ECLAMC at Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro.,INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro
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Wise AS, Shi M, Weinberg CR. Family-Based Multi-SNP X Chromosome Analysis Using Parent Information. Front Genet 2016; 7:20. [PMID: 26941777 PMCID: PMC4761843 DOI: 10.3389/fgene.2016.00020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 02/01/2016] [Indexed: 01/16/2023] Open
Abstract
We propose a method for association analysis of haplotypes on the X chromosome that offers both improved power and robustness to population stratification in studies of affected offspring and their parents if all three have been genotyped. The method makes use of assumed parental haplotype exchangeability (PHE), a weaker assumption than Hardy-Weinberg equilibrium (HWE). PHE requires that in the source population, of the three X chromosome haplotypes carried by the two parents, each is equally likely to be carried by the father. We propose a pseudo-sibling approach that exploits that exchangeability assumption. Our method extends the single-SNP PIX-LRT method to multiple SNPs in a high linkage block. We describe methods for testing the PHE assumption and also for determining how apparent violations can be distinguished from true fetal effects or maternally-mediated effects. We show results of simulations that demonstrate nominal type I error rate and good power. The methods are then applied to dbGaP data on the birth defect oral cleft, using both Asian and Caucasian families with cleft.
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Affiliation(s)
| | | | - Clarice R. Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health SciencesDurham, NC, USA
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8
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Fonseca RF, de Carvalho FM, Poletta FA, Montaner D, Dopazo J, Mereb JC, Moreira MAM, Seuanez HN, Vieira AR, Castilla EE, Orioli IM. Family-based genome-wide association study in Patagonia confirms the association of theDMDlocus and cleft lip and palate. Eur J Oral Sci 2015; 123:381-384. [DOI: 10.1111/eos.12212] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2015] [Indexed: 02/03/2023]
Affiliation(s)
- Renata F. Fonseca
- Department of Genetics; Institute of Biology, Federal University of Rio de Janeiro; Rio de Janeiro Brazil
- ECLAMC (Latin-American Collaborative Study of Congenital Malformations) at INAGEMP (National Institute of Population Medical Genetics); Rio de Janeiro Brazil
| | - Flávia M. de Carvalho
- Department of Genetics; Institute of Biology, Federal University of Rio de Janeiro; Rio de Janeiro Brazil
- ECLAMC (Latin-American Collaborative Study of Congenital Malformations) at INAGEMP (National Institute of Population Medical Genetics); Rio de Janeiro Brazil
- ECLAMC at LEMC (Laboratory of Congenital Malformation Epidemiology); Oswaldo Cruz Institute; FIOCRUZ; Rio de Janeiro Brazil
| | - Fernando A. Poletta
- ECLAMC (Latin-American Collaborative Study of Congenital Malformations) at INAGEMP (National Institute of Population Medical Genetics); Rio de Janeiro Brazil
- ECLAMC at LEMC (Laboratory of Congenital Malformation Epidemiology); Oswaldo Cruz Institute; FIOCRUZ; Rio de Janeiro Brazil
- ECLAMC at CEMIC (Center for Medical Education and Clinical Research) and CONICET (National Council for Scientific and Technical Investigation); Buenos Aires Argentina
| | - David Montaner
- CIPF (Computational Genomics Department, Centro de Investigación Príncipe Felipe); and CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras); Valencia Spain
| | - Joaquin Dopazo
- CIPF (Computational Genomics Department, Centro de Investigación Príncipe Felipe); and CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras); Valencia Spain
| | - Juan C. Mereb
- (In memoriam); ECLAMC at Hospital Zonal El Bolsón; El Bolsón Argentina
| | | | - Hector N. Seuanez
- Department of Genetics; Institute of Biology, Federal University of Rio de Janeiro; Rio de Janeiro Brazil
- Genetics Division; National Cancer Institute; Rio de Janeiro Brazil
| | - Alexandre R. Vieira
- Departments of Oral Biology and Pediatric Dentistry and Center for Craniofacial and Dental Genetics; School of Dental Medicine; University of Pittsburgh; Pittsburgh PA USA
| | - Eduardo E. Castilla
- ECLAMC (Latin-American Collaborative Study of Congenital Malformations) at INAGEMP (National Institute of Population Medical Genetics); Rio de Janeiro Brazil
- ECLAMC at LEMC (Laboratory of Congenital Malformation Epidemiology); Oswaldo Cruz Institute; FIOCRUZ; Rio de Janeiro Brazil
- ECLAMC at CEMIC (Center for Medical Education and Clinical Research) and CONICET (National Council for Scientific and Technical Investigation); Buenos Aires Argentina
| | - Iêda M. Orioli
- Department of Genetics; Institute of Biology, Federal University of Rio de Janeiro; Rio de Janeiro Brazil
- ECLAMC (Latin-American Collaborative Study of Congenital Malformations) at INAGEMP (National Institute of Population Medical Genetics); Rio de Janeiro Brazil
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9
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Wise AS, Shi M, Weinberg CR. Learning about the X from our parents. Front Genet 2015; 6:15. [PMID: 25713581 PMCID: PMC4322752 DOI: 10.3389/fgene.2015.00015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 01/12/2015] [Indexed: 11/30/2022] Open
Abstract
The X chromosome is generally understudied in association studies, in part because the analyst has had limited methodological options. For nuclear-family-based association studies, most current methods extend the transmission disequilibrium test (TDT) to the X chromosome. We present a new method to study association in case-parent triads: the parent-informed likelihood ratio test for the X chromosome (PIX-LRT). Our method enables estimation of relative risks and takes advantage of parental genotype information and the sex of the affected offspring to increase statistical power to detect an effect. Under a parental exchangeability assumption for the X, if case-parent triads are complete, the parents of affected offspring provide an independent replication sample for estimates based on transmission distortion to their affected offspring. For each offspring sex we combine the parent-level and the offspring-level information to form a likelihood ratio test statistic; we then combine the two to form a combined test statistic. Our method can estimate relative risks under different modes of inheritance or a more general co-dominant model. In triads with missing parental genotypes, the method accounts for missingness with the Expectation-Maximization algorithm. We calculate non-centrality parameters to assess the power gain and robustness of our method compared to alternative methods. We apply PIX-LRT to publically available data from an international consortium of genotyped families affected by the birth defect oral cleft and find a strong, internally-replicated signal for a SNP marker related to cleft lip with or without cleft palate.
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Affiliation(s)
- Alison S. Wise
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle ParkDurham, NC, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel HillChapel Hill, NC, USA
| | - Min Shi
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle ParkDurham, NC, USA
| | - Clarice R. Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle ParkDurham, NC, USA
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Watkins SE, Meyer RE, Strauss RP, Aylsworth AS. Classification, epidemiology, and genetics of orofacial clefts. Clin Plast Surg 2014; 41:149-63. [PMID: 24607185 DOI: 10.1016/j.cps.2013.12.003] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Orofacial clefts (OFCs) include a broad range of facial conditions that differ in cause and disease burden. In the published literature, there is substantial ambiguity in both terminology and classification of OFCs. This article discusses the terminology and classification of OFCs and the epidemiology of OFCs. Demographic, environmental, and genetic risk factors for OFCs are described, including suggestions for family counseling. This article enables clinicians to counsel families regarding the occurrence and recurrence of OFCs. Although much of the information is detailed, it is intended to be accessible to all health professionals for use in their clinical practices.
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Affiliation(s)
- Stephanie E Watkins
- Center for Health Promotion and Disease Prevention, University of North Carolina at Chapel Hill, 1700 Martin Luther King Jr Boulevard, Chapel Hill, NC, USA.
| | - Robert E Meyer
- Birth Defects Monitoring Program, Division of Public Health, North Carolina Department of Health and Human Services, State Center for Health Statistics, 222 North Dawson Street, Cotton Building, Raleigh, NC 27603, USA
| | - Ronald P Strauss
- UNC Center for AIDS Research, UNC School of Dentistry, UNC School of Medicine, University of North Carolina at Chapel Hill, 104 South Building, CB# 3000, Chapel Hill, NC 27599-3000, USA
| | - Arthur S Aylsworth
- Departments of Pediatrics and Genetics, University of North Carolina at Chapel Hill, CB# 7487, UNC Campus, Chapel Hill, NC 27599-7487, USA
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