1
|
Yankee TN, Oh S, Winchester EW, Wilderman A, Robinson K, Gordon T, Rosenfeld JA, VanOudenhove J, Scott DA, Leslie EJ, Cotney J. Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes. Nat Commun 2023; 14:4623. [PMID: 37532691 PMCID: PMC10397224 DOI: 10.1038/s41467-023-40363-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
Craniofacial disorders arise in early pregnancy and are one of the most common congenital defects. To fully understand how craniofacial disorders arise, it is essential to characterize gene expression during the patterning of the craniofacial region. To address this, we performed bulk and single-cell RNA-seq on human craniofacial tissue from 4-8 weeks post conception. Comparisons to dozens of other human tissues revealed 239 genes most strongly expressed during craniofacial development. Craniofacial-biased developmental enhancers were enriched +/- 400 kb surrounding these craniofacial-biased genes. Gene co-expression analysis revealed that regulatory hubs are enriched for known disease causing genes and are resistant to mutation in the normal healthy population. Combining transcriptomic and epigenomic data we identified 539 genes likely to contribute to craniofacial disorders. While most have not been previously implicated in craniofacial disorders, we demonstrate this set of genes has increased levels of de novo mutations in orofacial clefting patients warranting further study.
Collapse
Affiliation(s)
- Tara N Yankee
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT, 06030, USA
| | - Sungryong Oh
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA
| | | | - Andrea Wilderman
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT, 06030, USA
| | - Kelsey Robinson
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Tia Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratory, Houston, TX, 77021, USA
| | - Jennifer VanOudenhove
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Justin Cotney
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA.
| |
Collapse
|
2
|
Khan MI, C.S P, Mustak MS, Nizamuddin S. Maternal Transmission of the PAX7 Single Nucleotide Polymorphisms among Indian Cleft Trios. Glob Med Genet 2023; 10:6-11. [PMID: 36703778 PMCID: PMC9873478 DOI: 10.1055/s-0042-1760383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cleft lip and/or cleft palate (CL/P) is one of the most common congenital anomalies of the human face with a complex etiology involving multiple genetic and environmental factors. Several studies have shown the association of the paired box 7 ( PAX7 ) gene with CL/P in different populations worldwide. However, the current literature reveals no reported case-parent trio studies to evaluate the association between the PAX7 gene and the risk of nonsyndromic cleft lip and/or palate (NSCL/P) in the Indian population. Hence, the purpose of this study was to assess the PAX7 gene single nucleotide polymorphisms (SNPs) in the etiology of NSCL/P among the Indian cleft trios. Forty Indian case-parent trios of NSCL/P were included. The cases and their parents' genomic DNA were extracted. The SNPs rs9439714, rs1339062, rs6695765, rs742071, and rs618941of the PAX7 gene were genotyped using the Agena Bio MassARRAY analysis. The allelic transmission disequilibrium test was performed using PLINK software while pair-wise linkage disequilibrium by the Haploview program. The SNP rs9439714 showed evidence of association ( p -value = 0.02, odds ratio = 3) with NSCL/P. Considering the parent-of-origin effects, the SNPs rs9439714 and rs618941 showed an excess maternal transmission of allele C at rs9439714 ( p -value = 0.05) and G allele at rs618941 ( p -value = 0.04). The results of the present study suggested that the SNPs rs9439714 and rs618941 showed an excess maternal transmission of alleles suggestive of the possible role of the PAX7 gene involvement in the etiology of NSCL/P in the Indian population.
Collapse
Affiliation(s)
- Mahamad Irfanulla Khan
- Department of Orthodontics and Dentofacial Orthopedics, The Oxford Dental College, Bangalore, Karnataka, India,Address for correspondence Mahamad Irfanulla Khan, BDS, MDS Department of Orthodontics and Dentofacial Orthopedics, The Oxford Dental CollegeBangalore, Karnataka, 560068India
| | - Prashanth C.S
- Department of Orthodontics and Dentofacial Orthopedics, DAPM R.V Dental College, Bangalore, Karnataka, India
| | - Mohammed S. Mustak
- Department of Applied Zoology Mangalore University, Mangalore, Karnataka, India
| | - Sheikh Nizamuddin
- Department of Urology, Medical Center-University of Freiburg, Germany,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
3
|
Gowans LJJ, Comnick CL, Mossey PA, Eshete MA, Adeyemo WL, Naicker T, Awotoye WA, Petrin A, Adeleke C, Donkor P, Busch TD, James O, Ogunlewe MO, Li M, Olotu J, Hassan M, Adeniyan OA, Obiri-Yeboah S, Arthur FKN, Agbenorku P, Oti AA, Olatosi O, Adamson OO, Fashina AA, Zeng E, Marazita ML, Adeyemo AA, Murray JC, Butali A. Genome-Wide Scan for Parent-of-Origin Effects in a sub-Saharan African Cohort With Nonsyndromic Cleft Lip and/or Cleft Palate (CL/P). Cleft Palate Craniofac J 2022; 59:841-851. [PMID: 34382870 PMCID: PMC9884465 DOI: 10.1177/10556656211036316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
OBJECTIVE Nonsyndromic cleft lip and/or cleft palate (NSCL/P) have multifactorial etiology where genetic factors, gene-environment interactions, stochastic factors, gene-gene interactions, and parent-of-origin effects (POEs) play cardinal roles. POEs arise when the parental origin of alleles differentially impacts the phenotype of the offspring. The aim of this study was to identify POEs that can increase risk for NSCL/P in humans using a genome-wide dataset. METHODS The samples (174 case-parent trios from Ghana, Ethiopia, and Nigeria) included in this study were from the African only genome wide association studies (GWAS) that was published in 2019. Genotyping of individual DNA using over 2 million multiethnic and African ancestry-specific single-nucleotide polymorphisms from the Illumina Multi-Ethnic Genotyping Array v2 15070954 A2 (genome build GRCh37/hg19) was done at the Center for Inherited Diseases Research. After quality control checks, PLINK was employed to carry out POE analysis employing the pooled subphenotypes of NSCL/P. RESULTS We observed possible hints of POEs at a cluster of genes at a 1 mega base pair window at the major histocompatibility complex class 1 locus on chromosome 6, as well as at other loci encompassing candidate genes such as ASB18, ANKEF1, AGAP1, GABRD, HHAT, CCT7, DNMT3A, EPHA7, FOXO3, lncRNAs, microRNA, antisense RNAs, ZNRD1, ZFAT, and ZBTB16. CONCLUSION Findings from our study suggest that some loci may increase the risk for NSCL/P through POEs. Additional studies are required to confirm these suggestive loci in NSCL/P etiology.
Collapse
Affiliation(s)
- LJJ Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana,School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana,Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - CL Comnick
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - PA Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - MA Eshete
- Department of Surgery, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - WL Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - T Naicker
- Department of Pediatrics, University of KwaZulu-Natal and Inkosi Albert Luthuli Central Hospital, South Africa
| | - WA Awotoye
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - A Petrin
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - C Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - P Donkor
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - TD Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - O James
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - MO Ogunlewe
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - M Li
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - J Olotu
- Department of Anatomy, University of Port Harcourt, Nigeria
| | - M Hassan
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - OA Adeniyan
- NHS Foundation Trust (Queens Hospital, Belvedere Road, Burton-On-Trent), Staffordshire, UK
| | - S Obiri-Yeboah
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - FKN Arthur
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - P Agbenorku
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - AA Oti
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - O Olatosi
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - OO Adamson
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - AA Fashina
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - E Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - ML Marazita
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA,Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - AA Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - JC Murray
- Department of Pediatrics, University of Iowa, Iowa, IA, USA
| | - A Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| |
Collapse
|
4
|
Ray D, Vergara C, Taub MA, Wojcik G, Ladd‐Acosta C, Beaty TH, Duggal P. Benchmarking statistical methods for analyzing parent-child dyads in genetic association studies. Genet Epidemiol 2022; 46:266-284. [PMID: 35451532 PMCID: PMC9356976 DOI: 10.1002/gepi.22453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 02/06/2022] [Accepted: 03/15/2022] [Indexed: 11/24/2022]
Abstract
Genetic association studies of child health outcomes often employ family-based study designs. One of the most popular family-based designs is the case-parent trio design that considers the smallest possible nuclear family consisting of two parents and their affected child. This trio design is particularly advantageous for studying relatively rare disorders because it is less prone to type 1 error inflation due to population stratification compared to population-based study designs (e.g., case-control studies). However, obtaining genetic data from both parents is difficult, from a practical perspective, and many large studies predominantly measure genetic variants in mother-child dyads. While some statistical methods for analyzing parent-child dyad data (most commonly involving mother-child pairs) exist, it is not clear if they provide the same advantage as trio methods in protecting against population stratification, or if a specific dyad design (e.g., case-mother dyads vs. case-mother/control-mother dyads) is more advantageous. In this article, we review existing statistical methods for analyzing genome-wide marker data on dyads and perform extensive simulation experiments to benchmark their type I errors and statistical power under different scenarios. We extend our evaluation to existing methods for analyzing a combination of case-parent trios and dyads together. We apply these methods on genotyped and imputed data from multiethnic mother-child pairs only, case-parent trios only or combinations of both dyads and trios from the Gene, Environment Association Studies consortium (GENEVA), where each family was ascertained through a child affected by nonsyndromic cleft lip with or without cleft palate. Results from the GENEVA study corroborate the findings from our simulation experiments. Finally, we provide recommendations for using statistical genetic association methods for dyads.
Collapse
Affiliation(s)
- Debashree Ray
- Department of Epidemiology, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
- Department of Biostatistics, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Candelaria Vergara
- Department of Epidemiology, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Margaret A. Taub
- Department of Biostatistics, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Genevieve Wojcik
- Department of Epidemiology, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Christine Ladd‐Acosta
- Department of Epidemiology, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Priya Duggal
- Department of Epidemiology, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| |
Collapse
|
5
|
Rs9891446 in NTN1 is associated with right-side cleft lip in Han Chinese Population. Arch Oral Biol 2022; 141:105485. [DOI: 10.1016/j.archoralbio.2022.105485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/31/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022]
|
6
|
Martinelli M, Palmieri A, Carinci F, Scapoli L. Non-syndromic Cleft Palate: An Overview on Human Genetic and Environmental Risk Factors. Front Cell Dev Biol 2020; 8:592271. [PMID: 33195260 PMCID: PMC7606870 DOI: 10.3389/fcell.2020.592271] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/28/2020] [Indexed: 12/27/2022] Open
Abstract
The epithelial and mesenchymal cells involved in early embryonic facial development are guided by complex regulatory mechanisms. Any factor perturbing the growth, approach and fusion of the frontonasal and maxillary processes could result in orofacial clefts that represent the most common craniofacial malformations in humans. The rarest and, probably for this reason, the least studied form of cleft involves only the secondary palate, which is posterior to the incisive foramen. The etiology of cleft palate only is multifactorial and involves both genetic and environmental risk factors. The intention of this review is to give the reader an overview of the efforts made by researchers to shed light on the underlying causes of this birth defect. Most of the scientific papers suggesting potential environmental and genetic causes of non-syndromic cleft palate are summarized in this review, including genome-wide association and gene–environment interaction studies.
Collapse
Affiliation(s)
- Marcella Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Annalisa Palmieri
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Francesco Carinci
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Luca Scapoli
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| |
Collapse
|
7
|
[Exploring parent-of-origin effects for non-syndromic cleft lip with or without cleft palate on PTCH1, PTCH2, SHH, SMO genes in Chinese case-parent trios]. BEIJING DA XUE XUE BAO. YI XUE BAN = JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2020; 52. [PMID: 33047712 PMCID: PMC7653437 DOI: 10.19723/j.issn.1671-167x.2020.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
OBJECTIVE Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect, affecting 1.4 per 1 000 live births, and multiple genetic and environmental risk factors influencing its risk. All the known genetic risk factors accounted for a small proportion of the heritability. Several authors have suggested parent-of-origin effects (PoO) may play an important role in the etiology of this complex and heterogeneous malformation. To clarify the genetic association between PTCH1, PTCH2, SHH and SMO in hedgehog (HH) pathway and NSCL/P, as well as testing for potential PoO effects in Chinese case-parent trios. METHODS We tested for transmission disequilibrium tests (TDT) and PoO effects using 83 common single nucleotide polymorphic (SNP) markers of HH pathway genes from 806 NSCL/P case-parent trios. These trios were drawn from an international consortium established for a genome-wide association studies (GWAS) of non-syndromic oral clefts of multiple ethnicities. DNA samples were collected from each trio. Single marker and haplotype based analysis were performed both in TDT tests and PoO effects. SNPs were excluded if they (ⅰ) had a call rate of < 95%, (ⅱ) had a minor allele frequency (MAF) of < 0.05, (ⅲ) had Mendelian errors over all trios of >5%, (ⅳ) had a genotype distribution in the parents that deviated from the Hardy-Weinberg equilibrium (HWE) (P < 0.000 1). The process was done using Plink (version 1.07, <a href="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml" target="_blank">http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml</a>). TDT test was performed in Plink v1.07. A log-linear model was used to explore PoO effects using Haplin v6.2.1 as implemented in R package v3.4.2. Significance level was assessed using the Bonferroni correction. RESULTS A total of 18 SNPs were dropped due to low MAF, thus leaving 65 SNPs available for the analysis. Thus the Bonferroni threshold was 7.7×10-4 (0.05/65). Nominal significant association with NSCL/P was found at a SNP (rs4448343 in PTCH1, P=0.023) and six haplotypes (rs10512249-rs4448343, rs1461208-rs7786445, rs10512249-rs4448343, rs16909865-rs10512249-rs4448343, rs1461208-rs7786445-rs12698335, and rs288756-rs288758-rs1151790, P < 0.05). A total of six haplotypes (rs288765-rs1233563, rs12537550-rs11765352, rs872723-rs288765-rs1233563, rs288765-rs1233563-rs288756, rs6459952-rs12537550-rs11765352, and rs12537550-rs11765352-rs6971211) showed PoO effect (P < 0.05). None of the results remained significant after the Bonferroni correction (P>7.7×10-4). CONCLUSION Neither significant association between SNPs within HH pathway and the risk of NSCL/P nor PoO effects was seen in this study.
Collapse
|
8
|
Khan MI, CS P. Case-Parent Trio Studies in Cleft Lip and Palate. Glob Med Genet 2020; 7:75-79. [PMID: 33392609 PMCID: PMC7772012 DOI: 10.1055/s-0040-1722097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is one of the most common congenital malformations in humans involving various genetic and environmental risk factors. The prevalence of CL/P varies according to geographical location, ethnicity, race, gender, and socioeconomic status, affecting approximately 1 in 800 live births worldwide. Genetic studies aim to understand the mechanisms contributory to a phenotype by measuring the association between genetic variants and also between genetic variants and phenotype population. Genome-wide association studies are standard tools used to discover genetic loci related to a trait of interest. Genetic association studies are generally divided into two main design types: population-based studies and family-based studies. The epidemiological population-based studies comprise unrelated individuals that directly compare the frequency of genetic variants between (usually independent) cases and controls. The alternative to population-based studies (case-control designs) includes various family-based study designs that comprise related individuals. An example of such a study is a case-parent trio design study, which is commonly employed in genetics to identify the variants underlying complex human disease where transmission of alleles from parents to offspring is studied. This article describes the fundamentals of case-parent trio study, trio design and its significances, statistical methods, and limitations of the trio studies.
Collapse
Affiliation(s)
- Mahamad Irfanulla Khan
- Department of Orthodontics & Dentofacial Orthopedics, The Oxford Dental College, Bangalore, Karnataka, India
| | - Prashanth CS
- Department of Orthodontics & Dentofacial Orthopedics, DAPM RV Dental College, Bangalore, Karnataka, India
| |
Collapse
|
9
|
Lowry RB, Bedard T, Crawford S, Grevers X, Bernier FP, Thomas MA. Prevalence rates study of selected isolated non-Mendelian congenital anomalies in the Hutterite population of Alberta, 1980-2016. Am J Med Genet A 2020; 182:2594-2604. [PMID: 32893972 DOI: 10.1002/ajmg.a.61834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/29/2020] [Accepted: 08/01/2020] [Indexed: 11/10/2022]
Abstract
A study of the prevalence rates for selected isolated non-Mendelian congenital anomalies in the Hutterite Brethren of Alberta, Canada was undertaken to further examine longitudinal data in this isolated community that was last reported in 1985 (Lowry et al., 1985), although there are numerous publications on recessive disorders (Boycott et al., 2008; Triggs-Raine et al., 2016). Cases were ascertained from the Alberta Congenital Anomaly Surveillance System for the years 1997-2016. Since our initial results showed some surprising findings in the Hutterite Brethren, such as zero cases of spina bifida, cleft lip and palate, gastroschisis, and omphalocele, and a significant excess of cases with hypospadias, we extended the study to prior years (1980-1996) for selected anomalies. For the extended study period (1980-2016), there was a significant increased prevalence of hypospadias, tetralogy of Fallot and tricuspid atresia in the Hutterite population, and although not statistically significant, zero cases of cleft lip with cleft palate, gastroschisis and omphalocele were confirmed. Further research is needed to determine the precise effects of rural environmental exposures, lifestyle factors, and genetic associations for selected multifactorial congenital anomalies.
Collapse
Affiliation(s)
- R Brian Lowry
- Alberta Congenital Anomalies Surveillance System, Alberta Health Services, Calgary, Alberta, Canada.,Department of Pediatrics, University of Calgary and Alberta Children's Hospital, Calgary, Alberta, Canada.,Department of Medical Genetics, University of Calgary and Alberta Children's Hospital, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Tanya Bedard
- Alberta Congenital Anomalies Surveillance System, Alberta Health Services, Calgary, Alberta, Canada
| | - Susan Crawford
- Alberta Perinatal Health Program, Alberta Health Services, Calgary, Alberta, Canada
| | - Xin Grevers
- Alberta Congenital Anomalies Surveillance System, Alberta Health Services, Calgary, Alberta, Canada
| | - François P Bernier
- Department of Pediatrics, University of Calgary and Alberta Children's Hospital, Calgary, Alberta, Canada.,Department of Medical Genetics, University of Calgary and Alberta Children's Hospital, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mary Ann Thomas
- Alberta Congenital Anomalies Surveillance System, Alberta Health Services, Calgary, Alberta, Canada.,Department of Pediatrics, University of Calgary and Alberta Children's Hospital, Calgary, Alberta, Canada.,Department of Medical Genetics, University of Calgary and Alberta Children's Hospital, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
10
|
Sewda A, Agopian AJ, Goldmuntz E, Hakonarson H, Morrow BE, Musfee F, Taylor D, Mitchell LE. Gene-based analyses of the maternal genome implicate maternal effect genes as risk factors for conotruncal heart defects. PLoS One 2020; 15:e0234357. [PMID: 32516339 PMCID: PMC7282656 DOI: 10.1371/journal.pone.0234357] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Congenital heart defects (CHDs) affect approximately 1% of newborns. Epidemiological studies have identified several genetically-mediated maternal phenotypes (e.g., pregestational diabetes, chronic hypertension) that are associated with the risk of CHDs in offspring. However, the role of the maternal genome in determining CHD risk has not been defined. We present findings from gene-level, genome-wide studies that link CHDs to maternal effect genes as well as to maternal genes related to hypertension and proteostasis. Maternal effect genes, which provide the mRNAs and proteins in the oocyte that guide early embryonic development before zygotic gene activation, have not previously been implicated in CHD risk. Our findings support a role for and suggest new pathways by which the maternal genome may contribute to the development of CHDs in offspring.
Collapse
Affiliation(s)
- Anshuman Sewda
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, Texas, United States of America
| | - A. J. Agopian
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, Texas, United States of America
| | - Elizabeth Goldmuntz
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Division of Cardiology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Hakon Hakonarson
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Bernice E. Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Fadi Musfee
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, Texas, United States of America
| | - Deanne Taylor
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Laura E. Mitchell
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, Texas, United States of America
- * E-mail:
| | | |
Collapse
|
11
|
Gjerdevik M, Gjessing HK, Romanowska J, Haaland ØA, Jugessur A, Czajkowski NO, Lie RT. Design efficiency in genetic association studies. Stat Med 2020; 39:1292-1310. [PMID: 31943314 DOI: 10.1002/sim.8476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 12/20/2019] [Accepted: 12/21/2019] [Indexed: 11/07/2022]
Abstract
Selecting the best design for genetic association studies requires careful deliberation; different study designs can be used to scan for different genetic effects, and each design has its own set of strengths and limitations. A variety of family and unrelated control configurations are amenable to genetic association analyses, including the case-control design, case-parent triads, and case-parent triads in combination with unrelated controls or control-parent triads. Ultimately, the goal is to choose the design that achieves the highest statistical power using the lowest cost. For given parameter values and genotyped individuals, designs can be compared directly by computing the power. However, a more informative and general design comparison can be achieved by studying the relative efficiency, defined as the ratio of variances of two different parameter estimators, corresponding to two separate designs. Using log-linear modeling, we derive the relative efficiency from the asymptotic variance of the parameter estimators and relate it to the concept of Pitman efficiency. The relative efficiency takes into account the fact that different designs impose different costs relative to the number of genotyped individuals. We show that while optimal efficiency for analyses of regular autosomal effects is achieved using the standard case-control design, the case-parent triad design without unrelated controls is efficient when searching for parent-of-origin effects. Due to the potential loss of efficiency, maternal genes should generally not be adjusted for in an initial genome-wide association study scan of offspring genes but instead checked post hoc. The relative efficiency calculations are implemented in our R package Haplin.
Collapse
Affiliation(s)
- 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
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Astanand Jugessur
- 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.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nikolai O Czajkowski
- Department of Psychology, University of Oslo, Oslo, Norway.,Division of Mental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| |
Collapse
|
12
|
Park PG, Kim KH, Hyun HS, Lee CH, Park JS, Kie JH, Choi YH, Moon KC, Cheong HI. Three cases of multicentric carpotarsal osteolysis syndrome: a case series. BMC MEDICAL GENETICS 2018; 19:164. [PMID: 30208859 PMCID: PMC6134760 DOI: 10.1186/s12881-018-0682-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 09/06/2018] [Indexed: 11/30/2022]
Abstract
Background Multicentric carpotarsal osteolysis syndrome (MCTO) is characterized by progressive destruction and disappearance of the carpal and tarsal bones associated with nephropathy. MCTO is caused by loss-of-function mutations in the MAF bZIP transcription factor B (MAFB) gene. Case presentation This report describes three unrelated patients with MAFB mutations, including two male and one female patient. Osteolytic lesions in the carpal and tarsal bones were detected at 2 years, 12 years, and 14 months of age, respectively. Associated proteinuria was noted at 4 years, 12 years, and 3 months of age, respectively. Kidney biopsy was performed in two of them and revealed focal segmental glomerulosclerosis (FSGS). One patient showed progression to end-stage renal disease, that is by 1 year after the detection of proteinuria. The second patient had persistent proteinuria but maintained normal renal function. In the third patient, who did not undergo a kidney biopsy, the proteinuria disappeared spontaneously. The bony lesions worsened progressively in all three patients. Mutational study of MAFB revealed three different mutations, two novel mutations [c.183C > A (p.Ser61Arg) and c.211C > G (p.Pro71Ala)] and one known mutation [c.212C > T (p.Pro71Leu)]. Conclusion We report three cases with MCTO and two novel MAFB mutations. The renal phenotypes were different among the three patients, whereas progressive worsening of the bony lesions was common in all patients. We also confirmed FSGS to be an early renal pathologic finding in two cases. A diagnosis of MCTO should be considered in patients with progressive bone loss concentrated primarily in the carpal and tarsal bones and kidney involvement, such as proteinuria.
Collapse
Affiliation(s)
- Peong Gang Park
- Department of Pediatrics, Seoul National University Children's Hospital, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080, Korea
| | - Kee Hyuck Kim
- Department of Pediatrics, National Health Insurance Service Ilsan Hospital, Goyang, Korea
| | - Hye Sun Hyun
- Department of Pediatrics, Seoul National University Children's Hospital, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080, Korea
| | - Chan Hee Lee
- Division of Rheumatology, Department of Internal Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Korea
| | - Jin-Su Park
- Division of Rheumatology, Department of Internal Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Korea
| | - Jeong Hae Kie
- Department of Pathology, National Health Insurance Service Ilsan Hospital, Goyang, Korea
| | - Young Hun Choi
- Department of Radiology, Seoul National University College of Medicine, Seoul, Korea
| | - Kyung Chul Moon
- Department of Pathology, Seoul National University Hospital, Seoul, Korea
| | - Hae Il Cheong
- Department of Pediatrics, Seoul National University Children's Hospital, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080, Korea. .,Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea. .,Research Coordination Center for Rare Diseases, Seoul National University Hospital, Seoul, Korea. .,Kidney Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea.
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Yan C, Deng-Qi H, Li-Ya C, Mang Y, Ke-Hu Y. Transforming Growth Factor Alpha Taq I Polymorphisms and Nonsyndromic Cleft Lip and/or Palate Risk: A Meta-Analysis. Cleft Palate Craniofac J 2018; 55:814-820. [PMID: 28001102 DOI: 10.1597/16-008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND A series of epidemiological studies were conducted to investigate the association between transforming growth factor alpha ( TGFA) polymorphism and nonsyndromic cleft lip and/or palate (CL/P) risk, but the findings remain conflicting. The present meta-analysis summarizes the association between the TGFA Taq I polymorphisms and nonsyndromic CL/P risk. METHODS We searched PubMed, EMBASE, Web of Science, and Chinese Biomedical Literature databases from their inception to May 1, 2015. Fixed-effects or random-effects models were used to calculate the pooled odds ratio for two genetic comparisons (heterozygous mutation versus wild type, homozygous mutation versus wild type). All of the statistical tests were conducted by STATA 10.0 (StataCorp, College Station, TX). RESULTS A total of 26 case-control studies were identified for this meta-analysis. There was evidence of a significant association between the TGFA Taq I polymorphism and nonsyndromic CL/P risk in the overall population. The TGFA polymorphism was associated with nonsyndromic CL/P susceptibility in Asian populations under any of genetic models. However, in subgroup analysis, we did not find a significant association of TGFA gene polymorphisms with a reduced cancer risk in White and other populations and (recessive model, odds ratio = 2.37, 95% confidence intervals = 0.92-6.07; odds ratio = 3.45, 95% confidence intervals = 1.07-11.09, respectively). CONCLUSION Our study indicates that the TGFA gene polymorphism might be associated with nonsyndromic CL/P susceptibility. However, these findings still need to be confirmed by single, large, well-designed prospective studies.
Collapse
|
15
|
Bauer AE, Avery CL, Shi M, Weinberg CR, Olshan AF, Harmon QE, Luo J, Yang J, Manuck T, Wu MC, Williams N, McGinnis R, Morgan L, Klungsøyr K, Trogstad L, Magnus P, Engel SM. A Family Based Study of Carbon Monoxide and Nitric Oxide Signalling Genes and Preeclampsia. Paediatr Perinat Epidemiol 2018; 32:1-12. [PMID: 28881463 PMCID: PMC5771849 DOI: 10.1111/ppe.12400] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Preeclampsia is thought to originate during placentation, with incomplete remodelling and perfusion of the spiral arteries leading to reduced placental vascular capacity. Nitric oxide (NO) and carbon monoxide (CO) are powerful vasodilators that play a role in the placental vascular system. Although family clustering of preeclampsia has been observed, the existing genetic literature is limited by a failure to consider both mother and child. METHODS We conducted a nested case-control study within the Norwegian Mother and Child Birth Cohort of 1545 case-pairs and 995 control-pairs from 2540 validated dyads (2011 complete pairs, 529 missing mother or child genotype). We selected 1518 single-nucleotide polymorphisms (SNPs) with minor allele frequency >5% in NO and CO signalling pathways. We used log-linear Poisson regression models and likelihood ratio tests to assess maternal and child effects. RESULTS One SNP met criteria for a false discovery rate Q-value <0.05. The child variant, rs12547243 in adenylate cyclase 8 (ADCY8), was associated with an increased risk (relative risk [RR] 1.42, 95% confidence interval [CI] 1.20, 1.69 for AG vs. GG, RR 2.14, 95% CI 1.47, 3.11 for AA vs. GG, Q = 0.03). The maternal variant, rs30593 in PDE1C was associated with a decreased risk for the subtype of preeclampsia accompanied by early delivery (RR 0.45, 95% CI 0.27, 0.75 for TC vs. CC; Q = 0.02). None of the associations were replicated after correction for multiple testing. CONCLUSIONS This study uses a novel approach to disentangle maternal and child genotypic effects of NO and CO signalling genes on preeclampsia.
Collapse
Affiliation(s)
- Anna E. Bauer
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill
| | - Christy L. Avery
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill
- Carolina Population Center, University of North Carolina at Chapel Hill
| | - Min Shi
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | - Clarice R. Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | - Andrew F. Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill
| | - Quaker E. Harmon
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | - Jingchun Luo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill
| | - Jenny Yang
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill
| | - Tracy Manuck
- Department of Obstetrics and Gynecology, School of Medicine, University of North Carolina at Chapel Hill
| | - Michael C. Wu
- Biostatistics and Biomathematics Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Ralph McGinnis
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Linda Morgan
- School of Life Sciences, University of Nottingham, United Kingdom
| | | | | | - Per Magnus
- Norwegian Institute of Public Health, Oslo, Norway
| | - Stephanie M. Engel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill
| |
Collapse
|
16
|
Gjerdevik M, Haaland ØA, Romanowska J, Lie RT, Jugessur A, Gjessing HK. Parent-of-origin-environment interactions in case-parent triads with or without independent controls. Ann Hum Genet 2017; 82:60-73. [PMID: 29094765 PMCID: PMC5813215 DOI: 10.1111/ahg.12224] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 09/05/2017] [Indexed: 01/31/2023]
Abstract
With case–parent triad data, one can frequently deduce parent of origin of the child's alleles. This allows a parent‐of‐origin (PoO) effect to be estimated as the ratio of relative risks associated with the alleles inherited from the mother and the father, respectively. A possible cause of PoO effects is DNA methylation, leading to genomic imprinting. Because environmental exposures may influence methylation patterns, gene–environment interaction studies should be extended to allow for interactions between PoO effects and environmental exposures (i.e., PoOxE). One should thus search for loci where the environmental exposure modifies the PoO effect. We have developed an extensive framework to analyze PoOxE effects in genome‐wide association studies (GWAS), based on complete or incomplete case–parent triads with or without independent control triads. The interaction approach is based on analyzing triads in each exposure stratum using maximum likelihood estimation in a log‐linear model. Interactions are then tested applying a Wald‐based posttest of parameters across strata. Our framework includes a complete setup for power calculations. We have implemented the models in the R software package Haplin. To illustrate our PoOxE test, we applied the new methodology to top hits from our previous GWAS, assessing whether smoking during the periconceptional period modifies PoO effects on cleft palate only.
Collapse
Affiliation(s)
- Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetic Research and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Computional Biology Unit, University of Bergen, Bergen, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Health Registries, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetic Research and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, 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
| |
Collapse
|
17
|
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.
Collapse
|
18
|
Family-based exome-wide association study of childhood acute lymphoblastic leukemia among Hispanics confirms role of ARID5B in susceptibility. PLoS One 2017; 12:e0180488. [PMID: 28817678 PMCID: PMC5560704 DOI: 10.1371/journal.pone.0180488] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/15/2017] [Indexed: 12/30/2022] Open
Abstract
We conducted an exome-wide association study of childhood acute lymphoblastic leukemia (ALL) among Hispanics to confirm and identify novel variants associated with disease risk in this population. We used a case-parent trio study design; unlike more commonly used case-control studies, this study design is ideal for avoiding issues with population stratification bias among this at-risk ethnic group. Using 710 individuals from 323 Guatemalan and US Hispanic families, two inherited SNPs in ARID5B reached genome-wide level significance: rs10821936, RR = 2.31, 95% CI = 1.70–3.14, p = 1.7×10−8 and rs7089424, RR = 2.22, 95% CI = 1.64–3.01, p = 5.2×10−8. Similar results were observed when restricting our analyses to those with the B-ALL subtype: ARID5B rs10821936 RR = 2.22, 95% CI = 1.63–3.02, p = 9.63×10−8 and ARID5B rs7089424 RR = 2.13, 95% CI = 1.57–2.88, p = 2.81×10−7. Notably, effect sizes observed for rs7089424 and rs10821936 in our study were >20% higher than those reported among non-Hispanic white populations in previous genetic association studies. Our results confirmed the role of ARID5B in childhood ALL susceptibility among Hispanics; however, our assessment did not reveal any strong novel inherited genetic risks for acute lymphoblastic leukemia among this ethnic group.
Collapse
|
19
|
Moreno Uribe LM, Fomina T, Munger RG, Romitti PA, Jenkins MM, Gjessing HK, Gjerdevik M, Christensen K, Wilcox AJ, Murray JC, Lie RT, Wehby GL. A Population-Based Study of Effects of Genetic Loci on Orofacial Clefts. J Dent Res 2017; 96:1322-1329. [PMID: 28662356 DOI: 10.1177/0022034517716914] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Prior genome-wide association studies for oral clefts have focused on clinic-based samples with unclear generalizability. Prior samples were also small for investigating effects by cleft type and exclusively studied isolated clefts (those occurring without other birth defects). We estimated the effects of 17 top loci on cleft types in both isolated and nonisolated cases in the largest consortium to date of European-descent population-based studies. Our analytic approach focused on a mother-child dyad case-control design, but it also allowed analyzing mother-only or child-only genotypes to maximize power. Our total sample included 1,875 cases with isolated clefts, 459 cases with nonisolated clefts, and 3,749 controls. After correcting for multiple testing, we observed significant associations between fetal single-nucleotide polymorphisms (SNPs) at IRF6, PAX7, 8q21.3, 8q24, KIAA1598-VAX1, and MAFB and isolated cleft lip only (CLO) and cleft lip and palate (CLP). Significant associations were observed between isolated CLO and fetal SNPs near TPM1 and NOG1 and between CLP and fetal SNPs at ABCA4-ARHGAP29, THADA, FOXE1, and SPRY2. Overall, effects were similar for isolated CLO and CLP, except for ABCA4-ARHGAP29. A protective effect was observed for the fetal NOG1 SNP on cleft palate only, opposite in direction to the effect on CLO. For most fetal SNPs, a dose-response allelic effect was observed. No evidence of parent-of-origin or maternal genome effects was observed. Overall, effect direction and magnitude were similar between isolated and nonisolated clefts, suggesting that several loci are modifiers of cleft risk in both isolated and nonisolated forms. Our results provide reliable estimates of the effects of top loci on risks of oral clefts in a population of European descent.
Collapse
Affiliation(s)
- L M Moreno Uribe
- 1 Department of Orthodontics and Dows Institute, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - T Fomina
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - R G Munger
- 3 Department of Nutrition and Food Sciences, Utah State University, Logan, UT, USA
| | - P A Romitti
- 4 Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - M M Jenkins
- 5 National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - H K Gjessing
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,6 Norwegian Institute of Public Health, Bergen and Oslo, Norway
| | - M Gjerdevik
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,6 Norwegian Institute of Public Health, Bergen and Oslo, Norway
| | - K Christensen
- 7 Department of Public Health, University of Southern Denmark; Department of Clinical Genetics and Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - A J Wilcox
- 8 Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - J C Murray
- 9 Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - R T Lie
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,6 Norwegian Institute of Public Health, Bergen and Oslo, Norway
| | - G L Wehby
- 10 Departments of Health Management and Policy, Economics, and Preventive and Community Dentistry, and Public Policy Center, University of Iowa, Iowa City, IA, USA
| |
Collapse
|
20
|
Archer NP, Perez-Andreu V, Scheurer ME, Rabin KR, Peckham-Gregory EC, Plon SE, Zabriskie RC, De Alarcon PA, Fernandez KS, Najera CR, Yang JJ, Antillon-Klussmann F, Lupo PJ. Family-based exome-wide assessment of maternal genetic effects on susceptibility to childhood B-cell acute lymphoblastic leukemia in hispanics. Cancer 2016; 122:3697-3704. [PMID: 27529658 DOI: 10.1002/cncr.30241] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/31/2016] [Accepted: 07/06/2016] [Indexed: 11/11/2022]
Abstract
BACKGROUND Children of Hispanic ancestry have a higher incidence of acute lymphoblastic leukemia (ALL) compared with other ethnic groups, but to the authors' knowledge, the genetic basis for these racial disparities remain incompletely understood. Genome-wide association studies of childhood ALL to date have focused on inherited genetic effects; however, maternal genetic effects (the role of the maternal genotype on phenotype development in the offspring) also may play a role in ALL susceptibility. METHODS The authors conducted a family-based exome-wide association study of maternal genetic effects among Hispanics with childhood B-cell ALL using the Illumina Infinium HumanExome BeadChip. A discovery cohort of 312 Guatemalan and Hispanic American families and an independent replication cohort of 152 Hispanic American families were used. RESULTS Three maternal single-nucleotide polymorphisms (SNPs) approached the study threshold for significance after correction for multiple testing (P<1.0 × 10-6 ): MTL5 rs12365708 (testis expressed metallothionein-like protein [tesmin]) (relative risk [RR], 2.62; 95% confidence interval [95% CI], 1.61-4.27 [P = 1.8 × 10-5 ]); ALKBH1 rs6494 (AlkB homolog 1, histone H2A dioxygenase) (RR, 3.77; 95% CI, 1.84-7.74 [P = 3.7 × 10-5 ]); and NEUROG3 rs4536103 (neurogenin 3) (RR, 1.75; 95% CI, 1.30-2.37 [P = 1.2 × 10-4 ]). Although effect sizes were similar, these SNPs were not nominally significant in the replication cohort in the current study. In a meta-analysis comprised of the discovery cohort and the replication cohort, these SNPs were still not found to be statistically significant after correction for multiple comparisons (rs12365708: pooled RR, 2.27 [95% CI, 1.48-3.50], P = 1.99 × 10-4 ; rs6494: pooled RR, 2.31 [95% CI, 1.38-3.85], P = .001; and rs4536103: pooled RR, 1.67 [95% CI, 1.29-2.16] P = 9.23 × 10-5 ). CONCLUSIONS In what to the authors' knowledge is the first family-based based exome-wide association study to investigate maternal genotype effects associated with childhood ALL, the results did not implicate a strong role of maternal genotype on disease risk among Hispanics; however, 3 maternal SNPs were identified that may play a modest role in susceptibility. Cancer 2016;122:3697-704. © 2016 American Cancer Society.
Collapse
Affiliation(s)
- Natalie P Archer
- Austin Regional Campus, University of Texas School of Public Health, Austin, Texas
| | - Virginia Perez-Andreu
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee.,Hematologic Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael E Scheurer
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Karen R Rabin
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Erin C Peckham-Gregory
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Sharon E Plon
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Ryan C Zabriskie
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Pedro A De Alarcon
- Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, Illinois
| | - Karen S Fernandez
- Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, Illinois
| | - Cesar R Najera
- National Pediatric Oncology Unit, Guatemala City, Guatemala
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee.,Hematologic Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Federico Antillon-Klussmann
- National Pediatric Oncology Unit, Guatemala City, Guatemala.,School of Medicine, Francisco Marroquin University, Guatemala City, Guatemala
| | - Philip J Lupo
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
21
|
Current Controversies in Diagnosis and Management of Cleft Palate and Velopharyngeal Insufficiency. BIOMED RESEARCH INTERNATIONAL 2015; 2015:196240. [PMID: 26273595 PMCID: PMC4529889 DOI: 10.1155/2015/196240] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 02/16/2015] [Accepted: 03/02/2015] [Indexed: 12/20/2022]
Abstract
Background. One of the most controversial topics concerning cleft palate is the diagnosis and treatment of velopharyngeal insufficiency (VPI). Objective. This paper reviews current genetic aspects of cleft palate, imaging diagnosis of VPI, the planning of operations for restoring velopharyngeal function during speech, and strategies for speech pathology treatment of articulation disorders in patients with cleft palate. Materials and Methods. An updated review of the scientific literature concerning genetic aspects of cleft palate was carried out. Current strategies for assessing and treating articulation disorders associated with cleft palate were analyzed. Imaging procedures for assessing velopharyngeal closure during speech were reviewed, including a recent method for performing intraoperative videonasopharyngoscopy. Results. Conclusions from the analysis of genetic aspects of syndromic and nonsyndromic cleft palate and their use in its diagnosis and management are presented. Strategies for classifying and treating articulation disorders in patients with cleft palate are presented. Preliminary results of the use of multiplanar videofluoroscopy as an outpatient procedure and intraoperative endoscopy for the planning of operations which aimed to correct VPI are presented. Conclusion. This paper presents current aspects of the diagnosis and management of patients with cleft palate and VPI including 3 main aspects: genetics and genomics, speech pathology and imaging diagnosis, and surgical management.
Collapse
|
22
|
Sun Y, Huang Y, Yin A, Pan Y, Wang Y, Wang C, Du Y, Wang M, Lan F, Hu Z, Wang G, Jiang M, Ma J, Zhang X, Ma H, Ma J, Zhang W, Huang Q, Zhou Z, Ma L, Li Y, Jiang H, Xie L, Jiang Y, Shi B, Cheng J, Shen H, Wang L, Yang Y. Genome-wide association study identifies a new susceptibility locus for cleft lip with or without a cleft palate. Nat Commun 2015; 6:6414. [DOI: 10.1038/ncomms7414] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/27/2015] [Indexed: 01/24/2023] Open
|
23
|
Erickson PA, Cleves PA, Ellis NA, Schwalbach KT, Hart JC, Miller CT. A 190 base pair, TGF-β responsive tooth and fin enhancer is required for stickleback Bmp6 expression. Dev Biol 2015; 401:310-23. [PMID: 25732776 DOI: 10.1016/j.ydbio.2015.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/11/2015] [Indexed: 12/17/2022]
Abstract
The ligands of the Bone Morphogenetic Protein (BMP) family of developmental signaling molecules are often under the control of complex cis-regulatory modules and play diverse roles in vertebrate development and evolution. Here, we investigated the cis-regulatory control of stickleback Bmp6. We identified a 190bp enhancer ~2.5 kilobases 5' of the Bmp6 gene that recapitulates expression in developing teeth and fins, with a core 72bp sequence that is sufficient for both domains. By testing orthologous enhancers with varying degrees of sequence conservation from outgroup teleosts in transgenic reporter gene assays in sticklebacks and zebrafish, we found that the function of this regulatory element appears to have been conserved for over 250 million years of teleost evolution. We show that a predicted binding site for the TGFβ effector Smad3 in this enhancer is required for enhancer function and that pharmacological inhibition of TGFβ signaling abolishes enhancer activity and severely reduces endogenous Bmp6 expression. Finally, we used TALENs to disrupt the enhancer in vivo and find that Bmp6 expression is dramatically reduced in teeth and fins, suggesting this enhancer is necessary for expression of the Bmp6 locus. This work identifies a relatively short regulatory sequence that is required for expression in multiple tissues and, combined with previous work, suggests that shared regulatory networks control limb and tooth development.
Collapse
Affiliation(s)
- Priscilla A Erickson
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, United States
| | - Phillip A Cleves
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, United States
| | - Nicholas A Ellis
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, United States
| | - Kevin T Schwalbach
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, United States
| | - James C Hart
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, United States
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, United States.
| |
Collapse
|
24
|
Pan X, Wang P, Yin X, Liu X, Li D, Li X, Wang Y, Li H, Yu Z. Association between Maternal MTHFR Polymorphisms and Nonsyndromic Cleft Lip with or without Cleft Palate in Offspring, A Meta-Analysis Based on 15 Case-Control Studies. INTERNATIONAL JOURNAL OF FERTILITY & STERILITY 2015; 8:463-80. [PMID: 25780529 PMCID: PMC4355933 DOI: 10.22074/ijfs.2015.4186] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 11/25/2013] [Indexed: 11/30/2022]
Abstract
Background The methylenetetrahydrofolate reductase (MTHFR) is thought to be
involved in the development of nonsyndromic cleft lip with or without cleft palate
(NSCL/P). However, conflicting results have been obtained when evaluating the association between maternal MTHFR C677T and A1298C polymorphisms and the risk of
NSCL/P. In light of this gap, a meta-analysis of all eligible case-control studies was
conducted in the present study. Materials and Methods A total of 15 case-control studies were ultimately identified
after a comprehensive literature search and Hardy-Weinberg equilibrium (HWE) examination. Cochrane’s Q test and index of heterogeneity (I2) indicated no obvious heterogeneity among studies. Results Fixed or random-effects models were used to calculate the pooled odds ratios
(ORs). The results showed that the TT genotype in mothers increased the likelihood of having
NSCL/P offspring 1.25 times (95% CI: 1.047-1.494) more than the CC homozygotes. Meanwhile, maternal TT genotype increased the risk of producing NSCL/P offspring in recessive
model (OR=1.325, 95% CI: 1.124-1.562). However, the CT heterozygote and the CT+TT
dominant models had no association with NSCL/P offspring compared with the CC wild-type
homozygote model. Subgroup analyses based on ethnicity indicated that maternal TT genotype increased the likelihood of having NSCL/P offspring in Whites (OR=1.308, 95% CI:
1.059-1.617) and Asians (OR=1.726, 95% CI: 1.090-2.733) in recessive model. Also, subgroup analyses based on source of control showed that mothers with the 677TT genotype had
a significantly increased susceptibility of having NSCL/P children in hospital based population (HB) when compared with CC homozygotes (OR=1.248, 95% CI: 1.024-1.520) and un-
der the recessive model (OR=1.324, 95% CI: 1.104-1.588). Furthermore, maternal A1298C
polymorphism had no significant association with producing NSCL/P offspring (dominant
model OR=0.952, 95% CI: 0.816-1.111, recessive model OR=0.766, 95% CI: 0.567-1.036). Conclusion MTHFR C677T polymorphism is associated with the risk of generating NSCL/P
offspring, and being a 677TT homozygote is a risk factor. MTHFR A1298C polymorphism
was not associated with generating NSCL/P offspring. However, further work should be performed to confirm these findings.
Collapse
Affiliation(s)
- Xinjuan Pan
- College of Public Health, Zhengzhou University, Zhengzhou, China ; Medical College, Henan University of Science and Technology, Luoyang, China
| | - Ping Wang
- Medical College, Henan University of Science and Technology, Luoyang, China
| | - Xinjuan Yin
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xiaozhuan Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Di Li
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xing Li
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Yongchao Wang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Hongle Li
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Zengli Yu
- College of Public Health, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
25
|
Mitchell LE, Agopian AJ, Bhalla A, Glessner JT, Kim CE, Swartz MD, Hakonarson H, Goldmuntz E. Genome-wide association study of maternal and inherited effects on left-sided cardiac malformations. Hum Mol Genet 2014; 24:265-73. [PMID: 25138779 DOI: 10.1093/hmg/ddu420] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Congenital left-sided lesions (LSLs) are serious, heritable malformations of the heart. However, little is known about the genetic causes of LSLs. This study was undertaken to identify common variants acting through the genotype of the affected individual (i.e. case) or the mother (e.g. via an in utero effect) that influence the risk of LSLs. A genome-wide association study (GWAS) was performed using data from 377 LSL case-parent triads, with follow-up studies in an independent sample of 224 triads and analysis of the combined data. Associations with both the case and maternal genotypes were assessed using log-linear analyses under an additive model. An association between LSLs and the case genotype for one intergenic SNP on chromosome 16 achieved genome-wide significance in the combined data (rs8061121, combined P = 4.0 × 10(-9); relative risk to heterozygote: 2.6, 95% CI: 1.9-3.7). In the combined data, there was also suggestive evidence of association between LSLs and the case genotype for a variant in the synaptoporin gene (rs1975649, combined P = 3.4 × 10(-7); relative risk to heterozygote: 1.6, 95% CI: 1.4-2.0) and between LSLs and the maternal genotype for an intergenic SNP on chromosome 10 (rs11008222, combined P = 6.3 × 10(-7); relative risk to heterozygote: 1.6, 95% CI: 1.4-2.0). This is the first GWAS of LSLs to evaluate associations with both the case and maternal genotypes. The results of this study identify three candidate LSL susceptibility loci, including one that appears to be associated with the risk of LSLs via the maternal genotype.
Collapse
Affiliation(s)
- Laura E Mitchell
- Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX 77030, USA
| | - A J Agopian
- Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX 77030, USA
| | - Angela Bhalla
- Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX 77030, USA
| | | | | | - Michael D Swartz
- Division of Biostatistics, University of Texas School of Public Health, Houston, TX 77030, USA and
| | - Hakon Hakonarson
- The Center for Applied Genomics and Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elizabeth Goldmuntz
- Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
26
|
Garg P, Ludwig KU, Böhmer AC, Rubini M, Steegers-Theunissen R, Mossey PA, Mangold E, Sharp AJ. Genome-wide analysis of parent-of-origin effects in non-syndromic orofacial clefts. Eur J Hum Genet 2014; 22:822-30. [PMID: 24169523 PMCID: PMC4023210 DOI: 10.1038/ejhg.2013.235] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 09/02/2013] [Accepted: 09/04/2013] [Indexed: 02/04/2023] Open
Abstract
Parent-of-origin (PofO) effects, such as imprinting are a phenomenon where the effect of variants depends on parental origin. Conventional association studies assume that phenotypic effects are independent of parental origin, and are thus severely underpowered to detect such non-Mendelian effects. Risk of orofacial clefts is influenced by genetic and environmental effects, the latter including maternal-specific factors such as perinatal smoking and folate intake. To identify variants showing PofO effects in orofacial clefts we have used a modification of the family-based transmission disequilibrium test to screen for biased transmission from mothers and fathers to affected offspring, biased ratios of maternal versus paternal transmission, and biased frequencies of reciprocal classes of heterozygotes among offspring. We applied these methods to analyze published genome-wide single-nucleotide polymorphism (SNP) data from ∼2500 trios mainly of European and Asian ethnicity with non-syndromic orofacial clefts, followed by analysis of 64 candidate SNPs in a replication cohort of ∼1200 trios of European origin. In our combined analysis, we did not identify any SNPs achieving conventional genome-wide significance (P<5 × 10(-8)). However, we observed an overall excess of loci showing maternal versus paternal transmission bias (P=0.013), and identified two loci that showed nominally significant effects in the same direction in both the discovery and replication cohorts, raising the potential for PofO effects. These include a possible maternal-specific transmission bias associated with rs12543318 at 8q21.3, a locus identified in a recent meta-analysis of non-syndromic cleft (maternal-specific P=1.5 × 10(-7), paternal-specific P=0.17). Overall, we conclude from this analysis that there are subtle hints of PofO effects in orofacial clefting.
Collapse
Affiliation(s)
- Paras Garg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY, USA
| | - Kerstin U Ludwig
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Anne C Böhmer
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Michele Rubini
- Department of Experimental and Diagnostic Medicine, Medical Genetics Unit, University of Ferrara, Ferrara, Italy
| | - Regine Steegers-Theunissen
- Department of Obstetrics and Gynaecology, and Clinical Genetics, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Peter A Mossey
- Orthodontic Unit, Dental Hospital and School, University of Dundee, Dundee, UK
| | | | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY, USA
| |
Collapse
|
27
|
Agopian AJ, Mitchell LE, Glessner J, Bhalla AD, Sewda A, Hakonarson H, Goldmuntz E. Genome-wide association study of maternal and inherited loci for conotruncal heart defects. PLoS One 2014; 9:e96057. [PMID: 24800985 PMCID: PMC4011736 DOI: 10.1371/journal.pone.0096057] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 04/02/2014] [Indexed: 12/05/2022] Open
Abstract
Conotruncal and related heart defects (CTDs) are a group of serious and relatively common birth defects. Although both maternal and inherited genotypes are thought to play a role in the etiology of CTDs, few specific genetic risk factors have been identified. To determine whether common variants acting through the genotype of the mother (e.g. via an in utero effect) or the case are associated with CTDs, we conducted a genome-wide association study of 750 CTD case-parent triads, with follow-up analyses in 358 independent triads. Log-linear analyses were used to assess the association of CTDs with the genotypes of both the mother and case. No association achieved genomewide significance in either the discovery or combined (discovery+follow-up) samples. However, three loci with p-values suggestive of association (p<10−5) in the discovery sample had p-values <0.05 in the follow-up sample and p-values in the combined data that were lower than in the discovery sample. These included suggestive association with an inherited intergenic variant at 20p12.3 (rs6140038, combined p = 1.0×10−5) and an inherited intronic variant in KCNJ4 at 22q13.1 (rs2267386, combined p = 9.8×10−6), as well as with a maternal variant in SLC22A24 at 11q12.3 (rs11231379, combined p = 4.2×10−6). These observations suggest novel candidate loci for CTDs, including loci that appear to be associated with the risk of CTDs via the maternal genotype, but further studies are needed to confirm these associations.
Collapse
Affiliation(s)
- A. J. Agopian
- Human Genetics Center, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, Texas, United States of America
| | - Laura E. Mitchell
- Human Genetics Center, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, Texas, United States of America
- * E-mail:
| | - Joseph Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Angela D. Bhalla
- Human Genetics Center, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, Texas, United States of America
| | - Anshuman Sewda
- Human Genetics Center, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, Texas, United States of America
| | - Hakon Hakonarson
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Elizabeth Goldmuntz
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
28
|
Hassan WA, Lees CC. Facial cleft detected: Is the palate normal? Best Pract Res Clin Obstet Gynaecol 2014; 28:379-89. [DOI: 10.1016/j.bpobgyn.2014.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/22/2014] [Indexed: 10/25/2022]
|
29
|
Pan Y, Zhang W, Ma J, Du Y, Li D, Cai Q, Jiang H, Wang M, Zhang Z, Wang L. Infants'MTHFRpolymorphisms and nonsyndromic orofacial clefts susceptibility: A meta-analysis based on 17 case-control studies. Am J Med Genet A 2012; 158A:2162-9. [DOI: 10.1002/ajmg.a.35503] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 05/07/2012] [Indexed: 11/09/2022]
|
30
|
Candidate pathway based analysis for cleft lip with or without cleft palate. Stat Appl Genet Mol Biol 2012; 11:/j/sagmb.2012.11.issue-2/1544-6115.1717/1544-6115.1717.xml. [PMID: 22499695 DOI: 10.2202/1544-6115.1717] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The objective of this research was to identify potential biological pathways associated with non-syndromic cleft lip with or without cleft palate (NSCL/P), and to explore the potential biological mechanisms underlying these associated pathways on risk of NSCL/P. This project was based on the dataset of a previously published genome-wide association (GWA) study on NSCL/P (Beaty et al. 2010). Case-parent trios used here originated from an international consortium (The Gene, Environment Association Studies consortium, GENEVA) formed in 2007. A total of 5,742 individuals from 1,908 CL/P case-parents trios (1,591 complete trios and 317 incomplete trios where one parent was missing) were collected and genotyped using the Illumina Human610-Quad array. Candidate pathways were selected using a list of 356 genes that may be related to oral clefts. In total, 42 candidate pathways, which included 1,564 genes and 40,208 SNPs were tested. Using a pathway-based analysis approach proposed by Wang et al (2007), we conducted a permutation-based test to assess the statistical significance of the nominal p-values of 42 candidate pathways. The analysis revealed several pathways yielding nominally significant p-values. However, controlling for the family wise error rate, none of these pathways could retain statistical significance. Nominal p-values of these pathways were concentrated at the lower tail of the distribution, with more than expected low p-values. A permutation based test for examining this type of distribution pattern yielded an overall p-value of 0.029. Thus, while this pathway-based analysis did not yield a clear significant result for any particular pathway, we conclude that one or more of the genes and pathways considered here likely do play a role in oral clefting.
Collapse
|