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Cai M, Lin N, Su L, Wu X, Xie X, Li Y, Chen X, Lin Y, Huang H, Xu L. Copy number variations associated with fetal congenital kidney malformations. Mol Cytogenet 2020; 13:11. [PMID: 32211073 PMCID: PMC7092440 DOI: 10.1186/s13039-020-00481-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/17/2020] [Indexed: 01/19/2023] Open
Abstract
Background Congenital anomalies of the kidney and urinary tract (CAKUT) constitute 20–30% of all congenital malformations. Within the CAKUT phenotypic spectrum, renal hypodysplasia (RHD) is particularly severe. This study aimed to evaluate the applicability of single-nucleotide polymorphism (SNP) array test in prenatal diagnosis of RHD for improving prenatal genetic counseling and to search for evidence of a possible causative role of copy-number variations (CNVs) in RHD. Results We performed a systematic survey of CNV burden in 120 fetuses with RHD: 103 cases were isolated RHD and 17 were non-isolated RHD. Single-nucleotide polymorphism (SNP) array test was performed using the Affymetrix CytoScan HD platform. All annotated CNVs were validated by fluorescence in situ hybridization. We identified abnormal CNVs in 15 (12.5%) cases of RHD; of these CNVs, 11 were pathogenic and 4 were variants of uncertain significance. The detection rate of abnormal CNVs in non-isolated RHD was higher (29.4%, 5/17) than that in isolated RHD (9.7%, 10/103) (P = 0.060). Parents are more inclined to terminate the pregnancy if the fetuses have pathogenic results of the SNP-array test. Conclusions The variable phenotypes that abnormal CNVs may cause indicate the genetic counseling is needed for RHD cases.
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Affiliation(s)
- Meiying Cai
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Linjuan Su
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xiaoqing Wu
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xiaorui Xie
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Ying Li
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xuemei Chen
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yuan Lin
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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Mohamad Shah NS, Sulong S, Wan Sulaiman WA, Halim AS. Two novel genes TOX3 and COL21A1 in large extended Malay families with nonsyndromic cleft lip and/or palate. Mol Genet Genomic Med 2019; 7:e635. [PMID: 30924295 PMCID: PMC6503016 DOI: 10.1002/mgg3.635] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 01/09/2019] [Accepted: 02/11/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip and/or palate is one of the most common human birth defects worldwide that affects the lip and/or palate. The incidence of clefts varies among populations through ethnic, race, or geographical differences. The focus on Malay nonsyndromic cleft lip and/or palate (NSCL/P) is because of a scarce report on genetic study in relation to this deformity in Malaysia. We are interested to discuss about the genes that are susceptible to cause orofacial cleft formation in the family. METHODS Genome-wide linkage analysis was carried out on eight large extended families of NSCL/P with the total of 91 individuals among Malay population using microarray platform. Based on linkage analyses findings, copy number variation (CNV) of LPHN2, SATB2, PVRL3, COL21A1, and TOX3 were identified in four large extended families that showed linkage evidence using quantitative polymerase chain reaction (qPCR) as for a validation purpose. Copy number calculated (CNC) for each genes were determined with Applied Biosystems CopyCallerTM Software v2.0. Normal CNC of the target sequence expected was set at two. RESULTS Genome-wide linkage analysis had discovered several genes including TOX3 and COL21A1 in four different loci 4p15.2-p16.1, 6p11.2-p12.3, 14q13-q21, and 16q12.1. There was significant decreased, p < 0.05 of SATB2, COL21A1, and TOX3 copy number in extended families compared to the normal controls. CONCLUSION Novel linkage evidence and significant low copy number of COL21A1 and TOX3 in NSCLP family was confirmed. These genes increased the risks toward NSCLP formation in that family traits.
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Affiliation(s)
- Nurul Syazana Mohamad Shah
- Reconstructive Science Unit, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
| | - Wan Azman Wan Sulaiman
- Reconstructive Science Unit, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
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Mohamad Shah NS, Salahshourifar I, Sulong S, Wan Sulaiman WA, Halim AS. Discovery of candidate genes for nonsyndromic cleft lip palate through genome-wide linkage analysis of large extended families in the Malay population. BMC Genet 2016; 17:39. [PMID: 26868259 PMCID: PMC4751652 DOI: 10.1186/s12863-016-0345-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 02/02/2016] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Nonsyndromic orofacial clefts are one of the most common birth defects worldwide. It occurs as a result of genetic or environmental factors. This study investigates the genetic contribution to nonsyndromic cleft lip and/or palate through the analysis of family pedigrees. Candidate genes associated with the condition were identified from large extended families from the Malay population. RESULTS A significant nonparametric linkage (NPL) score was detected in family 100. Other suggestive NPL and logarithm of the odds (LOD) scores were attained from families 50, 58, 99 and 100 under autosomal recessive mode. Heterogeneity LOD (HLOD) score ≥ 1 was determined for all families, confirming genetic heterogeneity of the population and indicating that a proportion of families might be linked to each other. Several candidate genes in linkage intervals were determined; LPHN2 at 1p31, SATB2 at 2q33.1-q35, PVRL3 at 3q13.3, COL21A1 at 6p12.1, FOXP2 at 7q22.3-q33, FOXG1 and HECTD1 at 14q12 and TOX3 at 16q12.1. CONCLUSIONS We have identified several novel and known candidate genes for nonsyndromic cleft lip and/or palate through genome-wide linkage analysis. Further analysis of the involvement of these genes in the condition will shed light on the disease mechanism. Comprehensive genetic testing of the candidate genes is warranted.
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Affiliation(s)
| | - Iman Salahshourifar
- Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Isfahan, Iran.
| | - Sarina Sulong
- Human Genome Center, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.
| | - Wan Azman Wan Sulaiman
- Reconstructive Science Unit, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.
| | - Ahmad Sukari Halim
- School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia.
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Abstract
Oral clefts are common birth defects that have a major impact on the affected individual, their family and society. World-wide, the incidence of oral clefts is 1/700 live births, making them the most common craniofacial birth defects. The successful prediction of oral clefts may help identify sub-population at high risk, and promote new diagnostic and therapeutic strategies. Nevertheless, developing a clinically useful oral clefts risk prediction model remains a great challenge. Compelling evidences suggest the etiologies of oral clefts are highly heterogeneous, and the development of a risk prediction model with consideration of phenotypic heterogeneity may potentially improve the accuracy of a risk prediction model. In this study, we applied a previously developed statistical method to investigate the risk prediction on sub-phenotypes of oral clefts. Our results suggested subtypes of cleft lip (CL) and palate have similar genetic etiologies (AUC = 0.572) with subtypes of CL only (AUC = 0.589), while the subtypes of cleft palate only (CPO) have heterogeneous underlying mechanisms (AUCs for soft CPO and hard CPO are 0.617 and 0.623, respectively). This highlighted the potential that the hard and soft forms of CPO have their own mechanisms despite sharing some of the genetic risk factors. Comparing with conventional methods for risk prediction modeling, our method considers phenotypic heterogeneity of a disease, which potentially improves the accuracy for predicting each sub-phenotype of oral clefts.
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Affiliation(s)
- Yalu Wen
- Department of Statistics, University of Auckland, Auckland New Zealand
| | - Qing Lu
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI USA
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Rajendran R, Shaikh SF, Anil S. Tracing disease gene(s) in non-syndromic clefts of orofacial region: HLA haplotypic linkage by analyzing the microsatellite markers: MIB, C1_2_5, C1_4_1, and C1_2_A. Indian J Hum Genet 2012; 17:188-93. [PMID: 22345991 PMCID: PMC3276988 DOI: 10.4103/0971-6866.92101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND: Cleft lip with or without cleft palate (CL/P) is the most frequent craniofacial malformation seen in man. The etiology of CL/P is complex involving both genetic and epigenetic (environmental) factors, and the genes play an almost deterministic role in the normal development of craniofacial structures. This study was aimed at ascertaining the association of HLA microsatellites in CL/P patients. MATERIALS AND METHODS: Case DNA was obtained from 76 patients (40M and 36 F, average age 7.8 years, range 1-16 years). Unaffected individuals from the same geographical area without population mixing included as controls (n=154, 76 M and 78 F, average age 8.2 years, range 2-17 years). All DNA samples were purified from peripheral blood by standard techniques. RESULTS: Four microsatellites were compared in this case-control study. C1_2_5 locus was the most polymorphic marker with 15 observed alleles while C1_4_1 had the least number of alleles. Three of the four markers viz MIB,C1_4_1 and C1_2_5 showed a significant association of microsatellite alleles with CL/P. Five alleles (MIB_326,332,350; C1_4_1 – 213 and C1_2_5-204) were seen with an increased frequency among the test samples, whereas two alleles (C1-4_1_217, and C1_2_5_196) had an increased frequency among the control samples. One allele (C1-4-1-209) had an increased frequency in patient group but was not observed in the controls. CONCLUSION: The role of HLA complex in the pathogenesis of CL/P is speculative and has not been established so far. The result of this study shows that a few alleles have an increased frequency of expression in the diseased group which suggests that these alleles may predispose the individuals to clefting. This finding may be beneficial to aid in early diagnosis and plan intervention strategies.
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Affiliation(s)
- R Rajendran
- Department of Oral Medicine and Diagnostic Science, College of Dentistry, King Saud University, Post Box: 60169, Riyadh-11545, Kingdom of Saudi Arabia
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Abstract
Nonsyndromic cleft lip and palate is a complex genetic disorder with variable phenotype, largely attributed to the interactions of the environment and multiple genes, each potentially having certain effects. Numerous genes have been reported in studies demonstrating associations and/or linkage of the cleft lip and palate phenotypes to alleles of microsatellite markers and single nucleotide polymorphisms within specific genes that regulate transcription factors, growth factors, cell signalling and detoxification metabolisms. Although the studies reporting these observations are compelling, most of them lack statistical power. This review compiles the evidence that supports linkage and associations to the various genetic loci and candidate genes. Whereas significant progress has been made in the field of cleft lip and palate genetics in the past decade, the role of the genes and genetic variations within the numerous candidate genes that have been found to associate with the expression of the orofacial cleft phenotype remain to be determined.
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Affiliation(s)
- Jyotsna Murthy
- Department of Plastic Surgery, Sri Ramachandra Medical College, Chennai, India
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Abstract
The Indian sub-continent remains one of the most populous areas of the world with an estimated population of 1.1 billion in India alone. This yields an estimated 24.5 million births per year and the birth prevalence of clefts is somewhere between 27,000 and 33,000 clefts per year. Inequalities exist, both in access to and quality of cleft care with distinct differences in urban versus rural access and over the years the accumulation of unrepaired clefts of the lip and palate make this a significant health care problem in India. In recent years the situation has been significantly improved through the intervention of Non Governmental Organisations such as SmileTrain and Transforming Faces Worldwide participating in primary surgical repair programmes. The cause of clefts is multi factorial with both genetic and environmental input and intensive research efforts have yielded significant advances in recent years facilitated by molecular technologies in the genetic field. India has tremendous potential to contribute by virtue of improving research expertise and a population that has genetic, cultural and socio-economic diversity. In 2008, the World Health Organisation (WHO) has recognised that non-communicable diseases, including birth defects cause significant infant mortality and childhood morbidity and have included cleft lip and palate in their Global Burden of Disease (GBD) initiative. This will fuel the interest of India in birth defects registration and international efforts aimed at improving quality of care and ultimately prevention of non-syndromic clefts of the lip and palate.
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Affiliation(s)
- Peter Mossey
- Unit of Orthodontics, Dundee University Dental School, 1 Park Place, Dundee, DD1 4HR, Scotland, United Kingdom
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Zhu J, Hao L, Li S, Bailey LB, Tian Y, Li Z. MTHFR, TGFB3, and TGFA polymorphisms and their association with the risk of non-syndromic cleft lip and cleft palate in China. Am J Med Genet A 2010; 152A:291-8. [PMID: 20082468 DOI: 10.1002/ajmg.a.33113] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Our previous results indicated a moderate association between the methylenetetrahydrofolate reductase (MTHFR) gene 677C-T variant and an increased risk of non-syndromic cleft lip with or without cleft palate (nsCL/P) among the northern but not southern population in China, suggesting possible genetic heterogeneity in the etiology of nsCL/P between these two populations. It remains unknown whether the transforming growth factor alpha (TGFA) gene TaqI polymorphism and transforming growth factor beta 3 (TGFB3) gene CA repeats influence the risk of nsCL/P differently between the northern and southern Chinese populations. In this study of 188 Chinese case-parent triads, we found an independent association between the TGFB3 variant and risk of nsCL/P (OR = 2.10, 95% CI: 1.25-3.54 for heterozygotes; OR = 1.78, 95% CI: 0.83-3.83 for homozygotes). The MTHFR variant was associated with an increased risk of nsCL/P among children in the north (OR = 3.11, 95% CI: 1.18-8.23 for heterozygotes; OR = 3.36, 95%CI: 1.14-9.93 for homozygotes) and appear to interact marginally with the TGFB3 variant in the occurrence of nsCL/P among southern subjects (OR = 0.26, 95% CI: 0.06-1.07). No association was found between the TGFA variant and risk of nsCL/P in our data. Our results suggest that the TGFB3 gene variant may be an important genetic risk factor for nsCL/P occurrence in Chinese children, and we found no evidence of heterogeneity between northern and southern Chinese populations in the associations between TGFB3 and TGFA variants and risk of nsCL/P, but these results warrant further investigation.
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Affiliation(s)
- JiangHui Zhu
- National Reference Laboratory on Reproductive and Child Health, Ministry of Health, Peking University Health Science Center, Beijing, China
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9
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Abstract
Clefts of the lip and palate are generally divided into two groups, isolated cleft palate and cleft lip with or without cleft palate, representing a heterogeneous group of disorders affecting the lips and oral cavity. These defects arise in about 1.7 per 1000 liveborn babies, with ethnic and geographic variation. Effects on speech, hearing, appearance, and psychology can lead to longlasting adverse outcomes for health and social integration. Typically, children with these disorders need multidisciplinary care from birth to adulthood and have higher morbidity and mortality throughout life than do unaffected individuals. This Seminar describes embryological developmental processes, epidemiology, known environmental and genetic risk factors, and their interaction. Although access to care has increased in recent years, especially in developing countries, quality of care still varies substantially. Prevention is the ultimate objective for clefts of the lip and palate, and a prerequisite of this aim is to elucidate causes of the disorders. Technological advances and international collaborations have yielded some successes.
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Affiliation(s)
- Peter A Mossey
- Department of Dental and Oral Health, University of Dundee, Dental Hospital and School, Dundee, UK.
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Moreno LM, Mansilla MA, Bullard SA, Cooper ME, Busch TD, Machida J, Johnson MK, Brauer D, Krahn K, Daack-Hirsch S, L'heureux J, Valencia-Ramirez C, Rivera D, López AM, Moreno MA, Hing A, Lammer EJ, Jones M, Christensen K, Lie RT, Jugessur A, Wilcox AJ, Chines P, Pugh E, Doheny K, Arcos-Burgos M, Marazita ML, Murray JC, Lidral AC. FOXE1 association with both isolated cleft lip with or without cleft palate, and isolated cleft palate. Hum Mol Genet 2009; 18:4879-96. [PMID: 19779022 DOI: 10.1093/hmg/ddp444] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Nonsyndromic orofacial clefts are a common complex birth defect caused by genetic and environmental factors and/or their interactions. A previous genome-wide linkage scan discovered a novel locus for cleft lip with or without cleft palate (CL/P) at 9q22-q33. To identify the etiologic gene, we undertook an iterative and complementary fine mapping strategy using family-based CL/P samples from Colombia, USA and the Philippines. Candidate genes within 9q22-q33 were sequenced, revealing 32 new variants. Concurrently, 397 SNPs spanning the 9q22-q33 2-LOD-unit interval were tested for association. Significant SNP and haplotype association signals (P = 1.45E - 08) narrowed the interval to a 200 kb region containing: FOXE1, C9ORF156 and HEMGN. Association results were replicated in CL/P families of European descent and when all populations were combined the two most associated SNPs, rs3758249 (P = 5.01E - 13) and rs4460498 (P = 6.51E - 12), were located inside a 70 kb high linkage disequilibrium block containing FOXE1. Association signals for Caucasians and Asians clustered 5' and 3' of FOXE1, respectively. Isolated cleft palate (CP) was also associated, indicating that FOXE1 plays a role in two phenotypes thought to be genetically distinct. Foxe1 expression was found in the epithelium undergoing fusion between the medial nasal and maxillary processes. Mutation screens of FOXE1 identified two family-specific missense mutations at highly conserved amino acids. These data indicate that FOXE1 is a major gene for CL/P and provides new insights for improved counseling and genetic interaction studies.
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Affiliation(s)
- Lina M Moreno
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
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11
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Marazita ML, Lidral AC, Murray JC, Field LL, Maher BS, Goldstein McHenry T, Cooper ME, Govil M, Daack-Hirsch S, Riley B, Jugessur A, Felix T, Morene L, Mansilla MA, Vieira AR, Doheny K, Pugh E, Valencia-Ramirez C, Arcos-Burgos M. Genome scan, fine-mapping, and candidate gene analysis of non-syndromic cleft lip with or without cleft palate reveals phenotype-specific differences in linkage and association results. Hum Hered 2009; 68:151-70. [PMID: 19521098 DOI: 10.1159/000224636] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 02/12/2009] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVES Non-syndromic orofacial clefts, i.e. cleft lip (CL) and cleft palate (CP), are among the most common birth defects. The goal of this study was to identify genomic regions and genes for CL with or without CP (CL/P). METHODS We performed linkage analyses of a 10 cM genome scan in 820 multiplex CL/P families (6,565 individuals). Significant linkage results were followed by association analyses of 1,476 SNPs in candidate genes and regions, utilizing a weighted false discovery rate (wFDR) approach to control for multiple testing and incorporate the genome scan results. RESULTS Significant (multipoint HLOD >or=3.2) or genome-wide-significant (HLOD >or=4.02) linkage results were found for regions 1q32, 2p13, 3q27-28, 9q21, 12p11, 14q21-24 and 16q24. SNPs in IRF6 (1q32) and in or near FOXE1 (9q21) reached formal genome-wide wFDR-adjusted significance. Further, results were phenotype dependent in that the IRF6 region results were most significant for families in which affected individuals have CL alone, and the FOXE1 region results were most significant in families in which some or all of the affected individuals have CL with CP. CONCLUSIONS These results highlight the importance of careful phenotypic delineation in large samples of families for genetic analyses of complex, heterogeneous traits such as CL/P.
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Affiliation(s)
- Mary L Marazita
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
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Ding NS, Mao HR, Guo YM, Ren J, Xiao SJ, Wu GZ, Shen HQ, Wu LH, Ruan GF, Brenig B, Huang LS. A genome-wide scan reveals candidate susceptibility loci for pig hernias in an intercross between White Duroc and Erhualian. J Anim Sci 2009; 87:2469-74. [PMID: 19359506 DOI: 10.2527/jas.2008-1601] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pig scrotal/inguinal and umbilical hernias are the most prevalent congenital disorders in pigs and often cause animal welfare problems and economic loss. To identify susceptibility loci for these traits, a genome-wide scan with 194 microsatellite markers covering the pig genome was performed in a White Duroc x Erhualian resource population with 23 scrotal/inguinal F(2) animals, 50 umbilical F(2) animals, and their unaffected siblings. A sex-average linkage map with a total length of 2,350.3 cM and an average marker interval of 12.84 cM was constructed. Both nonparametric genome-wide linkage (NPL) analysis and transmission disequilibrium test (TDT) were implemented to detect closely linked markers. The NPL analysis revealed 11 chromosomal regions on SSC1, 2, 3, 6, 7, 8, 10, and 11 for umbilical hernia and 5 regions on SSC2, 4, 8, 13, and 16 for scrotal/inguinal hernia, whereas the TDT test identified susceptibility loci for umbilical hernia on SSC1, 2, 4, 7, 10, 13, 14, and 15 and for scrotal/inguinal hernias on SSC2, 8, 10, and 18. The most promising loci were SWR1928 on SSC7 and SW830 on SSC10 for umbilical hernia, and SW933 on SSC8 for scrotal hernia, which were consistently detected by both NPL and TDT. Several previously reported chromosomal regions for scrotal/inguinal hernia were confirmed, and new evidence for linkage with this pig defect was found. Moreover, susceptibility loci for pig umbilical hernia were detected for the first time.
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Affiliation(s)
- N S Ding
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, PR China
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Hildebrandt F, Heeringa SF, Rüschendorf F, Attanasio M, Nürnberg G, Becker C, Seelow D, Huebner N, Chernin G, Vlangos CN, Zhou W, O'Toole JF, Hoskins BE, Wolf MTF, Hinkes BG, Chaib H, Ashraf S, Schoeb DS, Ovunc B, Allen SJ, Vega-Warner V, Wise E, Harville HM, Lyons RH, Washburn J, MacDonald J, Nürnberg P, Otto EA. A systematic approach to mapping recessive disease genes in individuals from outbred populations. PLoS Genet 2009; 5:e1000353. [PMID: 19165332 PMCID: PMC2621355 DOI: 10.1371/journal.pgen.1000353] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 12/22/2008] [Indexed: 12/29/2022] Open
Abstract
The identification of recessive disease-causing genes by homozygosity mapping is often restricted by lack of suitable consanguineous families. To overcome these limitations, we apply homozygosity mapping to single affected individuals from outbred populations. In 72 individuals of 54 kindred ascertained worldwide with known homozygous mutations in 13 different recessive disease genes, we performed total genome homozygosity mapping using 250,000 SNP arrays. Likelihood ratio Z-scores (ZLR) were plotted across the genome to detect ZLR peaks that reflect segments of homozygosity by descent, which may harbor the mutated gene. In 93% of cases, the causative gene was positioned within a consistent ZLR peak of homozygosity. The number of peaks reflected the degree of inbreeding. We demonstrate that disease-causing homozygous mutations can be detected in single cases from outbred populations within a single ZLR peak of homozygosity as short as 2 Mb, containing an average of only 16 candidate genes. As many specialty clinics have access to cohorts of individuals from outbred populations, and as our approach will result in smaller genetic candidate regions, the new strategy of homozygosity mapping in single outbred individuals will strongly accelerate the discovery of novel recessive disease genes. Many childhood diseases are caused by single-gene mutations of recessive genes, in which a child has inherited one mutated gene copy from each parent causing disease in the child, but not in the parents who are healthy heterozygous carriers. As the two mutations represent the disease cause, gene mapping helped understand disease mechanisms. “Homozygosity mapping” has been particularly useful. It assumes that the parents are related and that a disease-causing mutation together with a chromosomal segment of identical markers (i.e., homozygous markers) is transmitted to the affected child through the paternal and the maternal line from an ancestor common to both parents. Homozygosity mapping seeks out those homozygous regions to map the disease-causing gene. Homozygosity mapping requires families, in which the parents are knowingly related, and have multiple affected children. To overcome these limitations, we applied homozygosity mapping to single affected individuals from outbred populations. In 72 individuals with known homozygous mutations in 13 different recessive disease genes, we performed homozygosity mapping. In 93% we detected the causative gene in a segment of homozygosity. We demonstrate that disease-causing homozygous mutations can be detected in single cases from outbred populations. This will strongly accelerate the discovery of novel recessive disease genes.
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Affiliation(s)
- Friedhelm Hildebrandt
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
- Howard Hughes Medical Institute, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
- * E-mail:
| | - Saskia F. Heeringa
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | | | - Massimo Attanasio
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Gudrun Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Christian Becker
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Dominik Seelow
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
- Department of Neuropaediatrics, Charite, Berlin, Germany
| | | | - Gil Chernin
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Christopher N. Vlangos
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Weibin Zhou
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - John F. O'Toole
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Bethan E. Hoskins
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Matthias T. F. Wolf
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Bernward G. Hinkes
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Hassan Chaib
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Shazia Ashraf
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Dominik S. Schoeb
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Bugsu Ovunc
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Susan J. Allen
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Virginia Vega-Warner
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Eric Wise
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Heather M. Harville
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Robert H. Lyons
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Joseph Washburn
- University of Michigan Cancer Center, Ann Arbor, Michigan, United States of America
| | - James MacDonald
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
- University of Michigan Cancer Center, Ann Arbor, Michigan, United States of America
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Edgar A. Otto
- Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
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14
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Beiraghi S, Nath SK, Gaines M, Mandhyan DD, Hutchings D, Ratnamala U, McElreavey K, Bartoloni L, Antonarakis GS, Antonarakis SE, Radhakrishna U. Autosomal dominant nonsyndromic cleft lip and palate: significant evidence of linkage at 18q21.1. Am J Hum Genet 2007; 81:180-8. [PMID: 17564975 PMCID: PMC1950911 DOI: 10.1086/518944] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Accepted: 04/05/2007] [Indexed: 01/10/2023] Open
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common congenital facial defects, with an incidence of 1 in 700-1,000 live births among individuals of European descent. Several linkage and association studies of NSCL/P have suggested numerous candidate genes and genomic regions. A genomewide linkage analysis of a large multigenerational family (UR410) with NSCL/P was performed using a single-nucleotide-polymorphism array. Nonparametric linkage (NPL) analysis provided significant evidence of linkage for marker rs728683 on chromosome 18q21.1 (NPL=43.33 and P=.000061; nonparametric LOD=3.97 and P=.00001). Parametric linkage analysis with a dominant mode of inheritance and reduced penetrance resulted in a maximum LOD score of 3.61 at position 47.4 Mb on chromosome 18q21.1. Haplotype analysis with informative crossovers defined a 5.7-Mb genomic region spanned by proximal marker rs1824683 (42,403,918 bp) and distal marker rs768206 (48,132,862 bp). Thus, a novel genomic region on 18q21.1 was identified that most likely harbors a high-risk variant for NSCL/P in this family; we propose to name this locus "OFC11" (orofacial cleft 11).
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Affiliation(s)
- Soraya Beiraghi
- Division of Pediatric Dentistry, University of Minnesota, Minneapolis, MN, USA
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15
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Beaty TH, Hetmanski JB, Fallin MD, Park JW, Sull JW, McIntosh I, Liang KY, Vanderkolk CA, Redett RJ, Boyadjiev SA, Jabs EW, Chong SS, Cheah FSH, Wu-Chou YH, Chen PK, Chiu YF, Yeow V, Ng ISL, Cheng J, Huang S, Ye X, Wang H, Ingersoll R, Scott AF. Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations. Hum Genet 2006; 120:501-18. [PMID: 16953426 DOI: 10.1007/s00439-006-0235-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Revised: 07/13/2006] [Accepted: 07/17/2006] [Indexed: 02/07/2023]
Abstract
Isolated oral clefts, including cleft lip with/without cleft palate (CL/P) and cleft palate (CP), have a complex and heterogeneous etiology. Case-parent trios from three populations were used to study genes spanning chromosome 2, where single nucleotide polymorphic (SNP) markers were analyzed individually and as haplotypes. Case-parent trios from three populations (74 from Maryland, 64 from Singapore and 95 from Taiwan) were genotyped for 962 SNPs in 104 genes on chromosome 2, including two well-recognized candidate genes: TGFA and SATB2. Individual SNPs and haplotypes (in sliding windows of 2-5 SNPs) were used to test for linkage and disequilibrium separately in CL/P and CP trios. A novel candidate gene (ZNF533) showed consistent evidence of linkage and disequilibrium in all three populations for both CL/P and CP. SNPs in key regions of ZNF533 showed considerable variability in estimated genotypic odds ratios and their significance, suggesting allelic heterogeneity. Haplotype frequencies for regions of ZNF533 were estimated and used to partition genetic variance into among-and within-population components. Wright's fixation index, a measure of genetic diversity, showed little difference between Singapore and Taiwan compared with Maryland. The tensin-1 gene (TNS1) also showed evidence of linkage and disequilibrium among both CL/P and CP trios in all three populations, albeit at a lower level of significance. Additional genes (VAX2, GLI2, ZHFX1B on 2p; WNT6-WNT10A and COL4A3-COL4A4 on 2q) showed consistent evidence of linkage and disequilibrium only among CL/P trios in all three populations, and TGFA showed significant evidence in two of three populations.
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Affiliation(s)
- T H Beaty
- Johns Hopkins University, Baltimore, MD, USA.
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16
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Watanabe A, Akita S, Tin NTD, Natsume N, Nakano Y, Niikawa N, Uchiyama T, Yoshiura KI. A mutation in RYK is a genetic factor for nonsyndromic cleft lip and palate. Cleft Palate Craniofac J 2006; 43:310-6. [PMID: 16681403 DOI: 10.1597/04-145.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE The RYK, EPHB2, and EPHB3 genes are attractive candidates for cleft lip and/or palate and cleft palate only pathogenesis. Both the Ryk-deficient mouse and Ephb2/Ephb3 (genes for interaction molecules with RYK) double-mutant mouse show cleft palate. SETTING Mutation searches for RYK, EPHB2, and EPHB3 were carried out in a large number of Japanese and Vietnamese patients with cleft lip and/or palate and cleft palate only. Case-control study and transmission disequilibrium tests were performed also, using three single nucleotide polymorphisms within a linkage disequilibrium block in RYK. Seven haplotypes were constructed from the single nucleotide polymorphisms. RESULTS A missense mutation, 1355G>A (Y452C), in RYK was identified in one Vietnamese patient with cleft lip and/or palate. This mutation was not found among 1646 Vietnamese, Japanese, and Caucasians, including 354 cleft lip and/ or palate and cleft palate only patients. Colony formation assay using NIH3T3 cells transfected with mutant cDNA revealed that mutant RYK had significantly reduced protein activity, compared with those with wild-type RYK, implying that the transformation ability of RYK is depleted by this mutation. Although a case-control study and transmission disequilibrium tests on three individual single nucleotide polymorphisms provided no evidence for association with oral clefts, a case-control study on one rare haplotype suggested a positive association in Japanese patients with cleft lip and/or palate and cleft palate only. No mutations in EPHB2 and EPHB3 were found in any patients examined. CONCLUSION The findings suggested that a missense mutation, 1355G>A, and one rare single nucleotide polymorphisms haplotype may play a role in the development of cleft lip and/or palate in the Vietnamese, and cleft lip and/ or palate and cleft palate only in the Japanese.
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Affiliation(s)
- Akira Watanabe
- The Second Department of Oral and Maxillofacial Surgery, Tokyo Dental College, Chiba, Japan
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17
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Abstract
Transforming growth factor alpha (TGFA) is a well-characterized mammalian growth factor. Since the first report of an association between DNA sequence variants at the TGFA genetic locus and nonsyndromic oral clefts, 47 studies have been carried out, producing conflicting results. In this review, the author synthesizes findings from published reports on the association between the TGFA gene and clefting in humans. Bias, lack of statistical power, and genuine population diversity can explain the diverse results. In the aggregate, TGFA is probably a genetic modifier of clefting in humans, which is consistent with the oligogenic model suggested for nonsyndromic oral clefts.
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Affiliation(s)
- Alexandre R Vieira
- Department of Oral Medicine and Pathology, School of Dental Medicine, University of Pittsburgh, 3501 Terrace Street, Pittsburgh, PA 15261, USA.
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18
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Park JW, Cai J, McIntosh I, Jabs EW, Fallin MD, Ingersoll R, Hetmanski JB, Vekemans M, Attie-Bitach T, Lovett M, Scott AF, Beaty TH. High throughput SNP and expression analyses of candidate genes for non-syndromic oral clefts. J Med Genet 2006; 43:598-608. [PMID: 16415175 PMCID: PMC2564555 DOI: 10.1136/jmg.2005.040162] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Recent work suggests that multiple genes and several environmental risk factors influence risk for non-syndromic oral clefts, one of the most common birth defects in humans. Advances in high-throughput genotyping technology now make it possible to test multiple markers in many candidate genes simultaneously. METHODS We present findings from family based association tests of single nucleotide polymorphism (SNP) markers in 64 candidate genes genotyped using the BeadArray approach in 58 case-parent trios from Maryland (USA) to illustrate how multiple markers in multiple genes can be analysed. To assess whether these genes were expressed in human craniofacial structures relevant to palate and lip development, we also analysed data from the Craniofacial and Oral Gene Expression Network (COGENE) consortium, and searched public databases for expression profiles of these genes. RESULTS Thirteen candidate genes showed significant evidence of linkage in the presence of disequilibrium, and ten of these were found to be expressed in relevant embryonic tissues: SP100, MLPH, HDAC4, LEF1, C6orf105, CD44, ALX4, ZNF202, CRHR1, and MAPT. Three other genes showing statistical evidence (ADH1C, SCN3B, and IMP5) were not expressed in the embryonic tissues examined here. CONCLUSIONS This approach demonstrates how statistical evidence on large numbers of SNP markers typed in case-parent trios can be combined with expression data to identify candidate genes for complex disorders. Many of the genes reported here have not been previously studied as candidates for oral clefts and warrant further investigation.
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Affiliation(s)
- J W Park
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
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19
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Abstract
PURPOSE OF REVIEW Orofacial clefts are common birth defects with a known genetic component to their etiology. Most orofacial clefts are nonsyndromic, isolated defects, which can be separated into two different phenotypes: (1) cleft lip with or without cleft palate and (2) cleft palate only. Both are genetically complex traits, which has limited the ability to identify disease loci or genes. The purpose of this review is to summarize recent progress of human genetic studies in identifying causal genes for isolated or nonsyndromic cleft lip with or without cleft palate. RECENT FINDINGS The results of multiple genome scans and a subsequent meta-analysis have significantly advanced our knowledge by revealing novel loci. Furthermore, candidate gene approaches have identified important roles for IRF6 and MSX1. To date, causal mutations with a known functional effect have not yet been described. SUMMARY With the implementation of genome-wide association studies and inexpensive sequencing, future studies will identify disease genes and characterize both gene-environment and gene-gene interactions to provide knowledge for risk counseling and the development of preventive therapies.
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Affiliation(s)
- Andrew C Lidral
- Department of Orthodontics, University of Iowa, Iowa City, Iowa 52242, USA.
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20
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Ounap K, Ilus T, Laidre P, Uibo O, Tammur P, Bartsch O. A new case of 2q duplication supports either a locus for orofacial clefting between markers D2S1897 and D2S2023 or a locus for cleft palate only on chromosome 2q13-q21. Am J Med Genet A 2005; 137A:323-7. [PMID: 16094674 DOI: 10.1002/ajmg.a.30890] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We report on a pure duplication of the proximal chromosome 2q in a 6.5-year-old boy with V-shaped midline cleft palate and bifid uvula, posteriorly located tongue, and micrognathia (Pierre Robin sequence), celiac disease, failure to thrive, and developmental delay. Cytogenetic and FISH analysis indicated a duplication of chromosome 2q13-q22. In general, pure proximal duplication or triplication of 2q is rare. The clinical features and chromosomal breakpoints of the 10 previously reported patients varied, and no common phenotype or proximal duplication/triplication 2q syndrome could be defined to date. However, based on four previous patients with different orofacial clefts and our case, a locus for orofacial clefting may be located at proximal 2q. The duplication/triplication comprised chromosome 2q13 in all five affected individuals including our patient. Our patient and three previous cases (two with cleft palate only (CPO) and one with cleft lip/palate (CL/P)) showed a cytogenetic breakpoint at 2q13, which could support the presence of a critical dominant gene disrupted by a common breakpoint, however, the fifth case with CPO showed different breakpoints, advocating against the disruption of a critical dominant gene and supporting that the overexpression of a gene(s) on chromosome 2q13-q21 may cause cleft palate only (CPO) and Pierre Robin sequence. Hence, our findings support either the presence of one locus for orofacial clefting (CL/P, CPO, and Pierre Robin sequence) between markers D2S1897 (chromosome 2q12.2) and D2S2023 (chromosome 2q14.2), or alternatively the presence of a locus for CPO and Pierre Robin sequence on chromosome 2q13-q21.
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Affiliation(s)
- Katrin Ounap
- Medical Genetics Center, United Laboratories, Tartu University Clinics, Tartu, Estonia.
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21
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Abstract
BACKGROUND Understanding the etiology of birth defects is an important step toward developing improved treatment and preventive strategies. Most birth defects have an underlying genetic basis, ranging from single genes playing dominant or recessive roles in Mendelian disorders to a mixture of contributions from multiple genes and environmental triggers in complex traits. The purpose of this article is to provide an overview of genetic approaches to identifying disease genes for genetically complex birth defects. METHODS A review of the literature describing successes and limitations for identifying disease genes for complex traits was conducted. RESULTS Cleft lip and cleft palate are common congenital anomalies with significant medical, psychological, social, and economic ramifications. The Online Mendelian Inheritance in Man catalog (OMIM; http://www3.ncbi.nlm.nih.gov/Omim) lists more than 400 single-gene causes of clefts of the lip and/or palate. Genetic causes of clefting also include chromosomal rearrangements, genetic susceptibility to teratogenic exposures, and complex genetic contributions of multiple genes. CONCLUSIONS Genetic causes of birth defects can be identified using an increasingly powerful combination of careful sample collection, molecular analytic methods, and statistical evaluations. We will describe a range of approaches to search for genetic factors of birth defects and use our own work with cleft lip and palate as a model.
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Affiliation(s)
- Andrew C Lidral
- Department of Orthodontics and Dows Institute for Dental Research, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA.
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22
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Marazita ML, Murray JC, Lidral AC, Arcos-Burgos M, Cooper ME, Goldstein T, Maher BS, Daack-Hirsch S, Schultz R, Mansilla MA, Field LL, Liu YE, Prescott N, Malcolm S, Winter R, Ray A, Moreno L, Valencia C, Neiswanger K, Wyszynski DF, Bailey-Wilson JE, Albacha-Hejazi H, Beaty TH, McIntosh I, Hetmanski JB, Tunçbilek G, Edwards M, Harkin L, Scott R, Roddick LG. Meta-analysis of 13 genome scans reveals multiple cleft lip/palate genes with novel loci on 9q21 and 2q32-35. Am J Hum Genet 2004; 75:161-73. [PMID: 15185170 PMCID: PMC1216052 DOI: 10.1086/422475] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2004] [Accepted: 05/07/2004] [Indexed: 11/03/2022] Open
Abstract
Isolated or nonsyndromic cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex etiology. A 10-cM genome scan of 388 extended multiplex families with CL/P from seven diverse populations (2,551 genotyped individuals) revealed CL/P genes in six chromosomal regions, including a novel region at 9q21 (heterogeneity LOD score [HLOD]=6.6). In addition, meta-analyses with the addition of results from 186 more families (six populations; 1,033 genotyped individuals) showed genomewide significance for 10 more regions, including another novel region at 2q32-35 (P=.0004). These are the first genomewide significant linkage results ever reported for CL/P, and they represent an unprecedented demonstration of the power of linkage analysis to detect multiple genes simultaneously for a complex disorder.
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Affiliation(s)
- Mary L Marazita
- Center for Craniofacial and Dental Genetics, Division of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
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