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CircFOXO3 rs12196996, a polymorphism at the gene flanking intron, is associated with circFOXO3 levels and the risk of coronary artery disease. Aging (Albany NY) 2020; 12:13076-13089. [PMID: 32614786 PMCID: PMC7377899 DOI: 10.18632/aging.103398] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/25/2020] [Indexed: 01/02/2023]
Abstract
CircFOXO3 plays an important role in the pathogenesis of coronary artery disease (CAD). Single nucleotide polymorphisms (SNPs) at circRNA flanking introns may change its back-splicing and influence circRNA formation. Here, we aimed to investigate the influence of the polymorphisms at the circFOXO3 flanking introns on individual susceptibility to CAD. A total of 1185 individuals were included in the case-control study. In a multivariate logistic regression analysis, we determined that the rs12196996 G variant was significantly associated with increased CAD risk (OR = 1.36, P = 0.014). A similar trend of the association was observed in the recessive model (OR = 2.57, P = 0.003). Stratified analysis revealed a more significant association with CAD risk among younger subjects and non-smokers. Consistent with these results, the haplotype rs12196996G-rs9398171C containing rs12196996G allele was also associated with increased CAD risk (OR = 1.31, P = 0.013). Further investigation revealed that the rs12196996 GG genotype was associated with decreased circFOXO3 expression, but not linear FOXO3 levels. Taken together, our data provide the first evidence that the rs12196996 polymorphism at the circFOXO3 gene flanking intron is associated with CAD risk in the Chinese Han population, which is probably due to influence circFOXO3 levels.
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Zhang JN, Song FQ, Zhou SN, Zheng H, Peng LY, Zhang Q, Zhao WH, Zhang TW, Li WR, Zhou ZB, Lin JX, Chen F. [Analysis of single-nucleotide polymorphism of Sonic hedgehog signaling pathway in non-syndromic cleft lip and/or palate in the Chinese population]. JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2019; 51:556-563. [PMID: 31209431 DOI: 10.19723/j.issn.1671-167x.2019.03.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To study the relationship between Sonic hedgehog (Shh) associated single-nucleotide polymorphism (SNP) and non-syndromic cleft lip and/or palate (NSCL/P), and to explore the risk factors of cleft lip and/or palate. Many studies suggest that the pathogenesis of NSCL/P could be related to genes that control early development, in which the Shh signaling pathway plays an important role. METHODS Peripheral blood was collected from 197 individuals (100 patients with NSCL/P and 97 healthy controls). Haploview software was used for haplotype analysis and Tag SNP were selected, based on the population data of Han Chinese in Beijing of the international human genome haplotype mapping project. A total of 27 SNP were selected for the 4 candidate genes of SHH, PTCH1, SMO and GLI2 in the Shh signaling pathway. The genotypes of 27 SNP were detected and analyzed by Sequenom mass spectrometry. The data were analyzed by chi-squared test and an unconditional Logistic regression model. RESULTS The selected SNP basically covered the potential functional SNP of the target genes, and its minimum allele frequency (MAF) was >0.05: GLI2 73.5%, PTCH1 91.0%, SMO 100.0%, and SHH 75.0%. It was found that the genotype frequency of SNP (rs12674259) located in SMO gene and SNP (rs2066836) located in PTCH1 gene were significantly different between the NSCL/P group and the control group. Linkage disequilibrium was also found on 3 chromosomes (chromosomes 2, 7 and 9) where the 4 candidate genes were located. However, in the analysis of linkage imbalance haplotype, there was no significant difference between the disease group and the control group. CONCLUSION In China, NSCL/P is the most common congenital disease in orofacial region. However, as it is a multigenic disease and could be affected by multiple factors, such as the external environment, the etiology of NSCL/P has not been clearly defined. This study indicates that Shh signaling pathway is involved in the occurrence of NSCL/P, and some special SNP of key genes in this pathway are related to cleft lip and/or palate, which provides a new direction for the etiology research of NSCL/P and may provide help for the early screening and risk prediction of NSCL/P.
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Affiliation(s)
- J N Zhang
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - F Q Song
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - S N Zhou
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - H Zheng
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - L Y Peng
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - Q Zhang
- Department of Center Laboratory, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - W H Zhao
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510000, China
| | - T W Zhang
- Department of Orthodontics, Yantai Stomatological Hospital, Yantai 264000, Shandong, China
| | - W R Li
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - Z B Zhou
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - J X Lin
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - F Chen
- Department of Center Laboratory, Peking University School and Hospital of Stomatology, Beijing 100081, China
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Hua F, Guo Y, Sun Q, Yang L, Gao F. HapMap-based study: CYP2A13 may be a potential key metabolic enzyme gene in the carcinogenesis of lung cancer in non-smokers. Thorac Cancer 2019; 10:601-606. [PMID: 30807688 PMCID: PMC6449263 DOI: 10.1111/1759-7714.12954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/03/2018] [Accepted: 12/03/2018] [Indexed: 12/30/2022] Open
Abstract
Background The aim of this study was to evaluate the association between CYP2A13 polymorphisms and lung cancer susceptibility using the HapMap database. Methods A case‐control analysis of 532 subjects with lung cancer and 614 controls with no personal history of the disease was performed. The tag SNPs rs1645690 and rs8192789 for CYP2A13 were selected, and the genetic polymorphisms were confirmed experimentally through real‐time PCR, cloning, and sequencing assay. Results SNP frequency in this study was consistent with the HapMap Project database of Han‐Chinese and lung cancer risk was associated with CYP2A13 polymorphisms in non‐smokers. CYP2A13 shares a 93.5% identity with CYP2A6 in the amino acid sequence and the homologous sequences may interfere with the study of SNPs of CYP2A13. Conclusions CYP2A13 may be a potential key metabolic enzyme gene in the carcinogenesis of lung cancer in non‐smokers. The common polymorphisms of CYP2A13 may be candidate biomarkers for lung cancer susceptibility in Han‐Chinese.
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Affiliation(s)
- Feng Hua
- Department of Thoracic Surgery, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, China
| | - Yonglu Guo
- Department of Respiratory, Jiuquan City People's Hospital, Jiuquan, China
| | - Qiang Sun
- Department of Infection, Jiuquan City People's Hospital, Jiuquan, China
| | - Leizhou Yang
- Department of Internal Medicine, Jining City Yanzhou District Railway Hospital, Jining, China
| | - Fang Gao
- Department of Thoracic Surgery, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, China
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Feintuch CM, Tare A, Cusumano LR, Benayoun J, Ryu S, Sixpence A, Seydel K, Laufer M, Taylor T, Suh Y, Daily JP. Type I Interferon Receptor Variants in Gene Regulatory Regions are Associated with Susceptibility to Cerebral Malaria in Malawi. Am J Trop Med Hyg 2018; 98:1692-1698. [PMID: 29637882 DOI: 10.4269/ajtmh.17-0887] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Cerebral malaria (CM) remains an important cause of morbidity and mortality. Risk for developing CM partially depends on host genetic factors, including variants encoded in the type I interferon (IFN) receptor 1 (IFNAR1). Type I IFNs bind to IFNAR1 resulting in increased expression of IFN responsive genes, which modulate innate and adaptive immune responses. To comprehensively study IFNAR1 genetic variant associations in Malawians with CM or uncomplicated malaria, we used a tag single nucleotide polymorphism approach, based on the HapMap Yoruba in Ibadan, Nigeria, population database. We identified three novel (rs914142, rs12626750, and rs1041867) and one previously published (Chr21:34696785 [C > G]) IFNAR1 variants to be associated with CM. Some of these variants are in gene regulatory regions. Chr21:34696785 (C > G) is in a region encoding histone modifications and transcription factor-binding sites, which suggests gene regulatory activity. Rs12626750 is predicted to bind embryonic lethal abnormal vision system-like RNA-binding protein 1, a RNA-binding protein which can increase the type I IFN response. Furthermore, we examined these variants in an expression quantitative trait loci database and found that a protective variant, rs914142, is associated with lower expression of IFNAR1, whereas the CM-associated variant rs12626750 was associated with increased IFNAR1 expression, suggesting that activation of the type I IFN pathway may contribute to pathogenesis of CM. Future functional studies of IFNAR1 variants are now needed to clarify the role of this pathway in severe malarial diseases.
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Affiliation(s)
| | - Archana Tare
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Lucas R Cusumano
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York
| | - Jacqueline Benayoun
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York
| | - Seungjin Ryu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Alick Sixpence
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi
| | - Karl Seydel
- Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan.,Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi
| | - Miriam Laufer
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Terrie Taylor
- Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan.,Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi
| | - Yousin Suh
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Johanna P Daily
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York
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Takeichi T, Nanda A, Liu L, Aristodemou S, McMillan JR, Sugiura K, Akiyama M, Al-Ajmi H, Simpson MA, McGrath JA. Founder mutation in dystonin-e underlying autosomal recessive epidermolysis bullosa simplex in Kuwait. Br J Dermatol 2014; 172:527-31. [PMID: 25059916 DOI: 10.1111/bjd.13294] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2014] [Indexed: 01/30/2023]
Abstract
Only two homozygous nonsense mutations in the epidermal isoform of the dystonin gene, DST-e, have been reported previously in autosomal recessive epidermolysis bullosa simplex (EBS); the affected pedigrees were Kuwaiti and Iranian. This subtype of EBS is therefore considered to be a rare clinicopathological entity. In this study, we identified four seemingly unrelated Kuwaiti families in which a total of seven individuals had predominantly acral trauma-induced blistering since infancy. All affected individuals were homozygous for the mutation p.Gln1124* in DST-e, the same mutation that was identified in the originally reported family from Kuwait. Haplotype analysis in the five pedigrees (including the previous case) revealed a shared block of ~60 kb of genomic DNA across the site of the mutation, consistent with a founder effect. Most heterozygotes had no clinical abnormalities although one subject had mild transient skin fragility during childhood, an observation noted in the previously reported Iranian pedigree, suggesting that the condition may also be semidominant in some pedigrees rather than purely autosomal recessive. Our study reveals propagation of a mutant ancestral allele in DST-e throughout Kuwait, indicating that this subtype of EBS may be more common in Kuwait, and perhaps other Middle Eastern countries, than is currently appreciated.
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Affiliation(s)
- T Takeichi
- St John's Institute of Dermatology, King's College London, Guy's Hospital, Great Maze Pond, London, SE1 9RT, U.K; Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Jiang Y, Zhang R, Lv H, Li J, Wang M, Chang Y, Lv W, Sheng X, Zhang J, Liu P, Zheng J, Shi M, Liu G. HGPGD: the human gene population genetic difference database. PLoS One 2013; 8:e64150. [PMID: 23717556 PMCID: PMC3661546 DOI: 10.1371/journal.pone.0064150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 04/11/2013] [Indexed: 11/18/2022] Open
Abstract
Demographic events such as migration, and evolutionary events like mutation and recombination, have contributed to the genetic variations that are found in the human genome. During the evolution and differentiation of human populations, different functional genes and pathways (a group of genes that act together to perform specific biological tasks) would have displayed different degrees of genetic diversity or evolutionary conservatism. To query the genetic differences of functional genes or pathways in populations, we have developed the human gene population genetic difference (HGPGD) database. Currently, 11 common population genetic features, 18,158 single human genes, 220 KEGG (Kyoto Encyclopedia of Genes and Genomes) human pathways and 4,639 Gene Ontology (GO) categories (3,269 in biological process; 862 in molecular function; and 508 in cellular component) are available in the HGPGD database. The 11 population genetic features are related mainly to three aspects: allele frequency, linkage disequilibrium pattern, and transferability of tagSNPs. By entering a list of Gene IDs, KEGG pathway IDs or GO category IDs and selecting a population genetic feature, users can search the genetic differences between pairwise HapMap populations. We hope that, when the researchers carry out gene-based, KEGG pathway-based or GO category-based research, they can take full account of the genetic differences between populations. The HGPGD database (V1.0) is available at http://www.bioapp.org/hgpgd.
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Affiliation(s)
- Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongchao Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Miao Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yiman Chang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenhua Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xin Sheng
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Jingjing Zhang
- Department of Epidemiology and Statistics, School of Public Health, Central South University, Changsha, China
| | - Panpan Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiajia Zheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Miao Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Guiyou Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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7
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Cauchi S, Ezzidi I, El Achhab Y, Mtiraoui N, Chaieb L, Salah D, Nejjari C, Labrune Y, Yengo L, Beury D, Vaxillaire M, Mahjoub T, Chikri M, Froguel P. European genetic variants associated with type 2 diabetes in North African Arabs. DIABETES & METABOLISM 2012; 38:316-23. [PMID: 22463974 DOI: 10.1016/j.diabet.2012.02.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 02/07/2012] [Accepted: 02/08/2012] [Indexed: 12/16/2022]
Abstract
AIMS Recent genome-wide association studies (GWAS) and previous approaches have identified many genetic variants associated with type 2 diabetes (T2D) in populations of European descent, but their contribution in Arab populations from North Africa is unknown. Our study aimed to validate these markers and to assess their combined effects, using large case-control studies of Moroccan and Tunisian individuals. METHODS Overall, 44 polymorphisms, located at 37 validated European loci, were first analyzed in 1055 normoglycaemic controls and 1193 T2D cases from Morocco. Associations and trends were then assessed in 942 normoglycaemic controls and 1446 T2D cases from Tunisia. Finally, their ability to discriminate cases from controls was evaluated. RESULTS Carrying a genetic variant in BCL11A, ADAMTS9, IGF2BP2, WFS1, CDKAL1, TP53INP1, CDKN2A/B, TCF7L2, KCNQ1, HNF1A, FTO, MC4R and GCK increased the risk of T2D when assessing the Moroccan and Tunisian samples together. Each additional risk allele increased the susceptibility for developing the disease by 12% (P = 9.0 × 10(-9)). Genotype information for 13 polymorphisms slightly improved the classification of North Africans with and without T2D, as assessed by clinical parameters, with an increase in the area under the receiver operating characteristic curve from 0.64 to 0.67 (P = 0.004). CONCLUSION In addition to TCF7L2, 12 additional loci were found to be shared between Europeans and North African Arabs. As for Europeans, the reliability of genetic testing based on these markers to determine the risk for T2D is low. More genome-wide studies, including next-generation sequencing, in North African populations are needed to identify the genetic variants responsible for ethnic disparities in T2D susceptibility.
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Affiliation(s)
- S Cauchi
- CNRS UMR 8199, Genomics and Metabolic Diseases, Lille, France
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Identifying highly conserved and highly differentiated gene ontology categories in human populations. PLoS One 2011; 6:e27871. [PMID: 22140477 PMCID: PMC3227580 DOI: 10.1371/journal.pone.0027871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 10/27/2011] [Indexed: 11/19/2022] Open
Abstract
Detecting and interpreting certain system-level characteristics associated with human population genetic differences is a challenge for human geneticists. In this study, we conducted a population genetic study using the HapMap genotype data to identify certain special Gene Ontology (GO) categories associated with high/low genetic difference among 11 Hapmap populations. Initially, the genetic differences in each gene region among these populations were measured using allele frequency, linkage disequilibrium (LD) pattern, and transferability of tagSNPs. The associations between each GO term and these genetic differences were then identified. The results showed that cellular process, catalytic activity, binding, and some of their sub-terms were associated with high levels of genetic difference, and genes involved in these functional categories displayed, on average, high genetic diversity among different populations. By contrast, multicellular organismal processes, molecular transducer activity, and some of their sub-terms were associated with low levels of genetic difference. In particular, the neurological system process under the multicellular organismal process category had low levels of genetic difference; the neurological function also showed high evolutionary conservation between species in some previous studies. These results may provide a new insight into the understanding of human evolutionary history at the system-level.
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Xing J, Watkins WS, Hu Y, Huff CD, Sabo A, Muzny DM, Bamshad MJ, Gibbs RA, Jorde LB, Yu F. Genetic diversity in India and the inference of Eurasian population expansion. Genome Biol 2010; 11:R113. [PMID: 21106085 PMCID: PMC3156952 DOI: 10.1186/gb-2010-11-11-r113] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 10/29/2010] [Accepted: 11/24/2010] [Indexed: 01/11/2023] Open
Abstract
Background Genetic studies of populations from the Indian subcontinent are of great interest because of India's large population size, complex demographic history, and unique social structure. Despite recent large-scale efforts in discovering human genetic variation, India's vast reservoir of genetic diversity remains largely unexplored. Results To analyze an unbiased sample of genetic diversity in India and to investigate human migration history in Eurasia, we resequenced one 100-kb ENCODE region in 92 samples collected from three castes and one tribal group from the state of Andhra Pradesh in south India. Analyses of the four Indian populations, along with eight HapMap populations (692 samples), showed that 30% of all SNPs in the south Indian populations are not seen in HapMap populations. Several Indian populations, such as the Yadava, Mala/Madiga, and Irula, have nucleotide diversity levels as high as those of HapMap African populations. Using unbiased allele-frequency spectra, we investigated the expansion of human populations into Eurasia. The divergence time estimates among the major population groups suggest that Eurasian populations in this study diverged from Africans during the same time frame (approximately 90 to 110 thousand years ago). The divergence among different Eurasian populations occurred more than 40,000 years after their divergence with Africans. Conclusions Our results show that Indian populations harbor large amounts of genetic variation that have not been surveyed adequately by public SNP discovery efforts. Our data also support a delayed expansion hypothesis in which an ancestral Eurasian founding population remained isolated long after the out-of-Africa diaspora, before expanding throughout Eurasia.
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Affiliation(s)
- Jinchuan Xing
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT 84112, USA
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Suazo J, Santos JL, Jara L, Blanco R. Parent-of-origin effects for MSX1 in a Chilean population with nonsyndromic cleft lip/palate. Am J Med Genet A 2010; 152A:2011-6. [DOI: 10.1002/ajmg.a.33528] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Thompson EE, Sun Y, Nicolae D, Ober C. Shades of gray: a comparison of linkage disequilibrium between Hutterites and Europeans. Genet Epidemiol 2010; 34:133-9. [PMID: 19697328 DOI: 10.1002/gepi.20442] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Founder or isolated populations have advantages for genetic studies due to decreased genetic and environmental heterogeneity. However, whereas longer-range linkage disequilibrium (LD) in these populations is expected to facilitate gene localization, extensive LD may actually limit the ability for gene discovery. The North American Hutterite population is one of the best characterized young founder populations and members of this isolate have been the subjects of our studies of complex traits, including fertility, asthma and cardiovascular disease, for >20 years. Here, we directly assess the patterns and extent of global LD using single nucleotide polymorphism genotypes with minor allele frequencies (MAFs) > or =5% from the Affymetrix GeneChip Mapping 500 K array in 60 relatively unrelated Hutterites and 60 unrelated Europeans (HapMap CEU). Although LD among some marker pairs extends further in the Hutterites than in Europeans, the pattern of LD and MAF are surprisingly similar. These results indicate that (1) identifying disease genes should be no more difficult in the Hutterites than in outbred European populations, (2) the same common susceptibility alleles for complex diseases should be present in the Hutterites and outbred European populations, and (3) imputation algorithms based on HapMap CEU should be applicable to the Hutterites.
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Affiliation(s)
- Emma E Thompson
- Department of Human Genetics, The University of Chicago, Illinois, USA.
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Rosenberg NA, Huang L, Jewett EM, Szpiech ZA, Jankovic I, Boehnke M. Genome-wide association studies in diverse populations. Nat Rev Genet 2010; 11:356-66. [PMID: 20395969 PMCID: PMC3079573 DOI: 10.1038/nrg2760] [Citation(s) in RCA: 410] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genome-wide association (GWA) studies have identified a large number of SNPs associated with disease phenotypes. As most GWA studies have been performed in populations of European descent, this Review examines the issues involved in extending the consideration of GWA studies to diverse worldwide populations. Although challenges exist with issues such as imputation, admixture and replication, investigation of a greater diversity of populations could make substantial contributions to the goal of mapping the genetic determinants of complex diseases for the human population as a whole.
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Affiliation(s)
- Noah A Rosenberg
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA.
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Suazo J, Santos JL, Jara L, Blanco R. Association between bone morphogenetic protein 4 gene polymorphisms with nonsyndromic cleft lip with or without cleft palate in a chilean population. DNA Cell Biol 2010; 29:59-64. [PMID: 19839778 DOI: 10.1089/dna.2009.0944] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCLP) is one of the most common birth defects in humans with both genetic and environmental components involved in its expression. Experimental evidences have postulated that bone morphogenetic protein 4 gene (Bmp4) is involved in the etiology of cleft lip with or without cleft palate (CL/P) in mice. In our study we analyzed the association between BMP4 and NSCLP in a sample of 150 unrelated trios ascertained through affected probands. Three BMP4 polymorphisms were analyzed, two intronic (rs762642 and rs2855532) and rs1957860, located 5.7 kb upstream from BMP4. Transmission/disequilibrium tests were performed at the allele and haplotype levels. Our results did not detect preferential transmission for individual single-nucleotide polymorphisms. Significant transmission distortion was observed for haplotypes rs1957860-rs762642 (p = 0.018), especially for C-T (p = 0.015) and T-T (p = 0.018) which include the genomic region where the promoter and an enhancer of BMP4 are located. Thus, despite the positive association detected between these haplotypes and NSCLP they probably do not have a functional effect on BMP4 expression or protein activity but possibly reflect NSCLP susceptibility changes which are in linkage disequilibrium with these polymorphisms. The findings of our study support a role for BMP4 in NSCLP in the admixed Chilean population.
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Affiliation(s)
- José Suazo
- 1 Human Genetics Program, Institute of Biomedical Sciences, School of Medicine, Catholic University of Chile, Santiago, Chile
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14
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Schisler JC, Charles PC, Parker JS, Hilliard EG, Mapara S, Meredith D, Lineberger RE, Wu SS, Alder BD, Stouffer GA, Patterson C. Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry. PLoS One 2009; 4:e8183. [PMID: 20016837 PMCID: PMC2790609 DOI: 10.1371/journal.pone.0008183] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 11/09/2009] [Indexed: 12/02/2022] Open
Abstract
Background Individuals of African descent in the United States suffer disproportionately from diseases with a metabolic etiology (obesity, metabolic syndrome, and diabetes), and from the pathological consequences of these disorders (hypertension and cardiovascular disease). Methodology/Principal Findings Using a combination of genetic/genomic and bioinformatics approaches, we identified a large number of genes that were both differentially expressed between American subjects self-identified to be of either African or European ancestry and that also contained single nucleotide polymorphisms that distinguish distantly related ancestral populations. Several of these genes control the metabolism of simple carbohydrates and are direct targets for the SREBP1, a metabolic transcription factor also differentially expressed between our study populations. Conclusions/Significance These data support the concept of stable patterns of gene transcription unique to a geographic ancestral lineage. Differences in expression of several carbohydrate metabolism genes suggest both genetic and transcriptional mechanisms contribute to these patterns and may play a role in exacerbating the disproportionate levels of obesity, diabetes, and cardiovascular disease observed in Americans with African ancestry.
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Affiliation(s)
- Jonathan C. Schisler
- McAllister Heart Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Peter C. Charles
- McAllister Heart Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Division of Cardiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Joel S. Parker
- Expression Analysis, Durham, North Carolina, United States of America
| | - Eleanor G. Hilliard
- McAllister Heart Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Sabeen Mapara
- McAllister Heart Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Dane Meredith
- Division of Cardiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Robert E. Lineberger
- McAllister Heart Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Samuel S. Wu
- Division of Cardiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Brian D. Alder
- School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - George A. Stouffer
- Division of Cardiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Cam Patterson
- McAllister Heart Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Division of Cardiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
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15
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Ding WJ, Zeng YZ, Li WH, Zhang TE, Liu WW, Teng XK, Ma YX, Yan SL, Wan JMF, Wang MQ. Identification of Linkage Disequilibrium SNPs from a Kidney-Yang Deficiency Syndrome Pedigree. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2009; 37:427-38. [PMID: 19606505 DOI: 10.1142/s0192415x09006953] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In order to probe the genetic traits of Kidney-yang Deficiency Syndrome (KDS), we employed a national standard of KDS diagnosis for the collection of KDS subjects. Each candidate KDS subject from a typical family was diagnosed by 5 independent physicians of Traditional Chinese Medicine (TCM), and repeated for 3 years, all on the first Saturday of December. Fifteen samples of genomic DNA were isolated and genotyped by Affymetrix 100 K arrays of single nucleotide polymorphism (SNP). Then appropriate tools were used for the analysis of linkage disequilibrium (LD) and bioinformatic mining of LD SNPs. The results indicated that our procedure of TCM diagnosis can effectively collect KDS subjects and therefore provide substantial basis for the linkage analysis of KDS. Five SNPs (i.e. rs514207, rs1054020, rs7685923, rs10515889 and rs10516202) were identified as LD SNPs from this KDS family, representing an unprecedented set of LD SNPs derived from TCM syndrome. These SNPs demonstrate midrange linkage disequilibrium within the KDS family. Two genes with established functions were identified within 100 bp of these SNPs. One is Homo sapiens double cortin domain containing 5, which interacts selectively with mono-, di- or tri-saccharide carbohydrate and involves certain signaling cascades. Another one, leucyl-tRNA synthetase, is also a pleiotropic gene response to cysteinyl-tRNA aminoacylation and protein biosynthesis. In conclusion, KDS is involved in special SNP linkage disequilibrium in the intragenic level, and genes within the flanks of these SNPs suggest some essential symptoms of KDS. However, definitive evidence to confirm or exclude these loci and to establish their biological activities will be required.
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Affiliation(s)
- Wei Jun Ding
- Department of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.
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16
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Lins TC, Abreu BS, Pereira RW. TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population. J Biomed Sci 2009; 16:73. [PMID: 19682379 PMCID: PMC2737315 DOI: 10.1186/1423-0127-16-73] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 08/14/2009] [Indexed: 01/30/2023] Open
Abstract
Background The application of a subset of single nucleotide polymorphisms, the tagSNPs, can be useful in capturing untyped SNPs information in a genomic region. TagSNP transferability from the HapMap dataset to admixed populations is of uncertain value due population structure, admixture, drift and recombination effects. In this work an empirical dataset from a Brazilian admixed sample was evaluated against the HapMap population to measure tagSNP transferability and the relative loss of variability prediction. Methods The transferability study was carried out using SNPs dispersed over four genomic regions: the PTPN22, HMGCR, VDR and CETP genes. Variability coverage and the prediction accuracy for tagSNPs in the selected genomic regions of HapMap phase II were computed using a prediction accuracy algorithm. Transferability of tagSNPs and relative loss of prediction were evaluated according to the difference between the Brazilian sample and the pooled and single HapMap population estimates. Results Each population presented different levels of prediction per gene. On average, the Brazilian (BRA) sample displayed a lower power of prediction when compared to HapMap and the pooled sample. There was a relative loss of prediction for BRA when using single HapMap populations, but a pooled HapMap dataset generated minor loss of variability prediction and lower standard deviations, except at the VDR locus at which loss was minor using CEU tagSNPs. Conclusion Studies that involve tagSNP selection for an admixed population should not be generally correlated with any specific HapMap population and can be better represented with a pooled dataset in most cases.
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Affiliation(s)
- Tulio C Lins
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil.
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17
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Frazer KA, Murray SS, Schork NJ, Topol EJ. Human genetic variation and its contribution to complex traits. Nat Rev Genet 2009; 10:241-51. [PMID: 19293820 DOI: 10.1038/nrg2554] [Citation(s) in RCA: 675] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The last few years have seen extensive efforts to catalogue human genetic variation and correlate it with phenotypic differences. Most common SNPs have now been assessed in genome-wide studies for statistical associations with many complex traits, including many important common diseases. Although these studies have provided new biological insights, only a limited amount of the heritable component of any complex trait has been identified and it remains a challenge to elucidate the functional link between associated variants and phenotypic traits. Technological advances, such as the ability to detect rare and structural variants, and a clear understanding of the challenges in linking different types of variation with phenotype, will be essential for future progress.
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Affiliation(s)
- Kelly A Frazer
- Scripps Genomic Medicine, Scripps Translational Science Institute and The Scripps Research Institute, La Jolla, California 92037, USA.
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18
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Huang L, Li Y, Singleton AB, Hardy JA, Abecasis G, Rosenberg NA, Scheet P. Genotype-imputation accuracy across worldwide human populations. Am J Hum Genet 2009; 84:235-50. [PMID: 19215730 DOI: 10.1016/j.ajhg.2009.01.013] [Citation(s) in RCA: 182] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Revised: 01/09/2009] [Accepted: 01/16/2009] [Indexed: 11/19/2022] Open
Abstract
A current approach to mapping complex-disease-susceptibility loci in genome-wide association (GWA) studies involves leveraging the information in a reference database of dense genotype data. By modeling the patterns of linkage disequilibrium in a reference panel, genotypes not directly measured in the study samples can be imputed and tested for disease association. This imputation strategy has been successful for GWA studies in populations well represented by existing reference panels. We used genotypes at 513,008 autosomal single-nucleotide polymorphism (SNP) loci in 443 unrelated individuals from 29 worldwide populations to evaluate the "portability" of the HapMap reference panels for imputation in studies of diverse populations. When a single HapMap panel was leveraged for imputation of randomly masked genotypes, European populations had the highest imputation accuracy, followed by populations from East Asia, Central and South Asia, the Americas, Oceania, the Middle East, and Africa. For each population, we identified "optimal" mixtures of reference panels that maximized imputation accuracy, and we found that in most populations, mixtures including individuals from at least two HapMap panels produced the highest imputation accuracy. From a separate survey of additional SNPs typed in the same samples, we evaluated imputation accuracy in the scenario in which all genotypes at a given SNP position were unobserved and were imputed on the basis of data from a commercial "SNP chip," again finding that most populations benefited from the use of combinations of two or more HapMap reference panels. Our results can serve as a guide for selecting appropriate reference panels for imputation-based GWA analysis in diverse populations.
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Affiliation(s)
- Lucy Huang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA.
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19
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Global similarity with local differences in linkage disequilibrium between the Dutch and HapMap-CEU populations. Eur J Hum Genet 2009; 17:802-10. [PMID: 19127282 DOI: 10.1038/ejhg.2008.248] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The HapMap project has facilitated the selection of tagging single nucleotide polymorphisms (tagSNPs) for genome-wide association studies (GWAS) under the assumption that linkage disequilibrium (LD) in the HapMap populations is similar to the populations under investigation. Earlier reports support this assumption, although in most of these studies only a few loci were evaluated. We compared pair-wise LD and LD block structure across autosomes between the Dutch population and the CEU-HapMap reference panel. The impact of sampling distribution on the estimation of LD blocks was studied by bootstrapping. A high Pearson correlation (genome-wide; 0.93) between pair-wise r(2) for the Dutch and the CEU populations was found, indicating that tagSNPs from the CEU-HapMap panel capture common variation in the Dutch population. However, some genomic regions exhibited, significantly lower correlation than the genome-wide estimate. This might decrease the validity of HapMap tagSNPs in these regions and the power of GWAS. The LD block structure differed considerably between the Dutch and CEU-HapMap populations. This was not explained by demographic differences between the CEU and Dutch samples, as testing for population stratification was not significant. We also found that sampling variation had a large effect on the estimation of LD blocks, as shown by the bootstrapping analysis. Thus, in small samples, most of the observed differences in LD blocks between populations are most likely the result of sampling variation. This poor concordance in LD block structure suggests that large samples are required for robust estimations of local LD block structure in populations.
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