1
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Hoehe MR, Herwig R. Analysis of 1276 Haplotype-Resolved Genomes Allows Characterization of Cis- and Trans-Abundant Genes. Methods Mol Biol 2023; 2590:237-272. [PMID: 36335503 DOI: 10.1007/978-1-0716-2819-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Many methods for haplotyping have materialized, but their application on a significant scale has been rare to date. Here we summarize analyses that were carried out in 1092 genomes from the 1000 Genomes Consortium and validated in an unprecedented number of 184 PGP genomes that have been experimentally haplotype-resolved by application of the Long-Fragment Read (LFR) technology. These analyses provided first insights into the diplotypic nature of human genomes and its potential functional implications. Thus, protein-changing variants were not randomly distributed between the two homologues of 18,121 autosomal protein-coding genes but occurred significantly more frequently in cis than in trans configurations in virtually each of the 1276 phased genomes. This resulted in global cis/trans ratios of ~60:40, establishing "cis abundance" as a universal characteristic of diploid human genomes. This phenomenon was based on two different classes of genes, a larger one exhibiting cis configurations of protein-changing variants in excess, so-called "cis-abundant" genes, and a smaller one of "trans-abundant" genes. These two gene classes, which together constitute a common diplotypic exome, were further functionally distinguished by means of gene ontology (GO) and pathway enrichment analysis. Moreover, they were distinguishable in terms of their effects on the human interactome, where they constitute distinct cis and trans modules, as shown with network propagation on a large integrated protein-protein interaction network. These analyses, recently performed with updated database and analysis tools, further consolidated the characterization of cis- and trans-abundant genes while expanding previous results. In this chapter, we present the key results along with the materials and methods to motivate readers to investigate these findings independently and gain further insights into the diplotypic nature of genes and genomes.
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Affiliation(s)
- Margret R Hoehe
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
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2
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Jiang K, Du F, Lv L, Zhuo H, Xu T, Peng L, Chen Y, Li L, Zhang J. Genetic Fine Mapping and Genomic Annotation Defines Causal Mechanisms at A Novel Colorectal Cancer Susceptibility Locus in Han Chinese. J Cancer 2020; 11:6841-6849. [PMID: 33123275 PMCID: PMC7592009 DOI: 10.7150/jca.47189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/14/2020] [Indexed: 12/30/2022] Open
Abstract
Genome-wide association studies of colorectal cancer (CRC) have identified two risk SNPs. The characterization of these risk regions in diverse racial groups with different linkage disequilibrium structure would aid in localizing the causal variants. Herein, fine mapping of the established CRC loci was carried out in 1,508 cases and 1,482 controls obtained from the Han Chinese population. One distinct association signal was identified at these loci, where fine mapping implicated rs1010208 as a functional locus. Next, the candidate target genes of functional SNP rs1010208 were analyzed using data from TCGA databases by expression quantitative trait loci analysis method; the data from Peking University People's Hospital were utilized for verification. The dual-luciferase reporter system analysis confirmed that rs1010208 is a regulatory region that can be mutated to decrease the expression of HINT1, resulting in proliferation and invasiveness of CRC.
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Affiliation(s)
- Kewei Jiang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China
| | - Fengying Du
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Liang Lv
- Department of General Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hongqing Zhuo
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Tao Xu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Lipan Peng
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yuezhi Chen
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Leping Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Jizhun Zhang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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3
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Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin CS, Fungtammasan A, Clarke WE, Cleary A, Ebler J, Eizenga J, Sibbesen JA, Markello CJ, Garrison E, Garg S, Hickey G, Lazo GR, Lin MF, Mahmoud M, Marschall T, Minkin I, Monlong J, Musunuri RL, Sagayaradj S, Novak AM, Rautiainen M, Regier A, Sedlazeck FJ, Siren J, Souilmi Y, Wagner J, Wrightsman T, Yokoyama TT, Zeng Q, Zook JM, Paten B, Busby B. A strategy for building and using a human reference pangenome. F1000Res 2019; 8:1751. [PMID: 34386196 PMCID: PMC8350888 DOI: 10.12688/f1000research.19630.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/23/2021] [Indexed: 01/27/2024] Open
Abstract
In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.
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Affiliation(s)
- Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | | | - Valerie Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Peter A. Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Evan Biederstedt
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02215, USA
| | - Lon Blauvelt
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Peter Bradbury
- Robert W. Holley Center, USDA-ARS, Ithaca, NY, 14853, USA
| | - Xian Chang
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | | | | | - Alan Cleary
- National Center for Genome Resources 87505, Santa Fe, NM, 87505, USA
| | - Jana Ebler
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Jordan Eizenga
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jonas A. Sibbesen
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Charles J. Markello
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Erik Garrison
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Shilpa Garg
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Glenn Hickey
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Gerard R. Lazo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710-1105, USA
| | | | - Medhat Mahmoud
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, TX, 77030, USA
| | | | - Ilia Minkin
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jean Monlong
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | - Sagayamary Sagayaradj
- Genome Center, University of California, Davis, Davis, CA, USA
- BASF, West Sacramento, CA, USA
| | - Adam M. Novak
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | - Allison Regier
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, 63108, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, TX, 77030, USA
| | - Jouni Siren
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Travis Wrightsman
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Toshiyuki T. Yokoyama
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Qiandong Zeng
- Laboratory Corporation of America Holdings, Westborough, MA, 01581, USA
| | - Justin M. Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Benedict Paten
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Ben Busby
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
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4
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Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin CS, Fungtammasan A, Clarke WE, Cleary A, Ebler J, Eizenga J, Sibbesen JA, Markello CJ, Garrison E, Garg S, Hickey G, Lazo GR, Lin MF, Mahmoud M, Marschall T, Minkin I, Monlong J, Musunuri RL, Sagayaradj S, Novak AM, Rautiainen M, Regier A, Sedlazeck FJ, Siren J, Souilmi Y, Wagner J, Wrightsman T, Yokoyama TT, Zeng Q, Zook JM, Paten B, Busby B. A strategy for building and using a human reference pangenome. F1000Res 2019; 8:1751. [PMID: 34386196 PMCID: PMC8350888 DOI: 10.12688/f1000research.19630.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/23/2021] [Indexed: 11/20/2022] Open
Abstract
In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.
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Affiliation(s)
- Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | | | - Valerie Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Evan Biederstedt
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02215, USA
| | - Lon Blauvelt
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Peter Bradbury
- Robert W. Holley Center, USDA-ARS, Ithaca, NY, 14853, USA
| | - Xian Chang
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | | | | | - Alan Cleary
- National Center for Genome Resources 87505, Santa Fe, NM, 87505, USA
| | - Jana Ebler
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Jordan Eizenga
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jonas A Sibbesen
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Charles J Markello
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Erik Garrison
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Shilpa Garg
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Glenn Hickey
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Gerard R Lazo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710-1105, USA
| | | | - Medhat Mahmoud
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, TX, 77030, USA
| | | | - Ilia Minkin
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jean Monlong
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | - Sagayamary Sagayaradj
- Genome Center, University of California, Davis, Davis, CA, USA.,BASF, West Sacramento, CA, USA
| | - Adam M Novak
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | - Allison Regier
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, 63108, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, TX, 77030, USA
| | - Jouni Siren
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Travis Wrightsman
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Toshiyuki T Yokoyama
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Qiandong Zeng
- Laboratory Corporation of America Holdings, Westborough, MA, 01581, USA
| | - Justin M Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Benedict Paten
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Ben Busby
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
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5
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Hoehe MR, Herwig R, Mao Q, Peters BA, Drmanac R, Church GM, Huebsch T. Significant abundance of cis configurations of coding variants in diploid human genomes. Nucleic Acids Res 2019; 47:2981-2995. [PMID: 30698752 PMCID: PMC6451136 DOI: 10.1093/nar/gkz031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/05/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022] Open
Abstract
To fully understand human genetic variation and its functional consequences, the specific distribution of variants between the two chromosomal homologues of genes must be known. The 'phase' of variants can significantly impact gene function and phenotype. To assess patterns of phase at large scale, we have analyzed 18 121 autosomal genes in 1092 statistically phased genomes from the 1000 Genomes Project and 184 experimentally phased genomes from the Personal Genome Project. Here we show that genes with cis-configurations of coding variants are more frequent than genes with trans-configurations in a genome, with global cis/trans ratios of ∼60:40. Significant cis-abundance was observed in virtually all genomes in all populations. Moreover, we identified a large group of genes exhibiting cis-configurations of protein-changing variants in excess, so-called 'cis-abundant genes', and a smaller group of 'trans-abundant genes'. These two gene categories were functionally distinguishable, and exhibited strikingly different distributional patterns of protein-changing variants. Underlying these phenomena was a shared set of phase-sensitive genes of importance for adaptation and evolution. This work establishes common patterns of phase as key characteristics of diploid human exomes and provides evidence for their functional significance, highlighting the importance of phase for the interpretation of protein-coding genetic variation and gene function.
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Affiliation(s)
- Margret R Hoehe
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Qing Mao
- Complete Genomics, Inc., San Jose, CA 95112, USA
| | - Brock A Peters
- Complete Genomics, Inc., San Jose, CA 95112, USA.,BGI-Shenzhen, Shenzhen 518083, China
| | - Radoje Drmanac
- Complete Genomics, Inc., San Jose, CA 95112, USA.,BGI-Shenzhen, Shenzhen 518083, China
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Huebsch
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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6
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Association between the SNPs in trace element-related metabolic genes and the risk of gastric cancer: a case–control study in Xianyou of China. J Genet 2019. [DOI: 10.1007/s12041-019-1110-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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7
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Yan B, Liu X, Wu J, Zhao S, Yuan W, Wang B, Wureli H, Tu C, Chen C, wang Y. Genetic Diversity of Echinococcus granulosus Genotype G1 in Xinjiang, Northwest of China. THE KOREAN JOURNAL OF PARASITOLOGY 2018; 56:391-396. [PMID: 30196674 PMCID: PMC6137305 DOI: 10.3347/kjp.2018.56.4.391] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/18/2018] [Accepted: 08/18/2018] [Indexed: 11/25/2022]
Abstract
Cystic echinococcosis (CE) caused by E. granulosus is a serious helminthic zoonosis in humans, livestock and wildlife. Xinjiang is one of high endemic province for CE in China. A total of 55 sheep and cattle livers containing echinococcal cysts were collected from slaughterhouses in Changji and Yining City, northern region of Xinjiang. PCR was employed for cloning 2 gene fragments, 12S rRNA and CO1 for analysis of phylogenetic diversity of E. granulosus. The results showed that all the samples collected were identified as G1 genotype of E. granulosus. Interestingly, YL5 and CJ75 strains were the older branches compared to those strains from France, Argentina, Australia. CO1 gene fragment showed 20 new genotype haploids and 5 new genotype haplogroups (H1-H5) by the analysis of Network 5.0 software, and the YLY17 strain was identified as the most ancestral haplotype. The major haplotypes, such as CJ75 and YL5 strains, showed identical to the isolates from Middle East. The international and domestic trade of livestock might contribute to the dispersal of different haplotypes for E. granulosus evolution.
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Affiliation(s)
- Bin Yan
- School of Medicine, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region 832002, People’s Republic of China
| | - Xiafei Liu
- School of Medicine, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region 832002, People’s Republic of China
| | - Junyuan Wu
- College of Animal Science, Tarim University, Alar City, Xinjiang 843300, PR China
| | - Shanshan Zhao
- School of Medicine, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region 832002, People’s Republic of China
| | - Wumei Yuan
- School of Medicine, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region 832002, People’s Republic of China
| | - Baoju Wang
- Department of Infectious Diseases, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hazi Wureli
- School of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region 832002, People’s Republic of China
| | - Changchun Tu
- Institue of Veterinary Sciences, Academy of Military Medical Sciences, Jilin, Changchun, 1300062, People’s Republic of China
| | - Chuangfu Chen
- School of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region 832002, People’s Republic of China
| | - Yuanzhi wang
- School of Medicine, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region 832002, People’s Republic of China
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8
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Rhee JK, Li H, Joung JG, Hwang KB, Zhang BT, Shin SY. Survey of computational haplotype determination methods for single individual. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0342-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Tao R, Chen Z, Wu P, Liu C, Peng Y, Zhao W, Hu C, Feng J. The possible role of EZH2 and DNMT1 polymorphisms in sporadic triple-negative breast carcinoma in southern Chinese females. Tumour Biol 2015; 36:9849-55. [PMID: 26162541 DOI: 10.1007/s13277-015-3754-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/02/2015] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancer (TNBC) has a more invasive and metastatic potential than the other types of breast cancer and hence is associated with poor prognosis. Zeste homolog 2 (EZH2) and DNA methyltransferase 1 (DNMT1) could lead to tumorigenesis by separately methylating histone H3K27 and CpG islands in tumor suppressor genes. In order to investigate the association between oncogenesis and the distribution of single nucleotide polymorphisms (SNPs) of EZH2, DNMT1, a case-control study on SNPs in TNBC cases from south China was conducted. A total of 13 SNPs were genotyped from 234 cases of TNBC tissues, and 300 normal blood samples from age-matched control group were analyzed using Snapshot technology. The expressions of EZH2 and DNMT1 were examined in the 234 cases of TNBC tissues by immunohistochemistry (IHC). The T allele of rs2288349 and the C allele of rs16999593 increase the risk of TNBC, with relative risk coefficients of 1.76 and 1.69, respectively (p < 0.001). The TC genotypes of rs2288349 and rs16999593 were higher in TNBC compared with the control group; the cancer risk increased to 5.27 and 4.13, respectively (p < 0.001). There were no significant differences between the frequencies of the other 10 SNPs and the risk of TNBC (p > 0.05). Five common haplotypes (>8 % frequency) were identified with a cumulative frequency of 96 % in the controls, while the haplotypes of AAGTAG, GGGTGA, and GACCAG were significantly increased in the control group compared to that in patients (p < 0.05). The G allele of rs10274701 significantly increased the EZH2 expression level in TNBC (p = 0.01). This is the first study to demonstrate a significant association between TNBC risk and the polymorphisms of EZH2 and DNMT1, and our researches indicate that the SNPs of EZH2 and DNMT1 are risk predictors for TNBC.
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Affiliation(s)
- Ran Tao
- Laboratory Medicine, Southern Medical University Affiliated Fengxian Hospital, Shanghai, 201400, China
- Guangzhou Kingmed Centre for Clinical Laboratory, Guangzhou, 510330, China
| | - Zekun Chen
- Third Clinical College, Southern Medical University, Guangzhou, 510515, China
| | - Pingping Wu
- Laboratory Medicine, Southern Medical University Affiliated Fengxian Hospital, Shanghai, 201400, China
| | - Cuicui Liu
- Laboratory Medicine, Southern Medical University Affiliated Fengxian Hospital, Shanghai, 201400, China
| | - You Peng
- Laboratory Medicine, Southern Medical University Affiliated Fengxian Hospital, Shanghai, 201400, China
| | - Weiwei Zhao
- Laboratory Medicine, Southern Medical University Affiliated Fengxian Hospital, Shanghai, 201400, China
| | - Chaohui Hu
- Guangzhou Kingmed Centre for Clinical Laboratory, Guangzhou, 510330, China
| | - Jing Feng
- Laboratory Medicine, Southern Medical University Affiliated Fengxian Hospital, Shanghai, 201400, China.
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10
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Stevens CW. Bioinformatics and evolution of vertebrate nociceptin and opioid receptors. VITAMINS AND HORMONES 2015; 97:57-94. [PMID: 25677768 DOI: 10.1016/bs.vh.2014.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
G protein-coupled receptors (GPCRs) are ancestrally related membrane proteins on cells that mediate the pharmacological effect of most drugs and neurotransmitters. GPCRs are the largest group of membrane receptor proteins encoded in the human genome. One of the most famous types of GPCRs is the opioid receptors. Opioid family receptors consist of four closely related proteins expressed in all vertebrate brains and spinal cords examined to date. The three classical types of opioid receptors shown unequivocally to mediate analgesia in animal models and in humans are the mu- (MOR), delta- (DOR), and kappa-(KOR) opioid receptor proteins. The fourth and most recent member of the opioid receptor family discovered is the nociceptin or orphanin FQ receptor (ORL). The role of ORL and its ligands in producing analgesia is not as clear, with both analgesic and hyperalgesic effects reported. All four opioid family receptor genes were cloned from expressed mRNA in a number of vertebrate species, and there are enough sequences presently available to carry out bioinformatic analysis. This chapter presents the results of a comparative analysis of vertebrate opioid receptors using pharmacological studies, bioinformatics, and the latest data from human whole-genome studies. Results confirm our initial hypotheses that the four opioid receptor genes most likely arose by whole-genome duplication, that there is an evolutionary vector of opioid receptor type divergence in sequence and function, and that the hMOR gene shows evidence of positive selection or adaptive evolution in Homo sapiens.
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Affiliation(s)
- Craig W Stevens
- Department of Pharmacology and Physiology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma, USA.
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11
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Hoehe MR, Church GM, Lehrach H, Kroslak T, Palczewski S, Nowick K, Schulz S, Suk EK, Huebsch T. Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes. Nat Commun 2014; 5:5569. [PMID: 25424553 PMCID: PMC4263165 DOI: 10.1038/ncomms6569] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 10/14/2014] [Indexed: 12/21/2022] Open
Abstract
To fully understand human biology and link genotype to phenotype, the phase of DNA variants must be known. Here we present a comprehensive analysis of haplotype-resolved genomes to assess the nature and variation of haplotypes and their pairs, diplotypes, in European population samples. We use a set of 14 haplotype-resolved genomes generated by fosmid clone-based sequencing, complemented and expanded by up to 372 statistically resolved genomes from the 1000 Genomes Project. We find immense diversity of both haploid and diploid gene forms, up to 4.1 and 3.9 million corresponding to 249 and 235 per gene on average. Less than 15% of autosomal genes have a predominant form. We describe a 'common diplotypic proteome', a set of 4,269 genes encoding two different proteins in over 30% of genomes. We show moreover an abundance of cis configurations of mutations in the 386 genomes with an average cis/trans ratio of 60:40, and distinguishable classes of cis- versus trans-abundant genes. This work identifies key features characterizing the diplotypic nature of human genomes and provides a conceptual and analytical framework, rich resources and novel hypotheses on the functional importance of diploidy.
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Affiliation(s)
- Margret R. Hoehe
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin D-14195, Germany
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin D-14195, Germany
| | - Thomas Kroslak
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin D-14195, Germany
| | - Stefanie Palczewski
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin D-14195, Germany
| | - Katja Nowick
- Department of Computer Science, University of Leipzig, Leipzig D-04107, Germany
| | - Sabrina Schulz
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin D-14195, Germany
| | - Eun-Kyung Suk
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin D-14195, Germany
- These authors contributed equally to this work
| | - Thomas Huebsch
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin D-14195, Germany
- These authors contributed equally to this work
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12
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Abstract
Genomic information reported as haplotypes rather than genotypes will be increasingly important for personalized medicine. Current technologies generate diploid sequence data that is rarely resolved into its constituent haplotypes. Furthermore, paradigms for thinking about genomic information are based on interpreting genotypes rather than haplotypes. Nevertheless, haplotypes have historically been useful in contexts ranging from population genetics to disease-gene mapping efforts. The main approaches for phasing genomic sequence data are molecular haplotyping, genetic haplotyping, and population-based inference. Long-read sequencing technologies are enabling longer molecular haplotypes, and decreases in the cost of whole-genome sequencing are enabling the sequencing of whole-chromosome genetic haplotypes. Hybrid approaches combining high-throughput short-read assembly with strategic approaches that enable physical or virtual binning of reads into haplotypes are enabling multi-gene haplotypes to be generated from single individuals. These techniques can be further combined with genetic and population approaches. Here, we review advances in whole-genome haplotyping approaches and discuss the importance of haplotypes for genomic medicine. Clinical applications include diagnosis by recognition of compound heterozygosity and by phasing regulatory variation to coding variation. Haplotypes, which are more specific than less complex variants such as single nucleotide variants, also have applications in prognostics and diagnostics, in the analysis of tumors, and in typing tissue for transplantation. Future advances will include technological innovations, the application of standard metrics for evaluating haplotype quality, and the development of databases that link haplotypes to disease.
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Affiliation(s)
- Gustavo Glusman
- Institute for Systems Biology, Terry Avenue North, Seattle, WA 98109 USA
| | - Hannah C Cox
- Institute for Systems Biology, Terry Avenue North, Seattle, WA 98109 USA
| | - Jared C Roach
- Institute for Systems Biology, Terry Avenue North, Seattle, WA 98109 USA
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Doleschall M, Szabó JA, Pázmándi J, Szilágyi Á, Koncz K, Farkas H, Tóth M, Igaz P, Gláz E, Prohászka Z, Korbonits M, Rácz K, Füst G, Patócs A. Common genetic variants of the human steroid 21-hydroxylase gene (CYP21A2) are related to differences in circulating hormone levels. PLoS One 2014; 9:e107244. [PMID: 25210767 PMCID: PMC4161435 DOI: 10.1371/journal.pone.0107244] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/08/2014] [Indexed: 12/01/2022] Open
Abstract
Purpose Systematic evaluation of the potential relationship between the common genetic variants of CYP21A2 and hormone levels. Methods The relationships of CYP21A2 intron 2 polymorphisms and haplotypes with diverse baseline and stimulated blood hormone levels were studied in 106 subjects with non-functioning adrenal incidentaloma (NFAI). The rationale for using NFAI subjects is dual: i) their baseline hormone profiles do not differ from those of healthy subjects and ii) hormone levels after stimulation tests are available. Results The carriers (N = 27) of a well-defined CYP21A2 haplotype cluster (c5) had significantly elevated levels of cortisol (p = 0.0110), and 17-hydroxyprogesterone (p = 0.0001) after ACTH stimulation, and 11-deoxycortisol after metyrapone administration (p = 0.0017), but the hormone values were in normal ranges. In addition, the carriers (N = 33) of the C allele of the rs6462 polymorphism had a higher baseline aldosterone level (p = 0.0006). The prevalence of these genetic variants of CYP21A2 did not differ between NFAI and healthy subjects. Conclusions The common CYP21A2 variants presumably exert the same effect on hormone levels in the healthy and disease-affected populations. Therefore, they may contribute to complex diseases such as some cardiovascular diseases, and may influence the genotype-phenotype correlation in patients with congenital adrenal hyperplasia (CAH) including the individual need for hormone substitution.
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Affiliation(s)
- Márton Doleschall
- 3rd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- * E-mail:
| | - Julianna Anna Szabó
- 3rd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Júlia Pázmándi
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Ágnes Szilágyi
- 3rd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Klára Koncz
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
- “Lendület” Hereditary Endocrine Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Henriette Farkas
- 3rd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Miklós Tóth
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Péter Igaz
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Edit Gláz
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Zoltán Prohászka
- 3rd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Márta Korbonits
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Károly Rácz
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - George Füst
- 3rd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Attila Patócs
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- “Lendület” Hereditary Endocrine Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
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14
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Yang J, Lin S, Zhou J, Wu B, Dong W, Arima H, Liu H, Zhang J, Li J, Liu M. Genetic variations of MMP9 gene and intracerebral hemorrhage outcome: a cohort study in Chinese Han population. J Neurol Sci 2014; 343:56-9. [PMID: 24881865 DOI: 10.1016/j.jns.2014.05.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 04/20/2014] [Accepted: 05/12/2014] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To investigate the association between genetic variations of matrix metalloproteinase 9 (MMP9) gene and intracerebral hemorrhage (ICH) outcome in Chinese Han population. METHODS The clinical data and peripheral blood samples from the patients with ICH were collected. The patients were followed up for 3 months, and poor outcome was defined as death or dependency (modified Rankin scale score of 3-6). MassARRAY Analyser was used to genotype the tagger single nucleotide polymorphisms (SNPs) of MMP9 gene. Construction of haplotypes and genetic comparisons were performed by employing PLINK 1.0.7 software. RESULTS 181 patients with ICH were recruited between September 2009 and October 2010. Information on genetic variations and follow-up assessments were available for 169 (93.4%) patients. Independent patients at 90 days were younger than those who died or dependent (57.82 ± 13.47 vs. 66.99 ± 11.49 years, p<0.01). In addition, independent patients had lower National Institutes of Health Stroke Scale (NIHSS) score (4[1-6] vs. 13[9-19], p<0.01). There were no significant associations (all p>0.05) between MMP9 genetic variations (alleles, genotypes and haplotypes) and ICH outcome after adjustment for conventional risk factors. CONCLUSIONS The genetic variations of MMP9 gene were not significantly associated with ICH outcome at 90 days in Chinese Han population.
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Affiliation(s)
- Jie Yang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu 610041, China; Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Sen Lin
- Department of Neurology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Junshan Zhou
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Bo Wu
- Department of Neurology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wei Dong
- Department of Neurology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hisatomi Arima
- The George Institute for Global Health, Royal Prince Alfred Hospital, University of Sydney, Sydney, NSW 2050, Australia
| | - Hua Liu
- Department of Neurology, The Third People's Hospital of Mianyang, Luzhou Medical College, Mianyang 621000, China
| | - Jing Zhang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jie Li
- Department of Neurology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ming Liu
- Department of Neurology, West China Hospital, Sichuan University, Chengdu 610041, China.
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15
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Bánlaki Z, Szabó JA, Szilágyi Á, Patócs A, Prohászka Z, Füst G, Doleschall M. Intraspecific evolution of human RCCX copy number variation traced by haplotypes of the CYP21A2 gene. Genome Biol Evol 2013; 5:98-112. [PMID: 23241443 PMCID: PMC3595039 DOI: 10.1093/gbe/evs121] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The RCCX region is a complex, multiallelic, tandem copy number variation (CNV). Two complete genes, complement component 4 (C4) and steroid 21-hydroxylase (CYP21A2, formerly CYP21B), reside in its variable region. RCCX is prone to nonallelic homologous recombination (NAHR) such as unequal crossover, generating duplications and deletions of RCCX modules, and gene conversion. A series of allele-specific long-range polymerase chain reaction coupled to the whole-gene sequencing of CYP21A2 was developed for molecular haplotyping. By means of the developed techniques, 35 different kinds of CYP21A2 haplotype variant were experimentally determined from 112 unrelated European subjects. The number of the resolved CYP21A2 haplotype variants was increased to 61 by bioinformatic haplotype reconstruction. The CYP21A2 haplotype variants could be assigned to the haplotypic RCCX CNV structures (the copy number of RCCX modules) in most cases. The genealogy network constructed from the CYP21A2 haplotype variants delineated the origin of RCCX structures. The different RCCX structures were located in tight groups. The minority of groups with identical RCCX structure occurred once in the network, implying monophyletic origin, but the majority of groups occurred several times and in different locations, indicating polyphyletic origin. The monophyletic groups were often created by single unequal crossover, whereas recurrent unequal crossover events generated some of the polyphyletic groups. As a result of recurrent NAHR events, more CYP21A2 haplotype variants with different allele patterns belonged to the same RCCX structure. The intraspecific evolution of RCCX CNV described here has provided a reasonable expectation for that of complex, multiallelic, tandem CNVs in humans.
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Affiliation(s)
- Zsófia Bánlaki
- 3rd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
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16
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Tyson J, Armour JAL. Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR. BMC Genomics 2012; 13:693. [PMID: 23231411 PMCID: PMC3543183 DOI: 10.1186/1471-2164-13-693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 12/07/2012] [Indexed: 12/26/2022] Open
Abstract
Background Genotyping and massively-parallel sequencing projects result in a vast amount of diploid data that is only rarely resolved into its constituent haplotypes. It is nevertheless this phased information that is transmitted from one generation to the next and is most directly associated with biological function and the genetic causes of biological effects. Despite progress made in genome-wide sequencing and phasing algorithms and methods, problems assembling (and reconstructing linear haplotypes in) regions of repetitive DNA and structural variation remain. These dynamic and structurally complex regions are often poorly understood from a sequence point of view. Regions such as these that are highly similar in their sequence tend to be collapsed onto the genome assembly. This is turn means downstream determination of the true sequence haplotype in these regions poses a particular challenge. For structurally complex regions, a more focussed approach to assembling haplotypes may be required. Results In order to investigate reconstruction of spatial information at structurally complex regions, we have used an emulsion haplotype fusion PCR approach to reproducibly link sequences of up to 1kb in length to allow phasing of multiple variants from neighbouring loci, using allele-specific PCR and sequencing to detect the phase. By using emulsion systems linking flanking regions to amplicons within the CNV, this led to the reconstruction of a 59kb haplotype across the DEFA1A3 CNV in HapMap individuals. Conclusion This study has demonstrated a novel use for emulsion haplotype fusion PCR in addressing the issue of reconstructing structural haplotypes at multiallelic copy variable regions, using the DEFA1A3 locus as an example.
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Affiliation(s)
- Jess Tyson
- School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
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17
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Zheng C, Fu Q, Shen Y, Xu Q. Investigation of allelic heterogeneity of the CCK-A receptor gene in paranoid schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2012; 159B:741-7. [PMID: 22825913 DOI: 10.1002/ajmg.b.32079] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 06/28/2012] [Indexed: 11/09/2022]
Abstract
The cholecystokinin type A receptor (CCKAR) gene has been found to be associated with positive symptoms in patients with schizophrenia but the results reported to date are inconsistent. Considering the involvement of allelic heterogeneity in poor replication of the CCKAR finding, we genotyped five single nucleotide polymorphisms (SNPs) located in the 5' putative regulatory region of the CCKAR gene in a Chinese case-control sample and then applied the 5-SNP haplotype analysis to extract allelic heterogeneity information. The results showed that three individual haplotypes were strongly associated with increased risk of schizophrenia (corrected P = 2.9 × 10(-4), P = 2.5 × 10(-5), and P = 1.4 × 10(-5), respectively) and their combination gave an odds ratio (OR) of 6.12 with 95% CI 3.67-10.21 (P = 6.7 × 10(-15)). The haplotypes were also associated with some clinical symptoms including hallucination, suspiciousness, and hostility. Our work provided further evidence in support of the CCKAR hypothesis of schizophrenia and also suggested that haplotype-based association analysis may be a powerful approach for identification of allelic heterogeneity of a disease-underlying gene, which is very likely to be attributable to poor replication of an initial finding due to the reduction of sample power and the complexity of genetic architectures.
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Affiliation(s)
- Chunming Zheng
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Science and Peking Union Medical College, Tsinghua University, Beijing, China
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18
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Kimmel G, Shamir R. THE INCOMPLETE PERFECT PHYLOGENY HAPLOTYPE PROBLEM. J Bioinform Comput Biol 2011; 3:359-84. [PMID: 15852510 DOI: 10.1142/s0219720005001090] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2004] [Revised: 08/21/2004] [Accepted: 08/30/2004] [Indexed: 11/18/2022]
Abstract
The problem of resolving genotypes into haplotypes, under the perfect phylogeny model, has been under intensive study recently. All studies so far handled missing data entries in a heuristic manner. We prove that the perfect phylogeny haplotype problem is NP-complete when some of the data entries are missing, even when the phylogeny is rooted. We define a biologically motivated probabilistic model for genotype generation and for the way missing data occur. Under this model, we provide an algorithm, which takes an expected polynomial time. In tests on simulated data, our algorithm quickly resolves the genotypes under high rates of missing entries.
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Affiliation(s)
- Gad Kimmel
- School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.
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19
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Duitama J, McEwen GK, Huebsch T, Palczewski S, Schulz S, Verstrepen K, Suk EK, Hoehe MR. Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques. Nucleic Acids Res 2011; 40:2041-53. [PMID: 22102577 PMCID: PMC3299995 DOI: 10.1093/nar/gkr1042] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Determining the underlying haplotypes of individual human genomes is an essential, but currently difficult, step toward a complete understanding of genome function. Fosmid pool-based next-generation sequencing allows genome-wide generation of 40-kb haploid DNA segments, which can be phased into contiguous molecular haplotypes computationally by Single Individual Haplotyping (SIH). Many SIH algorithms have been proposed, but the accuracy of such methods has been difficult to assess due to the lack of real benchmark data. To address this problem, we generated whole genome fosmid sequence data from a HapMap trio child, NA12878, for which reliable haplotypes have already been produced. We assembled haplotypes using eight algorithms for SIH and carried out direct comparisons of their accuracy, completeness and efficiency. Our comparisons indicate that fosmid-based haplotyping can deliver highly accurate results even at low coverage and that our SIH algorithm, ReFHap, is able to efficiently produce high-quality haplotypes. We expanded the haplotypes for NA12878 by combining the current haplotypes with our fosmid-based haplotypes, producing near-to-complete new gold-standard haplotypes containing almost 98% of heterozygous SNPs. This improvement includes notable fractions of disease-related and GWA SNPs. Integrated with other molecular biological data sets, this phase information will advance the emerging field of diploid genomics.
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Affiliation(s)
- Jorge Duitama
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, D-14195 Berlin, Germany.
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20
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Suk EK, McEwen GK, Duitama J, Nowick K, Schulz S, Palczewski S, Schreiber S, Holloway DT, McLaughlin S, Peckham H, Lee C, Huebsch T, Hoehe MR. A comprehensively molecular haplotype-resolved genome of a European individual. Genome Res 2011; 21:1672-85. [PMID: 21813624 DOI: 10.1101/gr.125047.111] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Independent determination of both haplotype sequences of an individual genome is essential to relate genetic variation to genome function, phenotype, and disease. To address the importance of phase, we have generated the most complete haplotype-resolved genome to date, "Max Planck One" (MP1), by fosmid pool-based next generation sequencing. Virtually all SNPs (>99%) and 80,000 indels were phased into haploid sequences of up to 6.3 Mb (N50 ~1 Mb). The completeness of phasing allowed determination of the concrete molecular haplotype pairs for the vast majority of genes (81%) including potential regulatory sequences, of which >90% were found to be constituted by two different molecular forms. A subset of 159 genes with potentially severe mutations in either cis or trans configurations exemplified in particular the role of phase for gene function, disease, and clinical interpretation of personal genomes (e.g., BRCA1). Extended genomic regions harboring manifold combinations of physically and/or functionally related genes and regulatory elements were resolved into their underlying "haploid landscapes," which may define the functional genome. Moreover, the majority of genes and functional sequences were found to contain individual or rare SNPs, which cannot be phased from population data alone, emphasizing the importance of molecular phasing for characterizing a genome in its molecular individuality. Our work provides the foundation to understand that the distinction of molecular haplotypes is essential to resolve the (inherently individual) biology of genes, genomes, and disease, establishing a reference point for "phase-sensitive" personal genomics. MP1's annotated haploid genomes are available as a public resource.
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Affiliation(s)
- Eun-Kyung Suk
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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21
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IL4 gene polymorphisms and their relation to periodontal disease in a Macedonian population. Hum Immunol 2011; 72:446-50. [DOI: 10.1016/j.humimm.2011.02.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 02/06/2011] [Accepted: 02/22/2011] [Indexed: 11/18/2022]
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Tan IKL, Mackin L, Wang N, Papenfuss AT, Elso CM, Ashton MP, Quirk F, Phipson B, Bahlo M, Speed TP, Smyth GK, Morahan G, Brodnicki TC. A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility. Genome Res 2010; 20:1629-38. [PMID: 21051460 DOI: 10.1101/gr.101881.109] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
More than 25 loci have been linked to type 1 diabetes (T1D) in the nonobese diabetic (NOD) mouse, but identification of the underlying genes remains challenging. We describe here the positional cloning of a T1D susceptibility locus, Idd11, located on mouse chromosome 4. Sequence analysis of a series of congenic NOD mouse strains over a critical 6.9-kb interval in these mice and in 25 inbred strains identified several haplotypes, including a unique NOD haplotype, associated with varying levels of T1D susceptibility. Haplotype diversity within this interval between congenic NOD mouse strains was due to a recombination hotspot that generated four crossover breakpoints, including one with a complex conversion tract. The Idd11 haplotype and recombination hotspot are located within a predicted gene of unknown function, which exhibits decreased expression in relevant tissues of NOD mice. Notably, it was the recombination hotspot that aided our mapping of Idd11 and confirms that recombination hotspots can create genetic variation affecting a common polygenic disease. This finding has implications for human genetic association studies, which may be affected by the approximately 33,000 estimated hotspots in the genome.
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Affiliation(s)
- Iris K L Tan
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
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23
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Orzack SH. The consensus approach to resolving heterogeneity among haplotype inferrals: a comment on Huang et al. (2008). Mol Ecol 2009; 18:1553-5; discussion 1556-9. [PMID: 19302347 DOI: 10.1111/j.1365-294x.2009.04146.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
The proteins that mediate the analgesic and other effects of opioid drugs and endogenous opioid peptides are known as opioid receptors. Opioid receptors consist of a family of four closely-related proteins belonging to the large superfamily of G-protein coupled receptors. The three types of opioid receptors shown unequivocally to mediate analgesia in animal models are the mu (MOR), delta (DOR), and kappa (KOR) opioid receptor proteins. The role of the fourth member of the opioid receptor family, the nociceptin or orphanin FQ receptor (ORL), is not as clear as hyperalgesia, analgesia, and no effect was reported after administration of ORL agonists. There are now cDNA sequences for all four types of opioid receptors that are expressed in the brain of six species from three different classes of vertebrates. This review presents a comparative analysis of vertebrate opioid receptors using bioinformatics and data from recent human genome studies. Results indicate that opioid receptors arose by gene duplication, that there is a vector of opioid receptor divergence, and that MOR shows evidence of rapid evolution.
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Affiliation(s)
- Craig W Stevens
- Department of Pharmacology and Physiology, Oklahoma State University-Center for Health Sciences, Tulsa, OK, USA.
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25
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Holla LI, Fassmann A, Augustin P, Halabala T, Znojil V, Vanek J. The Association of Interleukin-4 Haplotypes With Chronic Periodontitis in a Czech Population. J Periodontol 2008; 79:1927-33. [DOI: 10.1902/jop.2008.080035] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Polymorphisms of the serotonin transporter gene (5-HTTLPR, A/G SNP in 5-HTTLPR, and STin2 VNTR) and their relation to personality traits in healthy individuals from Russia. Psychiatr Genet 2008; 18:167-76. [PMID: 18628678 DOI: 10.1097/ypg.0b013e328304deb8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
OBJECTIVE Numerous studies have reported association of the serotonin transporter gene (5-HTT) polymorphisms and neuroticism and traits characterizing sociability and activity. This study aimed to define a single genotype effect of three polymorphic markers in the 5-HTT gene (5-HTTLPR, A/G SNP in 5-HTTLPR and STin2 VNTR) and to check possible association of the 5-HTT haplotypes and personality traits [assessed with Eysenck Personality Inventory (EPI) and Temperament and Character Inventory (TCI) questionnaires] in 301 healthy young individuals. METHODS To investigate single genotype and haplotype effects of all polymorphic markers, multivariate analysis of variance and haplotype trend regression analyses were conducted correspondingly. RESULTS Individuals with STin2.10 allele scored significantly lower on Neuroticism (EPI) (P=0.007) and Harm Avoidance (P=0.005) in the overall sample. The same pattern of association was reported in women: carriers of STin2.10 allele scored lower on Harm Avoidance (TCI) (P=0.008). Haplotype trend regression analyses revealed that carriers of S12 haplotype had lower sociability-related traits such as Extraversion (EPI) and Novelty Seeking (TCI), whereas Harm Avoidance (TCI) (anxiety-related trait) was higher. Opposite association was observed for S10 haplotype: Extraversion (EPI) score was higher, whereas Harm Avoidance (TCI) score was lower in carriers of this haplotype. CONCLUSION As single polymorphism effect of STin2 was observed in relation to anxiety-related traits, opposite S10 and S12 haplotype effects on Neuroticism and Harm Avoidance could be explained by the larger impact of STin2 polymorphism. Controversially, we consider that the variance in sociability-related traits is related to specific haplotypes of 5-HTT gene.
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Holla LI, Jurajda M, Pohunek P, Znojil V. Haplotype analysis of the endothelial nitric oxide synthase gene in asthma. Hum Immunol 2008; 69:306-13. [PMID: 18486767 DOI: 10.1016/j.humimm.2008.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Revised: 03/11/2008] [Accepted: 03/18/2008] [Indexed: 10/22/2022]
Abstract
Nitric oxide (NO) is an important mediator of physiologic processes in the airways. Evidence exists that genetic factors affect NO formation and contribute to the pathophysiology of asthma. The aims of this study were to determine the endothelial NO synthase (eNOS) haplotypes in Czech asthmatics and control subjects and examine their relation to asthma. We analyzed a total of six polymorphisms. Two SNPs in the promoter (C-786T and C-691T), two variants in the introns (27-bp repeat in intron 4 and G11T in intron 23), and two others in the exons (C774T in exon 6 and G894T in exon 7) were genotyped in 610 subjects (asthma, n = 294; healthy controls, n = 316), and a case-control association study was conducted. No significant differences in allele or genotype frequencies for individual polymorphisms were observed between patients with asthma and controls after correction for multiple comparisons. Nevertheless, a G to T exchange in intron 23 was related with specific sensitization for feather (p = 0.008, p(corr) < 0.05). However, the common haplotype -786T/-691C/27-bp 5 repeat variant/774C/894G/11T was associated with lower risk of asthma (p = 0.001, p(corr) < 0.05, odds ratio = 0.58, 95% confidence interval = 0.46-0.73). These findings suggest that endothelial NOS variants may be one of the factors participating in protection or susceptibility to asthma in our population.
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Affiliation(s)
- Lydie Izakovicova Holla
- Department of Pathophysiology, Medical Faculty, Masaryk University Brno, Brno, Czech Republic.
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28
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Huo L, Straub RE, Schmidt PJ, Shi K, Vakkalanka R, Weinberger DR, Rubinow DR. Risk for premenstrual dysphoric disorder is associated with genetic variation in ESR1, the estrogen receptor alpha gene. Biol Psychiatry 2007; 62:925-33. [PMID: 17599809 PMCID: PMC2762203 DOI: 10.1016/j.biopsych.2006.12.019] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 10/19/2006] [Accepted: 12/08/2006] [Indexed: 11/29/2022]
Abstract
BACKGROUND Premenstrual dysphoric disorder (PMDD) is a heritable mood disorder that is triggered by gonadal steroids during the luteal phase in susceptible women. METHODS We performed haplotype analyses of estrogen receptors alpha and beta (ESR1 and ESR2) in 91 women with prospectively confirmed PMDD and 56 control subjects to investigate possible sources of the genetic susceptibility to affective dysregulation induced by normal levels of gonadal steroids. We also examined associations with the valine (Val)158methionine (Met) single nucleotide polymorphism (SNP) of the gene for catechol-O-methyltransferase (COMT), an enzyme involved in estrogen metabolism and prefrontal cortical activation. RESULTS Four SNPs in intron 4 of ESR1 showed significantly different genotype and allele distributions between patients and control subjects. Significant case-control differences were seen in sliding-window analyses of two-, three-, and four-marker haplotypes but only in those haplotypes containing SNPs in intron 4 that were positive in the single-locus analysis. No significant associations were observed with ESR2 or with the COMT Val158Met polymorphism, although the significant associations with ESR1 were observed only in those with the Val/Val genotype. CONCLUSIONS These are the first positive (albeit preliminary) genetic findings in this reproductive endocrine-related mood disorder and involve the receptor for a hormone that is pathogenically relevant.
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Affiliation(s)
- Liang Huo
- Behavioral Endocrinology Branch, NIMH, NIH
| | | | | | - Kai Shi
- Behavioral Endocrinology Branch, NIMH, NIH
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29
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Ozdemir V, Williams-Jones B, Cooper DM, Someya T, Godard B. Mapping translational research in personalized therapeutics: from molecular markers to health policy. Pharmacogenomics 2007; 8:177-85. [PMID: 17286540 DOI: 10.2217/14622416.8.2.177] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Translational research is frequently used in the bioscience literature to refer to the translation of basic science into practical applications at the point of patient care. With the introduction of theragnostics, a new medical subspecialty that fuses therapeutics and diagnostic medicine with the goal of providing individualized pharmacotherapy, we suggest that the focus of translational research is shifting. We identify two bottlenecks or gaps in translational research for theragnostics: GAP1 translation from basic science to first-in-human proof-of-concept; and GAP2 translation from clinical proof-of-concept to development of evidence-based personalized treatment guidelines. GAP1 translational research in theragnostics is usually performed in traditional craft-based studies with small sample sizes and led by independent academic or industry researchers. In contrast, GAP2 translational investigations typically rely on large research consortiums and population-based biobanks that couple biomarker information with longitudinal ‘real-life’ observational data on a broad range of pharmacological phenotypes. Despite an abundance of research on the use of biobanks in disease gene discovery, there has been little conceptual work on whether and to what extent population biobanks can be utilized for translating genomics discoveries to practical treatment guidelines for theragnostic tests.
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Affiliation(s)
- Vural Ozdemir
- General Clinical Research Center, School of Medicine, University of California, Irvine, CA, USA.
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30
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Zaboli G, Jönsson EG, Gizatullin R, Asberg M, Leopardi R. Tryptophan hydroxylase-1 gene variants associated with schizophrenia. Biol Psychiatry 2006; 60:563-9. [PMID: 16806098 DOI: 10.1016/j.biopsych.2006.03.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Revised: 03/16/2006] [Accepted: 03/22/2006] [Indexed: 11/16/2022]
Abstract
BACKGROUND Serotonin (5-HT) has been implicated in the pathophysiology of schizophrenia. Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in the biosynthesis of serotonin (5-HT), and as such it might be related to the pathogenesis of schizophrenia. Two isoforms are known, TPH-1 and TPH-2. TPH-1 association with schizophrenia is debated. METHODS A case-control design was employed for gene-disease association in 155 schizophrenic psychosis patients and 253 healthy controls, all North European Caucasians. Six single nucleotide polymorphisms (SNPs) with a haplotype block structure spanning over 23 kb of the total TPH-1 29 kb were analyzed. Linkage disequilibrium and haplotype analyses were performed. Bonferroni correction was used for multiple testing. RESULTS Single marker association analyses showed two SNPs significantly associated with schizophrenia. Several haplotypes were associated with the disease. A "sliding window" analysis attributed the strongest disease association to a haplotype configuration localized between the promoter region and intron 3. CONCLUSIONS Our data indicate that TPH-1 associates with schizophrenia. It appears that specific combinations of promoter variants vis-à-vis gene transcript variants contribute to genetic predisposition to the disease.
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Affiliation(s)
- Ghazal Zaboli
- Department of Clinical Neuroscience, Psychiatry Section, Karolinska Institute and Hospital, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden.
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31
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Zaboli G, Gizatullin R, Nilsonne A, Wilczek A, Jönsson EG, Ahnemark E, Asberg M, Leopardi R. Tryptophan hydroxylase-1 gene variants associate with a group of suicidal borderline women. Neuropsychopharmacology 2006; 31:1982-90. [PMID: 16495936 DOI: 10.1038/sj.npp.1301046] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alterations in the serotonin (5-HT) system have been related to impulsive aggression and suicidal behavior, common features of the borderline personality disorder (BPD). Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in 5-HT biosynthesis. Two isoforms are known, TPH-1 and TPH-2. TPH-1 has been correlated to various psychiatric and behavioral disorders by gene polymorphism association studies. We aimed to determine whether specific TPH-1 haplotypes associate with BPD. A case-control design was employed. The control group included 98 women without psychiatric history. In all, 95 patients were included, all Caucasian women with a BPD diagnosis who had attempted suicide at least twice during their lifetime. Exclusion criteria were: (i) substance dependence; (ii) dementia or other irreversible organic brain syndromes; (iii) psychotic disorders or major depressive illness with melancholic features; (iv) life-threatening eating disorders. Six single-nucleotide polymorphisms (SNPs) were found at significant linkage disequilibrium across 23 kb of the TPH-1 gene in both patients and controls, suggesting a haplotype block structure. While no individual SNP showed association, several haplotypes associated with the BPD group. In particular, one six-SNP haplotype was absent from the control group while representing about one-quarter of all haplotypes in the BPD group (corrected P<<10(-5)). A 'sliding window' analysis attributed the strongest disease association to haplotype configurations located between the gene promoter and intron 3. We conclude that TPH-1 associates with BPD in suicidal women. Our data support the expectation that haplotype analysis is superior to single locus analysis in gene-disease, case-control association studies.
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Affiliation(s)
- Ghazal Zaboli
- Psychiatry Section, Department of Clinical Neuroscience, Karolinska Institute and Hospital, Stockholm, Sweden.
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32
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Gizatullin R, Zaboli G, Jönsson EG, Asberg M, Leopardi R. Haplotype analysis reveals tryptophan hydroxylase (TPH) 1 gene variants associated with major depression. Biol Psychiatry 2006; 59:295-300. [PMID: 16165107 DOI: 10.1016/j.biopsych.2005.07.034] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2005] [Revised: 07/12/2005] [Accepted: 07/27/2005] [Indexed: 11/28/2022]
Abstract
BACKGROUND Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in the biosynthesis of serotonin (5-HT) and might be related to the pathogenesis of major depression (MD). Two isoforms are known, TPH-1 and TPH-2. Tryptophan hydroxylase-1 association with MD is still debated. METHODS A single nucleotide polymorphism (SNP) screening strategy was used to define TPH-1 haplotypes spanning over 23 kilobase (kb) of the 29 kb gene length. Genotyping was performed in 228 MD patients and 253 healthy control subjects. RESULTS Six SNPs were found at linkage disequilibrium in both patients and control subjects, suggesting a haplotype block structure. Single marker association analyses showed only one SNP significantly associated with MD. Several haplotypes were associated with MD. When all six locus haplotypes were divided into two groups, above or below a 5% threshold, the compound haplotype group below a 5% frequency resulted as associated with the disease (31.6% vs. 18.0% in control subjects, p < 10(-5)). A "sliding window" analysis attributed the strongest disease association to a haplotype configuration localized between introns 7 and 8 (p < 10(-5)). CONCLUSIONS Haplotype analysis indicates that TPH-1 associates with MD. The most common TPH-1 variants appear to carry no risk, while some of the less frequent variants might contribute to genetic predisposition to MD.
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Affiliation(s)
- Rinat Gizatullin
- Department of Clinical Neuroscience, Psychiatry Section, Karolinska Institute and Hospital, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
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Kathiresan S, Larson MG, Vasan RS, Guo CY, Vita JA, Mitchell GF, Keyes MJ, Newton-Cheh C, Musone SL, Lochner AL, Drake JA, Levy D, O'Donnell CJ, Hirschhorn JN, Benjamin EJ. Common Genetic Variation at the Endothelial Nitric Oxide Synthase Locus and Relations to Brachial Artery Vasodilator Function in the Community. Circulation 2005; 112:1419-27. [PMID: 16129794 DOI: 10.1161/circulationaha.105.544619] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background—
Sequence variants at the endothelial nitric oxide synthase (
NOS3
) locus have been associated with endothelial function measures, but replication has been limited.
Methods and Results—
In reference pedigrees, we characterized linkage disequilibrium structure at the
NOS3
locus using 33 common single nucleotide polymorphisms (SNPs). Eighteen SNPs that capture underlying common variation were genotyped in unrelated Framingham Heart Study participants (49.5% women; mean age, 62 years) with measured brachial artery flow-mediated dilation (n=1446) or hyperemic flow velocity (n=1043). Within 3 defined blocks of strong linkage disequilibrium that spanned
NOS3
, 11 SNPs captured >80% of common haplotypic variation. Among men, there were nominally significant associations between 8
NOS3
SNPs (minimum
P
=0.002) and between haplotypes (minimum
P
=0.002) and either flow-mediated dilation or hyperemic flow velocity. In women, we did not observe significant associations between
NOS3
SNPs or haplotypes and endothelial function measures. To correct for multiple testing, we constructed 1000 bootstrapped null data sets and found that empirical probability values exceeded 0.05 for both phenotypes.
Conclusions—
A parsimonious set of SNPs captures common genetic variation at the
NOS3
locus. A conservative interpretation of our results is that, accounting for multiple testing, we did not observe statistically significant relations between
NOS3
sequence variants and endothelial function measures in either sex. The nominal associations of select
NOS3
variants with endothelial function in men (unadjusted for multiple testing) should be viewed as hypothesis-generating observations and may merit testing in other cohorts and experimental designs.
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Affiliation(s)
- Sekar Kathiresan
- Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA, USA
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Ozdemir V, Lerer B. Pharmacogenomics and the Promise of Personalized Medicine. DRUGS AND THE PHARMACEUTICAL SCIENCES 2005. [DOI: 10.1201/9780849359507.ch2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Aplenc R. Genetic polymorphisms of CYP1A1, CYP2D6, GSTM1, and GSTT1 and susceptibility to acute lymphoblastic leukemia in Indian children. Pediatr Blood Cancer 2004; 43:539-41. [PMID: 15382269 DOI: 10.1002/pbc.20167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Richard Aplenc
- Pediatric Oncology/Stem Cell Transplant, Children's Hospital of Philadelphia, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Philadelphia, Pennsylvania, USA.
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Abstract
With the genome assembly archive, it is possible to examine the raw data that underlies the DNA sequence in any sequenced genome
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Wedrén S, Lovmar L, Humphreys K, Magnusson C, Melhus H, Syvänen AC, Kindmark A, Landegren U, Fermér ML, Stiger F, Persson I, Baron J, Weiderpass E. Oestrogen receptor alpha gene haplotype and postmenopausal breast cancer risk: a case control study. Breast Cancer Res 2004; 6:R437-49. [PMID: 15217512 PMCID: PMC468663 DOI: 10.1186/bcr811] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2004] [Revised: 05/05/2004] [Accepted: 05/11/2004] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Oestrogen receptor alpha, which mediates the effect of oestrogen in target tissues, is genetically polymorphic. Because breast cancer development is dependent on oestrogenic influence, we have investigated whether polymorphisms in the oestrogen receptor alpha gene (ESR1) are associated with breast cancer risk. METHODS We genotyped breast cancer cases and age-matched population controls for one microsatellite marker and four single-nucleotide polymorphisms (SNPs) in ESR1. The numbers of genotyped cases and controls for each marker were as follows: TAn, 1514 cases and 1514 controls; c.454-397C --> T, 1557 cases and 1512 controls; c.454-351A --> G, 1556 cases and 1512 controls; c.729C --> T, 1562 cases and 1513 controls; c.975C --> G, 1562 cases and 1513 controls. Using logistic regression models, we calculated odds ratios (ORs) and 95% confidence intervals (CIs). Haplotype effects were estimated in an exploratory analysis, using expectation-maximisation algorithms for case-control study data. RESULTS There were no compelling associations between single polymorphic loci and breast cancer risk. In haplotype analyses, a common haplotype of the c.454-351A --> G or c.454-397C --> T and c.975C --> G SNPs appeared to be associated with an increased risk for ductal breast cancer: one copy of the c.454-351A --> G and c.975C --> G haplotype entailed an OR of 1.19 (95% CI 1.06-1.33) and two copies with an OR of 1.42 (95% CI 1.15-1.77), compared with no copies, under a model of multiplicative penetrance. The association with the c.454-397C --> T and c.975C --> G haplotypes was similar. Our data indicated that these haplotypes were more influential in women with a high body mass index. Adjustment for multiple comparisons rendered the associations statistically non-significant. CONCLUSION We found suggestions of an association between common haplotypes in ESR1 and the risk for ductal breast cancer that is stronger in heavy women.
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Affiliation(s)
- Sara Wedrén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Lovisa Lovmar
- Department of Medical Sciences, Uppsala University, Sweden
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Cecilia Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Håkan Melhus
- Department of Medical Sciences, Uppsala University, Sweden
| | | | | | - Ulf Landegren
- Department of Genetics and Pathology, Uppsala University, Sweden
| | | | - Fredrik Stiger
- Department of Medical Sciences, Uppsala University, Sweden
| | - Ingemar Persson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Swedish Medical Products Agency, Uppsala, Sweden
| | - John Baron
- Dartmouth Medical School, Hanover, New Hampshire, USA
| | - Elisabete Weiderpass
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- International Agency for Research on Cancer, Lyon, France
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Hoehe MR. Genetic variation and pharmacogenomics: concepts, facts, and challenges. DIALOGUES IN CLINICAL NEUROSCIENCE 2004. [PMID: 22033504 PMCID: PMC3181790 DOI: 10.31887/dcns.2004.6.1/mhoehe] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The analysis of genetic variation in candidate genes is an issue of central importance in pharmacogenomics. The specific approaches taken will have a critical impact on the successful identification of disease genes, the molecular correlates of drug response, and the establishment of meaningful relationships between genetic variants and phenotypes of biomedical and pharmaceutical importance in general. Against a historical background, this article distinguishes different approaches to candidate gene analysis, reflecting different stages in human genome research. Only recently has it become feasible to analyze genetic variation systematically at the ultimate level of resolution, ie, the DNA sequence. In this context, the importance of haplotype-based approaches to candidate gene analysis has at last been recognized; the determination of the specific combinations of variants for each of the two sequences of a gene defined as a haplotype is essential. An up-to-date summary of such maximum resolution data on the amount, nature, and structure of genetic variation in candidate genes will be given. These data demonstrate abundant gene sequence and haplotype diversity. Numerous individually different forms of a gene may exist. This presents major challenges to the analysis of relationships between genetic variation, gene function, and phenotype. First solutions seem within reach. The implications of naturally occurring variation for pharmacogenomics and “personalized” medicine are now evident. Future approaches to the identification, evaluation, and prioritization of drug targets, the optimization of clinical trials, and the development of efficient therapies must be based on in-depth knowledge of candidate gene variation as an essential prerequisite.
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Hennah W, Varilo T, Paunio T, Peltonen L. Haplotype analysis and identification of genes for a complex trait: examples from schizophrenia. Ann Med 2004; 36:322-31. [PMID: 15478307 DOI: 10.1080/07853890410029824] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
For more than a decade there has been intensive research into the genetic etiology of schizophrenia, yet it is only recently that the first findings of promising genes associating with the disorder have been reported. Linkage analyses in families collected from different populations have provided relatively well defined genomic loci. These have been typically followed by fine mapping studies using single nucleotide polymorphisms (SNPs). A number of analysis programs have been produced to test SNPs and their haplotypes for association. Typically association has been established to specific haplotypes representing an allelic variant of the corresponding gene. The inherent problem of multiple testing in the analysis of haplotypes needs to be addressed fully, to determine if any of these recent findings can be considered as confirmed susceptibility genes for schizophrenia. However, informative haplotypes have provided a way to define allelic variants of genes associated with schizophrenia in numerous study samples, and are a useful tool in characterizing the extent of allelic diversity of putative schizophrenia susceptibility genes within different populations.
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MESH Headings
- Chromosome Mapping/methods
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 13/genetics
- Chromosomes, Human, Pair 22/genetics
- Chromosomes, Human, Pair 6/genetics
- Chromosomes, Human, Pair 8/genetics
- Genetic Predisposition to Disease/genetics
- Genome, Human
- Haplotypes/genetics
- Humans
- Linkage Disequilibrium/genetics
- Polymorphism, Single Nucleotide
- Schizophrenia/genetics
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Affiliation(s)
- William Hennah
- Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland.
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