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Chen YL, Ho CL, Hung CY, Chen WL, Chang C, Hou YH, Chen JR, Chen PJ, Chow NH, Huang W, Hsu YT, Chen TY, Liu T. Enhancing diagnosis of T-cell lymphoma using non-recombined T-cell receptor sequences. Front Oncol 2022; 12:1014132. [PMID: 36568146 PMCID: PMC9772823 DOI: 10.3389/fonc.2022.1014132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Clonality assessment, which can detect neoplastic T cells by identifying the uniquely recombined T-cell receptor (TCR) genes, provides important support in the diagnosis of T-cell lymphoma (TCL). BIOMED-2 is the gold standard clonality assay and has proven to be effective in European TCL patients. However, we failed to prove its sensitivity in Taiwanese TCL patients, especially based on the TCRβ gene. To explore potential impact of genetic background in the BIOMED-2 test, we analyzed TCRβ sequences of 21 healthy individuals and two TCL patients. This analysis suggests that genetic variations in the BIOMED-2 primer sites could not explain the difference in sensitivity. The BIOMED-2 test results of the two TCL patients were positive and negative, respectively. Interestingly, a higher percentage (>81%) of non-recombined TCRβ sequences was observed in the test-negative patient than those of the test-positive patient and all healthy individuals (13~66%). The result suggests a new TCR target for enhancing TCL diagnosis. To further explore the hypothesis, we proposed a cost-effective digital PCR assay that quantifies the relative abundance of non-recombined TCRβ sequences containing a J2-2P~J2-3 segment. With the digital PCR assay, bone marrow specimens from TCL patients (n=9) showed a positive outcome (i.e., the relative abundance of the J2-2P~J2-3 sequences ≧5%), whereas non-TCL patients (n=6) gave a negative result. As five of nine TCL patients had a negative BIOMED-2 test result, the J2-2P~J2-3 sequences may improve TCL detection. This is the first report showing the capability of characterizing non-recombined TCR sequences as a supplementary strategy for the BIOMED-2 clonality test.
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Affiliation(s)
- Yi-Lin Chen
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan,Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chung-Liang Ho
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan,Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chen-Yan Hung
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Wan-Li Chen
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Chen Chang
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Yi-Hsin Hou
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Jian-Rong Chen
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Pin-Jun Chen
- Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Nan-Haw Chow
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan,Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wenya Huang
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan,Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Ting Hsu
- Section of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Tsai-Yun Chen
- Section of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Tsunglin Liu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan,*Correspondence: Tsunglin Liu,
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2
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Omer A, Peres A, Rodriguez OL, Watson CT, Lees W, Polak P, Collins AM, Yaari G. T cell receptor beta germline variability is revealed by inference from repertoire data. Genome Med 2022; 14:2. [PMID: 34991709 PMCID: PMC8740489 DOI: 10.1186/s13073-021-01008-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND T and B cell receptor (TCR, BCR) repertoires constitute the foundation of adaptive immunity. Adaptive immune receptor repertoire sequencing (AIRR-seq) is a common approach to study immune system dynamics. Understanding the genetic factors influencing the composition and dynamics of these repertoires is of major scientific and clinical importance. The chromosomal loci encoding for the variable regions of TCRs and BCRs are challenging to decipher due to repetitive elements and undocumented structural variants. METHODS To confront this challenge, AIRR-seq-based methods have recently been developed for B cells, enabling genotype and haplotype inference and discovery of undocumented alleles. However, this approach relies on complete coverage of the receptors' variable regions, whereas most T cell studies sequence a small fraction of that region. Here, we adapted a B cell pipeline for undocumented alleles, genotype, and haplotype inference for full and partial AIRR-seq TCR data sets. The pipeline also deals with gene assignment ambiguities, which is especially important in the analysis of data sets of partial sequences. RESULTS From the full and partial AIRR-seq TCR data sets, we identified 39 undocumented polymorphisms in T cell receptor Beta V (TRBV) and 31 undocumented 5 ' UTR sequences. A subset of these inferences was also observed using independent genomic approaches. We found that a single nucleotide polymorphism differentiating between the two documented T cell receptor Beta D2 (TRBD2) alleles is strongly associated with dramatic changes in the expressed repertoire. CONCLUSIONS We reveal a rich picture of germline variability and demonstrate how a single nucleotide polymorphism dramatically affects the composition of the whole repertoire. Our findings provide a basis for annotation of TCR repertoires for future basic and clinical studies.
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Affiliation(s)
- Aviv Omer
- Faculty of Engineering, Bar Ilan University, Ramat Gan, 5290002, Israel
- Bar Ilan institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Ayelet Peres
- Faculty of Engineering, Bar Ilan University, Ramat Gan, 5290002, Israel
- Bar Ilan institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - William Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - Pazit Polak
- Faculty of Engineering, Bar Ilan University, Ramat Gan, 5290002, Israel
- Bar Ilan institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Andrew M Collins
- School of Biotechnology and Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, 5290002, Israel.
- Bar Ilan institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, 5290002, Israel.
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3
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Wang Q, Gu J, Wang L, Chang DW, Ye Y, Huang M, Roth JA, Wu X. Genetic associations of T cell cancer immune response-related genes with T cell phenotypes and clinical outcomes of early-stage lung cancer. J Immunother Cancer 2021; 8:jitc-2019-000336. [PMID: 32764075 PMCID: PMC7412613 DOI: 10.1136/jitc-2019-000336] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2020] [Indexed: 12/14/2022] Open
Abstract
Background Recent advances in T cell-related immunotherapy have brought remarkable progress in the treatment of non-small cell lung cancer (NSCLC). However, whether and how genetic variations of T cell cancer immune response genes can influence clinical outcomes of NSCLC patients remain obscure. Methods In this multiphase study, we assessed 2450 single-nucleotide polymorphisms (SNPs) from 280 T cell cancer immune response-related genes in 941 early-stage NSCLC patients (discovery n=536; validation n=405) to analyze the variants’ associations with outcomes and to observe the effects on T cell phenotypes. Results We found 14 SNPs in 10 genes were associated with NSCLC outcomes (p<0.05) in both phases. Among them, TRB:rs1964986 was the most significant variant associated with recurrence risk after meta-analysis (HR 1.84, 95% CI 1.35 to 2.52, p=1.15E-04), while IDO1:rs10108662 was the most significant SNP associated with death risk (HR 1.87, 95% CI 1.40 to 2.51, p=2.17E-05). Analysis of unfavorable genotypes indicated cumulative effects on death and recurrence risks. Seven treatment-specific variants were found to predict opposite outcomes in surgery-only and surgery-plus-chemotherapy subgroups. Expression quantitative trait loci analysis indicated that six SNPs significantly correlated with their corresponding gene expression. T cells from high-risk subjects displayed reduced degranulation (p=0.02) and decreased cytotoxicity against cancer cells (p<0.01). Gene expression profile indicated increased IDO1 expression and decreased IL2, PRF and GZMB expression in high-risk subjects. Conclusions Genetic variations in T cell cancer immune response pathways can impact outcomes and may be served as predictors for treatment efficacy in early-stage NSCLC patients. The correlation between immune genotypes and T cell antitumor immunity suggests a biological link between host immune genetics and NSCLC prognosis.
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Affiliation(s)
- Qinchuan Wang
- Department of Surgical Oncology, Affiliated Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States.,Department of Epidemiology, Center for Biostatistics, Bioinformatics, and Big Data, Second Affiliated Hospital and Department of Big Data in Health Science, School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jianchun Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States.,Department of Epidemiology, Medical Oncology, Shanghai Jiaotong University School of Medicine Xinhua Hospital, Shanghai, China
| | - Linbo Wang
- Department of Surgical Oncology, Affiliated Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - David W Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States .,Department of Epidemiology, Center for Biostatistics, Bioinformatics, and Big Data, Second Affiliated Hospital and Department of Big Data in Health Science, School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Maosheng Huang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Jack A Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States .,Department of Epidemiology, Center for Biostatistics, Bioinformatics, and Big Data, Second Affiliated Hospital and Department of Big Data in Health Science, School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,National Institute for Data Science in Health and Medicine, Hangzhou, Zhejiang, China
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4
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Sex-Related Differences in Allelic Frequency of the Human Beta T Cell Receptor SNP rs1800907: A Retrospective Analysis from Milan Metropolitan Area. Vaccines (Basel) 2021; 9:vaccines9040333. [PMID: 33915945 PMCID: PMC8066715 DOI: 10.3390/vaccines9040333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/01/2021] [Accepted: 03/18/2021] [Indexed: 11/30/2022] Open
Abstract
This paper aims at retrospectively re-analyzing the different distribution, between males and females, in the allelic frequency of the human β T cell receptor (TCR β) single nucleotide polymorphism (SNPs) rs1800907 in Caucasian patients in the Milan metropolitan area. The allelic frequency significantly differed between sexes. Females showed higher frequency of C/C genotype than males, but lower T/C genotype (p < 0.0001). Heterozygous (T/C) versus homozygous (T/T + C/C) genotypes resulted in a different distribution of frequencies in males than in females, the latter possessing higher homozygosis (p < 0.0001). Within the limitations of this work (small number of included studies that concerned just a specific geographical area), allelic distribution according to sex might account the role of TCRβ-related SNPs in autoimmune diseases and further investigations are required to explain better this genetic background, in the perspective of a sex-related T cell immune responsiveness and auto-immunity.
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5
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Nunes JRS, Pértille F, Andrade SCS, Perazza CA, Villela PMS, Almeida-Val VMF, Gao ZX, Coutinho LL, Hilsdorf AWS. Genome-wide association study reveals genes associated with the absence of intermuscular bones in tambaqui (Colossoma macropomum). Anim Genet 2020; 51:899-909. [PMID: 33006182 DOI: 10.1111/age.13001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 01/21/2023]
Abstract
The presence of intermuscular bones in fisheries products limits the consumption and commercialization potential of many fish species, including tambaqui (Colossoma macropomum). These bones have caused medical emergencies and are an undesirable characteristic for fish farming because their removal is labor-intensive during fish processing. Despite the difficulty in identifying genes related to the lack of intermuscular bone in diverse species of fish, the discovery of individuals lacking intermuscular bones in a Neotropical freshwater characiform fish has provided a unique opportunity to delve into the genetic mechanisms underlying the pathways of intermuscular bone formation. In this study, we carried out a GWAS among boneless and wt tambaqui populations to identify markers associated with a lack of intermuscular bone. After analyzing 11 416 SNPs in 360 individuals (12 boneless and 348 bony), we report 675 significant (Padj < 0.003) associations for this trait. Of those, 13 associations were located near candidate genes related to the reduction of bone mass, promotion of bone formation, inhibition of bone resorption, central control of bone remodeling, bone mineralization and other related functions. To the best of our knowledge, for the first time, we have successfully identified genes related to a lack of intermuscular bones using GWAS in a non-model species.
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Affiliation(s)
- J R S Nunes
- Nature and Culture Institute, Federal University of Amazon (UFAM), Benjamin Constant, Amazonas, 69630-000, Brazil.,Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - F Pértille
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil.,Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58 183, Sweden
| | - S C S Andrade
- Genetics and Evolutionary Biology Department, University of São Paulo (USP)/Bioscience Institute (IB), São Paulo, São Paulo, 05508-090, Brazil
| | - C A Perazza
- Unit of Biotechnology, University of Mogi das Cruzes, Mogi das Cruzes, São Paulo, 08780-911, Brazil
| | - P M S Villela
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - V M F Almeida-Val
- Brazilian National Institute for Research of the Amazon, Laboratory of Ecophysiology and Molecular Evolution, Manaus, Amazonas, 69067-375, Brazil
| | - Z-X Gao
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Hongshan District, Wuhan, 430070, China
| | - L L Coutinho
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - A W S Hilsdorf
- Unit of Biotechnology, University of Mogi das Cruzes, Mogi das Cruzes, São Paulo, 08780-911, Brazil
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6
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Luo S, Yu JA, Li H, Song YS. Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans. Life Sci Alliance 2019; 2:2/2/e201800221. [PMID: 30808649 PMCID: PMC6391684 DOI: 10.26508/lsa.201800221] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/14/2019] [Accepted: 02/14/2019] [Indexed: 12/31/2022] Open
Abstract
This article presents a comprehensive study of the IGHV and TRBV gene families in a globally diverse sample of humans and shows that the two gene families exhibit starkly different patterns of variation. The immunoglobulin heavy variable (IGHV) and T cell beta variable (TRBV) loci are among the most complex and variable regions in the human genome. Generated through a process of gene duplication/deletion and diversification, these loci can vary extensively between individuals in copy number and contain genes that are highly similar, making their analysis technically challenging. Here, we present a comprehensive study of the functional gene segments in the IGHV and TRBV loci, quantifying their copy number and single-nucleotide variation in a globally diverse sample of 109 (IGHV) and 286 (TRBV) humans from over a 100 populations. We find that the IGHV and TRBV gene families exhibit starkly different patterns of variation. In addition to providing insight into the different evolutionary paths of the IGHV and TRBV loci, our results are also important to the adaptive immune repertoire sequencing community, where the lack of frequencies of common alleles and copy number variants is hampering existing analytical pipelines.
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Affiliation(s)
- Shishi Luo
- Computer Science Division, University of California, Berkeley, Berkeley, CA, USA.,Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Jane A Yu
- Computer Science Division, University of California, Berkeley, Berkeley, CA, USA
| | - Heng Li
- Department of Biostatistics, Harvard Medical School, Boston, MA, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, Berkeley, CA, USA .,Department of Statistics, University of California, Berkeley, Berkeley, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
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7
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Crawford DC, Bailey JNC, Miskimen K, Miron P, McCauley JL, Sedor JR, ƠToole JF, Bush WS. Somatic T-cell Receptor Diversity in a Chronic Kidney Disease PatientPopulation Linked to Electronic Health Records. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2018; 2017:63-71. [PMID: 29888042 PMCID: PMC5961818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Germline and somatic genomic variation represent the bulk of 'omics data available for precision medicine research. These data, however, may fail to capture the dynamic biological processes that underlie disease development, particularly for chronic diseases of aging such as chronic kidney disease (CKD). To demonstrate the value of additional dynamic precision medicine data, we sequenced somatic T-cell receptor rearrangements, markers of the adaptive immune response, from genomic DNA collected during a clinical encounter from 15 participants with CKD and associated co-morbidities. Participants were consented as part of a larger precision medicine research project at the MetroHealth System, a large urban public hospital in Cleveland, Ohio. Despite the limited sample size, we observed reduced T-cell receptor diversity in relation to biomarkers (creatinine and BUN) of CKD status in this older and mostly African American sample. Overall, these data suggest a relationship between advanced CKD and premature aging of the adaptive immune system and highlight the potential of dynamic 'omic data to generate novel hypotheses about disease mechanisms and unique opportunities for precision medicine applications.
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Affiliation(s)
- Dana C. Crawford
- Institute for Computational Biology, Departments of,Population and Quantitative Health Sciences and,Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Kristy Miskimen
- Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Penelope Miron
- Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Jacob L. McCauley
- John P. Hussman Institute for Human Genomics, Dr. John T Macdonald Department of Human Genetics, University of Miami, Miami, FL, USA; Departments of
| | - John R. Sedor
- Medicine and,Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | | | - William S. Bush
- Institute for Computational Biology, Departments of,Population and Quantitative Health Sciences and
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8
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Jackson KJL, Kidd MJ, Wang Y, Collins AM. The shape of the lymphocyte receptor repertoire: lessons from the B cell receptor. Front Immunol 2013; 4:263. [PMID: 24032032 PMCID: PMC3759170 DOI: 10.3389/fimmu.2013.00263] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/19/2013] [Indexed: 11/13/2022] Open
Abstract
Both the B cell receptor (BCR) and the T cell receptor (TCR) repertoires are generated through essentially identical processes of V(D)J recombination, exonuclease trimming of germline genes, and the random addition of non-template encoded nucleotides. The naïve TCR repertoire is constrained by thymic selection, and TCR repertoire studies have therefore focused strongly on the diversity of MHC-binding complementarity determining region (CDR) CDR3. The process of somatic point mutations has given B cell studies a major focus on variable (IGHV, IGLV, and IGKV) genes. This in turn has influenced how both the naïve and memory BCR repertoires have been studied. Diversity (D) genes are also more easily identified in BCR VDJ rearrangements than in TCR VDJ rearrangements, and this has allowed the processes and elements that contribute to the incredible diversity of the immunoglobulin heavy chain CDR3 to be analyzed in detail. This diversity can be contrasted with that of the light chain where a small number of polypeptide sequences dominate the repertoire. Biases in the use of different germline genes, in gene processing, and in the addition of non-template encoded nucleotides appear to be intrinsic to the recombination process, imparting "shape" to the repertoire of rearranged genes as a result of differences spanning many orders of magnitude in the probabilities that different BCRs will be generated. This may function to increase the precursor frequency of naïve B cells with important specificities, and the likely emergence of such B cell lineages upon antigen exposure is discussed with reference to public and private T cell clonotypes.
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Affiliation(s)
- Katherine J. L. Jackson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Marie J. Kidd
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Yan Wang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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9
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Burrows SR, Miles JJ. Immune parameters to consider when choosing T-cell receptors for therapy. Front Immunol 2013; 4:229. [PMID: 23935599 PMCID: PMC3733007 DOI: 10.3389/fimmu.2013.00229] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 07/22/2013] [Indexed: 11/13/2022] Open
Abstract
T-cell receptor (TCR) therapy has arrived as a realistic treatment option for many human diseases. TCR gene therapy allows for the mass redirection of T-cells against a defined antigen while high affinity TCR engineering allows for the creation of a new class of soluble drugs. However, deciding which TCR blueprint to take forward for gene therapy or engineering is difficult. More than one quintillion TCR combinations can be generated by somatic recombination and we are only now beginning to appreciate that not all are functionally equal. TCRs can exhibit high or low degrees of HLA-restricted cross-reactivity and alloreact against one or a combination of HLA alleles. Identifying TCR candidates with high specificity and minimal cross-reactivity/alloreactivity footprints before engineering is obviously highly desirable. Here we will summarize what we currently know about TCR biology with regard to immunoengineering.
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Affiliation(s)
- Scott R Burrows
- Human Immunity Laboratory and Cellular Immunology Laboratory, Queensland Institute of Medical Research , Brisbane, QLD , Australia ; School of Medicine, The University of Queensland , Brisbane, QLD , Australia
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10
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Gras S, Burrows SR, Turner SJ, Sewell AK, McCluskey J, Rossjohn J. A structural voyage toward an understanding of the MHC-I-restricted immune response: lessons learned and much to be learned. Immunol Rev 2012; 250:61-81. [DOI: 10.1111/j.1600-065x.2012.01159.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stephanie Gras
- Department of Biochemistry and Molecular Biology; School of Biomedical Sciences; Monash University; Clayton; Australia
| | - Scott R. Burrows
- Queensland Institute of Medical Research and Australian Centre for Vaccine Development; Brisbane; Australia
| | - Stephen J. Turner
- Department of Microbiology and Immunology; University of Melbourne; Parkville; Australia
| | - Andrew K. Sewell
- Institute of Infection and Immunity; Cardiff University School of Medicine; Cardiff; UK
| | - James McCluskey
- Department of Microbiology and Immunology; University of Melbourne; Parkville; Australia
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11
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Brennan RM, Petersen J, Neller MA, Miles JJ, Burrows JM, Smith C, McCluskey J, Khanna R, Rossjohn J, Burrows SR. The Impact of a Large and Frequent Deletion in the Human TCR β Locus on Antiviral Immunity. THE JOURNAL OF IMMUNOLOGY 2012; 188:2742-8. [DOI: 10.4049/jimmunol.1102675] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Qin J, Munyard K, Lee CY, Wetherall JD, Groth DM. Characterization of the sheep Complement Factor B gene (CFB). Vet Immunol Immunopathol 2011; 140:170-4. [PMID: 21163535 DOI: 10.1016/j.vetimm.2010.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 11/04/2010] [Accepted: 11/11/2010] [Indexed: 10/18/2022]
Abstract
The Complement Factor B gene (CFB) of the alternative complement pathway has been identified in the sheep Major Histocompatibility Complex (MHC) and its genomic sequence determined. CFB is located approximately 600 bp upstream of the complement C2 gene, contains 18 exons, and manifests the domain signature characteristic of CFB protein. Thirteen single nucleotide polymorphisms were identified in merino sheep and interbreed variation was identified by comparison with International Sheep Genomics Consortium data. Two predicted non synonymous substitutions were observed and in-silico analysis indicates that these are likely to have a destabilizing effect on the protein structure. Sheep and cattle CFB were compared and shown to contain a common nine nucleotide deletion in exon 18 relative to human CFB. Predicted CFB amino acid sequences for these two species contain 761 aa relative to 764 aa in the human orthologue. Sequencing of the cosmid and BAC clones used in this study permitted the relative positions of three adjacent loci to be determined and showed that the previously described microsatellite locus (BfMs) is located within SKIV2L.
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Affiliation(s)
- Jinyi Qin
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, Curtin University, GPO Box U1987, Perth, 6845 Western Australia, Australia
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13
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Miles JJ, Douek DC, Price DA. Bias in the αβ T-cell repertoire: implications for disease pathogenesis and vaccination. Immunol Cell Biol 2011; 89:375-87. [PMID: 21301479 DOI: 10.1038/icb.2010.139] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The naïve T-cell repertoire is vast, containing millions of unique T-cell receptor (TCR) structures. Faced with such diversity, the mobilization of TCR structures from this enormous pool was once thought to be a stochastic, even chaotic, process. However, steady and systematic dissection over the last 20 years has revealed that this is not the case. Instead, the TCR repertoire deployed against individual antigens is routinely ordered and biased. Often, identical and near-identical TCR repertoires can be observed across different individuals, suggesting that the system encompasses an element of predictability. This review provides a catalog of αβ TCR bias by disease and by species, and discusses the mechanisms that govern this inherent and widespread phenomenon.
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Affiliation(s)
- John J Miles
- T Cell Modulation Laboratory, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff, UK.
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14
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Gras S, Chen Z, Miles JJ, Liu YC, Bell MJ, Sullivan LC, Kjer-Nielsen L, Brennan RM, Burrows JM, Neller MA, Khanna R, Purcell AW, Brooks AG, McCluskey J, Rossjohn J, Burrows SR. Allelic polymorphism in the T cell receptor and its impact on immune responses. ACTA ACUST UNITED AC 2010; 207:1555-67. [PMID: 20566715 PMCID: PMC2901058 DOI: 10.1084/jem.20100603] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
In comparison to human leukocyte antigen (HLA) polymorphism, the impact of allelic sequence variation within T cell receptor (TCR) loci is much less understood. Particular TCR loci have been associated with autoimmunity, but the molecular basis for this phenomenon is undefined. We examined the T cell response to an HLA-B*3501-restricted epitope (HPVGEADYFEY) from Epstein-Barr virus (EBV), which is frequently dominated by a TRBV9*01(+) public TCR (TK3). However, the common allelic variant TRBV9*02, which differs by a single amino acid near the CDR2beta loop (Gln55-->His55), was never used in this response. The structure of the TK3 TCR, its allelic variant, and a nonnaturally occurring mutant (Gln55-->Ala55) in complex with HLA-B*3501(HPVGEADYFEY) revealed that the Gln55-->His55 polymorphism affected the charge complementarity at the TCR-peptide-MHC interface, resulting in reduced functional recognition of the cognate and naturally occurring variants of this EBV peptide. Thus, polymorphism in the TCR loci may contribute toward variability in immune responses and the outcome of infection.
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Affiliation(s)
- Stephanie Gras
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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15
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Bonfigli S, Fozza C, Contini S, Buzzetti R, Cucca F, Longinotti M. High frequency of the TCRBV20S1 null allele in the Sardinian population. Hum Immunol 2007; 68:426-9. [PMID: 17462510 DOI: 10.1016/j.humimm.2007.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 01/16/2007] [Accepted: 01/17/2007] [Indexed: 11/26/2022]
Abstract
Single nucleotide polymorphisms (SNPs) in the T-cell receptor (TCR) gene segments might play a role in shaping the TCR repertoire. Three polymorphisms have been described for the TCRBV20S1 gene segment, one of which is responsible for a nucleotide substitution at position 524, resulting in the introduction of a stop codon. Individuals homozygous for this inactivating polymorphism ("null allele") are unable to express TCRBV20 gene products. Using DNA restriction digestion analysis, we investigated the frequency of this polymorphism in 111 healthy Sardinian subjects. Inhabitants of the Mediterranean island of Sardinia are considered to represent a genetically isolated population. Our analyses revealed an incidence of 19.8% of homozygosity for the null allele, corresponding to an allele frequency of 0.45. Such an incidence, significantly higher than the one detected in 83 non-Sardinian Caucasians (6%), is the most elevated so far reported in the literature. BV20 is a single member subfamily and the null allele produces a gap in the potential TCR repertoire. Therefore, it is possible that an undetermined selective pressure could have played a role in determining the high frequency of this inactivating polymorphism in Sardinians. Alternatively, this finding could be related to a founder effect in this ancient island population.
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16
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Smith WP, Vu Q, Li SS, Hansen JA, Zhao LP, Geraghty DE. Toward understanding MHC disease associations: partial resequencing of 46 distinct HLA haplotypes. Genomics 2006; 87:561-71. [PMID: 16434165 DOI: 10.1016/j.ygeno.2005.11.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 11/28/2005] [Accepted: 11/29/2005] [Indexed: 11/23/2022]
Abstract
We carried out a resequencing project that examined 552 kb of sequence from each of 46 individual HLA haplotypes representing a diversity of HLA allele types, generating nearly 27 Mb of fully phased genomic sequence. Haplotype blocks were defined extending from telomeric of HLA-F to centromeric of HLA-DP including in total 5186 MHC SNPs. To investigate basic questions about the evolutionary origin of common HLA haplotypes, and to obtain an estimate of rare variation in the MHC, we similarly examined two additional sets of samples. In 19 independent HLA-A1, B8, DR3 chromosomes, the most common HLA haplotype in Northern European Caucasians, variation was found at 11 SNP positions in the 3600-kb region from HLA-A to DR. Partial resequencing of 282 individuals in the gene-dense class III region identified significant variability beyond what could have been detected by linkage to common SNPs.
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Affiliation(s)
- Wade P Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA
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17
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Mackelprang R, Livingston RJ, Eberle MA, Carlson CS, Yi Q, Akey JM, Nickerson DA. Sequence diversity, natural selection and linkage disequilibrium in the human T cell receptor alpha/delta locus. Hum Genet 2006; 119:255-66. [PMID: 16425038 DOI: 10.1007/s00439-005-0111-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2005] [Accepted: 11/16/2005] [Indexed: 12/22/2022]
Abstract
T cell receptors (TR), through their interaction with the major histocompatibility complex, play a central role in immune responsiveness and potentially immune-related disorders. We resequenced all 57 variable (V) genes in the human T cell receptor alpha and delta (TRA/TRD) locus in 40 individuals of Northern European, Mexican, African-American and Chinese descent. Two hundred and eighty-four single nucleotide polymorphisms (SNPs) were identified. The distribution of SNPs between V genes was heterogeneous, with an average of five SNPs per gene and a range of zero to 15. We describe the patterns of linkage disequilibrium for these newly discovered SNPs and compare these patterns with other emerging large-scale datasets (e.g. Perlegen and HapMap projects) to place our findings into a framework for future analysis of genotype-phenotype associations across this locus. Furthermore, we explore signatures of natural selection across V genes. We find evidence of strong directional selection at this locus as evidenced by unusually high values of Fst.
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Affiliation(s)
- Rachel Mackelprang
- Department of Genome Sciences, University of Washington, 357730, Seattle, WA, 98195-7730, USA.
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18
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Abstract
Currently, more than 10 million DNA sequence variations have been uncovered in the human genome. The most detailed variation discovery efforts have focused on candidate genes involved in cardiovascular disease or in susceptibilities associated with exposure to environmental agents. Here we provide an overview of natural genetic variation from the literature and in 510 human candidate genes resequenced for variation discovery. The average human gene contains 126 biallelic polymorphisms, 46 of which are common (> or =5% minor allele frequency) and 5 of which are found in coding regions. Using this complete picture of genetic diversity, we explore conservation, signatures of selection, and historical recombination to mine information useful for candidate gene association studies. In general, we find that the patterns of human gene variation suggest that no one approach will be appropriate for genetic association studies across all genes. Therefore, many different approaches may be required to identify the elusive genotypes associated with common human phenotypes.
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Affiliation(s)
- Dana C Crawford
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
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19
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Verzilli CJ, Stallard N, Whittaker JC. Bayesian modelling of multivariate quantitative traits using seemingly unrelated regressions. Genet Epidemiol 2005; 28:313-25. [PMID: 15789447 DOI: 10.1002/gepi.20072] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We investigate a Bayesian approach to modelling the statistical association between markers at multiple loci and multivariate quantitative traits. In particular, we describe the use of Bayesian Seemingly Unrelated Regressions (SUR) whereby genotypes at the different loci are allowed to have non-simultaneous effects on the phenotypes considered with residuals from each regression assumed correlated. We present results from simulations showing that, under rather general conditions that are likely to hold in real situations, the Bayesian SUR approach has increased probability of selecting the true model compared to univariate analyses. Finally, we apply our methods to data from subjects genotyped for 12 SNPs in the apolipoprotein E (APOE) gene. Phenotypes relate to response to treatment with atorvastatin and include changes in total cholesterol, low-density lipoprotein cholesterol, and triglycerides. Missing genotype data are naturally accommodated in our Bayesian framework by imputing them using a nested haplotype phasing algorithm.
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Affiliation(s)
- Claudio J Verzilli
- Department of Epidemiology and Public Health, Imperial College London, London, United Kingdom.
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20
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Nothnagel M, Rohde K. The effect of single-nucleotide polymorphism marker selection on patterns of haplotype blocks and haplotype frequency estimates. Am J Hum Genet 2005; 77:988-98. [PMID: 16380910 PMCID: PMC1285181 DOI: 10.1086/498175] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2004] [Accepted: 09/16/2004] [Indexed: 11/03/2022] Open
Abstract
The definition of haplotype blocks of single-nucleotide polymorphisms (SNPs) has been proposed so that the haplotypes can be used as markers in association studies and to efficiently describe human genetic variation. The International Haplotype Map (HapMap) project to construct a comprehensive catalog of haplotypic variation in humans is underway. However, a number of factors have already been shown to influence the definition of blocks, including the population studied and the sample SNP density. Here, we examine the effect that marker selection has on the definition of blocks and the pattern of haplotypes by using comparable but complementary SNP sets and a number of block definition methods in various genomic regions and populations that were provided by the Encyclopedia of DNA Elements (ENCODE) project. We find that the chosen SNP set has a profound effect on the block-covered sequence and block borders, even at high marker densities. Our results question the very concept of discrete haplotype blocks and the possibility of generalizing block findings from the HapMap project. We comparatively apply the block-free tagging-SNP approach and discuss both the haplotype approach and the tagging-SNP approach as means to efficiently catalog genetic variation.
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Affiliation(s)
- Michael Nothnagel
- Department of Bioinformatics, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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21
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Abstract
Advances in genotyping and sequencing technologies, coupled with the development of sophisticated statistical methods, have afforded investigators novel opportunities to define the role of sequence variation in the development of common human diseases. At the forefront of these investigations is the use of dense maps of single-nucleotide polymorphisms (SNPs) and the haplotypes derived from these polymorphisms. Here we review basic concepts of high-density genetic maps of SNPs and haplotypes and how they are typically generated and used in human genetic research. We also provide useful examples and tools available for researchers interested in incorporating haplotypes into their studies. Finally, we discuss the latest concepts for the analysis of haplotypes related to human disease, including haplotype blocks, the International HapMap Project, and the future directions of these resources.
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Affiliation(s)
- Dana C Crawford
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
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22
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Bernig T, Taylor JG, Foster CB, Staats B, Yeager M, Chanock SJ. Sequence analysis of the mannose-binding lectin (MBL2) gene reveals a high degree of heterozygosity with evidence of selection. Genes Immun 2005; 5:461-76. [PMID: 15306844 DOI: 10.1038/sj.gene.6364116] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human mannose-binding protein (MBL) is a component of innate immunity. To capture the common genetic variants of MBL2, we resequenced a 10.0 kb region that includes MBL2 in 102 individuals representing four major US ethnic groups. In all, 87 polymorphic sites were observed, indicating a high level of heterozygosity (total pi=18.3 x 10(-4)). Estimates of linkage disequilibrium across MBL2 indicate that it is divided into two blocks, with a probable recombination hot spot in the 3' end. Three non-synonymous SNPs in exon 1 of the encoding MBL2 gene and three upstream SNPs form common 'secretor haplotypes' that can predict circulating levels. Common variants have been associated with increased susceptibility to infection and autoimmune diseases. The high frequencies of B, C and D alleles in certain populations suggest a possible selective advantage for heterozygosity. There is limited diversity of haplotype structure; the 'secretor haplotypes' lie on a restricted number of extended haplotypes, which could include additional linked SNPs, which might also have possible functional implications. There is evidence for gene conversion in the region between the two blocks, in the last exon. Our data should form the basis for conducting MBL2 candidate gene association studies using a locus-wide approach.
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Affiliation(s)
- T Bernig
- Section on Genomic Variation, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4605, USA
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23
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Verhoeven KJF, Simonsen KL. Genomic haplotype blocks may not accurately reflect spatial variation in historic recombination intensity. Mol Biol Evol 2004; 22:735-40. [PMID: 15563716 DOI: 10.1093/molbev/msi058] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Recently, genomic data have revealed a "block-like" structure of haplotype diversity on human chromosomes. This structure is anticipated to facilitate gene mapping studies, because strong associations among loci within a block may allow haplotype variation to be tagged with a limited number of markers. But its usefulness to mapping efforts depends on the consistency of the block structure within and among populations, which in turn depends on how the block structure arises. Recombination hot spots are generally thought to underlie the block structure, but haplotype blocks can also develop stochastically under random recombination, in which case the block structure will show limited consistency among populations. Using coalescent models, which we upscaled to simulate the evolution of haplotypes with many markers at fixed distances, we show that the relationship between block boundaries and historic recombination intensity may be surprisingly weak. The majority of historic recombinations do not leave a footprint in present-day linkage disequilibrium patterns, and the block structure is sensitive to factors that affect the timing of recombination relative to marker mutation events in the genealogy, such as marker frequency bias and historic population size changes. Our results give insight into the potential of stochastic events to affect haplotype block structure, which can limit the usefulness of the block structure to mapping studies.
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Affiliation(s)
- Koen J F Verhoeven
- Computational Genomics and Department of Agronomy, Purdue University, USA.
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24
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Ke X, Durrant C, Morris AP, Hunt S, Bentley DR, Deloukas P, Cardon LR. Efficiency and consistency of haplotype tagging of dense SNP maps in multiple samples. Hum Mol Genet 2004; 13:2557-65. [PMID: 15367493 DOI: 10.1093/hmg/ddh294] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Haplotype tagging is a means of retaining most of the information in high density marker maps, while reducing genotyping requirements. Estimates of the numbers of tagging SNPs required to cover the human genome have varied widely, ranging from 100,000 to 1,000,000. Tagging has been applied to a number of gene-based datasets but has not been evaluated in contexts reflecting those of genome-wide association studies--large chromosome regions and multiple samples drawn from the same population. We analysed 5000 common markers across a 10 Mb segment of human chromosome 20 in three samples (UK Caucasian, CEPH Caucasian, African American) to evaluate tagging efficiency and consistency. Overall, the results indicate a high degree of efficiency, yielding 3-5-fold savings in Caucasians and 2-3-fold savings in African Americans. These levels varied according to linkage disequilibrium (LD) levels, tagging thresholds and allele frequencies, but in high LD regions they did not vary markedly due to marker density. However, a strong positive relationship between marker density and tagging was observed, relating to the fact that increasing marker density yields greater sequence coverage in high LD, thus requiring more tag SNPs to cover a greater fraction of the genome. Encouragingly, whatever the density employed, a high level of robustness was observed between UK and CEPH samples, as most of the htSNPs selected in one sample were also appropriate as tags in the other.
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Affiliation(s)
- Xiayi Ke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
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25
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Crawford DC, Carlson CS, Rieder MJ, Carrington DP, Yi Q, Smith JD, Eberle MA, Kruglyak L, Nickerson DA. Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am J Hum Genet 2004; 74:610-22. [PMID: 15015130 PMCID: PMC1181939 DOI: 10.1086/382227] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2003] [Accepted: 12/17/2003] [Indexed: 01/15/2023] Open
Abstract
Recent studies have suggested that a significant fraction of the human genome is contained in blocks of strong linkage disequilibrium, ranging from ~5 to >100 kb in length, and that within these blocks a few common haplotypes may account for >90% of the observed haplotypes. Furthermore, previous studies have suggested that common haplotypes in candidate genes are generally shared across populations and represent the majority of chromosomes in each population. The conclusions drawn from these preliminary studies, however, are based on an incomplete knowledge of the variation in the regions examined. To bridge this gap in knowledge, we have completely resequenced 100 candidate genes in a population of African descent and one of European descent. Although these genes have been well studied because of their medical importance, we demonstrate that a large amount of sequence variation has not yet been described. We also report that the average number of inferred haplotypes per gene, when complete data is used, is higher than in previous reports and that the number and proportion of all haplotypes represented by common haplotypes per gene is variable. Furthermore, we demonstrate that haplotypes shared between the two populations constitute only a fraction of the total number of haplotypes observed and that these shared haplotypes represent fewer of the African-descent chromosomes than was expected from previous studies. Finally, we show that restricting variation discovery to coding regions does not adequately describe all common haplotypes or the true haplotype block structure observed when all common variation is used to infer haplotypes. These data, derived from complete knowledge of genetic variation in these genes, suggest that the haplotype architecture of candidate genes across the human genome is more complex than previously suggested, with important implications for candidate gene and genomewide association studies.
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Affiliation(s)
- Dana C. Crawford
- Department of Genome Sciences, University of Washington, and Division of Human Biology and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle
| | - Christopher S. Carlson
- Department of Genome Sciences, University of Washington, and Division of Human Biology and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle
| | - Mark J. Rieder
- Department of Genome Sciences, University of Washington, and Division of Human Biology and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle
| | - Dana P. Carrington
- Department of Genome Sciences, University of Washington, and Division of Human Biology and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle
| | - Qian Yi
- Department of Genome Sciences, University of Washington, and Division of Human Biology and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle
| | - Joshua D. Smith
- Department of Genome Sciences, University of Washington, and Division of Human Biology and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle
| | - Michael A. Eberle
- Department of Genome Sciences, University of Washington, and Division of Human Biology and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle
| | - Leonid Kruglyak
- Department of Genome Sciences, University of Washington, and Division of Human Biology and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, and Division of Human Biology and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle
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26
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Abstract
Human geneticists working on systems for which it is possible to make a strong case for a set of candidate genes face the problem of whether it is necessary to consider the variation in those genes as phased haplotypes, or whether the one-SNP-at-a-time approach might perform as well. There are three reasons why the phased haplotype route should be an improvement. First, the protein products of the candidate genes occur in polypeptide chains whose folding and other properties may depend on particular combinations of amino acids. Second, population genetic principles show us that variation in populations is inherently structured into haplotypes. Third, the statistical power of association tests with phased data is likely to be improved because of the reduction in dimension. However, in reality it takes a great deal of extra work to obtain valid haplotype phase information, and inferred phase information may simply compound the errors. In addition, if the causal connection between SNPs and a phenotype is truly driven by just a single SNP, then the haplotype-based approach may perform worse than the one-SNP-at-a-time approach. Here we examine some of the factors that affect haplotype patterns in genes, how haplotypes may be inferred, and how haplotypes have been useful in the context of testing association between candidate genes and complex traits.
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Affiliation(s)
- Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.
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27
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Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 2004; 74:106-20. [PMID: 14681826 PMCID: PMC1181897 DOI: 10.1086/381000] [Citation(s) in RCA: 1226] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2003] [Accepted: 10/23/2003] [Indexed: 01/23/2023] Open
Abstract
Common genetic polymorphisms may explain a portion of the heritable risk for common diseases. Within candidate genes, the number of common polymorphisms is finite, but direct assay of all existing common polymorphism is inefficient, because genotypes at many of these sites are strongly correlated. Thus, it is not necessary to assay all common variants if the patterns of allelic association between common variants can be described. We have developed an algorithm to select the maximally informative set of common single-nucleotide polymorphisms (tagSNPs) to assay in candidate-gene association studies, such that all known common polymorphisms either are directly assayed or exceed a threshold level of association with a tagSNP. The algorithm is based on the r(2) linkage disequilibrium (LD) statistic, because r(2) is directly related to statistical power to detect disease associations with unassayed sites. We show that, at a relatively stringent r(2) threshold (r2>0.8), the LD-selected tagSNPs resolve >80% of all haplotypes across a set of 100 candidate genes, regardless of recombination, and tag specific haplotypes and clades of related haplotypes in nonrecombinant regions. Thus, if the patterns of common variation are described for a candidate gene, analysis of the tagSNP set can comprehensively interrogate for main effects from common functional variation. We demonstrate that, although common variation tends to be shared between populations, tagSNPs should be selected separately for populations with different ancestries.
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28
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Kittles RA, Weiss KM. Race, ancestry, and genes: implications for defining disease risk. Annu Rev Genomics Hum Genet 2003; 4:33-67. [PMID: 14527296 DOI: 10.1146/annurev.genom.4.070802.110356] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Geneticists are interested in finding genes associated with disease. Because of widespread health disparities, race is a variable that is often said to be relevant in this context. The idea is that members of a preconceived "race" share common ancestry that may include genetic risk factors. Human variation has been shaped by the long-term processes of population history, and population samples that reflect that history carry statistical information about shared genetic variation or "ancestry." But race is an elusive concept and a term difficult even to define rigorously. Unfortunately, these problems are neither new nor related to recent genetic knowledge. Race is also one of the most politically charged subjects in American life because its associated sociocultural component has notoriously led to categorical treatment that has been misleading and politically misused. There are ways in which the concept of race (whether or not the term is used) can be a legitimate tool in the search for disease-associated genes. But in that context race reflects deeply confounded cultural as well as biological factors, and a careful distinction must be made between race as a statistical risk factor and causal genetic variables.
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Affiliation(s)
- Rick A Kittles
- National Human Genome Center, Howard University, Washington, D.C. 20060, USA.
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29
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Wang Z, Moult J. Three-dimensional structural location and molecular functional effects of missense SNPs in the T cell receptor V? domain. Proteins 2003; 53:748-57. [PMID: 14579365 DOI: 10.1002/prot.10522] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The mechanisms by which human single nucleotide polymorphisms (SNPs) influence susceptibility to disease are not yet well understood. In a previous study, we developed a structure-based model that may be used to identify which missense SNPs are neutral and which are deleterious to protein function and so potentially involved in disease (Wang and Moult, Hum Mutat 2001;263-270). The model has now been applied to a set of 54 missense cSNPs in the 46 functional T-cell receptor Vbeta-genes. Most of these missense cSNPs are found to be neutral, but 10 are identified as likely deleterious to protein function. Only one was previously associated with disease. We suggest that the others may be disease related but that redundancy in the T-cell response prevents any simple, monogenic effect. Therefore, these SNPs are the most likely contributors to complex, polygenic disease traits. It has been noted that there is a surprisingly high (74%) fraction of nonsynonymous SNPs in these genes. Contrary to expectation, the analysis shows that these are not associated with an unusually high fraction of deleterious SNPs, nor do they significantly contribute to a larger range of antigen recognition or a reduced superantigen-binding repertoire.
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MESH Headings
- Binding Sites
- Genes, Immunoglobulin
- Genetic Predisposition to Disease
- Immunoglobulin Variable Region/chemistry
- Immunoglobulin Variable Region/genetics
- Models, Molecular
- Mutation, Missense
- Polymorphism, Single Nucleotide
- Protein Binding
- Protein Structure, Tertiary
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
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Affiliation(s)
- Zhen Wang
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA
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30
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Zhang K, Akey JM, Wang N, Xiong M, Chakraborty R, Jin L. Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: an act of genetic drift. Hum Genet 2003; 113:51-9. [PMID: 12677424 DOI: 10.1007/s00439-003-0941-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2002] [Accepted: 02/08/2003] [Indexed: 11/30/2022]
Abstract
There is considerable interest in identifying and characterizing block-like patterns of linkage disequilibrium (LD; haplotype blocks) in the human genome as these may facilitate the identification of complex disease genes via genome-wide association studies. Although recombination hot-spots have been suggested as the primary mechanism to explain the block-like pattern of LD, other forces, such as genetic drift, may also be important. To this end, we have studied the effect of various recombination models on patterns of LD by using extensive simulations. As expected, haplotype blocks were observed under a model allowing recombination hot-spots. However, we also observed similar block-like patterns in the models where recombination crossovers are randomly and uniformly distributed, and we demonstrate that these blocks are generated by genetic drift. We caution that genetic drift may be an alternative mechanism (in addition to recombination hot-spots) that can lead to block-like patterns of LD. Our findings highlight the necessity of characterizing haplotype blocks in world-wide populations.
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Affiliation(s)
- Kun Zhang
- Center for Genome Information, 130 Kettering, Department of Environmental Health, University of Cincinnati, OH 45215, Cincinnati, USA
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31
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Meng Z, Zaykin DV, Xu CF, Wagner M, Ehm MG. Selection of genetic markers for association analyses, using linkage disequilibrium and haplotypes. Am J Hum Genet 2003; 73:115-30. [PMID: 12796855 PMCID: PMC1180574 DOI: 10.1086/376561] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2003] [Accepted: 04/24/2003] [Indexed: 11/04/2022] Open
Abstract
The genotyping of closely spaced single-nucleotide polymorphism (SNP) markers frequently yields highly correlated data, owing to extensive linkage disequilibrium (LD) between markers. The extent of LD varies widely across the genome and drives the number of frequent haplotypes observed in small regions. Several studies have illustrated the possibility that LD or haplotype data could be used to select a subset of SNPs that optimize the information retained in a genomic region while reducing the genotyping effort and simplifying the analysis. We propose a method based on the spectral decomposition of the matrices of pairwise LD between markers, and we select markers on the basis of their contributions to the total genetic variation. We also modify Clayton's "haplotype tagging SNP" selection method, which utilizes haplotype information. For both methods, we propose sliding window-based algorithms that allow the methods to be applied to large chromosomal regions. Our procedures require genotype information about a small number of individuals for an initial set of SNPs and selection of an optimum subset of SNPs that could be efficiently genotyped on larger numbers of samples while retaining most of the genetic variation in samples. We identify suitable parameter combinations for the procedures, and we show that a sample size of 50-100 individuals achieves consistent results in studies of simulated data sets in linkage equilibrium and LD. When applied to experimental data sets, both procedures were similarly effective at reducing the genotyping requirement while maintaining the genetic information content throughout the regions. We also show that haplotype-association results that Hosking et al. obtained near CYP2D6 were almost identical before and after marker selection.
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Affiliation(s)
- Zhaoling Meng
- Bioinformatics Research Center, Campus Box 7566, North Carolina State University, Raleigh, NC 27695-7566, USA.
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32
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Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA, Studebaker JF, Ankener WM, Alfisi SV, Kuo FS, Camisa AL, Pazorov V, Scott KE, Carey BJ, Faith J, Katari G, Bhatti HA, Cyr JM, Derohannessian V, Elosua C, Forman AM, Grecco NM, Hock CR, Kuebler JM, Lathrop JA, Mockler MA, Nachtman EP, Restine SL, Varde SA, Hozza MJ, Gelfand CA, Broxholme J, Abecasis GR, Boyce-Jacino MT, Cardon LR. Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat Genet 2003; 33:382-7. [PMID: 12590262 DOI: 10.1038/ng1100] [Citation(s) in RCA: 217] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2002] [Accepted: 01/16/2003] [Indexed: 01/30/2023]
Abstract
Recent studies of human populations suggest that the genome consists of chromosome segments that are ancestrally conserved ('haplotype blocks'; refs. 1-3) and have discrete boundaries defined by recombination hot spots. Using publicly available genetic markers, we have constructed a first-generation haplotype map of chromosome 19. As expected for this marker density, approximately one-third of the chromosome is encompassed within haplotype blocks. Evolutionary modeling of the data indicates that recombination hot spots are not required to explain most of the observed blocks, providing that marker ascertainment and the observed marker spacing are considered. In contrast, several long blocks are inconsistent with our evolutionary models, and different mechanisms could explain their origins.
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Affiliation(s)
- M S Phillips
- Orchid Biosciences Inc., 303A College Road East, Princeton, New Jersey 08540, USA
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33
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Noonan JP, Li J, Nguyen L, Caoile C, Dickson M, Grimwood J, Schmutz J, Feldman MW, Myers RM. Extensive linkage disequilibrium, a common 16.7-kilobase deletion, and evidence of balancing selection in the human protocadherin alpha cluster. Am J Hum Genet 2003; 72:621-35. [PMID: 12577201 PMCID: PMC1180238 DOI: 10.1086/368060] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2002] [Accepted: 12/05/2002] [Indexed: 02/03/2023] Open
Abstract
Regions of extensive linkage disequilibrium (LD) appear to be a common feature of the human genome. However, the mechanisms that maintain these regions are unknown. In an effort to understand whether gene density contributes to LD, we determined the degree of promoter sequence variation in a large tandem-arrayed gene family, the human protocadherin alpha cluster, on chromosome 5. These genes are expressed at synaptic junctions in the developing brain and the adult brain and may be involved in the determination of synaptic complexity. We sequenced the promoters of all 13 alpha protocadherin genes in 96 European Americans and identified polymorphisms in the promoters alpha 1, alpha 3, alpha 4, alpha 5, alpha 7, alpha 9, alpha 11, and alpha 13. In these promoters, 11 common SNPs are in extensive LD, forming two 48-kb haplotypes of equal frequency, in this population, that extend from the alpha1 through alpha 7 genes. We sequenced these promoters in East Asians and African Americans, and we estimated haplotype frequencies and calculated LD statistics for all three populations. Our results indicate that, although extensive LD is an ancient feature of the alpha cluster, it has eroded over time. SNPs 3' of alpha 7 are involved in ancestral recombination events in all populations, and overall alpha-cluster LD is reduced in African Americans. We obtained significant positive values for Tajima's D test for all alpha promoter SNPs in Europeans (D=3.03) and East Asians (D=2.64), indicating an excess of intermediate-frequency variants, which is a signature of balancing selection. We also discovered a 16.7-kb deletion that truncates the alpha 8 gene and completely removes the alpha 9 and alpha 10 genes. This deletion appears in unaffected individuals from multiple populations, suggesting that a reduction in protocadherin gene number is not obviously deleterious.
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Affiliation(s)
- James P. Noonan
- Department of Genetics, Stanford University School of Medicine, and Department of Biological Sciences, Herrin Laboratories, Stanford University, Stanford, CA; and Stanford Human Genome Center, Stanford University School of Medicine, Palo Alto, CA
| | - Jun Li
- Department of Genetics, Stanford University School of Medicine, and Department of Biological Sciences, Herrin Laboratories, Stanford University, Stanford, CA; and Stanford Human Genome Center, Stanford University School of Medicine, Palo Alto, CA
| | - Loan Nguyen
- Department of Genetics, Stanford University School of Medicine, and Department of Biological Sciences, Herrin Laboratories, Stanford University, Stanford, CA; and Stanford Human Genome Center, Stanford University School of Medicine, Palo Alto, CA
| | - Chenier Caoile
- Department of Genetics, Stanford University School of Medicine, and Department of Biological Sciences, Herrin Laboratories, Stanford University, Stanford, CA; and Stanford Human Genome Center, Stanford University School of Medicine, Palo Alto, CA
| | - Mark Dickson
- Department of Genetics, Stanford University School of Medicine, and Department of Biological Sciences, Herrin Laboratories, Stanford University, Stanford, CA; and Stanford Human Genome Center, Stanford University School of Medicine, Palo Alto, CA
| | - Jane Grimwood
- Department of Genetics, Stanford University School of Medicine, and Department of Biological Sciences, Herrin Laboratories, Stanford University, Stanford, CA; and Stanford Human Genome Center, Stanford University School of Medicine, Palo Alto, CA
| | - Jeremy Schmutz
- Department of Genetics, Stanford University School of Medicine, and Department of Biological Sciences, Herrin Laboratories, Stanford University, Stanford, CA; and Stanford Human Genome Center, Stanford University School of Medicine, Palo Alto, CA
| | - Marcus W. Feldman
- Department of Genetics, Stanford University School of Medicine, and Department of Biological Sciences, Herrin Laboratories, Stanford University, Stanford, CA; and Stanford Human Genome Center, Stanford University School of Medicine, Palo Alto, CA
| | - Richard M. Myers
- Department of Genetics, Stanford University School of Medicine, and Department of Biological Sciences, Herrin Laboratories, Stanford University, Stanford, CA; and Stanford Human Genome Center, Stanford University School of Medicine, Palo Alto, CA
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Abstract
Several studies of haplotype structures in the human genome in various populations have been published recently. Such knowledge may provide valuable information on human evolutionary history and lead to the development of more efficient strategies to identify genetic variants that increase susceptibility to human diseases. In this review, we summarize the current understanding of haplotype structure, diversity, and distribution in the human genome, with a focus on statistical issues in using haplotypes for studies of population genetics and evolutionary history, as well as to identify genetic variants underlying complex human traits.
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Affiliation(s)
- Hongyu Zhao
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06520, USA.
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35
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Geraghty DE, Daza R, Williams LM, Vu Q, Ishitani A. Genetics of the immune response: identifying immune variation within the MHC and throughout the genome. Immunol Rev 2002; 190:69-85. [PMID: 12493007 DOI: 10.1034/j.1600-065x.2002.19006.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
With the advent of modern genomic sequencing technology the ability to obtain new sequence data and to acquire allelic polymorphism data from a broad range of samples has become routine. In this regard, our investigations have started with the most polymorphic of genetic regions fundamental to the immune response in the major histocompatibility complex (MHC). Starting with the completed human MHC genomic sequence, we have developed a resource of methods and information that provide ready access to a large portion of human and nonhuman primate MHCs. This resource consists of a set of primer pairs or amplicons that can be used to isolate about 15% of the 4.0 Mb MHC. Essentially similar studies are now being carried out on a set of immune response loci to broaden the usefulness of the data and tools developed. A panel of 100 genes involved in the immune response have been targeted for single nucleotide polymorphism (SNP) discovery efforts that will analyze 120 Mb of sequence data for the presence of immune-related SNPs. The SNP data provided from the MHC and from the immune response panel has been adapted for use in studies of evolution, MHC disease associations, and clinical transplantation.
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Affiliation(s)
- Daniel E Geraghty
- Reseach Division, Fred Hutchinson Cancer Research Center, N. Seattle, WA 98109, USA.
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36
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Mackelprang R, Carlson CS, Subrahmanyan L, Livingston RJ, Eberle MA, Nickerson DA. Sequence variation in the human T-cell receptor loci. Immunol Rev 2002; 190:26-39. [PMID: 12493004 DOI: 10.1034/j.1600-065x.2002.19003.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Identifying common sequence variations known as single nucleotide polymorphisms (SNPs) in human populations is one of the current objectives of the human genome project. Nearly 3 million SNPs have been identified. Analysis of the relative allele frequency of these markers in human populations and the genetic associations between these markers, known as linkage disequilibrium, is now underway to generate a high-density genetic map. Because of the central role T cells play in immune reactivity, the T-cell receptor (TCR) loci have long been considered important candidates for common disease susceptibility within the immune system (e.g., asthma, atopy and autoimmunity). Over the past two decades, hundreds of SNPs in the TCR loci have been identified. Most studies have focused on defining SNPs in the variable gene segments which are involved in antigenic recognition. On average, the coding sequence of each TCR variable gene segment contains two SNPs, with many more found in the 5', 3' and intronic sequences of these segments. Therefore, a potentially large repertoire of functional variants exists in these loci. Association between SNPs (linkage disequilibrium) extends approximately 30 kb in the TCR loci, although a few larger regions of disequilibrium have been identified. Therefore, the SNPs found in one variable gene segment may or may not be associated with SNPs in other surrounding variable gene segments. This suggests that meaningful association studies in the TCR loci will require the analysis and typing of large marker sets to fully evaluate the role of TCR loci in common disease susceptibility in human populations.
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Affiliation(s)
- Rachel Mackelprang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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37
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Wang N, Akey JM, Zhang K, Chakraborty R, Jin L. Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation. Am J Hum Genet 2002; 71:1227-34. [PMID: 12384857 PMCID: PMC385104 DOI: 10.1086/344398] [Citation(s) in RCA: 323] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2002] [Accepted: 08/21/2002] [Indexed: 11/03/2022] Open
Abstract
Recent studies suggest that haplotypes are arranged into discrete blocklike structures throughout the human genome. Here, we present an alternative haplotype block definition that assumes no recombination within each block but allows for recombination between blocks, and we use it to study the combined effects of demographic history and various population genetic parameters on haplotype block characteristics. Through extensive coalescent simulations and analysis of published haplotype data on chromosome 21, we find that (1) the combined effects of population demographic history, recombination, and mutation dictate haplotype block characteristics and (2) haplotype blocks can arise in the absence of recombination hot spots. Finally, we provide practical guidelines for designing and interpreting studies investigating haplotype block structure.
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Affiliation(s)
- Ning Wang
- Center for Genome Information, University of Cincinnati, Cincinnati, OH 45267-0056, USA
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38
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Weber JL, David D, Heil J, Fan Y, Zhao C, Marth G. Human diallelic insertion/deletion polymorphisms. Am J Hum Genet 2002; 71:854-62. [PMID: 12205564 PMCID: PMC378541 DOI: 10.1086/342727] [Citation(s) in RCA: 245] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2002] [Accepted: 07/09/2002] [Indexed: 12/20/2022] Open
Abstract
We report the identification and characterization of 2,000 human diallelic insertion/deletion polymorphisms (indels) distributed throughout the human genome. Candidate indels were identified by comparison of overlapping genomic or cDNA sequences. Average confirmation rate for indels with a > or =2-nt allele-length difference was 58%, but the confirmation rate for indels with a 1-nt length difference was only 14%. The vast majority of the human diallelic indels were monomorphic in chimpanzees and gorillas. The ratio of deletionrcolon;insertion mutations was 4.1. Allele frequencies for the indels were measured in Europeans, Africans, Japanese, and Native Americans. New alleles were generally lower in frequency than old alleles. This tendency was most pronounced for the Africans, who are likely to be closest among the four groups to the original modern human population. Diallelic indels comprise approximately 8% of all human polymorphisms. Their abundance and ease of analysis make them useful for many applications.
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Affiliation(s)
- James L Weber
- Center for Medical Genetics, Marshfield Medical Research Foundation, Marshfield, WI 54449, USA.
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39
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Tabor HK, Risch NJ, Myers RM. Candidate-gene approaches for studying complex genetic traits: practical considerations. Nat Rev Genet 2002; 3:391-7. [PMID: 11988764 DOI: 10.1038/nrg796] [Citation(s) in RCA: 637] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Association studies with candidate genes have been widely used for the study of complex diseases. However, this approach has been criticized because of non-replication of results and limits on its ability to include all possible causative genes and polymorphisms. These challenges have led to pessimism about the candidate-gene approach and about the genetic analysis of complex diseases in general. We believe that these criticisms can be usefully countered with an appeal to the principles of epidemiological investigation.
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Affiliation(s)
- Holly K Tabor
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California 94305-5120, USA
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40
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Ardlie KG, Kruglyak L, Seielstad M. Patterns of linkage disequilibrium in the human genome. Nat Rev Genet 2002; 3:299-309. [PMID: 11967554 DOI: 10.1038/nrg777] [Citation(s) in RCA: 736] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Particular alleles at neighbouring loci tend to be co-inherited. For tightly linked loci, this might lead to associations between alleles in the population a property known as linkage disequilibrium (LD). LD has recently become the focus of intense study in the hope that it might facilitate the mapping of complex disease loci through whole-genome association studies. This approach depends crucially on the patterns of LD in the human genome. In this review, we draw on empirical studies in humans and Drosophila, as well as simulation studies, to assess the current state of knowledge about patterns of LD, and consider the implications for the use of LD as a mapping tool.
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Affiliation(s)
- Kristin G Ardlie
- Genomics Collaborative, 99 Erie Street, Cambridge, Massachusetts 02139, USA
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41
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Abstract
The potential value of haplotypes defined by several single nucleotide polymorphisms has attracted recent interest. With sufficient linkage disequilibrium (LD), haplotypes could be used in association studies to map common alleles that might influence the susceptibility to common diseases, as well as for reconstructing the evolution of the genome. It has been proposed that a globally useful resource need only be based on high frequency variants, identified from a few modest samples. Rapid progress has been made in quantifying the pattern of human LD and haplotypes defined by such common variants within and among populations. However, the quality and utility of the proposed LD-based resource could be seriously compromised if important sampling and analytical factors are overlooked in its design. The LD map should be based on adequately justified criteria defined by sound population genetic principles.
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Affiliation(s)
- Kenneth M Weiss
- Department of Anthropology, Penn State University, 409 Carpenter Bldg, University Park, PA 16802-3404, USA.
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