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Kim JW, Kim MJ, Paik K, Kim BR, Choi CW, Na JI. Genome-wide Association Study of Susceptibility Loci for Self-Reported Atopic Dermatitis and Allergic Rhinitis in the Korean Population. Ann Dermatol 2024; 36:74-80. [PMID: 38576245 PMCID: PMC10995615 DOI: 10.5021/ad.22.160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 11/19/2023] [Accepted: 12/27/2023] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Allergic diseases include atopic dermatitis (AD) and allergic rhinitis (AR), which are chronic, relapsing inflammatory disorders of the skin or mucosa that usually accompany immunoglobulin E-mediated immune responses. They are complex, multifactorial diseases with an etiology involving interactions between genetic and environmental factors. OBJECTIVE We performed a genome-wide association study (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with allergic diseases in the Korean population. METHODS A total of 8,840 samples were obtained from the Korean Association Resource Consortium dataset of the Korean Genome and Epidemiology Study Ansan-Anseong cohort. The allergic disease phenotype was determined based on self-reported physician diagnoses. After quality control, 8,823 subjects with 877,242 variants remained for the final analysis. The GWAS was performed using logistic regression analysis in an additive model adjusted for age and sex. RESULTS A total of 636 patients with allergic disease and 8,176 controls were analyzed. Three SNPs were associated with allergic disease at a level of genome-wide suggestive significance (p<1.0×10-5) in the Korean population: rs7275360, located in neural cell adhesion molecule 2; rs698195; and rs3750552, located in family with sequence similarity 189, member A2. These polymorphisms were on chromosomes 21q21.1, 7q31.1, and 9q21.12, respectively. CONCLUSION We identified 3 novel SNPs significantly associated with allergic diseases in the Korean population. Further research is required to confirm the association between these novel SNPs and allergic disease in the Korean population and in other ethnicities.
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Affiliation(s)
- Jee Woo Kim
- Department of Dermatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Min Jae Kim
- Department of Dermatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Kyungho Paik
- Department of Dermatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Bo Ri Kim
- Department of Dermatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Chong Won Choi
- Department of Dermatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jung-Im Na
- Department of Dermatology, Seoul National University Bundang Hospital, Seongnam, Korea.
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An J, Do AR, Kang HY, Kim WJ, Lee S, Lee JH, Song WJ, Kwon HS, Cho YS, Moon HB, Hu S, Adcock IM, Chung KF, Won S, Kim TB. Genome-Wide Association Study of Korean Asthmatics: A Comparison With UK Asthmatics. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2021; 13:609-622. [PMID: 34212547 PMCID: PMC8255356 DOI: 10.4168/aair.2021.13.4.609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/19/2021] [Accepted: 05/12/2021] [Indexed: 12/23/2022]
Abstract
PURPOSE Although genome-wide association studies (GWASs) represent the most powerful approach for identifying genes that influence asthma, to date, no studies have established genetic susceptibility to asthma in the Korean population. This study aimed to identify genetic variants associated with adult Korean asthmatics and compare them with the significant single nucleotide polymorphisms (SNPs) of UK asthmatics from the UK Biobank. METHODS Patients were defined as having asthma if they were diagnosed by a doctor or taking medications for asthma. Controls were defined as individuals without asthma or chronic obstructive pulmonary disease. We performed quality control, genotype imputation, GWAS, and PrediXcan analyses. In the GWAS, a P value of < 5 × 10-8 was considered significant. We compared significant SNPs between Korean and UK patients with asthma. RESULTS A total of 1,386 asthmatic patients and 5,205 controls were analyzed. The SNP rs1770, located near the human leukocyte antigen (HLA)-DQB1, was the most significant SNP (P = 4.5 × 10-10). In comparison with 24 SNPs in a GWAS of UK asthmatics, six SNPs were significant with the same odds ratio (OR) direction, including signals related to type 2 inflammation (e.g., IL1RL1, TSLP, and GATA3) and mucus plugging (e.g., MUC5AC). HLA-DQA1 showed an opposite OR direction. The HLA-DQB1 gene demonstrated significantly imputed mRNA expression in the lung tissue and whole blood. CONCLUSIONS The SNP rs1770 of HLA-DQB1 was the most significant in Korean asthmatics. Similarities and discrepancies were found in the genetic variants between Korean and UK asthmatics. GWAS of Korean asthmatics should be replicated and compared with those of GWAS of other ethnicities.
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Affiliation(s)
- Jin An
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Pulmonary, Allergy and Critical Care Medicine, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Ah Ra Do
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, Korea
| | - Hae Yeon Kang
- Department of Internal Medicine, Healthcare Research Institute, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Korea
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, School of Medicine, Kangwon National University, Chuncheon, Korea
| | - Sanghun Lee
- Department of Medical Consilience, Graduate School, Dankook university, Yongin, Korea
| | - Ji Hyang Lee
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Woo Jung Song
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyouk Soo Kwon
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - You Sook Cho
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hee Bom Moon
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sile Hu
- Experimental Studies, Airways Disease Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Ian M Adcock
- Experimental Studies, Airways Disease Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Kian Fan Chung
- Experimental Studies, Airways Disease Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Sungho Won
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, Korea.,Department of Public Health Sciences, School of Public Health, Seoul National University, Seoul, Korea.,Institute of Health and Environment, Seoul National University, Seoul, Korea.
| | - Tae Bum Kim
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
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Ran H, Xiao H, Zhou X, Guo L, Lu S. Single-nucleotide polymorphisms and haplotypes in the interleukin-33 gene are associated with a risk of allergic rhinitis in the Chinese population. Exp Ther Med 2020; 20:102. [PMID: 32973951 DOI: 10.3892/etm.2020.9232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/23/2020] [Indexed: 11/05/2022] Open
Abstract
Allergic rhinitis (AR) is a common upper airway disease attributed to a variety of risk factors, such as environmental exposures and genetic susceptibility. The commonly observed comorbidity of asthma and AR in the clinic suggests the presence of shared genetic risk factors and biological mechanisms between these diseases. Interleukin (IL)-33 has been indicated to be an important factor driving asthma susceptibility and pathogenesis using both genome-wide association studies and functional studies in model animals. Although previous studies have reported the putative association of this gene with AR, evidence for the association of genetic variations of IL-33 with the disease is still missing. To examine whether variations in the IL-33 gene confer a genetic risk of AR, a total of 769 patients with AR and 769 age- and sex-matched healthy controls were recruited among Han Chinese residents in the Hubei province, and 14 single-nucleotide polymorphisms (SNPs) spanning the IL-33 gene were examined for their association with the risk of AR. The results indicated that five SNPs, which were in a moderate linkage disequilibrium and were located in the 5'-flanking region of IL-33, exhibited significant associations with the risk of AR, and these associations were additionally supported by genotypic and haplotypic analyses. Notably, three of the five IL-33 SNPs have been previously reported to exhibit genome-wide associations with asthma, and their alleles were also revealed to confer an increased risk of AR in the present study. In summary, the results of the current study suggested that certain variations in the IL-33 gene represent a potential risk for AR, and indicated a shared genetic basis between AR and asthma.
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Affiliation(s)
- He Ran
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jingzhou, Jingzhou, Hubei 434000, P.R. China
| | - Hua Xiao
- Hubei College of Chinese Medicine, Jingzhou, Hubei 434020, P.R. China
| | - Xing Zhou
- Department of Otolaryngology Head and Neck Surgery, Shishou People's Hospital, Jingzhou, Hubei 434400, P.R. China
| | - Lijun Guo
- Hubei College of Chinese Medicine, Jingzhou, Hubei 434020, P.R. China
| | - Shuang Lu
- Hubei College of Chinese Medicine, Jingzhou, Hubei 434020, P.R. China
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Mei Q, Qu J. Interleukin-13 +2044 G/A and +1923C/T polymorphisms are associated with asthma susceptibility in Asians: A meta-analysis. Medicine (Baltimore) 2017; 96:e9203. [PMID: 29390465 PMCID: PMC5758167 DOI: 10.1097/md.0000000000009203] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A number of studies have reported that the interleukin 13 (IL-13) gene is associated with asthma susceptibility. However, the reported relationships between the +2044G/A and +1923C/T polymorphisms and asthma susceptibility are inconsistent, especially in Asian adults and children with atopic status. Meta-analysis was used to analyze combined data.The +2044G/A and +1923C/T polymorphisms were investigated using data from 18 and 11 studies, respectively. The results suggested that there was an association between asthma and the IL-13 +2044G/A polymorphisms: odds ratio (OR) 1.34, 95% confidence interval (CI) 1.03-1.75 for AA versus GG + GA and +1923C/T; OR 1.50, 95% CI 1.26-1.78 for TT versus CC; and OR 1.15, 95% CI 1.10-1.21 for TC versus CC. The subgroup meta-analysis demonstrated that IL-13 +2044G/A polymorphisms are associated with asthma: OR 1.47, 95% CI 1.06-2.04 for AA versus GG + GA and +1923C/T; OR 1.70, 95% CI 1.26-2.30 for TT versus CC; and OR 1.27, 95% CI 1.03-1.56 for TC versus CC. In particular, IL-13 +2044G/A polymorphisms are specifically associated with Asian ethnicity in both adults and children with atopic status. However, the 1923C/T polymorphisms were not significantly associated with age group or atopic status within the Asian subgroups. Further investigation using larger samples and meta-analysis is required. No publication bias was detected.This meta-analysis indicates that the IL13 +2044G/A and +1923C/T polymorphisms are risk factors for asthma, especially among Asians.
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Affiliation(s)
- Quanhui Mei
- Department of Intensive Care Unit, The First People's Hospital of Changde City, Changde, Hunan
| | - Jingjing Qu
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, China
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Association between IL-13 +1923C/T polymorphism and asthma risk: a meta-analysis based on 26 case-control studies. Biosci Rep 2017; 37:BSR20160505. [PMID: 28057889 PMCID: PMC5270317 DOI: 10.1042/bsr20160505] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/02/2017] [Accepted: 01/05/2017] [Indexed: 01/22/2023] Open
Abstract
Asthma is a serious and hereditary respiratory disorder affecting all age groups. Interleukin-13 (IL-13) is a central regulator of allergic inflammation. The purpose of the present study was to estimate the relationship between IL-13 +1923C/T polymorphism and asthma susceptibility. Relevant case-control studies published between January 2000 and July 2016 were searched in the online databases. Review Manage (RevMan) 5.3 was used to conduct the statistical analysis. The pooled odds ratio (OR) with its 95% confidence interval (CI) was employed to calculate the strength of association. A total of 26 articles were retrieved, including 17642 asthma patients and 42402 controls. Overall, our results found that IL-13 +1923C/T polymorphism was significantly associated with increased risk of asthma under each genetic model (P<0.00001). Subgroup analysis by ethnicity showed that alleles and genotypes of this variant correlated with asthma among Asians and Caucasians, but only TT genotype under the homozygote model in Africans. When stratified by age group, this variant highly correlated with asthma in children and moderately in adults. Furthermore, the TT, CT and CC genotypes in asthma group were all significantly associated with increased IgE levels in sera of asthma patients when compared with controls. Our results suggested that IL-13 +1923C/T polymorphism contributed to the development of asthma. Further case-control studies with more ethnicities are still needed.
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Kim KW, Myers RA, Lee JH, Igartua C, Lee KE, Kim YH, Kim EJ, Yoon D, Lee JS, Hirota T, Tamari M, Takahashi A, Kubo M, Choi JM, Kim KE, Nicolae DL, Ober C, Sohn MH. Genome-wide association study of recalcitrant atopic dermatitis in Korean children. J Allergy Clin Immunol 2015; 136:678-684.e4. [PMID: 25935106 DOI: 10.1016/j.jaci.2015.03.030] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/05/2015] [Accepted: 03/13/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Atopic dermatitis (AD) is a heterogeneous chronic inflammatory skin disease. Most AD during infancy resolves during childhood, but moderate-to-severe AD with allergic sensitization is more likely to persist into adulthood and more often occurs with other allergic diseases. OBJECTIVE We sought to find susceptibility loci by performing the first genome-wide association study (GWAS) of AD in Korean children with recalcitrant AD, which was defined as moderate-to-severe AD with allergic sensitization. METHODS Our study included 246 children with recalcitrant AD and 551 adult control subjects with a negative history of both allergic disease and allergic sensitization. DNA from these subjects was genotyped; sets of common single nucleotide polymorphisms (SNPs) were imputed and used in the GWAS after quality control checks. RESULTS SNPs at a region on 13q21.31 were associated with recalcitrant AD at a genome-wide threshold of significance (P < 2.0 × 10(-8)). These associated SNPs are more than 1 Mb from the closest gene, protocadherin (PCDH)9. SNPs at 4 additional loci had P values of less than 1 × 10(-6), including SNPs at or near the neuroblastoma amplified sequence (NBAS; 2p24.3), thymus-expressed molecule involved in selection (THEMIS; 6q22.33), GATA3 (10p14), and S-phase cyclin A-associated protein in the ER (SCAPER; 15q24.3) genes. Further analysis of total serum IgE levels suggested 13q21.31 might be primarily an IgE locus, and analyses of published data demonstrated that SNPs at the 15q24.3 region are expression quantitative trait loci for 2 nearby genes, ISL2 and proline-serine-threonine phosphatase interacting protein 1 (PSTPIP1), in immune cells. CONCLUSION Our GWAS of recalcitrant AD identified new susceptibility regions containing genes involved in epithelial cell function and immune dysregulation, 2 key features of AD, and potentially extend our understanding of their role in pathogenesis.
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Affiliation(s)
- Kyung Won Kim
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 PLUS project for Medical Science, Yonsei University College of Medicine, Seoul, Korea; Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Rachel A Myers
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Ji Hyun Lee
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul, Korea
| | | | - Kyung Eun Lee
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 PLUS project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Yoon Hee Kim
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 PLUS project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Eun-Jin Kim
- Division of Allergy and Chronic Respiratory Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Osong, Korea
| | - Dankyu Yoon
- Division of Allergy and Chronic Respiratory Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Osong, Korea
| | - Joo-Shil Lee
- Division of Allergy and Chronic Respiratory Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Osong, Korea
| | - Tomomitsu Hirota
- Laboratory for Respiratory and Allergic Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Mayumi Tamari
- Laboratory for Respiratory and Allergic Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Je-Min Choi
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, Korea
| | - Kyu-Earn Kim
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 PLUS project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Dan L Nicolae
- Department of Human Genetics, University of Chicago, Chicago, Ill; Department of Medicine and Statistics, University of Chicago, Chicago, Ill
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Myung Hyun Sohn
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 PLUS project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.
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Genome-wide association studies in asthma: what they really told us about pathogenesis. Curr Opin Allergy Clin Immunol 2013; 13:112-8. [PMID: 23222155 DOI: 10.1097/aci.0b013e32835c1674] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Over the past years, several consortia have provided a data deluge from large-scale, genome-wide association studies (GWASs) for numerous asthma and allergy related traits. Dozens of reviews have already summarized the main results, although a coherent picture is still missing, referred to as 'missing' or 'unexplained' heritability. RECENT FINDINGS We identify the factors responsible for the unexplained heritability including imprecise phenotyping, biased single-nucleotide polymorphism selection (preferentially gene-based and high allele frequency with poor linkage disequilibrium tagging capacity), heterogeneity and insufficient significance ranking test statistics. In spite of these problems, three major outcomes can already be identified. First, rare variants give the highest risk estimates but are limited to small subgroups indicating a complex origin of asthma that may involve hundreds of variants that are either population, family or individual specific. Second, only a few common variants are shared amongst all asthmatics where the IL33/ST2 pathway turns out to be the most relevant factor. Third, transcription factor binding sites are enriched amongst the top association results pointing towards disturbed regulatory network function in asthma. SUMMARY The next wave of asthma genetic studies will use full-genome sequencing and overcome most GWAS-associated problems. It will be the last step of a century-long search for asthma genes, satisfying scientific curiosity and, hopefully, also providing data applicable in translational medicine.
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Park SJ, Yang JO, Kim SC, Kwon J, Lee S, Lee B. Inference of kinship coefficients from Korean SNP genotyping data. BMB Rep 2013; 46:305-9. [PMID: 23790973 PMCID: PMC4133901 DOI: 10.5483/bmbrep.2013.46.6.177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The determination of relatedness between individuals in a family is crucial in analysis of common complex diseases. We present a method to infer close inter-familial relationships based on SNP genotyping data and provide the relationship coefficient of kinship in Korean families. We obtained blood samples from 43 Korean individuals in two families. SNP data was obtained using the Affymetrix Genome-wide Human SNP array 6.0 and the Illumina Human 1M-Duo chip. To measure the kinship coefficient with the SNP genotyping data, we considered all possible pairs of individuals in each family. The genetic distance between two individuals in a pair was determined using the allele sharing distance method. The results show that genetic distance is proportional to the kinship coefficient and that a close degree of kinship can be confirmed with SNP genotyping data. This study represents the first attempt to identify the genetic distance between very closely related individuals.
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Affiliation(s)
- Seong-Jin Park
- Korean BioInformation Center (KOBIC), KRIBB, Daejeon 305-333, Korea
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Interleukin-13 +1923C/T polymorphism is associated with asthma risk: a meta-analysis. BIOMED RESEARCH INTERNATIONAL 2013; 2013:394316. [PMID: 23841068 PMCID: PMC3693103 DOI: 10.1155/2013/394316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 05/22/2013] [Indexed: 11/17/2022]
Abstract
There are controversies on the association between interleukin-13 (IL-13) +1923C/T polymorphism (rs1295686) and the risk of asthma. We performed this study to assess the association by the method of meta-analysis. A systematic search current to October 16, 2012, was conducted using PubMed, EMBASE, and China National Knowledge Infrastructure (CNKI) and identified ten studies comprising 13698 cases and 38209 controls. The pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. There was a significant association between IL-13 +1923C/T polymorphism and asthma risk in codominant model. When stratified by ethnicity, IL-13 +1923C/T polymorphism remained significantly associated with higher asthma risk in Asians and Caucasians. In the subgroup analysis by study quality, a significantly increased asthma risk was observed in high quality studies. Sensitivity analysis and cumulative analysis further strengthened the validity of the results. No publication bias was found in this meta-analysis. In conclusion, results from this meta-analysis suggested that IL-13 +1923C/T polymorphism was a risk factor of asthma.
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Thompson EA. Identity by descent: variation in meiosis, across genomes, and in populations. Genetics 2013; 194:301-26. [PMID: 23733848 PMCID: PMC3664843 DOI: 10.1534/genetics.112.148825] [Citation(s) in RCA: 199] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Accepted: 03/10/2013] [Indexed: 01/04/2023] Open
Abstract
Gene identity by descent (IBD) is a fundamental concept that underlies genetically mediated similarities among relatives. Gene IBD is traced through ancestral meioses and is defined relative to founders of a pedigree, or to some time point or mutational origin in the coalescent of a set of extant genes in a population. The random process underlying changes in the patterns of IBD across the genome is recombination, so the natural context for defining IBD is the ancestral recombination graph (ARG), which specifies the complete ancestry of a collection of chromosomes. The ARG determines both the sequence of coalescent ancestries across the chromosome and the extant segments of DNA descending unbroken by recombination from their most recent common ancestor (MRCA). DNA segments IBD from a recent common ancestor have high probability of being of the same allelic type. Non-IBD DNA is modeled as of independent allelic type, but the population frame of reference for defining allelic independence can vary. Whether of IBD, allelic similarity, or phenotypic covariance, comparisons may be made to other genomic regions of the same gametes, or to the same genomic regions in other sets of gametes or diploid individuals. In this review, I present IBD as the framework connecting evolutionary and coalescent theory with the analysis of genetic data observed on individuals. I focus on the high variance of the processes that determine IBD, its changes across the genome, and its impact on observable data.
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Affiliation(s)
- Elizabeth A Thompson
- Department of Statistics, University of Washington, Seattle, WA 98195-4322, USA.
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