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Hashimoto S, Nakajima F, Imanishi T, Kawai Y, Kato K, Kimura T, Miyata S, Takanashi M, Nishio M, Tokunaga K, Satake M. Implications of HLA diversity among regions for bone marrow donor searches in Japan. HLA 2020; 96:24-42. [PMID: 32222025 DOI: 10.1111/tan.13881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/03/2020] [Accepted: 03/18/2020] [Indexed: 12/20/2022]
Abstract
Japan is an island country, and the Japanese people have had minimal genetic exchange with other ethnolinguistic groups. Consequently, the population is highly uniform and has limited HLA diversity relative to people from other countries. However, Japan has three ethnolinguistic groups, and HLA distributions differ depending on geographic region. To collect an HLA-rich variety of bone marrow bank donor registrants, it is essential to know the precise distribution of HLA in Japan. We analyzed HLA alleles and haplotypes based on HLA information of 177 041 bone marrow donor registrants. Registrants were grouped depending on the prefecture and region (a group of prefectures) as commonly used in Japan. The prefectures did not show the same distributions, but the tendency was similar for each region. We found that Okinawa Prefecture and the mainland can be clearly divided as haplotypes: [A*24:02-C*01:02-B*54:01-DRB1*04:05] and [A*24:02-C*01:02-B*59:01-DRB1*04:05] were typically found in Okinawa (P = .02, P < .001). Moreover, these types were found almost exclusively in Japan and Korea. Donor registration centers of the Japan Marrow Donor Program are currently located in all prefectures. It is essential to deploy registration centers to collect registrants with a large variety of HLA types covering all of Japan.
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Affiliation(s)
- Shiho Hashimoto
- Department of Laboratory Molecular Genetics of Hematology, Tokyo Medical and Dental University, Tokyo, Japan.,Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Fumiaki Nakajima
- Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Tadashi Imanishi
- Graduate School of Medicine, Tokai University School of Medicine, Kanagawa, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazue Kato
- Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Takafumi Kimura
- Japanese Red Cross Society Kinki Block Blood Center, Osaka, Japan
| | - Shigeki Miyata
- Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Minoko Takanashi
- Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Miwako Nishio
- Department of Laboratory Molecular Genetics of Hematology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masahiro Satake
- Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
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Zhong JL, Xu JW, Wang J, Wen YF, Niu H, Zheng L, He H, Peng K, He P, Shi SY, Huang YQ, Lei CZ, Dang RH, Lan XY, Qi XL, Chen H, Huang YZ. A novel SNP of PLAG1 gene and its association with growth traits in Chinese cattle. Gene 2018; 689:166-171. [PMID: 30580072 DOI: 10.1016/j.gene.2018.12.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/29/2018] [Accepted: 12/06/2018] [Indexed: 12/20/2022]
Abstract
Genetic polymorphism has great influences on the improvement of cattle traits. The polymorphism of the same gene family will greatly change the growth traits of cattle, such as the pleomorphic adenoma gene (PLAG) family. Many studies have shown that the PLAG family proteins are the transcription regulators of nuclear protein, which mainly regulates the expression of many important genes in the body. In cattle, single nucleotide polymorphisms (SNPs) within or near the PLAG1 gene is associated with economic traits of height in cattle. Here we investigate a SNPs of bovine PLAG1 in 646 cattle from five breeds. We found three different genotypes by using cleaved amplification polymorphism sequence-tagged sites (CAPs), includes some significant differences in body height, chest circumference and other shapes (P < 0.05), also we found that the TT genotype had no advantage in body shape. These results indicate that the selection of PLAG1 gene could be used to ensure the breeding direction for growth traits of the beef cattle.
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Affiliation(s)
- Jia-Lin Zhong
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jia-Wei Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jian Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yi-Fan Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Hui Niu
- Henan University of Animal Husbandry and Economy, Zhengzhou, Henan 450046, People's Republic of China
| | - Li Zheng
- Henan University of Animal Husbandry and Economy, Zhengzhou, Henan 450046, People's Republic of China
| | - Hua He
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China; College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Kun Peng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Pan He
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Shu-Yue Shi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yin-Qi Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chu-Zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Rui-Hua Dang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xian-Yong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xing-Lei Qi
- Bureau of Animal Husbandry of Biyang County, Biyang, Henan 463700, People's Republic of China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yong-Zhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Lv YF, Chang X, Hua RX, Yan GN, Meng G, Liao XY, Zhang X, Guo QN. The risk of new-onset cancer associated with HFE C282Y and H63D mutations: evidence from 87,028 participants. J Cell Mol Med 2016; 20:1219-33. [PMID: 26893171 PMCID: PMC4929296 DOI: 10.1111/jcmm.12764] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/26/2015] [Indexed: 12/13/2022] Open
Abstract
To investigate the association between mutation of HFE (the principal pathogenic gene in hereditary haemochromatosis) and risk of cancer, we conducted a meta‐analysis of all available case–control or cohort studies relating to two missense mutations, C282Y and H63D mutations. Eligible studies were identified by searching databases including PubMed, Embase and the ISI Web of Knowledge. Overall and subgroup analyses were performed and odds ratios (ORs) combined with 95% confidence intervals (CIs) were applied to evaluate the association between C282Y mutation, H63D mutation and cancer risk. Sensitivity and cumulative analyses were used to evaluate the stability of the results. A total of 36 eligible studies were included, comprising 13,680 cases and 73,348 controls. C282Y was significantly associated with elevated cancer risk in a recessive genetic model (OR: 1.991, 95% CI: 1.448–2.737). On subgroup analysis stratified by cancer type, statistically significantly increased cancer risks were found for breast cancer, colorectal cancer and hepatocellular carcinoma in a recessive model. When stratified by territory, a significantly increased risk of cancer was found in Oceanic populations in a recessive model and in Asian populations in an allele model and dominant model. H63D mutation did not significantly increase overall cancer risk in any genetic model. However, when, stratified by territory, an increased cancer risk was found in the Asian population in an allele and dominant. C282Y but not H63D mutation was related to elevated cancer risk. Further large‐scale studies considering gene–environment interactions and functional research should be conducted to further investigate this association.
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Affiliation(s)
- Yang-Fan Lv
- Department of Pathology, Xinqiao Hospital, The Third Military Medical University, Chongqing, China
| | - Xian Chang
- Department of Orthopedics, Xinqiao Hospital, The Third Military Medical University, Chongqing, China
| | - Rui-Xi Hua
- Department of Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Guang-Ning Yan
- Department of Pathology, Xinqiao Hospital, The Third Military Medical University, Chongqing, China
| | - Gang Meng
- Department of Pathology, Xinqiao Hospital, The Third Military Medical University, Chongqing, China
| | - Xiao-Yu Liao
- Department of Endocrinology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Xi Zhang
- Department of Pathology, Xinqiao Hospital, The Third Military Medical University, Chongqing, China
| | - Qiao-Nan Guo
- Department of Pathology, Xinqiao Hospital, The Third Military Medical University, Chongqing, China
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Zhou JJ, Lange K, Papp JC, Sinsheimer JS. A heterozygote-homozygote test of Hardy-Weinberg equilibrium. Eur J Hum Genet 2009; 17:1495-500. [PMID: 19367317 PMCID: PMC2986695 DOI: 10.1038/ejhg.2009.57] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Revised: 01/15/2009] [Accepted: 02/11/2009] [Indexed: 01/03/2023] Open
Abstract
The century-old Hardy-Weinberg law remains fundamental to population genetics. Typically Hardy-Weinberg equilibrium is tested in unrelated individuals using a chi(2) goodness-of-fit test that compares expected and observed numbers of heterozygotes and homozygotes. In this report, we propose a likelihood ratio test for Hardy-Weinberg equilibrium that accommodates a mixture of pedigree and random sample data. The underlying statistical model depends on a parameter gamma determining the ratio of heterozygous genotypes to homozygous genotypes among pedigree founders. As our heterozygous-homozygous test accommodates markers with dominant and recessive alleles, it can handle the phase ambiguities encountered in combining several linked single nucleotide polymorphisms into a single supermarker. No prior haplotyping is necessary. Our experience on real and simulated data suggests that the heterozygous-homozygous test has good type-one error and power.
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Affiliation(s)
- Jin J Zhou
- Department of Biomathematics, The University of California, Los Angeles, CA, USA
| | - Kenneth Lange
- Department of Biomathematics, The University of California, Los Angeles, CA, USA
- Department of Human Genetics, The University of California, Los Angeles, CA, USA
| | - Jeanette C Papp
- Department of Human Genetics, The University of California, Los Angeles, CA, USA
| | - Janet S Sinsheimer
- Department of Biomathematics, The University of California, Los Angeles, CA, USA
- Department of Human Genetics, The University of California, Los Angeles, CA, USA
- Department of Biostatistics, The University of California, Los Angeles, CA, USA
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Lachance J. Detecting selection-induced departures from Hardy-Weinberg proportions. Genet Sel Evol 2009; 41:15. [PMID: 19284519 PMCID: PMC2660905 DOI: 10.1186/1297-9686-41-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 01/21/2009] [Indexed: 11/20/2022] Open
Abstract
Viability selection influences the genotypic contexts of alleles and leads to quantifiable departures from Hardy-Weinberg proportions. One measure of these departures is Wright's inbreeding coefficient (F), where observed heterozygosity is compared with expected heterozygosity. Here, I extend population genetics theory to describe post-selection genotype frequencies in terms of post-selection allele frequencies and fitness dominance. The resulting equations correspond to non-equilibrium populations, allowing the following questions to be addressed: When selection is present, how large a sample size is needed to detect significant departures from Hardy-Weinberg? How do selection-induced departures from Hardy-Weinberg vary with allele frequencies and levels of fitness dominance? For realistic selection coefficients, large sample sizes are required and departures from Hardy-Weinberg proportions are small.
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Affiliation(s)
- Joseph Lachance
- Graduate Program in Genetics, Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, NY 11794-5222, USA.
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Lee HJ, Choi SJ, Hong JM, Lee WK, Baek JI, Kim SY, Park EK, Kim SY, Kim TH, Kim UK. Association of a Polymorphism in the Intron 7 of theSREBF1Gene with Osteonecrosis of the Femoral Head in Koreans. Ann Hum Genet 2009; 73:34-41. [DOI: 10.1111/j.1469-1809.2008.00490.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Deviations from Hardy-Weinberg proportions for multiple alleles under viability selection. Genet Res (Camb) 2008; 90:209-16. [PMID: 18426624 DOI: 10.1017/s0016672307009068] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Departures of genotype frequencies from Hardy-Weinberg proportions (HWP) for a single autosomal locus due to viability selection in a random mating population have been studied only for the two-allele case. In this article, the analysis of deviations from HWP due to constant viability selection is extended to multiple alleles. The deviations for an autosomal locus with k alleles are measured by means of k fii fixation indices for homozygotes and k(k-1)/2 fij fixation indices for heterozygotes, and expressions are obtained for these indices (FIS statistics) under the multiallele viability model. Furthermore, expressions for fii and fij when the multiallele polymorphism is at stable equilibrium are also derived and it is demonstrated that the pattern of multiallele Hardy-Weinberg deviations at equilibrium is characterized by a global heterozygote excess and a deficiency of each of the homozygotes. This pattern may be useful for detecting whether a given multiallelic polymorphism is at stable equilibrium in the population due to viability selection. An analysis of Hardy-Weinberg deviations from published data for the three-allele polymorphism at the beta-globin locus in human populations from West Africa is presented for illustration.
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Zou GY, Donner A. The merits of testing Hardy-Weinberg equilibrium in the analysis of unmatched case-control data: a cautionary note. Ann Hum Genet 2006; 70:923-33. [PMID: 17044866 DOI: 10.1111/j.1469-1809.2006.00267.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Testing for departures from the assumption of Hardy-Weinberg equilibrium (HWE) has been widely recommended as a preliminary step in the analysis of genetic case-control studies. Some authors suggest using a two-stage procedure in which gene/disease associations are ultimately evaluated using either the Pearson chi-square procedure or the Cochran-Armitage test for trend. Other authors go further and encourage investigators to discard data that are in violation of HWE, essentially using the test as a tool for identifying genotyping errors. In this paper we show that 1) testing for HWE should not be used as a tool to identify genotyping errors; and 2) it is not necessary, and possibly even harmful, to test the HWE assumption before testing for association between alleles and disease. Instead one should inherently account for deviations from HWE with an adjusted chi-square test statistic, a procedure which in the present context is identical to the trend test. Examples from previous reports are used to illustrate the methodology.
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Affiliation(s)
- Guang Yong Zou
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada.
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Zhang H, Luo X, Kranzler HR, Lappalainen J, Yang BZ, Krupitsky E, Zvartau E, Gelernter J. Association between two mu-opioid receptor gene (OPRM1) haplotype blocks and drug or alcohol dependence. Hum Mol Genet 2006; 15:807-19. [PMID: 16476706 PMCID: PMC3164878 DOI: 10.1093/hmg/ddl024] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We examined 13 single nucleotide polymorphisms (SNPs) spanning the coding region of the mu-opioid receptor gene (OPRM1), among 382 European Americans (EAs) affected with substance dependence [alcohol dependence (AD) and/or drug dependence (DD)] and 338 EA healthy controls. These SNPs delineated two haplotype blocks. Genotype distributions for all SNPs were in Hardy-Weinberg equilibrium (HWE) in controls, but in cases, four SNPs in Block I and three SNPs in Block II showed deviation from HWE. Significant differences were found between cases and controls in allele and/or genotype frequencies for six SNPs in Block I and two SNPs in Block II. Association of SNP4 in Block I with DD (allele: P=0.004), SNP5 in Block I with AD and DD (allele: P< or =0.005 for both) and two SNPs in Block II with AD (SNP11 genotype: P=0.002; SNP12 genotype: P=0.001) were significant after correction for multiple testing. Frequency distributions of haplotypes (constructed by five tag SNPs) differed significantly for cases and controls (P<0.001 for both AD and DD). Logistic regression analyses confirmed the association between OPRM1 variants and substance dependence, when sex and age of subjects and alleles, genotypes, haplotypes or diplotypes of five tag SNPs were considered. Population structure analyses excluded population stratification artifact. Additional supporting evidence for association between OPRM1 and AD was obtained in a smaller Russian sample (247 cases and 100 controls). These findings suggest that OPRM1 intronic variants play a role in susceptibility to AD and DD in populations of European ancestry.
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Affiliation(s)
- Huiping Zhang
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, Psychiatry 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, Psychiatry 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA
| | - Henry R. Kranzler
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Jaakko Lappalainen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, Psychiatry 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA
| | - Bao-Zhu Yang
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, Psychiatry 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA
| | - Evgeny Krupitsky
- St Petersburg State Pavlov Medical University, St Petersburg, Russia
| | - Edwin Zvartau
- St Petersburg State Pavlov Medical University, St Petersburg, Russia
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, Psychiatry 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA
- To whom correspondence should be addressed. Tel: +1 2039325711 ext. 3599; Fax: +1 2039373897;
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