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Khan F, Liacini A, Arora E, Wang S, Assad M, Doulla J, Faridi RM, Berka N. Assessment of fidelity and utility of the whole-genome amplification for the clinical tests offered in a histocompatibility and immunogenetics laboratory. ACTA ACUST UNITED AC 2012; 79:372-9. [PMID: 22489946 DOI: 10.1111/j.1399-0039.2012.01857.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Increasing emphasis on the use of molecular tests in a histocompatibility and immunogenetics laboratory (HIL) poses a potential problem of lack of sufficient DNA to perform multiple genetic analyses. In this study, we report the feasibility, fidelity and utility of multiple displacement amplification (MDA) method to perform whole-genome amplification (WGA) to generate DNA specimens that can be analyzed by multiple molecular techniques and can be used for different clinical tests offered by an HIL. The MDA-generated DNA when compared with the native DNA showed 100% congruency in genotyping of 37 genes/loci using multiple downstream molecular techniques: sequence-based typing and sequence-specific primer-based typing for 5 human leukocyte antigen (HLA) class I and II genes (HLA-A, B, C, DRB1 and DQB1), luminex-based sequence-specific oligonucleotide (SSO) genotyping for a panel of 16 killer immunoglobulin-like receptor (KIR) genes and automated fragment size analysis for a panel of 15 short tandem repeat (STR) loci and amelogenin gene. For post-allogeneic hematopoietic cell transplantation (HCT) chimerism analysis, MDA-generated DNA appeared useful for enriching pre-transplant DNA but not for enriching post-transplant chimeric DNA. Overall, our results show that MDA-based WGA could generate DNA of high yield and fidelity that can be used for various clinical tests and research purposes.
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Affiliation(s)
- F Khan
- Tissue Typing Laboratory, Calgary Laboratory Services, Calgary, Alberta, Canada.
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2
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Ndlovu BG, Danaviah S, Moodley E, Ghebremichael M, Bland R, Viljoen J, Newell ML, Ndung'u T, Carr WH. Use of dried blood spots for the determination of genetic variation of interleukin-10, killer immunoglobulin-like receptor and HLA class I genes. TISSUE ANTIGENS 2012; 79:114-22. [PMID: 22107032 PMCID: PMC3253194 DOI: 10.1111/j.1399-0039.2011.01807.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Optimal methods for using dried blood spots (DBSs) for population genetics-based studies have not been well established. Using DBS stored for 8 years from 21 pregnant South African women, we evaluated three methods of gDNA extraction with and without whole-genome amplification (WGA) to characterize immune-related genes: interleukin-10 (IL-10), killer immunoglobulin-like receptors (KIRs) and human leukocyte antigen (HLA) class I. We found that the QIAamp DNA mini kit yielded the highest gDNA quality (P< 0.05; Wilcoxon signed rank test) with sufficient yield for subsequent analyses. In contrast, we found that WGA was not reliable for sequence-specific primer polymerase chain reaction (SSP-PCR) analysis of KIR2DL1, KIR2DS1, KIR2DL5 and KIR2DL3 or high-resolution HLA genotyping using a sequence-based approach. We speculate that unequal template amplification by WGA underrepresents gene repertoires determined by sequence-based approaches.
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Affiliation(s)
- B G Ndlovu
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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3
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Protocol for analyzing human leukocyte antigen variants and sexually transmitted infections: from genotyping to immunoassays. Methods Mol Biol 2012; 903:359-80. [PMID: 22782832 DOI: 10.1007/978-1-61779-937-2_25] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This chapter describes experimental and analytical procedures that can be used to decipher the specific role of human leukocyte antigen (HLA) variants in infectious diseases. The techniques are distilled from more than one decade of active immunogenetics research, primarily on sexually transmitted infections (STIs) caused by viral and bacterial pathogens, including human immunodeficiency virus type 1 (HIV-1), hepatitis B virus (HBV), and Chlamydia trachomatis. The specific approaches cover (1) sequence-specific oligonucleotide (SSO) probe hybridization for low-resolution genotyping, (2) sequencing-based typing (SBT) for high-resolution, (3) statistical methods for testing associations between HLA variants and phenotypic traits, and (4) enzyme-linked immunospot (ELISpot) assay for enumerating HLA-restricted and epitope-specific T-lymphocyte responses. Proper application of these mature and robust techniques should help establish the importance of individual HLA alleles, haplotypes, and supertypes to host-pathogen interactions.
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Pajewski NM, Parker SD, Poland GA, Ovsyannikova IG, Song W, Zhang K, McKinney BA, Pankratz VS, Edberg JC, Kimberly RP, Jacobson RM, Tang J, Kaslow RA. The role of HLA-DR-DQ haplotypes in variable antibody responses to anthrax vaccine adsorbed. Genes Immun 2011; 12:457-65. [PMID: 21368772 DOI: 10.1038/gene.2011.15] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Host genetic variation, particularly within the human leukocyte antigen (HLA) loci, reportedly mediates heterogeneity in immune response to certain vaccines; however, no large study of genetic determinants of anthrax vaccine response has been described. We searched for associations between the immunoglobulin G antibody to protective antigen (AbPA) response to Anthrax Vaccine Adsorbed (AVA) in humans, and polymorphisms at HLA class I (HLA-A, -B, and -C) and class II (HLA-DRB1, -DQA1, -DQB1, -DPB1) loci. The study included 794 European-Americans and 200 African-Americans participating in a 43-month, double-blind and placebo-controlled clinical trial of AVA (clinicaltrials.gov identifier NCT00119067). Among European-Americans, genes from tightly linked HLA-DRB1, -DQA1, -DQB1 haplotypes displayed significant overall associations with longitudinal variation in AbPA levels at 4, 8, 26 and 30 weeks from baseline in response to vaccination with three or four doses of AVA (global P=6.53 × 10(-4)). In particular, carriage of the DRB1-DQA1-DQB1 haplotypes (*)1501-(*)0102-(*)0602 (P=1.17 × 10(-5)), (*)0101-(*)0101-(*)0501 (P=0.009) and (*)0102-(*)0101-(*)0501 (P=0.006) was associated with significantly lower AbPA levels. In carriers of two copies of these haplotypes, lower AbPA levels persisted following subsequent vaccinations. No significant associations were observed amongst African-Americans or for any HLA class I allele/haplotype. Further studies will be required to replicate these findings and to explore the role of host genetic variation outside of the HLA region.
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Affiliation(s)
- N M Pajewski
- Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0022, USA
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Chainonthee W, Böttcher G, Gagne K, Füssel M, Bignon JD, Wassmuth R. Improved KIR gene and HLA-C KIR ligand sequence-specific primer polymerase chain reaction genotyping using whole genome amplification. ACTA ACUST UNITED AC 2010; 76:135-43. [PMID: 20403144 DOI: 10.1111/j.1399-0039.2010.01479.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular analysis of genetic polymorphism for clinical or research purposes may be compromised by genomic DNA of limited quality and quantity. In this study, we have successfully tested the feasibility of using whole genome amplification (WGA) to allow genotyping for killer cell immunoglobulin-like receptor (KIR) genes and human leucocyte antigen (HLA)-C KIR ligand dimorphism on HLA-C. WGA was achieved by multiple displacement amplification (MDA) using bacteriophage phi29 polymerase. For KIR genotyping, a revised sequence-specific primer polymerase chain reaction protocol consisting of 23 primer pairs was used avoiding hitherto undetected cross-priming involving KIR2DL1, KIR2DS1, KIR3DL1 and KIR3DS1 alleles. Similarly, MDA-amplified genomic DNA was analyzed for the detection of the HLA-C KIR ligand groups C1 and C2, based on the amino acid K/N dimorphism in position 80.
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Affiliation(s)
- W Chainonthee
- Medizinische Klinik u. Poliklinik I, Universitätsklinikum Carl Gustav Carus der Technischen Universität Dresden, Dresden, Germany
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Li Y, Ni R, Song W, Shao W, Shrestha S, Ahmad S, Cunningham CK, Flynn PM, Kapogiannis BG, Wilson CM, Tang J. Clear and independent associations of several HLA-DRB1 alleles with differential antibody responses to hepatitis B vaccination in youth. Hum Genet 2009; 126:685-96. [PMID: 19597844 PMCID: PMC2771141 DOI: 10.1007/s00439-009-0720-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 07/05/2009] [Indexed: 12/18/2022]
Abstract
To confirm and refine associations of human leukocyte antigen (HLA) genotypes with variable antibody (Ab) responses to hepatitis B vaccination, we have analyzed 255 HIV-1 seropositive (HIV(+)) youth and 80 HIV-1 seronegatives (HIV(-)) enrolled into prospective studies. In univariate analyses that focused on HLA-DRB1, -DQA1, and -DQB1 alleles and haplotypes, the DRB1*03 allele group and DRB1*0701 were negatively associated with the responder phenotype (serum Ab concentration > or = 10 mIU/mL) (P = 0.026 and 0.043, respectively). Collectively, DRB1*03 and DRB1*0701 were found in 42 (53.8%) out of 78 non-responders (serum Ab <10 mIU/mL), 65 (40.6%) out of 160 medium responders (serum Ab 10-1,000 mIU/mL), and 27 (27.8%) out of 97 high responders (serum Ab >1,000 mIU/mL) (P < 0.001 for trend). Meanwhile, DRB1*08 was positively associated with the responder phenotype (P = 0.010), mostly due to DRB1*0804 (P = 0.008). These immunogenetic relationships were all independent of non-genetic factors, including HIV-1 infection status and immunodeficiency. Alternative analyses confined to HIV(+) youth or Hispanic youth led to similar findings. In contrast, analyses of more than 80 non-coding, single nucleotide polymorphisms within and beyond the three HLA class II genes revealed no clear associations. Overall, several HLA-DRB1 alleles were major predictors of differential Ab responses to hepatitis B vaccination in youth, suggesting that T-helper cell-dependent pathways mediated through HLA class II antigen presentation are critical to effective immune response to recombinant vaccines.
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Affiliation(s)
- Yufeng Li
- Department of Medicine, University of Alabama at Birmingham, Birmingham, USA
| | - Rong Ni
- Department of Medicine, University of Alabama at Birmingham, Birmingham, USA
| | - Wei Song
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
| | - Wenshuo Shao
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
| | - Sadeep Shrestha
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
| | - Sushma Ahmad
- Westat, 1650 Research Boulevard, Rockville, MD USA
| | | | - Patricia M. Flynn
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Bill G. Kapogiannis
- Pediatric, Adolescent, and Maternal AIDS Branch, National Institute of Child Health and Human Development, Bethesda, MD USA
| | - Craig M. Wilson
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, 1665 University Boulevard, Birmingham, AL 35294 USA
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Song W, Ruder AM, Hu L, Li Y, Ni R, Shao W, Kaslow RA, Butler M, Tang J. Genetic epidemiology of glioblastoma multiforme: confirmatory and new findings from analyses of human leukocyte antigen alleles and motifs. PLoS One 2009; 4:e7157. [PMID: 19774073 PMCID: PMC2742900 DOI: 10.1371/journal.pone.0007157] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Accepted: 09/01/2009] [Indexed: 11/19/2022] Open
Abstract
Background Human leukocyte antigen (HLA) class I genes mediate cytotoxic T-lymphocyte responses and natural killer cell function. In a previous study, several HLA-B and HLA-C alleles and haplotypes were positively or negatively associated with the occurrence and prognosis of glioblastoma multiforme (GBM). Methodology/Principal Findings As an extension of the Upper Midwest Health Study, we have performed HLA genotyping for 149 GBM patients and 149 healthy control subjects from a non-metropolitan population consisting almost exclusively of European Americans. Conditional logistic regression models did not reproduce the association of HLA-B*07 or the B*07-Cw*07 haplotype with GBM. Nonetheless, HLA-A*32, which has previously been shown to predispose GBM patients to a favorable prognosis, was negatively associated with occurrence of GBM (odds ratio = 0.41, p = 0.04 by univariate analysis). Other alleles (A*29, A*30, A*31 and A*33) within the A19 serology group to which A*32 belongs showed inconsistent trends. Sequencing-based HLA-A genotyping established that A*3201 was the single A*32 allele underlying the observed association. Additional evaluation of HLA-A promoter and exon 1 sequences did not detect any unexpected single nucleotide polymorphisms that could suggest differential allelic expression. Further analyses restricted to female GBM cases and controls revealed a second association with a specific HLA-B sequence motif corresponding to Bw4-80Ile (odds ratio = 2.71, p = 0.02). Conclusions/Significance HLA-A allelic product encoded by A*3201 is likely to be functionally important to GBM. The novel, sex-specific association will require further confirmation in other representative study populations.
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Affiliation(s)
- Wei Song
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Avima M. Ruder
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio, United States of America
| | - Liangyuan Hu
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Yufeng Li
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Rong Ni
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Wenshuo Shao
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Richard A. Kaslow
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - MaryAnn Butler
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio, United States of America
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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Creary LE, Girdlestone J, Zamora J, Brown J, Navarrete CV. Molecular typing of HLA genes using whole genome amplified DNA. Transfusion 2008; 49:57-63. [PMID: 18954395 DOI: 10.1111/j.1537-2995.2008.01943.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The outcome of clinical transplantation and a number of disease susceptibilities show very strong associations with genetic variants within the major histocompatibility complex, particularly in the human leukocyte antigen (HLA) genes. A problem with many association studies is the lack of sufficient DNA to perform multiple genetic analyses, particularly with transplantation outcomes where donor and recipient DNA are often in short supply. This study assesses whether a multiple-strand displacement whole genome amplification (WGA) method could generate sufficient template of high quality to perform unbiased amplification for analysis of the HLA-A, -B, -C, -DRB1, and -DQB1 genes. STUDY DESIGN AND METHODS A panel of DNA samples from various biological sources was subjected to WGA reaction using Phi29 DNA polymerase. The HLA genotypes were subsequently determined using standard polymerase chain reaction (PCR)-based methods including sequence-specific oligonucleotide probes (PCR-SSOP, Luminex, Luminex Corp.) and sequence-based typing (PCR-SBT). WGA products and original DNA samples were used to determine the sensitivity of the Luminex assay; in addition, reamplified WGA products were also genotyped. RESULTS The WGA templates, as well as serially amplified DNA for two successive rounds, yielded HLA genotypes fully concordant with those determined for the original DNA samples. WGA products and original DNA gave reproducible HLA-DQB1 genotypes with 100 to 10 ng of template. Purification of the WGA products was required for successful PCR-SBT, but not for the PCR-SSOP method. CONCLUSION Our study suggests that WGA can be a reliable method for generating unlimited DNA for medium- or high-resolution HLA typing using the techniques described above.
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Affiliation(s)
- Lisa E Creary
- Histocompatibility and Immunogenetics Research Group, Department of Histocompatibility and Immunogenetics, Colindale Centre, NHSBT, NHSBT, London, UK
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Tang J, Shao W, Yoo YJ, Brill I, Mulenga J, Allen S, Hunter E, Kaslow RA. Human leukocyte antigen class I genotypes in relation to heterosexual HIV type 1 transmission within discordant couples. THE JOURNAL OF IMMUNOLOGY 2008; 181:2626-35. [PMID: 18684953 DOI: 10.4049/jimmunol.181.4.2626] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Differences in immune control of HIV-1 infection are often attributable to the highly variable HLA class I molecules that present viral epitopes to CTL. In our immunogenetic analyses of 429 HIV-1 discordant Zambian couples (infected index partners paired with cohabiting seronegative partners), several HLA class I variants in index partners were associated with contrasting rates and incidence of HIV-1 transmission within a 12-year study period. In particular, A*3601 on the A*36-Cw*04-B*53 haplotype was the most unfavorable marker of HIV-1 transmission by index partners, while Cw*1801 (primarily on the A*30-Cw*18-B*57 haplotype) was the most favorable, irrespective of the direction of transmission (male to female or female to male) and other commonly recognized cofactors of infection, including age and GUI. The same HLA markers were further associated with contrasting viral load levels in index partners, but they had no clear impact on HIV-1 acquisition by the seronegative partners. Thus, HLA class I gene products not only mediate HIV-1 pathogenesis and evolution but also influence heterosexual HIV-1 transmission.
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Affiliation(s)
- Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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10
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Yu RB, Hong X, Ding WL, Tan YF, Zhang YX, Sun NX, Wu GL, Zhan SW, Ge DF. The association between the genetic polymorphism of HLA-DQA1, DQB1, and DRB1 and serum alanine aminotransferase levels in chronic hepatitis C in the Chinese population. J Gastroenterol Hepatol 2008; 23:1394-402. [PMID: 18028350 DOI: 10.1111/j.1440-1746.2007.05215.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
BACKGROUND AND AIM To investigate a possible association between HLA genes with serum alanine aminotransferase (ALT) levels and evaluate whether the HLA-DQA1, DQB1, and DRB1 genes could influence the development of liver damage in chronic hepatitis C. METHODS A total of 145 patients with chronic hepatitis C virus (HCV) infection (36 patients with persistently normal ALT values; 109 patients with elevated ALT levels) and 160 uninfected healthy controls were examined for HLA-DQA1, DQB1, and DRB1 molecules by using polymerase chain reaction-sequencing based typing (PCR-SBT). RESULTS Among the patients chronically infected with HCV, the frequencies of DQA1*0501, DQB1*0301, and DRB1*0401 alleles were significantly increased in the normal ALT group compared with those with abnormal ALT levels, whereas that of DQB1*0201 was significantly lower. As compared to uninfected healthy controls, DQA1*0501, DQB1*0301, and DRB1*0401 allele frequencies were also statistically higher in the normal ALT group, whereas that of DQB1*0201 was the inverse. The haplotype frequencies of DQA1*0301-DQB1*0301, DQA1*0501-DQB1*0301, and DRB1*1101-DQB1*0301 were found to be significantly higher in the normal ALT group. Multivariate logistic regression indicated that female sex, and the DQB1*0301 allele and DRB1*0401 allele were independently associated with normal ALT values, whereas DQB1*0201 allele was the inverse. CONCLUSIONS These results suggest that particular HLA alleles may have an influence on the serum ALT level of chronic HCV infection as a host genetic factor in the Chinese population. The DQA1*0501, DQB1*0301, and DRB1*0401 alleles, and the DQA1*0301-DQB1*0301, DQA1*0501-DQB1*0301, and DRB1*1101-DQB1*0301 haplotypes seem to be associated with low hepatitis activity; whereas DQB1*0201 allele is closely correlated with the progression of liver injury in chronic HCV infection.
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Affiliation(s)
- Rong-Bin Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Province Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing, China
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11
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Dorak MT. Role of natural killer cells and killer immunoglobulin-like receptor polymorphisms: association of HLA and KIRs. ACTA ACUST UNITED AC 2007; 134:123-44. [PMID: 17666748 DOI: 10.1007/978-1-59745-223-6_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Natural killer cells play an important role in innate immunity. They act against infected and transformed cells as part of the immune surveillance process. Their interactions with the human leukocyte antigens (HLAs) create a situation where they may act against donor hematopoietic cells following stem cell transplantation. Both killer immunoglobulin-like receptors (KIRs) and HLA types of donor and recipient are relevant in the generation of graft-vs-leukemia or graft-vs-host reactions. This chapter reviews the current knowledge on the involvement of natural killer cells in the events following hematopoietic stem cell transplantation, the structure of the genetic complex encoding the KIRs and provides a PCR-based genotyping scheme for KIR genes.
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Affiliation(s)
- M Tevfik Dorak
- School of Clinical Medical Sciences, University of Newcastle, UK
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12
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Liang X, Trentham-Dietz A, Titus-Ernstoff L, Newcomb PA, Welch RA, Hutchinson AA, Hampton JM, Sutcliffe CB, Haines JL, Egan KM. Whole-genome amplification of oral rinse self-collected DNA in a population-based case-control study of breast cancer. Cancer Epidemiol Biomarkers Prev 2007; 16:1610-4. [PMID: 17684135 DOI: 10.1158/1055-9965.epi-07-0110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The availability of large amounts of genomic DNA (gDNA) is the limiting factor for many of the molecular biology assays in genetic epidemiologic studies. Whole-genome amplification using multiple displacement amplification is used to amplify a representative sample of gDNA from small amounts of gDNA to optimize gDNA yield. We collected oral rinse DNA samples through the mail from 3,377 women enrolled in a population-based U.S. breast cancer case-control study and did whole-genome amplification by multiple displacement amplification. Genotyping was done for 66 single nucleotide polymorphisms (SNP) in 18 candidate susceptibility genes using amplified DNA with genomic replicates included for quality control. The concordance rates (percentages of agreement) in 95 quality control replicates of gDNA and amplified DNA for 66 SNPs ranged from 88% to 100% (median, 97%). The average allelic error rate was 0.9%. However, in further analyses based on the full control series (n = 1,492), >60% of the SNPs failed tests for Hardy-Weinberg equilibrium (P < 0.05), with evidence of heterozygote loss in the great majority. Even eliminating the 9% of samples with lower quality or input DNA, tests for Hardy-Weinberg equilibrium indicated persistent allele bias in nearly a third of the SNPs. Whole-genome amplification may introduce substantial allele amplification bias in gDNA collected using a common protocol in population-based epidemiologic studies.
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Affiliation(s)
- Xueying Liang
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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13
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Moore LE, Bergen AW, Haque KA, Qi Y, Castle P, Chanock SJ, Egan K, Newcomb P, Titus-Ernstoff L, Alguacil J, Rothman N, Garcia-Closas M. Whole genome amplification of buccal cytobrush DNA collected for molecular epidemiology studies. Biomarkers 2007; 12:303-12. [PMID: 17453743 DOI: 10.1080/13547500601162011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
When cytobrush buccal cell samples have been collected as a genomic DNA (gDNA) source for an epidemiological study, whole genome amplification (WGA) can be critical to maintain sufficient DNA for genotyping. We evaluated REPLI-g WGA using gDNA from two paired cytobrushes (cytobush 'A' kept in a cell lysis buffer, and 'B' dried and kept at room temperature for 3 days, and frozen until DNA extraction) in a pilot study (n=21), and from 144 samples collected by mail in a breast cancer study. WGA success was assessed as the per cent completion/concordance of STR/SNP genotypes. Locus amplification bias was assessed using quantitative PCR of 23 human loci. The pilot study showed > 98% completion but low genotype concordance between cytobrush wgaDNA and paired blood gDNA (82% and 84% for cytobrushes A and B, respectively). Substantial amplification bias was observed with significantly lower human gDNA amplification from cytobrush B than A. Using cytobrush gDNA samples from the breast cancer study (n =20), an independent laboratory demonstrated that increasing template gDNA to the REPLI-g reaction improved genotype performance for 49 SNPs; however, average completion and concordance remained below 90%. To reduce genotype misclassification when cytobrush wgaDNA is used, inclusion of paired gDNA/wgaDNA and/or duplicate wgaDNA samples is critical to monitor data quality.
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Affiliation(s)
- L E Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20852-7240, USA.
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14
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Singh KK, Spector SA. Fidelity of whole-genome amplification of blood spot DNA for HLA typing and SNP analyses. Clin Genet 2007; 72:156-9. [PMID: 17661821 DOI: 10.1111/j.1399-0004.2007.00808.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Schmidt H, Williamson D, Ashley-Koch A. HLA-DR15 haplotype and multiple sclerosis: a HuGE review. Am J Epidemiol 2007; 165:1097-109. [PMID: 17329717 DOI: 10.1093/aje/kwk118] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
An association between multiple sclerosis (MS) and the human leukocyte antigen (HLA) complex, a dense cluster of genes on the short arm of chromosome 6, was first noted over 30 years ago. In Caucasian populations of Northern European descent, the DR15 haplotype (DRB1*1501-DQA1*0102-DQB1*0602) has been hypothesized to be the primary HLA genetic susceptibility factor for MS. However, studies of other populations have produced varying results. Thus, the authors reviewed the literature for articles on the association between the DR15 haplotype and MS. They identified 72 papers meeting the inclusion criteria: human genetic studies written in English that were published between 1993 and 2004 and that reported allele frequencies for HLA-DRB1*1501, HLA-DQA1*0102, or HLA-DQB1*0602 or the frequency of the DRB1*1501-DQA1*0102-DQB1*0602 haplotype. Most of the studies identified used a case-control design (n = 60), while the remainder used a family-based design (n = 22). In most of these papers, investigators reported a higher frequency of the DR15 haplotype and/or its component alleles among MS cases than among controls. However, the authors' confidence in these results is tempered by factors related to study design that may have biased the outcomes.
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Affiliation(s)
- Hollie Schmidt
- Accelerated Cure Project for Multiple Sclerosis, Waltham, MA 02451, USA.
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Polymorphism of the HLA-DQA1 and -DQB1 genes of Han population in Jiangsu Province, China. Chin Med J (Engl) 2006. [DOI: 10.1097/00029330-200611020-00014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Tang J, Shao W, Dorak MT, Li Y, Miike R, Lobashevsky E, Wiencke JK, Wrensch M, Kaslow RA, Cobbs CS. Positive and negative associations of human leukocyte antigen variants with the onset and prognosis of adult glioblastoma multiforme. Cancer Epidemiol Biomarkers Prev 2005; 14:2040-4. [PMID: 16103458 DOI: 10.1158/1055-9965.epi-05-0136] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Associations of genetic factors with malignant gliomas have been modest. We examined the relationships of human leukocyte antigen (HLA) and related polymorphisms to glioblastoma multiforme in adult Caucasians (non-Hispanic Whites) from the San Francisco Bay area. For 155 glioblastoma multiforme patients and 157 control subjects closely matched by ethnicity, age, and gender, PCR-based techniques resolved alleles at HLA-A, -B, -C, and -DRB1 loci along with short tandem repeat polymorphisms of MICA exon 5 and TNFb. By multivariable logistic regression, B*13 and the B*07-Cw*07 haplotype were positively associated with glioblastoma multiforme (P=0.01 and <0.001, respectively), whereas Cw*01 was the only variant showing a negative association (P=0.05). Among glioblastoma multiforme patients, progression to death after diagnosis was slower in those with A*32 (relative hazard, 0.45; P<0.01) and faster in those with B*55 (relative hazard, 2.27; P<0.01). Thus, both the occurrence and the prognosis of glioblastoma multiforme could be associated with specific but different HLA genotypes. B*07 and the B*07-Cw*07 haplotype are much more common in Caucasians than other ethnic groups in the U.S., which may partially explain the higher incidence of glioblastoma multiforme in Caucasians.
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Affiliation(s)
- Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, 1665 University Boulevard, RPHB Room 220A, Birmingham, AL 35294-0022, USA
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Wormser GP, Kaslow R, Tang J, Wade K, Liveris D, Schwartz I, Klempner M. Association between human leukocyte antigen class II alleles and genotype of Borrelia burgdorferi in patients with early lyme disease. J Infect Dis 2005; 192:2020-6. [PMID: 16267776 PMCID: PMC2776636 DOI: 10.1086/497693] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Accepted: 06/30/2005] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND On the basis of a polymerase chain reaction-restriction fragment-length polymorphism analysis of the 16S-23S ribosomal DNA intergenic spacer, clinical isolates of Borrelia burgdorferi can be classified into 3 genotypes designated as RST1, RST2, and RST3. RST1 strains are the most pathogenic, and RST3 strains are the least pathogenic. METHODS Human leukocyte antigen (HLA) class II alleles were determined for a group of culture-positive patients with Lyme disease-associated erythema migrans and were evaluated for an association with the genotype of the infecting B. burgdorferi strain. RESULTS The DRB1*0101 allele carriage rate was higher in patients infected with RST3 strains (9/25 [36.0%]) than in patients infected with RST1 strains (2/28 [7.1%]) or RST2 strains (7/36 [19.4%]) (P=.010). The same relationship was found for carriage of the DRB1*0101-DQB1*0501 haplotype (P=.018), because of tight linkage disequilibrium. Similar associations could not be demonstrated for any of the other DRB1 and DQB1 alleles or haplotypes that were assessed. CONCLUSION The DRB1*0101 allele and the DRB1*0101-DQB1*0501 haplotype may be relevant to the development of infection with strains from the least invasive genotypes of B. burgdorferi.
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Affiliation(s)
- Gary P Wormser
- Department of Medicine, Division of Infectious Diseases, New York Medical College, Valhalla, NY 10595, USA.
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Csako G. Present and future of rapid and/or high-throughput methods for nucleic acid testing. Clin Chim Acta 2005; 363:6-31. [PMID: 16102738 DOI: 10.1016/j.cccn.2005.07.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 07/03/2005] [Accepted: 07/03/2005] [Indexed: 12/21/2022]
Abstract
BACKGROUND Behind the success of 'completing' the human genome project was a more than 30-year history of technical innovations for nucleic acid testing. METHODS Discovery of specific restriction endonucleases and reverse transcriptase was followed shortly by the development of the first diagnostic nucleic acid tests in the early 1970s. Introduction of Southern, Northern and dot blotting and DNA sequencing later in the 1970s considerably advanced the diagnostic capabilities. Nevertheless, it was the discovery of the polymerase chain reaction (PCR) in 1985 that led to an exponential growth in molecular biology and the introduction of practicable nucleic acid tests in the routine laboratory. The past two decades witnessed a continuing explosion of technological innovations in molecular diagnostics. In addition to classic PCR and reverse transcriptase PCR, numerous variations of PCR and alternative amplification techniques along with an ever-increasing variety of detection chemistries, closed tube (homogeneous) assays, and automated systems were developed. Discovery of real-time quantitative PCR and the development of oligonucleotide microarrays, the 'DNA chip', in the 1990s heralded the beginning of another revolution in molecular biology and diagnostics that is still in progress.
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Affiliation(s)
- Gyorgy Csako
- Department of Laboratory Medicine, W.G. Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892-1508, USA.
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