Analysis of the frequencies of HLA-A, B, and C alleles and haplotypes in the five major ethnic groups of the United States reveals high levels of diversity in these loci and contrasting distribution patterns in these populations

Changes in impact of HLA class I allele expression on HIV-1 plasma virus loads at a population level over time

HLA class I allele types have differential impacts on the level of the pVL and outcome of HIV-1 infection. While accumulations of CTL escape mutations at population levels have been reported, their actual impact on the level of the pVL remains unknown. In this study HLA class I types from 141 untreated, chronically HIV-1 infected Japanese patients diagnosed from 1995-2007 were determined, and the associations between expression of individual HLA alleles and level of pVL analyzed. It was found that the Japanese population has an extremely narrow HLA distribution compared to other ethnic groups, which may facilitate accumulation of CTL escape mutations at the population level. Moreover while they uniquely lack the most protective HLA-B27/B57, they commonly express the alleles that are protective in Caucasians (A11:10.4%, A26:11.55%, B51:8.6% and Cw14:12.7%). Cross-sectional analyses revealed no significant associations between expression of individual alleles and the level of the pVL. The patients were then stratified by the date of HIV diagnosis and the analyses repeated. It was found that, before 2001, B51+ individuals displayed significantly lower pVL than the other patients (median: 5150 vs. 18,000 RNA copies/ml, P=0.048); however thereafter this protective effect waned and disappeared, whereas no changes were observed for any other alleles over time. These results indicate that, at a population level, some HLA alleles have been losing their beneficial effects against HIV disease progression over time, thereby possibly posing a significant challenge for HIV vaccine development. However such detrimental effects may be limited to particular HLA class I alleles.

Human leukocyte antigen-A, -B, and -DRB1 allele and haplotype frequencies in the Mozambican population: a blood donor-based population study

Human leukocyte antigen (HLA) has been used for several decades as genetic markers for analyzing diversity of gene pool origin, platelet transfusion, tissue transplantation, disease susceptibility or resistance, and forensic and anthropological studies. In the present study, the allele and haplotype frequencies of HLA-A, -B, and -DRB1 were studied in 250 unrelated Mozambican individuals (black African from south of Mozambique Basin) by using a low-medium resolution polymerase chain reaction-Luminex typing method. A total of 18 A, 25 B, and 13 DRB1 alleles were identified. The most frequent HLA-A, -B, and -DRB1 alleles were HLA-A*30 (23.9%), HLA-B*15 (15.6%), and HLA-DRB1*13 (19.8%), respectively. The most frequent two-locus haplotypes were HLA-A*30-B*42 (7.4%) and HLA-B*42-DRB1*03 (5.4%), and three-locus haplotypes were HLA-A*30-B*42-DRB1*03 (4.9%), and HLA-A*02-B*58-DRB1*11 (4.1%). Allele distribution and haplotype analysis demonstrated that Mozambican population shares HLA patterns with sub-Saharan populations.

HLA-A, -B, -DRB1 allele frequencies and haplotypic association from DNA typing data of 7096 Korean cord blood units

Human leukocyte antigen (HLA) distribution in 7096 Korean cord blood (CB) units preserved at the public CB bank was analyzed by using the polymerase chain reaction with sequence-specific oligonucleotide probe (PCR-SSOP) method. A total of 14 HLA-A, 33 HLA-B, 13 HLA-DRB1 alleles and 2470 three-locus haplotypes were identified. The results are generally similar to those from the previous Korean studies, but the frequencies of less frequent haplotypes < 0.1% are more relevant and infrequent haplotypes with strong linkage disequilibrium were newly found because of the large sample size. Our results showed some similarities to those of other Asians but also some differences, suggesting a rationale for an Asian network for a hematopoietic stem-cell donor registry. Results from this large-scale analysis will be useful in Korean and Asian registry planning.

Natural epitope variants of the hepatitis C virus impair cytotoxic T lymphocyte activity

AIM: To understand how interactions between hepatitis C virus (HCV) and the host’s immune system might lead to viral persistence or effective elimination of HCV.

METHODS: Nucleotides 3519-3935 of the non-structural 3 (NS3) region were amplified by using reverse transcription polymerase chain reaction (PCR). PCR products of the HCV NS3 regions were integrated into a PCR^® T7TOPO^® TA vector and then sequenced in both directions using an automated DNA sequencer. Relative major histocompatibility complex binding levels of wild-type and variant peptides were performed by fluorescence polarization-based peptide competition assays. Peptides with wild type and variant sequences of NS3 were synthesized locally using F-moc chemistry and purified by high-performance liquid chromatography. Specific cytotoxic T lymphocytes (CTLs) clones toward HCV NS3 wild-type peptides were generated through limiting dilution cloning. The CTL clones specifically recognizing HCV NS3 wild-type peptides were tested by tetramer staining and flow cytometry. Cytolytic activity of CTL clones was measured using target cells labeled with the fluorescence enhancing ligand, DELFIA EuTDA.

RESULTS: The pattern of natural variants within three human leukocyte antigen (HLA)-A2-restricted NS3 epitopes has been examined in one patient with chronic HCV infection at 12, 28 and 63 mo post-infection. Results obtained may provide convincing evidence of immune selection pressure for all epitopes investigated. Statistical analysis of the extensive sequence variation found within these NS3 epitopes favors a Darwinian selection model of variant viruses. Mutations within the epitopes coincided with the decline of CTL responses, and peptide-binding studies suggested a significant impact of the mutation on T cell recognition rather than peptide presentation by HLA molecules. While most variants were either not recognized or elicited low responses, such could antagonize CTL responses to target cells pulsed with wild-type peptides.

CONCLUSION: Cross-recognition of CTL epitopes from wild-type and naturally-occurring HCV variants may lead to impaired immune responses and ultimately contribute to viral persistence.

Distributions of HLA-A and -B alleles and haplotypes in the Yi ethnic minority of Yunnan, China: relationship to other populations

Objective: To investigate the distributions of human leukocyte antigen (HLA)-A and -B alleles and HLA-A-B haplotypes in the Yi ethnic minority of the Yunnan Province, situated in southwestern China. Methods: DNA typing for HLA-A and -B loci was performed using the polymerase chain reaction-sequence-based typing (PCR-SBT) method on 114 randomly selected healthy individuals of the Yi population. The allelic frequencies of HLA-A and -B loci were calculated by direct counting and HLA-A-B haplotypes were estimated using the expectation maximization algorithm. Results: A total of 17 HLA-A and 38 HLA-B alleles were found in the Yi population. The most frequent alleles were A*2402 (32.46%), A*1101 (26.32%), and A*0203 (10.09%) at the HLA-A locus and B*4601 (12.28%), B*1525 (10.09%), B*4001 (8.77%), and B*3802 (7.89%) at the HLA-B locus. The predominant HLA-A-B haplotypes were A*2402-B*1525 (7.86%) and A*0203-B*3802 (5.64%), followed by A*1101-B*4001 (4.69%). Phylogenetic analysis indicates that the Yi population in the Honghe, Yunnan Province of China basically belongs to groups of southeastern Asian origin, but shares some characteristics with northeastern Asian groups. Conclusion: The present study may add to the understanding of HLA polymorphism in the Yi ethnic group that was poorly defined previously, and provide useful information for bone marrow transplantation, anthropological research, and forensic sciences as well as for disease-association studies.

Adaptive interactions between HLA and HIV-1: highly divergent selection imposed by HLA class I molecules with common supertype motifs

Currently, 1.1 million individuals in the United States are living with HIV-1 infection. Although this is a relatively small proportion of the global pandemic, the remarkable mix of ancestries in the United States, drawn together over the past two centuries of continuous population migrations, provides an important and unique perspective on adaptive interactions between HIV-1 and human genetic diversity. HIV-1 is a rapidly adaptable organism and mutates within or near immune epitopes that are determined by the HLA class I genotype of the infected host. We characterized HLA-associated polymorphisms across the full HIV-1 proteome in a large, ethnically diverse national United States cohort of HIV-1-infected individuals. We found a striking divergence in the immunoselection patterns associated with HLA variants that have very similar or identical peptide-binding specificities but are differentially distributed among racial/ethnic groups. Although their similarity in peptide binding functionally clusters these HLA variants into supertypes, their differences at sites within the peptide-binding groove contribute to race-specific selection effects on circulating HIV-1 viruses. This suggests that the interactions between the HLA/HIV peptide complex and the TCR vary significantly within HLA supertype groups, which, in turn, influences HIV-1 evolution.

HLA-C polymorphisms and PCR dropout in exons 2 and 3 of the Cw*0706 allele in sequence-based typing for unrelated Chinese marrow donors

To evaluate the accuracy of SBT protocols for HLA-C and to better understand the HLA-C polymorphism in Chinese, 1795 unrelated CMDP donors were typed at exons 2, 3, and 4 of the HLA-C gene using the Atria commercial kit. Of the study subjects, 1768 showed conclusive typing results, whereas the other 27 showed inconclusive results. Subsequent full-length cloning and haplotype sequencing showed that 11 of the 27 inconclusive results could be explained by the presence of nine novel alleles identified: Cw*0130, 0624, 070206, 075602, 0766, 0767, 0820, 0821, and 0827. These novel alleles were generated by a total of 10 coding-region substitutions, eight of them being located in the antigen-binding groove. Cw*0766 and Cw*075602 were detected three and two times, respectively, in the 1795 donors. The other 16 inconclusive samples were retested by SBT using our in-house PCR primers; all of them were found to carry Cw*0706, which dropped out in exons 2 and 3 in the initial PCR using the commercial primers amplifying from 5' UTR to intron 3. Our results showed the importance of the full-length genomic sequence and intronic SNPs for the development of more accurate SBT. The allele distribution and novel alleles detected in this study also provide further insights into the HLA-C polymorphism in the Chinese Han population.

Human leukocyte antigens and HIV type 1 viral load in early and chronic infection: predominance of evolving relationships

BACKGROUND

During untreated, chronic HIV-1 infection, plasma viral load (VL) is a relatively stable quantitative trait that has clinical and epidemiological implications. Immunogenetic research has established various human genetic factors, especially human leukocyte antigen (HLA) variants, as independent determinants of VL set-point.

METHODOLOGY/PRINCIPAL FINDINGS

To identify and clarify HLA alleles that are associated with either transient or durable immune control of HIV-1 infection, we evaluated the relationships of HLA class I and class II alleles with VL among 563 seroprevalent Zambians (SPs) who were seropositive at enrollment and 221 seroconverters (SCs) who became seropositive during quarterly follow-up visits. After statistical adjustments for non-genetic factors (sex and age), two unfavorable alleles (A*3601 and DRB1*0102) were independently associated with high VL in SPs (p<0.01) but not in SCs. In contrast, favorable HLA variants, mainly A*74, B*13, B*57 (or Cw*18), and one HLA-A and HLA-C combination (A*30+Cw*03), dominated in SCs; their independent associations with low VL were reflected in regression beta estimates that ranged from -0.47+/-0.23 to -0.92+/-0.32 log(10) in SCs (p<0.05). Except for Cw*18, all favorable variants had diminishing or vanishing association with VL in SPs (p

CONCLUSIONS/SIGNIFICANCE

Overall, each of the three HLA class I genes had at least one allele that might contribute to effective immune control, especially during the early course of HIV-1 infection. These observations can provide a useful framework for ongoing analyses of viral mutations induced by protective immune responses.

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Key Words Collapse

MESH Headings

• Adult
• Age Factors
• Alleles
• Chronic Disease
• Female
• Genetic Variation
• HIV Seropositivity
• HIV-1/metabolism
• Histocompatibility Antigens Class I/immunology
• Histocompatibility Antigens Class II/immunology
• Humans
• Male
• Middle Aged
• Models, Genetic
• Mutation
• Regression Analysis
• Seroepidemiologic Studies
• Viral Load
• Zambia

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Grants

• AI064060 NIAID NIH HHS
• R01 AI064060 NIAID NIH HHS
• K02 AI076123 NIAID NIH HHS
• AI040951 NIAID NIH HHS
• AI071906 NIAID NIH HHS
• AI76123 NIAID NIH HHS
• R01 AI071906 NIAID NIH HHS

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Affiliation(s)

Jianming Tang Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
Rakhi Malhotra Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
Wei Song Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
Ilene Brill Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
Liangyuan Hu Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
Paul K. Farmer Vaccine Research Center, Emory University, Atlanta, Georgia, United States of America
Joseph Mulenga Rwanda-Zambia HIV-1 Research Group, Lusaka, Zambia
Susan Allen Rwanda-Zambia HIV-1 Research Group, Lusaka, Zambia Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
Eric Hunter Vaccine Research Center, Emory University, Atlanta, Georgia, United States of America
Richard A. Kaslow Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America

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Safety and efficacy of a 36-week induction regimen of abacavir/lamivudine and ritonavir-boosted atazanavir in HIV-infected patients

PURPOSE

The ARIES study assessed safety and efficacy of an induction regimen with atazanavir/ritonavir (ATV/RTV) + abacavir/lamivudine (ABC/3TC) followed by simplification to ATV + ABC/3TC in antiretroviral-naïve patients.

METHODS

This report includes a noncomparative analysis of all patients in the induction phase of the ARIES study through 36 weeks (clinicaltrials.gov: NCT00440947). This open-label study included 515 antiretroviral-naïve,HLA-B*5701-negative patients receiving a regimen of ATV 300 mg, RTV 100 mg, and ABC/3TC 600 mg/300 mg once daily for 36 weeks; eligible patients were then randomized to continue the induction regimen or simplify to ATV 400 mg plus ABC/3TC 600 mg/300 mg once daily.

RESULTS

Eighty-six percent (442/515) of patients completed 36 weeks on study; 80% (410/515) achieved HIV RNA <50 copies/mL (84% and 76% of patients with baseline HIV RNA of < and >or=100,000 copies/mL achieved this endpoint). Virologic failure (VF) was uncommon (3%); treatment-emergent major protease inhibitor and nucleoside reverse transcriptase inhibitor mutations were detected in 0/15 and 4/15 patients, respectively. Median CD4+ cell increase was 171 (range, -176 to 718) cells/mm(3). Hyperbilirubinemia (13%), diarrhea (4%), nausea (2%), and rash (2%) were the most frequent drug-related Grade 2-4 adverse events. Few adverse events (3%) led to study discontinuation.

CONCLUSIONS

Induction with ATV/RTV + ABC/3TC once daily provides an efficacious and well-tolerated regimen for the initial treatment of HIV.

Association of HLA-A, -B and -DRB1 genotype with birthweight and CD34+ cell content: analysis of Korean newborns and their cord blood

Birthweight and the hematopoietic progenitor cell content in cord blood affect and reflect fetal development, and MHC has been reported to play an important role in intrauterine growth. In this study, we assessed HLA-A, -B and -DRB1 polymorphisms, birthweight and cord blood CD34(+) cell content in 1628 full-term healthy neonates to identify the HLA alleles that are associated with fetal growth in Koreans. HLA-A*31, B*47, B*51, DRB1*04 showed positive association and HLA-A*03, A*24, A*30, B*07, B*52, B*58, DRB1*03 showed negative association with birthweight and/or CD34(+) cell content; additionally, there was a greater association in homozygotes than heterozygotes revealed in the trend analysis of birthweight centile with candidate allele zygosity (A*24, P= 0.018; DRB1*04, P= 0.047). Among these alleles, HLA-A*24 and DRB1*03 showed significant negative association with birthweight and/or CD34(+) cell content after Bonferroni correction, suggesting a significant association of these alleles with fetal growth in late pregnancy (A*24, P= 0.002, P(c) = 0.026; DRB1*03, P < 0.001, P(c) < 0.001). Various populations should be analyzed to identify different or consistent factors among ethnicities. Furthermore, a larger scale study that includes pre-terms will aid in the comprehensive understanding of these associations.

Virus-specific CD8+ T-cell responses better define HIV disease progression than HLA genotype

HLA alleles B57/58, B27, and B35 have the strongest genetic associations with HIV-1 disease progression. The mechanisms of these relationships may be host control of HIV-1 infection via CD8(+) T-cell responses. We examined these immune responses in subjects from the Seattle Primary Infection Cohort with these alleles. CD8(+) T-cell responses to conserved HIV epitopes within B57/58 alleles (TW10 and KF11) and B27 alleles (KK10 and FY10) delayed declines in CD4(+) T-cell counts (4 to 8 times longer), while responses to variable epitopes presented by B35 alleles (DL9 and IL9) resulted in more rapid progression. The plasma viral load was higher in B57/58(+) and B27(+) subjects lacking the conserved B57/58- and B27-restricted responses. The presence of certain B57/58-, B27-, and B35-restricted HIV-specific CD8(+) T-cell responses after primary HIV-1 infection better defined disease progression than the HLA genotype alone, suggesting that it is the HIV-specific CD8(+) T cells and not the presence of a particular HLA allele that determine disease progression. Further, the most effective host CD8(+) T-cell responses to HIV-1 were prevalent within an HLA allele, represented a high total allele fraction of the host CD8(+) T-cell response, and targeted conserved regions of HIV-1. These data suggest that vaccine immunogens should contain only conserved regions of HIV-1.

Infections, antigen-presenting cells, T cells, and immune tolerance: their role in the pathogenesis of immune thrombocytopenia

In the last 20 years, many publications have shed new light on the complex immunopathogenesis of immune thrombocytopenic purpura. They are associated with 3 interrelated areas of environmental autoimmunity, for example, infectious influences, antigen-presenting cell (APC) function, and T-cell abnormalities, particularly tolerance induction. This article highlights the recent literature and argues that infectious agents and platelets can significantly modulate APCs, which create an environment that dysregulates autoreactive T cells, leading to the production of autoantibodies.

Immunogenetic susceptibility to diabetes mellitus in patients with liver disease

BACKGROUND/AIM

Genetic, environmental, metabolic and infectious influences, such as hepatitis C virus (HCV) infection, are thought to impact on the development of diabetes in patients with liver disease. As specific human leucocyte antigen (HLA) alleles provide the major genetic risk factors for type 1 diabetes, our aim was to investigate whether HLA class I and II alleles constitute additional risk factors for diabetes in patients with liver disease.

METHODS

We evaluated two independent databases of 193 and 728 adult patients with chronic liver disease for the diagnosis of diabetes and the presence of specific HLA subtypes.

RESULTS

In each database, 24 and 19% of patients met criteria for diabetes. In the first database, specific class I and II alleles were observed more frequently in diabetics compared with non-diabetics: Cw7 (50 vs. 32%, P=0.04), DR51 (17 vs. 3%P=0.003) and DQ6 (37 vs. 18%, P=0.02). In the second database, DQ6 was observed in 16% of diabetics vs. 8% of non-diabetics (P=0.04). The DR2-DR51-DQ6 haplotype was higher in patients with diabetes in both databases (22 vs.7%, P=0.02 and 12 vs. 5%, P=0.02). In a subgroup analysis of patients with HCV infection, increased frequencies of Cw7, DR2/DR51, DQ6 and DR2-DR51-DQ6 were also observed to be higher in subjects with diabetes compared with those without diabetes.

CONCLUSIONS

Patients with chronic liver disease, especially those with HCV infection, have an immunogenetic risk for diabetes characterized by the presence of Cw7, DR51, DQ6 and DR2-DR51-DQ6.

A study of HIV provider attitudes toward HLA-B 5701 testing in the United States

Screening for HLA-B 5701 reduces the risk of developing an abacavir hypersensitivity reaction (ABC HSR) and is recommended in all patients before initiating highly active antiretroviral therapy (HAART) with abacavir. Between September 2007 and March 2008 we conducted a study of the attitudes and practice patterns of HIV providers in the United States to identify barriers to HLA-B 5701 testing in clinical practice. Study participants who completed an educational program could receive HLA-B 5701 test kits for use in their clinical practice. Surveys were administered before and after the educational program. A total of 477 HIV providers registered to participate in the survey, and 134 providers tested a total of 874 HIV-infected subjects, of which 6% (49/874) were HLA-B 5701 positive. Of 433 providers who completed the preeducation survey, 97% indicated that the test provided clinical value and 77% anticipated barriers to testing, with cost/reimbursement the most frequently cited. Among 202 providers who completed the posteducation survey, perceptions of the test's value remained largely unchanged while the proportion of providers who anticipated or encountered barriers to testing decreased. Of providers who used HLA-B 5701 test kits, 86% (115/134) found it "very easy" or "easy" to obtain test results, 95% (127/134) found it "very easy" or "easy" to interpret results, and 89% (119/134) indicated that they planned to continue HLA-B 5701 testing after the study. The results of this study suggest that HLA-B 5701 testing is easy to use in clinical practice and is a valuable tool to help reduce the risk of developing ABC HSR.

Successful implementation of a national HLA-B*5701 genetic testing service in Canada

Abacavir is a nucleoside reverse transcriptase inhibitor (NRTI) that is used in combination antiretroviral therapy in HIV-infected patients. It is currently recommended as a preferred or an alternative NRTI in antiretroviral-naïve patients. The major toxicity of abacavir is a hypersensitivity reaction (HSR), which occurs in approximately 5% of treated patients. There is a strong association between the human leukocyte antigen (HLA)-B*5701 allele and abacavir HSR, which has allowed for rapid acceptance of genetic screening for HLA-B*5701 in clinical use. Canadian clinicians working in hospital centers with HLA typing capacity opted to launch a pilot project in 2006 to offer the screening test as standard of care to HIV-infected patients. Currently, more than 11,000 HLA-B*5701 tests have been performed, among which 6.3% are positive. Continued efforts have been made to ensure that testing is available to all HIV-infected patients to widen the patients' therapeutic options. HLA-B*5701 screening shows clinical use and preliminary data suggest cost-effectiveness.

Genetic epidemiology of glioblastoma multiforme: confirmatory and new findings from analyses of human leukocyte antigen alleles and motifs

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.

HLA-B*5701 screening prior to abacavir prescription: clinical and laboratory aspects

This review focuses on the development of HLA-B*5701 genetic screening as a means of preventing drug hypersensitivity reactions caused by a commonly prescribed antiretroviral drug, abacavir. This strongly predictive genetic association, which in many respects represents a test case for the clinical application of pharmacogenetics, highlights the fine specificity of HLA-restricted immunity, here directed against a drug-specific antigen rather than an allogeneic molecule (as occurs in transplantation) or a pathogenic organism (as in viral infection). However, this example also demonstrates that successful implementation of pharmacogenetic screening requires that a range of criteria be adequately addressed. These include pharmaceutical factors (e.g. lack of alternative treatments with similar or improved cost effectiveness, safety, and efficacy), clinical factors (e.g. accurate diagnosis of the adverse event, in this case provided by clinical diagnostic criteria and adjunctive epicutaneous patch testing), sufficient objective evidence of the test's predictive value and generalizability (in this case provided by the first large-scale randomized trial of a pharmacogenetic test), as well as availability of quality-assured laboratory services that are responsive to the needs of targeted genetic screening. This example is intended to serve as a precedent for other pharmacogenetic screening strategies, particularly those aimed at reducing rates of serious drug hypersensitivity reactions in clinical practice.

Immunogenetics of drug-induced skin blistering disorders. Part I: Perspective

The overall immunopathogenesis relevant to a large series of disorders caused by a drug or its associated hyperimmune condition is discussed based upon the examination of the genetics of severe drug-induced bullous skin problems (sporadic idiosyncratic adverse events, including Stevens-Johnson syndrome and toxic epidermal necrolysis). An overarching pharmacogenetic schema is proposed. Immune cognition and early-effector processes are focused upon and a challenging synthesis around systems evolution is explained by a variety of projective analogies. Etiology, human leukocyte antigen-B, immune stability, dysregulation, pharmacomimicry, viruses and an aggressive ethnically differentiated 'karmic' response are discussed.

HLA-B51 and haplotypic diversity of B-Cw associations: implications for matching in unrelated hematopoietic stem cell transplantation

In unrelated hematopoietic stem cell transplantation (HSCT), human leukocyte antigen (HLA)-C locus incompatibilities occur frequently and are associated with increased risk of posttransplant complications. Because HLA-B51 is associated with a high rate of Cw disparities, we performed a comprehensive four-digit typing analysis of 140 ABCDRB1 B51 genotypes proven by pedigree analysis and 311 unrelated donors selected for 75 B51-positive patients. In addition, 145 A1/Ax-B8/B51-DR3/DRx donors were HLA typed at a high-resolution level and tested for three microsatellite (Msat) polymorphisms located in the HLA class I and III regions. Based on these data sets, 182 different ABCDR haplotypes with 14 different B-Cw associations were detected. Rates of Cw mismatches were shown to be highly correlated with the ABDRB1 haplotypes. We have computed 21 B51 haplotypes that disclose a high probability of HLA-C allele matching and 30 haplotypes with a low (<25%) probability. The HLA-C allele frequency profiles were quite different in these two groups, with a more heterogeneous distribution in the low matching probability group. HLA-Cw*1502 was inversely correlated with the likelihood to identify a Cw-mismatched donor: it was present in 61% of the high vs 18% of the low probability group (P < 0.0001). The analysis of three Msats in the class I and III regions showed a higher allelic diversity in B51-positive haplotypes compared with the conserved A1-B8-DR3 haplotype. HLA-B51 haplotypes therefore exhibit a high diversity at the level of B-Cw associations and of non-HLA polymorphisms in the class I and III regions. Such heterogeneity negatively impacts on overall matching in HSCT.

HLA class I allele and haplotype diversity in Ugandans supports the presence of a major east African genetic cluster

The objective of this study was to characterize the class I human leukocyte antigen (HLA) genetic composition of the Ugandan population to better define its relationship with other African groups. Samples from 175 individuals from Kampala (Uganda) were subjected to class I HLA-A, -B, and -C sequence-based typing. The high concordance between the major alleles and haplotypes found in the current and Kenyan populations and interpopulation genetic distance analysis strongly supported the presence of an East African cluster that contained the current Ugandan population along with Kenyan Luo and Nandi populations. The congruence of major alleles in different populations would permit consideration of East Africa as an integrated setting when designing and evaluating much needed malaria, tuberculosis, and AIDS vaccines.

Impact of HLA on the underlying primary diseases in Turkish patients with end-stage renal disease

The number of patients with end stage renal disease (ESRD) is increasing faster than the number of renal transplantations performed per year worldwide. Of the primary diseases leading to ESRD, diabetic nephropathy is the leading cause. The purpose of the present study is to investigate the association of HLA with the primary diseases leading to ESRD in Turkish patients. A total of 3230 individuals comprising 587 ESRD patients and 2643 healthy controls were enrolled into the study. Class I HLA-A, -B typing was performed by CDC method, while class II HLA-DRB1 typing was performed by low resolution PCR-SSP. We found a significant negative association between almost all A locus antigens and primary disease groups classified as chronic glomerulonephritis and hypertensive nephrosclerosis (p < 0.05). HLA-B58 and HLA-DRB1*03 significantly correlated with amyloidosis and diabetic nephropathy, respectively. Determination of HLAs as risk factors for primary diseases leading to ESRD might be beneficial in preventing progression to ESRD and recurrence of the primary disease post-transplantation.

Genetic susceptibility to haemorrhagic fever with renal syndrome caused by Hantaan virus in Chinese Han population

We report a significantly higher occurrence of HLA-DRB1*09 (51% vs. 23%, P = 0.002, OR = 3.57) and HLA-B*46-DRB1*09 (26% vs. 8%, P = 0.018, OR = 3.76) in patients with haemorrhagic fever with renal syndrome (HFRS) compared to the control group, suggesting Hantaan virus-induced HFRS is associated with a genetic predisposition in the Chinese Han population.

Racial, ethnic and socioeconomic disparities in the treatment of brain tumors

Disparities in American health care based on socially-defined patient characteristics such as race, ethnicity, and socioeconomic position are well-documented. We review differences and disparities in incidence, pathobiology, processes and outcomes of care, and survival based on social factors for brain tumors of all histologies. In the US, black patients have lower incidences of most brain tumor types and lower-income patients have lower incidences of low grade glioma, meningioma and acoustic neuroma; ascertainment bias may contribute to these findings. Pathogenetic differences between malignant gliomas in patients of different races have been demonstrated, but their clinical significance is unclear. Patients in disadvantaged groups are less often treated by high-volume providers. Mortality and morbidity of initial treatment are higher for brain tumor patients in disadvantaged groups, and they present with markers of more severe disease. Long term survival differences between malignant glioma patients of different races have not yet been shown. Clinical trial enrollment appears to be lower among brain tumor patients from disadvantaged groups. We propose future research both to better define disparities and to alleviate them.

Host genetics and HIV-1 viral load set-point in African-Americans

OBJECTIVE

In a recent genome-wide association study of HIV-1-infected individuals in the Euro-CHAVI cohort, viral load set-point was strongly associated with genotypes defined by two single nucleotide polymorphisms (SNPs) (rs9264942 and rs2395029) within the human major histocompatibility complex (MHC) region on chromosome 6. We attempted to confirm this finding in African-Americans and to address whether these SNPs are in linkage disequilibrium with human leukocyte antigen (HLA) class I alleles that mediate innate and adaptive immunity.

DESIGN

Our analyses relied on 121 African-American adolescents with chronic HIV-1 infection and quarterly immunological and virological outcome measures in the absence of therapy.

METHODS

PCR-based techniques were used to genotype two SNPs along with HLA class I alleles. Their associations with HIV-1 viral load set-point and longitudinal CD4+ and CD8+CD38+ T cell counts were tested in univariate and multivariable models.

RESULTS

The CC genotype at rs9264942 was associated with reduced viral load, but not with immunological outcomes or category of disease control. Consistent associations of favorable virologic outcomes were observed with B*57 (mostly B*5703) but not with rs2395029G allele at the HCP5 locus, which is in absolute linkage disequilibrium with B*5701 (in individuals of European descent), and not B*5703.

CONCLUSION

Although rs9264942 and B*57 (but not rs2395029G) are clearly associated with control of viral load set-point among African-Americans, fine-mapping of MHC SNPs in populations of African and European descent should help reveal the causative variants and the underlying functional mechanisms.

Novel approach to recognition of predicted HIV-1 Gag B3501-restricted CD8 T-cell epitopes by HLA-B3501(+) patients: confirmation by quantitative ELISpot analyses and characterisation using multimers

Exploring the intricacies of CD8(+) T-cell epitope recognition using emerging technologies to combine assessment of affinity, phenotype and resulting polyfunctional efficacy advances our understanding of HIV-1 immunopathogenesis and disease progression. Complexities within T-cell antigen recognition, such as epitope:MHC binding, stability and affinity, appear to influence the distinction between protective and ineffective anti-HIV-1 immune responses, which are thought to govern rate of disease progression. This study utilises the novel ProImmune REVEAL and ProVE(R) technology of rapid peptide synthesis, binding and affinity assays, and pentamer synthesis in conjunction with flow cytometry and simultaneous assessment of multiple CD8(+) T-cell effector functions in response to HLA-B3501-restricted HIV-1 Gag peptides, to discover new T-cell epitopes. The predicted HLA-B3501-restricted peptides, HPVHAGPIA and YPLTSLRSL, and relevant pentamers were used in parallel to validate T-cell epitopes on clinical HIV-1(+) samples, confirming correlation between the expected superior immunogenicity of newly discovered epitopes and the ex vivo T-cell response. Such a platform should be employed in prophylactic and therapeutic vaccine settings.

HLA-A, B, Cw, DRB1, DQB1 and DPB1 alleles and haplotypes in the genetically homogenous Irish population

The frequencies of human leucocyte antigen (HLA) class I and II alleles and haplotypes of 250 Irish unrelated bone marrow donors were determined by high resolution polymerase chain reaction (PCR), using a combination of reverse line blot hybridization and PCR with sequence-specific primers. Phylogenetic analyses indicate that this Irish population is closely related to British, North-western European, American and Australian Caucasian populations. These observations are consistent with recognized historical, geographical, cultural, ethnic and linguistic relationships between these populations and suggest that Irish haematopoietic stem cell transplant recipients have a greater likelihood of finding a phenotypically matched donor within registries based on these populations. HLA-A, B, Cw, DRB1, DQB1 and DPB1 analysis confirms that this young homogenous population is characterized by features of a North-western European anthropological type with limited influence of additional ethnic haplotypes.

High-resolution human leukocyte antigen (HLA) haplotypes and linkage disequilibrium of HLA-B and -C and HLA-DRB1 and -DQB1 alleles in a Taiwanese population

Using the maximum-likelihood method with the expectation-maximization (EM) algorithm of PYPOP, high-resolution human leukocyte antigen (HLA) three-locus haplotypes (HLA-A, -B, and -C; HLA-A, -B, and -DRB1) and four-locus haplotypes (HLA-A, -B, -C, and -DRB1) were determined. Linkage disequilibrium of high-resolution HLA-B and -C alleles and HLA-DRB1 and -DQB1 alleles was also calculated. Comparison of the Taiwanese haplotypes and haplotypes from donors in the Chinese Han population, the Asia Pacific Islander ethnic category of the NMDP (National Marrow Donor Program), and the Taiwanese cord blood units demonstrated similarities and dissimilarities among the four populations. HLA allele frequencies of our study suggested that the Taiwanese have a relative population relationship with the southern Han Chinese with regard to HLA. Our results also indicated that the Taiwanese population exhibits genetic proximity with Asian Americans with regard to HLA-A and -DRB1 but not HLA-B.

Current trends in screening across ethnicities for hypersensitivity to abacavir

Abacavir is a potent nucleoside analog reverse transcriptase inhibitor approved for the treatment of HIV infection. Approximately 5-8% of Caucasian patients receiving abacavir develop a hypersensitivity reaction, characterized by rash, fever and, occasionally, multisystemic involvement. Rechallenge with the drug can be fatal. The discovery of the mechanisms involved in this hypersensitivity reaction and the identification of tools for its prediction are the subject of this review. The most relevant finding is the recognition of a strong association between one specific haplotype at the HLA complex type I, HLA-B*5701, and the abacavir hypersensitivity reaction. The heterogeneity in the prevalence of HLA-B*5701 across distinct ethnicities accounts for differences in the risk of abacavir hypersensitivity reactions in distinct populations.

Identification and characterization of 2 HIV-1 Gag immunodominant epitopes restricted by Asian HLA allele HLA-B*4801

HLA-B*4801 is frequently found in Asian populations but rarely in Caucasian or African populations. Although HLA-B*4801-restricted human immunodeficiency virus-1 (HIV-1) epitopes would be useful for acquired immune deficiency syndrome (AIDS) vaccine development in Asia, they have not been reported so far. In the present study, we sought to identify HLA-B*4801-restricted HIV-1 epitopes by using 17-mer overlapping peptides derived from HIV-1 Gag, Pol, and Nef as well as 8- to 11-mer truncated peptides, and thereby identified two HLA-B*4801-restricted Gag epitopes. These epitope-specific CD8(+) T cells strongly responded to HIV-1-infected cells expressing HLA-B*4801, confirming that these Gag epitopes were endogenously presented by HLA-B*4801. These epitope-specific CD8(+) T cells were elicited in five of the seven tested chronically HIV-1-infected individuals with HLA-B*4801, suggesting them to be immunodominant epitopes. These epitopes will be useful for the studies of AIDS immunopathogenesis and the development of an HIV-1 vaccine in Asia.

Design, expression, and processing of epitomized hepatitis C virus-encoded CTL epitopes

Hepatitis C virus (HCV) vaccine efficacy may crucially depend on immunogen length and coverage of viral sequence diversity. However, covering a considerable proportion of the circulating viral sequence variants would likely require long immunogens, which for the conserved portions of the viral genome, would contain unnecessarily redundant sequence information. In this study, we present the design and in vitro performance analysis of a novel "epitome" approach that compresses frequent immune targets of the cellular immune response against HCV into a shorter immunogen sequence. Compression of immunological information is achieved by partial overlapping shared sequence motifs between individual epitopes. At the same time, sequence diversity coverage is provided by taking advantage of emerging cross-reactivity patterns among epitope variants so that epitope variants associated with the broadest variant cross-recognition are preferentially included. The processing and presentation analysis of specific epitopes included in such a compressed, in vitro-expressed HCV epitome indicated effective processing of a majority of tested epitopes, although re-presentation of some epitopes may require refined sequence design. Together, the present study establishes the epitome approach as a potential powerful tool for vaccine immunogen design, especially suitable for the induction of cellular immune responses against highly variable pathogens.

Essential differences in ligand presentation and T cell epitope recognition among HLA molecules of the HLA-B44 supertype

Human leukocyte antigens (HLA) have long been grouped into supertypes to facilitate peptide-based immunotherapy. Analysis of several hundreds of peptides presented by all nine antigens of the HLA-B44 supertype (HLA-B*18, B*37, B*40, B*41, B*44, B*45, B*47, B*49 and B*50) revealed unique peptide motifs for each of them. Taking all supertype members into consideration only 25 out of 670 natural ligands were found on more than one HLA molecule. Further direct comparisons by two mass spectrometric methods--isotope labeling as well as a label-free approach--consistently demonstrated only minute overlaps of below 3% between the ligandomes of different HLA antigens. In addition, T cell reactions of healthy donors against immunodominant HLA-B*44 and HLA-B*40 epitopes from EBV lacked promiscuous T-cell recognition within the HLA-B44 supertype. Taken together, these results challenge the common paradigm of broadly presented epitopes within this supertype.

High frequency of prostate antigen-directed T cells in cancer patients compared to healthy age-matched individuals

BACKGROUND

In order to obtain a sustained cytotoxic T lymphocyte (CTL) response against cancer cells it is preferable to have CTLs directed against multiple peptide epitopes from numerous tumor-associated antigens.

METHODS

We used a Flow Cytometry-based interferon (IFN)-gamma secretion assay with peptide-pulsed C1R-A2 as antigen-presenting cells to analyze whether CD8+ T cells directed against any of 24 HLA-A*0201-binding peptides from 15 prostate-associated proteins can be found in the peripheral blood of patients with localized prostate cancer. We also investigated whether multiple prostate antigen-specific CD8+ T cells can be generated simultaneously, from a naïve T cell repertoire. In that case, dendritic cells (DCs) from peripheral blood of healthy donors were divided in six portions and separately pulsed with six peptides. The peptide-pulsed DCs were then pooled and used to stimulate autologous T cells. The T cells were re-stimulated with peptide-pulsed monocytes.

RESULTS

We found prostate antigen-restricted CD8+ T cells in the peripheral blood in 48 out of 184 (26.1%) analyzed samples from 25 cancer patients. This is significantly higher than 17 out of 214 analyzed samples (7.9%) from 10 healthy age-matched male individuals (P = 0.0249). In the cases when antigen-specific T cells could not be detected, we were able to generate IFN-gamma-producing CD8+ T cells specific for up to three prostate antigens simultaneously from a naïve T cell repertoire.

CONCLUSIONS

CD8+ T cells directed against prostate antigen peptides can be found in, or generated from, peripheral blood. This indicates that such T cells could be expanded ex vivo for adoptive transfer to prostate cancer patients.

Multiplex HLA-typing by pyrosequencing

Class I and II loci of the human leukocyte antigens (HLA) represent the most polymorphic region of the genome. Evolutionary pressure has resulted in a large number of allelic variants of these loci ensuring the high frequency of heterozygous genotypes observed in human populations. Molecular techniques, including sequencing, are capable of precisely defining HLA alleles. Sequencing by synthesis methodology employed by pyrosequencing represents a complementary approach to other molecular methods of HLA genotyping. Out-of-phase sequencing of HLA alleles by pyrosequencing can resolve certain cis/trans ambiguities that would otherwise require the sequencing of cloned DNA. Genotyping of HLA loci for the presence of specific amino acid variants is beneficial for proper matching of organ donor to recipient, the monitoring of HLA associated genetic risk to autoimmune diseases, population genetic studies, as well as evaluation of the genetics of human host-human pathogen interaction.

HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies distinguish Eastern European Americans from the general European American population

Sequence-based typing was used to identify human leukocyte antigen (HLA)-A, -B, -C, and -DRB1 alleles from 558 consecutively recruited US volunteers with Eastern European ancestry for an unrelated hematopoietic stem cell registry. Four of 31 HLA-A alleles, 29 HLA-C alleles, 59 HLA-B alleles, and 42 HLA-DRB1 alleles identified (A*0325, B*440204, Cw*0332, and *0732N) are novel. The HLA-A*02010101g allele was observed at a frequency of 0.28. Two-, three-, and four-locus haplotypes were estimated using the expectation-maximization algorithm. The highest frequency extended haplotypes (A*010101g-Cw*070101g-B*0801g-DRB1*0301 and A*03010101g-Cw*0702-B*0702-DRB1*1501) were observed at frequencies of 0.04 and 0.03, respectively. Linkage disequilibrium values (Dij') of the constituent two-locus haplotypes were highly significant for both extended haplotypes (P values were less than 8 x 10(-10)) but were consistently higher for the more frequent haplotype. Balancing selection was inferred to be acting on all the four loci, with the strongest evidence of balancing selection observed for the HLA-C locus. Comparisons of the A-C-B haplotypes and DRB1 frequencies in this population with those for African, European, and western Asian populations showed high degrees of identity with Czech, Polish, and Slovenian populations and significant differences from the general European American population.

HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1

Human immunodeficiency virus type 1 (HIV-1)-infected persons who maintain plasma viral loads of <50 copies RNA/ml without treatment have been termed elite controllers (EC). Factors contributing to durable control of HIV in EC are unknown, but an HLA-dependent mechanism is suggested by overrepresentation of "protective" class I alleles, such as B*27, B*51, and B*57. Here we investigated the relative replication capacity of viruses (VRC) obtained from EC (n = 54) compared to those from chronic progressors (CP; n = 41) by constructing chimeric viruses using patient-derived gag-protease sequences amplified from plasma HIV RNA and inserted into an NL4-3 backbone. The chimeric viruses generated from EC displayed lower VRC than did viruses from CP (P < 0.0001). HLA-B*57 was associated with lower VRC (P = 0.0002) than were other alleles in both EC and CP groups. Chimeric viruses from B*57(+) EC (n = 18) demonstrated lower VRC than did viruses from B*57(+) CP (n = 8, P = 0.0245). Differences in VRC between EC and CP were also observed for viruses obtained from individuals expressing no described "protective" alleles (P = 0.0065). Intriguingly, two common HLA alleles, A*02 and B*07, were associated with higher VRC (P = 0.0140 and 0.0097, respectively), and there was no difference in VRC between EC and CP sharing these common HLA alleles. These findings indicate that cytotoxic T-lymphocyte (CTL) selection pressure on gag-protease alters VRC, and HIV-specific CTLs inducing escape mutations with fitness costs in this region may be important for strict viremia control in EC of HIV.

HLA-A amino acid polymorphism and delayed kidney allograft function

Delayed allograft function (DGF) is a common adverse event in postrenal transplantation. The etiology of DGF is thought to include both nonimmunologic (donor age, cold ischemia time, and recipient race) and immunologic factors. We examined the association of DGF with amino acid mismatches at 66 variable sites of the HLA-A molecule in a prospective cohort study of 697 renal transplant recipients of deceased donors. Using a multivariate logistic regression model adjusted for nonimmunologic risk factors, we show that combinations of a few amino acid mismatches at crucial sites of HLA-A molecules were associated with DGF. In Caucasian recipients, a mismatch at position 62, 95, or 163, all known to be functionally important within the antigen recognition site, was associated with an increased risk for DGF. Furthermore, a decreased risk for DGF was associated with a mismatch at HLA-A family-specific sites (149, 184, 193, or 246), indicating that evolutionary features of HLA-A polymorphism separating HLA-A families and lineages among donor-recipient pairs may correlate with the magnitude of alloreactivity influencing the development of DGF. These findings suggest that amino acid polymorphisms at functionally important positions at the antigen recognition site of the HLA-A molecule have a significant influence on DGF.

Differential pathways govern CD4+ CD28- T cell proinflammatory and effector responses in patients with coronary artery disease

Patients with acute coronary syndromes experience circulatory and intraplaque expansion of an aggressive and unusual CD4(+) lymphocyte subpopulation lacking the CD28 receptor. These CD4(+)CD28(-) cells produce IFN-gamma and perforin, and are thought to play an important role in coronary atheromatous plaque destabilization. Aberrant expression of killer Ig-like receptors (KIRs) in CD4(+)CD28(-) cells is broadly thought to be responsible for their cytotoxicity, but the mechanisms involved remain poorly defined. We therefore sought to investigate the mechanism and regulation of CD4(+)CD28(-) cell functionality using T cell clones (n = 536) established from patients with coronary artery disease (n = 12) and healthy volunteers (n = 3). Our functional studies demonstrated that KIR2DS2 specifically interacted with MHC class I-presenting human heat shock protein 60 (hHSP60) inducing cytotoxicity. Further investigations revealed the novel finding that hHSP60 stimulation of TCR alone could not induce a cytotoxic response, and that this response was specific and KIR dependent. Analysis of CD4(+)CD28(-)2DS2(+) clones (n = 162) showed that not all were hHSP60 cytotoxic; albeit, their prevalence correlated with coronary disease status (p = 0.017). A higher proportion of clones responded to hHSP60 by IFN-gamma compared with perforin (p = 0.008). In this study, for the first time, we define the differential regulatory pathways involved in CD4(+)CD28(-) cell proinflammatory and effector responses. We describe in this study that, contrary to previous reports, CD4(+)CD28(-) cell recognition and killing can be specific and discriminate. These results, in addition to contributing to the understanding of CD4(+)CD28(-) cell functionality, may have implications for the monitoring and management of coronary artery disease progression.

Human leukocyte antigen class I genotypes in relation to heterosexual HIV type 1 transmission within discordant couples

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.

Clozapine-induced agranulocytosis and its genetic determinants

Clozapine-induced agranulocytosis (CiA) is a potentially life-threatening pharmacological adverse drug reaction, which limits a broader application of this highly effective atypical antipsychotic in schizophrenic patients. Although this adverse reaction has been well known for almost 30 years, only few genetically based determinants can be identified to date. Furthermore, owing to rare occurrence, specific clinical course and complexity of pathomechanisms of antipsychotic-induced agranulocytosis, only a few of the findings met the criteria of replication. The most promising susceptibility genes for CiA include genes involved in the human leukocyte antigen system and in specific metabolizing enzyme systems. However, complex idiosyncratic drug reactions such as CiA are considered to be determined by multiple, possibly interacting genetic variations, rather than by a single causative variant.

Identification of two novel HLA alleles, HLA-A*02010103 and HLA-B*4455, and characterization of the complete genomic sequence of HLA-A*290201

We describe two novel human leukocyte antigen (HLA) alleles, HLA-A*02010103 and HLA-B*4455, that were discovered in two unrelated Caucasian individuals. In addition, we report the full-length genomic sequence of HLA-A*290201. Compared with HLA-A*02010101, HLA-A*02010103 has three nucleotide (nt) changes within intron 1, which is altered to a sequence typical of the HLA-A*23/A*24 allele group. In HLA-B*4455, an nt exchange occurred in codon 9 of HLA-B*44020101, resulting in a change of the amino acid coding from tyrosine to histidine. We sequenced HLA-A*290201 from nt -108 to nt 2922, encompassing all exons and introns as well as parts of the 5' and 3' untranslated regions. Previously, the full-length genomic sequence was known only for HLA-A*29010101, which is found at a lower frequency in Caucasians than HLA-A*290201.

Immunogenetic correlates of Neisseria gonorrhoeae infection in adolescents

BACKGROUND

Understanding host factors modulating immunity to Neisseria gonorrhoeae infection may benefit work on vaccine development.

METHODS

We analyzed longitudinal data collected from 485 male and female adolescents to determine genetic correlates of genital gonorrhea. Cytokine data from 388 females were analyzed to assess immunologic markers of gonorrhea and their relationship to genetic correlates.

RESULTS

The T-G haplotype defining interleukin-2 (IL-2) gene promoter and intron 1 polymorphisms (-330T and -166G) was more frequently found in individuals who had gonorrhea (relative odds = 3.2, P = 0.01). Among 3 endocervical cytokines measured, IL-10 and IL-12 concentrations were higher and IL-2 lower when gonorrhea was detected. The decrease in endocervical IL-2 after gonorrhea acquisition was mostly restricted to subjects with the IL2 T-G haplotype, which may reflect involvement of a pathogen-specific and genetically mediated mechanism for differential IL-2 responses at genital mucosa. In addition, 2 human leukocyte antigen variants (Cw*04 and DQB1*05) were also independently associated with gonorrhea (adjusted relative odds = 1.9 and 0.5, respectively; P <0.05 for both).

CONCLUSIONS

Confirmation of immunogenetic correlates of gonorrhea in larger cohorts may be useful in guiding further research on both innate and adaptive immune responses to N. gonorrhoeae.

Molecular evolution of human immunodeficiency virus type 1 upon transmission between human leukocyte antigen disparate donor-recipient pairs

Background

To address evolution of HIV-1 after transmission, we studied sequence dynamics in and outside predicted epitopes of cytotoxic T lymphocytes (CTL) in subtype B HIV-1 variants that were isolated from 5 therapy-naive horizontal HLA-disparate donor-recipient pairs from the Amsterdam Cohort Studies on HIV-1 infection and AIDS.

Methodology/Principal Findings

In the first weeks after transmission, the majority of donor-derived mutations in and outside donor-HLA-restricted epitopes in Gag, Env, and Nef, were preserved in the recipient. Reversion to the HIV-1 subtype B consensus sequence of mutations in- and outside donor-HLA-restricted CTL epitopes, and new mutations away from the consensus B sequence mostly within recipient-HLA-restricted epitopes, contributed equally to the early sequence changes. In the subsequent period (1–2 years) after transmission, still only a low number of both reverting and forward mutations had occurred. During subsequent long-term follow-up, sequence dynamics were dominated by forward mutations, mostly (50–85%) in recipient-HLA-restricted CTL epitopes. At the end of long-term follow-up, on average 43% of the transmitted CTL escape mutations in donor-HLA-restricted epitopes had reverted to the subtype B consensus sequence.

Conclusions/Significance

The relatively high proportion of long-term preserved mutations after transmission points to a lack of back selection even in the absence of CTL pressure, which may lead to an accumulating loss of critical CTL epitopes. Our data are supportive for a continuous adaptation of HIV-1 to host immune pressures which may have implications for vaccine design.

High sensitivity of human leukocyte antigen-b*5701 as a marker for immunologically confirmed abacavir hypersensitivity in white and black patients

BACKGROUND

Although the human leukocyte antigen (HLA)-B*5701 is highly associated with a hypersensitivity reaction (HSR) to abacavir (ABC), variable sensitivities have been reported when clinical data alone have been used to define an ABC HSR. This study evaluated the sensitivity of detection of the HLA-B*5701 allele as a marker of ABC HSRs in both white and black patients, using skin patch testing to supplement clinical diagnosis.

METHODS

White and black patients, identified through chart review, were classified as having received a diagnosis of an ABC HSR based on clinical findings only (a clinically suspected ABC HSR) or based on clinical findings and a positive skin patch test result (an immunologically confirmed [IC] ABC HSR). Control subjects were racially matched subjects who tolerated ABC for >/=12 weeks without experiencing an ABC HSR. Patients and control subjects were tested for the presence of HLA-B*5701. Sensitivity, specificity, and odds ratios for the detection of HLA-B*5701 as a marker for an ABC HSR were calculated for white and black participants.

RESULTS

Forty-two (32.3%) of 130 white patients and 5 (7.2%) of 69 black patients who met the criteria for clinically suspected HSRs had IC HSRs. All 42 white patients with IC HSRs were HLA-B*5701 positive (sensitivity, 100%; odds ratio, 1945; 95% confidence interval, 110-34,352). Among all white patients with clinically suspected HSRs, sensitivity was 44% (57 of 130 patients tested positive for HLA-B*5701); specificity among white control subjects was 96%. Five of 5 black patients with IC HSRs were HLA-B*5701 positive (sensitivity, 100%; odds ratio, 900; 95% confidence interval, 38-21,045). Among black patients with clinically suspected HSRs, the sensitivity was 14% (10 of 69 tested positive for HLA-B*5701); specificity among black control subjects was 99%.

CONCLUSIONS

Although IC ABC HSRs are uncommon in black persons, the 100% sensitivity of HLA-B*5701 as a marker for IC ABC HSRs in both US white and black patients suggests similar implications of the association between HLA-B*5701 positivity and risk of ABC HSRs in both races.

Good genes, complementary genes and human mate preferences

The past decade has witnessed a rapidly growing interest in the biological basis of human mate choice. Here we review recent studies that demonstrate preferences for traits which might reveal genetic quality to prospective mates, with potential but still largely unknown influence on offspring fitness. These include studies assessing visual, olfactory and auditory preferences for potential good-gene indicator traits, such as dominance or bilateral symmetry. Individual differences in these robust preferences mainly arise through within and between individual variation in condition and reproductive status. Another set of studies have revealed preferences for traits indicating complementary genes, focussing on discrimination of dissimilarity at genes in the major histocompatibility complex (MHC). As in animal studies, we are only just beginning to understand how preferences for specific traits vary and inter-relate, how consideration of good and compatible genes can lead to substantial variability in individual mate choice decisions and how preferences expressed in one sensory modality may reflect those in another. Humans may be an ideal model species in which to explore these interesting complexities.

Statistical resolution of ambiguous HLA typing data

High-resolution HLA typing plays a central role in many areas of immunology, such as in identifying immunogenetic risk factors for disease, in studying how the genomes of pathogens evolve in response to immune selection pressures, and also in vaccine design, where identification of HLA-restricted epitopes may be used to guide the selection of vaccine immunogens. Perhaps one of the most immediate applications is in direct medical decisions concerning the matching of stem cell transplant donors to unrelated recipients. However, high-resolution HLA typing is frequently unavailable due to its high cost or the inability to re-type historical data. In this paper, we introduce and evaluate a method for statistical, in silico refinement of ambiguous and/or low-resolution HLA data. Our method, which requires an independent, high-resolution training data set drawn from the same population as the data to be refined, uses linkage disequilibrium in HLA haplotypes as well as four-digit allele frequency data to probabilistically refine HLA typings. Central to our approach is the use of haplotype inference. We introduce new methodology to this area, improving upon the Expectation-Maximization (EM)-based approaches currently used within the HLA community. Our improvements are achieved by using a parsimonious parameterization for haplotype distributions and by smoothing the maximum likelihood (ML) solution. These improvements make it possible to scale the refinement to a larger number of alleles and loci in a more computationally efficient and stable manner. We also show how to augment our method in order to incorporate ethnicity information (as HLA allele distributions vary widely according to race/ethnicity as well as geographic area), and demonstrate the potential utility of this experimentally. A tool based on our approach is freely available for research purposes at http://microsoft.com/science.

Epitope landscape in breast and colorectal cancer

The finding that individual cancers contain many mutant genes not present in normal tissues has prompted considerable interest in the cancer epitope landscape. To further understand such effects, we applied in silico-based epitope prediction algorithms and high throughput post hoc analysis to identify candidate tumor antigens. Analysis of 1,152 peptides containing missense mutations previously identified in breast and colorectal cancer revealed that individual cancers accumulate on average approximately 10 and approximately 7 novel and unique HLA-A*0201 epitopes, respectively, including genes implicated in the neoplastic process. These data suggest that, with appropriate manipulation of the immune system, tumor cell destruction in situ may provide a polyvalent tumor vaccine without a requirement for knowledge of the targeted antigens.