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1.  ASSOCIATION BETWEEN GENETIC VARIANTS IN ADHESION MOLECULES AND OUTCOMES AFTER HEMATOPOIETIC CELL TRANSPLANTS 
Allogeneic hematopoietic cell transplant (HCT) is associated with a high morbidity and mortality. Adhesion molecules play an important role in endothelial activation and initiation of inflammatory response. We hypothesized that single nucleotide polymorphisms (SNPs) in the endothelial molecules may contribute to heterogeneity in HCT outcomes. We evaluated the association of 4 SNPs in ICAM1 (rs5498), PECAM1 (rs668 and rs1131012) and SELL (rs2229569) genes with acute and chronic graft versus host disease (GvHD) and those experiencing transplant related mortality (TRM) within one year among 425 allogeneic HCT recipient-donor pairs. Using a Fine and Gray proportional hazards model to evaluate the association between genetic variants and clinical outcomes, after adjustment for recipient age, race, diagnosis, disease status, gender mismatch, CMV serostatus, gender, donor type, conditioning regimen and year of transplant, only rs5498 in the ICAM1 gene among both recipients and donors was associated with a decreased risk of TRM (p≤0.02). None of the SNPs were associated with acute or chronic GvHD risk. These findings suggest that genetic variants in the vascular adhesion molecules may be used to identify patients at high risk for TRM.
doi:10.1111/j.1744-313X.2012.01131.x
PMCID: PMC3458148  PMID: 22646485
Adhesion molecules; hematopoietic cell transplantation; single nucleotide polymorphisms
2.  Report from the Immunogenomic Data Analysis Working Group (IDAWG) 16th International HLA and Immunogenetics Workshop (IHIW) Project: Immunogenomic Data-Management Methods 
Summary
The goal of the IDAWG is to facilitate the consistent analysis of HLA and KIR data, and the sharing of those data among the immunogenomic and larger genomic communities. However, the data-management approaches currently applied by immunogenomic researchers are not widely discussed or reported in the literature, and the effect of different approaches on data-analyses is not known.
With ASHI’s support, the IDAWG developed a forty-five question survey on HLA and KIR data-generation, data-management, and data-analysis practices. Survey questions detailed the loci genotyped, typing systems used, nomenclature versions reported, computer operating systems and software used to manage and transmit data, the approaches applied to resolve HLA ambiguity, and the methods used for basic population-level analyses. Respondents were invited to demonstrate their HLA ambiguity resolution approaches in simulated data sets.By May 2012, 156 respondents from 35 nations had completed the survey . These survey respondents represent a broad sampling of the Immunogenomic community; 52% were European, 30% North American, 10% Asian, 4% South American, and 4% from the Pacific.
The project will continue in conjunction with the 17th Workshop, with the aim of developing community data-sharing standards, ambiguity resolution documentation formats, single-task data-Management tools, and, novel data-analysis methods and applications. While additional project details and plans for the 17th IHIW will be forthcoming, we welcome the input and participation in these projects from the histocompatibility and immunogenetics community.
doi:10.1111/iji.12026
PMCID: PMC3789600  PMID: 23280068
Meta-analysis; Statistics; HLA; Genetics
3.  Report from the 16th International Histocompatibility and Immunogenetics Workshop (IHIW) Component: Population Global Distribution of Killer Immunoglobulin-like Receptor (KIR) and Ligands 
In the last fifteen years published reports have described KIR gene-content frequency distributions in more than 120 populations worldwide. However, there have been limited studies examining these data in aggregate in order to detect overall patterns of variation at regional and global levels. Here, we present a summary of the collection of KIR gene-content data for 105 worldwide populations collected as part of the 15th and 16th International Histocompatibility and Immunogenetics Workshops, and preliminary results for data analysis.
The data were contributed by thirty-four laboratories during the four-year course of this project, including data for the HGDP-CEPH populations. Additionally, data from the 15th IHIW and data contributed to the allelefrequencies.net (AFND) database were combined with the current workshop dataset
doi:10.1111/iji.12028
PMCID: PMC3789603  PMID: 23280119
KIR; HLA; workshop; report
4.  The International Histocompatibility Working Group in Hematopoietic Cell Transplantation 
International journal of immunogenetics  2012;40(1):10.1111/iji.12022.
Summary
The International Histocompatibility Working Group is a collaborative international effort to understand the HLA and non-HLA genetics of the transplantation barrier. The Working Group is comprised of experts in the fields of histocompatibility and immunogenetics, hematopoietic cell transplantation, and outcomes research. Data for 25855 unrelated donor transplants was submitted in support of research studies for the 16th International Histocompatibility Workshop. Active investigation is in progress in 7 key areas: the impact of HLA matching, role of race and ethnicity, identification of permissible HLA mismatches, haplotype-associated determinants, minor histocompatibility antigens, immune response genes, and KIR genetics. New hypotheses for the 16th workshop were developed for immunogenetic studies in cord blood and haploidentical related donor transplantation.
doi:10.1111/iji.12022
PMCID: PMC3887040  PMID: 23279968
5.  An important role for autoimmunity in the immunopathogenesis of chronic allograft rejection 
Summary
Organ transplantation is the treatment of choice for patients with end-stage organ dysfunction. In spite of advances in understanding of donor and recipient physiology, organ preservation, operative techniques, and immunosuppression long term graft survival still remains a major problem primarily due to chronic rejection. Alloimmune responses to mismatched major histocompatibility antigens have been implicated as an important factor leading to rejection. However, there is increasing evidence pointing towards cross talk between the alloimmune and autoimmune responses creating a local inflammatory milieu which eventually leads to fibrosis and occlusion of the lumen in the transplanted organ i.e., chronic rejection. In this review, we will discuss recent studies and emerging concepts for the interdependence of alloimmune and autoimmune responses in the immunopathogenesis of chronic allograft rejection. The role of autoimmunity in the development of chronic rejection is an intriguing and exciting area of research in the field of solid-organ transplantation with significant potential to develop novel therapeutic strategies towards preventing chronic allograft rejection.
doi:10.1111/j.1744-313X.2012.01112.x
PMCID: PMC3396719  PMID: 22486939
chronic rejection; TH17; regulatory T-cells; autoimmunity
6.  Mannose binding lectin genotype and serum levels in patients with chronic and allergic pulmonary aspergillosis 
Background
Several studies suggest mannose binding lectin (MBL) deficiency is associated with various manifestations of aspergillosis. MBL serum levels and function are genetically determined, but levels rise during inflammation.
Objective
We address the relative frequency of deficient genotypes, the relationship between serum level and genotype and both age and disease manifestations in patients with chronic pulmonary (CPA) and allergic bronchopulmonary aspergillosis (ABPA) and severe asthma with fungal sensitisation (SAFS).
Method
DNA was extracted from blood samples and MBL2 genotyping was performed using the INNO-LiPA MBL2 kit. Serum MBL concentrations were determined by ELISA.
Results
108 patients were evaluated, 70 (65%) with CPA, 38 (35%) with allergic disease (ABPA, SAFS or undefined) and 13 (12%) had both CPA and ABPA. The mean MBL serum level was 1849μg/L and did not differ between groups. 40 subjects (37%) had exon 1 genotypes producing non-functional MBL (A/B, A/C, A/D and O/O), a frequency not different from published normal controls. A/A subjects with CPA had higher levels (2,981μg/L) compared with allergic A/A subjects (2202μg/L) (p=0.012). No single haplotype, genotype or allele was significantly related to any aspergillosis phenotype. Worse breathlessness was associated with higher MBL levels among A/A subjects (p=0.009) and conversely non-functional genotypes. Mean MBL values were higher in those with an MRC score of 5 compared with those with and MRC score of 1 (p=0.023).A/A allergic subjects (n=27) in this study were ~11 years younger than allergic A/O subjects (n=11, p=0.02). Subjects with worse respiratory status or more severe CPA had higher MBL serum levels (p=0.023; p=0.034). Bronchiectasis was not associated with MBL levels in CPA or allergic aspergillosis.
Conclusion
MBL genotype and serum level modulates progression of aspergillosis.
doi:10.1111/j.1744-313X.2011.01078.x
PMCID: PMC3326202  PMID: 22225939
Aspergillosis; Aspergillus; innate immunity; mannose binding lectin; MBL
7.  CCR5, RANTES, and SDF-1 polymorphisms and mother-to-child HIV-1 transmission 
SUMMARY
Among 288 HIV-1-infected, breastfeeding women who received zidovudine prophylaxis and were followed with their infants in Nairobi, we found no associations between maternal genetic polymorphisms in CCR5 (59029G/A, 59353T/C, 59356T/C, 59402G/A), RANTES (−403G/A), and SDF-1 (3′801G/A) and mother-to-child HIV-1 transmission; plasma, cervical, and breastmilk viral loads; or breastmilk chemokine concentrations.
doi:10.1111/j.1744-313X.2010.00924.x
PMCID: PMC2922909  PMID: 20518834
chemokines; CCR5; RANTES; SDF-1; HIV-1 transmission
8.  Genetic Variation in CXCL12 and Risk of Cervical Carcinoma: a Population-Based Case-Control Study 
Summary
CXCL12 provides a chemotactic signal directing leukocyte migration and regulates metastatic behavior of tumor cells. We conducted a population-based case-control study to test the hypothesis that common genetic variation in CXCL12 (single SNP alleles and haplotypes) is associated with the risk of cervical carcinoma. Cases (N=917) were women diagnosed with invasive squamous cell cervical carcinoma (SCC), adenocarcinoma or adenosquamous carcinoma or adenocarcinoma in situ (ACIS) of the cervix, while residents of western Washington State. Control participants (N=849) were identified from the source population by random digit telephone dialing and frequency matched to cases on county and age. Nine CXCL12 tagSNPs chosen from the SeattleSNPs database were genotyped. The minor allele of intronic SNP rs266085 was inversely associated with cervical cancer under a recessive genetic effects model (OR=0.74, 95% C.I. 0.56–0.98). Among the ten common haplotypes inferred from the 9 tagSNPs, one haplotype defined by minor alleles at 5’ flanking SNP rs17885289 and rs266085, and common alleles at the other 7 SNPs occurred among 7.8% of cases and 10.6% of controls (dominant model OR=0.72, 95% C.I. 0.56–0.93; recessive model OR=0.35, 95% C.I. 0.12–0.97; and log additive model OR=0.72, 95% C.I. 0.57–0.90). A stepwise procedure identified rs17885289, rs266085, and 3’ UTR SNP rs266093 as the most parsimonious subset of SNPs necessary to define the haplotype inversely associated with cervical cancer risk in our study. A 3’ UTR SNP, rs1801157, previously found to be related to HIV pathogenesis, was not associated with cervical cancer risk. Further population-based studies are warranted to confirm these associations between genetic variation in CXCL12 and cervical cancer risk.
doi:10.1111/j.1744-313X.2009.00877.x
PMCID: PMC2784202  PMID: 19788587
cervical cancer; HPV epidemiology; CXCL12; single nucleotide polymorphism
10.  Evaluation of IL10, IL19, and IL20 gene polymorphisms and chronic hepatitis B infection outcome 
Summary
Hepatitis B viral infection remains a serious global health problem despite the availability of a highly effective vaccine. Approximately 5% of HBV-infected adults develop chronic hepatitis B, which may result in liver cirrhosis or hepatocellular carcinoma. Variants of interleukin-10 (IL10) have been previously associated with chronic hepatitis B infection and progression to hepatocellular carcinoma. Single nucleotide polymorphisms (SNPs, n = 42) from the IL10, IL19, and IL20 gene regions were examined for an association with HBV infection outcome, either chronic or recovered, in a nested case-control study of African Americans and European Americans. Among African Americans, three nominally statistically significant SNP associations in IL10, two in IL20, and one haplotype association were observed with different HBV infection outcomes (P = 0.005–0.04). The SNP, rs1518108, in IL20 nominally deviated significantly from Hardy-Weinberg equilibrium in African Americans, with a large excess of heterozygotes in chronic HBV-infected cases (P = 0.0006), which suggests a strong genetic effect. Among European Americans, a nominally statistically significant SNP association in IL20, as well as an IL20 haplotype were associated with HBV recovery (P = 0.01–0.04). These results suggest that IL10 and IL20 gene variants influence HBV infection outcome and encourage the pursuit of further studies of these cytokines in HBV pathogenesis.
doi:10.1111/j.1744-313X.2008.00770.x
PMCID: PMC2874896  PMID: 18479293
Interleukin-10; Inflammation; African American; Immunogenetics; Hepatitis b; HIV co-infection
11.  Erythrocyte complement receptor 1 (CR1) expression level is not associated with polymorphisms in the promoter or 3′ untranslated regions of the CR1 gene 
Summary
Complement receptor 1 (CR1) expression level on erythrocytes is genetically determined and is associated with high (H) and low (L) expression alleles identified by a HindIII restriction fragment-length polymorphism (RFLP) in intron 27 of the CR1 gene. The L allele confers protection against severe malaria in Papua New Guinea, probably because erythrocytes with low CR1 expression, are less able to form pathogenic rosettes with Plasmodium falciparum-infected erythrocytes. Despite the biological importance of erythrocyte CR1, the genetic mutation controlling CR1 expression level remains unknown. We investigated the possibility that mutations in the upstream or 3′ untranslated regions of the CR1 gene could control erythrocyte CR1 level. We identified several novel polymorphisms; however, the mutations did not segregate with erythrocyte CR1 expression level or the H and L alleles. Therefore, high and low erythrocyte CR1 levels cannot be explained by polymorphisms in transcriptional control elements in the upstream or 3′ untranslated regions of the CR1 gene.
doi:10.1111/j.1744-313X.2005.00552.x
PMCID: PMC2869022  PMID: 16426237
12.  Understanding the genetics of autoimmune disease: two loci that regulate late onset Addison’s disease in Portuguese Water Dogs 
Summary
Addison’s disease, an immune-mediated disorder caused by destruction of the adrenal glands, is a rare disorder of Western European populations. Studies indicate that the disorder is polygenic in nature, involving specific alleles of the CTLA-4, DRB1*04 and DQ, Cyp27B1, VDR and MIC-A and -B loci. A similar immune form of Addison’s disease occurs in several breeds of domestic dog, with frequencies ranging from 1.5 to 9.0%. The high frequency of the disease in domestic dog breeds likely reflects the small number of founders associated with many breeds, subsequent inbreeding, and the frequent use of popular sires.
The Portuguese Water Dog (PWD) is a significantly affected breed. An analysis of 11 384 PWDs surveyed between 1985 and 1996 suggests a breed-specific disease incidence of 1.5%. As with humans, the disease is typically of late onset.
This study involves a genetic comparison of Addison’s disease in the PWD to the analogous disease in humans. The study is facilitated by the existence of complete pedigrees and a relatively high degree of inbreeding among PWDs. The breed originated from 31 founders, with 10 animals responsible for 90% of the current gene pool. We describe, specifically, the identification of two disease-associated loci, on Canis familiaris (CFA) chromosomes CFA12 and 37, which are syntenic with the human DRB1 histocompatibility locus alleles HLA-DRB1* 04 and DRB1*0301, and to a locus for immunosuppression syntenic with CTLA-4. Strong similarities exist therefore in the complex genetic background of Addison’s disease in humans and in the PWD. With the completion of the canine and human genome sequence, the purebred dog is set to become an important comparative model for Addison’s as well as other human immune disorders.
doi:10.1111/j.1744-313X.2006.00593.x
PMCID: PMC2775482  PMID: 16712648
13.  Human MHC architecture and evolution: implications for disease association studies 
Major histocompatibility complex (MHC) variation is a key determinant of susceptibility and resistance to a large number of infectious, autoimmune and other diseases. Identification of the MHC variants conferring susceptibility to disease is problematic, due to high levels of variation and linkage disequilibrium. Recent cataloguing and analysis of variation over the complete MHC has facilitated localization of susceptibility loci for autoimmune diseases, and provided insight into the MHC's evolution. This review considers how the unusual genetic characteristics of the MHC impact on strategies to identify variants causing, or contributing to, disease phenotypes. It also considers the MHC in relation to novel mechanisms influencing gene function and regulation, such as epistasis, epigenetics and microRNAs. These developments, along with recent technological advances, shed light on genetic association in complex disease.
doi:10.1111/j.1744-313X.2008.00765.x
PMCID: PMC2408657  PMID: 18397301
14.  Association of MCP-1 and CCR2 polymorphisms with the risk of late acute rejection after renal transplantation in Korean patients 
Among the factors modulating transplant rejection, chemokines and their respective receptors deserve special attention. Increased expression of monocyte chemoattractant protein-1 (MCP-1) and its corresponding receptor (chemokine receptor-2, CCR2) has been implicated in renal transplant rejection. To determine the impact of the MCP-1-2518G and CCR2-64I genotypes on renal allograft function, 167 Korean patients who underwent transplantation over a 25-year period were evaluated. Genomic DNA was genotyped using polymerase chain reaction followed by restriction fragment length polymorphism analysis. Fifty-five (32.9%) patients were homozygous for the MCP-1-2518G polymorphism. Nine (5.4%) patients were homozygous for the CCR2-64I polymorphism. None of the investigated polymorphism showed a significant shift in long-term allograft survival. However, a significant increase was noted for the risk of late acute rejection in recipients who were homozygous for the MCP-1-2518G polymorphism (OR, 2.600; 95% CI, 1.125–6.012; P = 0.022). There was also an association between the MCP-1-2518G/G genotype and the number of late acute rejection episodes (P = 0.024). Although there was no difference in the incidence of rejection among recipients stratified by the CCR2-V64I genotype, recipients with the CCR2-V64I GG genotype in combination with the MCP-1-2518G/G genotype had a significantly higher risk of acute or late acute rejection among the receptor-ligand combinations (P = 0.006, P = 0.008, respectively). The MCP-1 variant may be a marker for risk of late acute rejection in Korean patients.
doi:10.1111/j.1744-313X.2007.00725.x
PMCID: PMC2228509  PMID: 18186797
15.  Genetic analysis of HLA, NA and HPA typing in type 2 diabetes and ASO 
Summary
We examined the genetic status of human leucocyte antigens (HLA), human platelet alloantigens (HPA) and neutrophil-specific antigens (NA) in patients with type 2 diabetes mellitus and diabetic arteriosclerosis obliterans (ASO). To our knowledge, the present study is the first report showing the relationship among three genetic factors in type 2 diabetes mellitus and ASO patients. HLA typing was performed by the polymerase chain reaction (PCR)–restriction fragment length polymorphism method. HPA-typing and NA-typing were by a PCR-sequence-specific primer method. The incidence of HLA-DRB1* 1501 was found to be significant in type 2 diabetes and non-diabetic, particularly ASO-positive patients, compared to control subjects. There were no differences in NA1/NA2 between the control and diabetic or non-diabetic ASO groups. However, the frequency of NA2/NA2 in ASO-positive diabetes and non-diabetic ASO patients was significantly higher than controls. The a/b genotype of HPA-5a/5b was significantly lower in type 2 diabetes and non-diabetic ASO-positive patients than in controls. These findings suggest that genetic studies of HLA, NA and HPA could be useful to understand the pathogenesis of type 2 diabetes and ASO.
doi:10.1111/j.1744-313X.2006.00581.x
PMCID: PMC1464425  PMID: 16611256
16.  Genetic defects in common variable immunodeficiency 
Common variable immunodeficiency (CVID) is the most frequent clinically manifested primary immunodeficiency. According to clinical and laboratory findings, CVID is a heterogeneous group of diseases. Recently, the defects of molecules regulating activation and terminal differentiation of B lymphocytes have been described in some patients with CVID. In this study, we show the overview of deficiencies of inducible costimulator, transmembrane activator and calcium-modulator and cytophilin ligand interactor, CD19 molecules, their genetic basis, pathogenesis and clinical manifestations.
doi:10.1111/j.1744-313X.2007.00681.x
PMCID: PMC1974825  PMID: 17627754
17.  HLA antibody testing: a tool to facilitate not to prevent organ transplantation 
The introduction of very sensitive HLA antibody screening assays has destroyed the old dogma that pre-existence of donor specific HLA antibodies in the patient is a contra-indication for transplantation. The challenge is now to reach consensus on the parameters which predict the clinical relevance of donor specific HLA antibodies. Antibody screening assays should not only be used to prevent transplantation of patients with donor specific antibodies but also to facilitate transplantation of highly sensitized patients, both by defining acceptable HLA mismatches and non-detrimental donor specific HLA antibodies.
doi:10.1111/j.1744-313X.2008.00800.x
PMCID: PMC2610396  PMID: 18988321
18.  Strategies to work with HLA data in human populations for histocompatibility, clinical transplantation, epidemiology and population genetics: HLA-NET methodological recommendations 
HLA-NET (a European COST Action) aims at networking researchers working in bone marrow transplantation, epidemiology and population genetics to improve the molecular characterization of the HLA genetic diversity of human populations, with an expected strong impact on both public health and fundamental research. Such improvements involve finding consensual strategies to characterize human populations and samples and report HLA molecular typings and ambiguities; proposing user-friendly access to databases and computer tools and defining minimal requirements related to ethical aspects. The overall outcome is the provision of population genetic characterizations and comparisons in a standard way by all interested laboratories. This article reports the recommendations of four working groups (WG1-4) of the HLA-NET network at the mid-term of its activities. WG1 (Population definitions and sampling strategies for population genetics’ analyses) recommends avoiding outdated racial classifications and population names (e.g. ‘Caucasian’) and using instead geographic and/or cultural (e.g. linguistic) criteria to describe human populations (e.g. ‘pan-European’). A standard ‘HLA-NET POPULATION DATA QUESTIONNAIRE’ has been finalized and is available for the whole HLA community. WG2 (HLA typing standards for population genetics analyses) recommends retaining maximal information when reporting HLA typing results. Rather than using the National Marrow Donor Program coding system, all ambiguities should be provided by listing all allele pairs required to explain each genotype, according to the formats proposed in ‘HLA-NET GUIDELINES FOR REPORTING HLA TYPINGS’. The group also suggests taking into account a preliminary list of alleles defined by polymorphisms outside the peptide-binding sites that may affect population genetic statistics because of significant frequencies. WG3 (Bioinformatic strategies for HLA population data storage and analysis) recommends the use of programs capable of dealing with ambiguous data, such as the ‘gene[rate]’ computer tools to estimate frequencies, test for Hardy–Weinberg equilibrium and selective neutrality on data containing any number and kind of ambiguities. WG4 (Ethical issues) proposes to adopt thorough general principles for any HLA population study to ensure that it conforms to (inter)national legislation or recommendations/guidelines. All HLA-NET guidelines and tools are available through its website http://hla-net.eu.
doi:10.1111/j.1744-313X.2012.01113.x
PMCID: PMC3533781  PMID: 22533604
19.  16th IHIW: Global analysis of registry HLA haplotypes from 20 Million individuals: Report from the IHIW Registry Diversity Group 
This project has the goal to validate bioinformatics methods and tools for HLA haplotype frequency analysis specifically addressing unique issues of haematopoietic stem cell registry data sets. In addition to generating new methods and tools for the analysis of registry data sets, the intent is to produce a comprehensive analysis of HLA data from 20 million donors from the Bone Marrow Donors Worldwide (BMDW) database. This report summarizes the activity on this project as of the 16IHIW meeting in Liverpool.
doi:10.1111/iji.12031
PMCID: PMC3561701  PMID: 23280139

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