Major Histocompatibility Region Research Articles

Genetic Uniqueness for Immune Response Traits in Native Animal Genetic Resources

Breeding of animals for disease resistance is an important intervention in the era of emerging and re-emerging pathogens in livestock and poultry. Livestock and poultry species of India are considered as an important genetic resource for climate resilience as well as relative less susceptibility to tropical diseases. Indian livestock populations with a broad genetic base, due to availability of diverse breeds and populations, have advantage over the exotic counterpart. Introduction of cross breeding in India, cattle in particular, with exotic germplasm, has further helped in identification of several genes and pathways involved in gaining better immunity against the prevalent diseases. Unique alleles have been identified in the major histocompatibility region and other immune response genes, including toll-like receptors, having important role in disease resistance. Major impediment in associating genetic polymorphism with the disease resistance however, is the non-availability of standardized phenotypic data. Though attention is being diverted towards understanding the genetic basis of disease resistance in native livestock and poultry, there is a need to utilize the latest genome based technologies for fully understanding as well as exploiting the genetic potential of indigenous breeds.

Multilocus evaluation of genetic predictors of multiple sclerosis.

Genome-wide association studies identified numerous susceptibility loci for multiple sclerosis in populations of European ancestry, but the associations are not always reproducible in other populations due to admixture and different linkage disequilibrium patterns obscuring true association signals. Our aim was to identify genetic predictors of multiple sclerosis in three ethnically homogenous populations from the Volga-Ural region of Russian Federation. In the largest to date study of multiple sclerosis in Russian population, involving 2048 participants from the Republic of Bashkortostan, Russian Federation (641 patients with multiple sclerosis and 1407 unaffected individuals), we performed replication analysis of previously identified genome-wide signals for multiple sclerosis. Associations were tested using logistic regression analysis under additive genetic model adjusted for sex. Meta-analysis of the study results in three populations was performed under fixed effects and random effects models. We demonstrate the association with multiple sclerosis of the five variants (INAVA rs7522462, EOMES rs11129295, C6orf10 rs3129934, CD86 rs9282641, and GPR65 rs2119704). The strongest association (OR=2.16, CI:1.85-2.74, P=2.53x10-13) was detected for rs3129934 polymorphism in the major histocompatibility region. Multilocus analysis has revealed 322 and 27 allelic patterns associated with multiple sclerosis in women and men, respectively. In women, the highest risk of MS was conferred by C6orf10 rs3129934*T/T+STAT3 rs744166*T combination (OR=11.87), in men - by C6orf10 rs3129934*T+EOMES rs11129295*C+RPS6KB1 rs180515*C combination (OR=3.25). We confirm five associations with multiple sclerosis previously reported in genome-wide scans in Europeans in three ethnic groups from the Volga-Ural region of Russia.

A genome-wide association study in Japanese identified one variant associated with a preference for a Japanese dietary pattern

Individual eating habits may be influenced by genetic factors, in addition to environmental factors. Previous studies suggested that adherence to Japanese food patterns was associated with a decreased risk of all-cause and cardiovascular disease mortality. We conducted a genome-wide association study (GWAS) in a Japanese population to find genetic variations that affect adherence to a Japanese food pattern. We analyzed GWAS data using 14,079 participants from the Japan Multi-Institutional Collaborative Cohort study. We made a Japanese food score based on six food groups. Association of the imputed variants with the Japanese food score was performed by linear regression analysis with adjustments for age, sex, total energy intake, alcohol intake (g/day), and principal components 1-10 omitting variants in the major histocompatibility region. We found one SNP in the 14q11.2 locus that was significantly associated with the Japanese food score with P values <5 × 10-8. Functional annotation revealed that the expression levels of two genes (BCL2L2, SLC22A17) were significantly inversely associated with this SNP. These genes are known to be related to olfaction and obesity. We found a new SNP that was associated with the Japanese food score in a Japanese population. This SNP is inversely associated with genes link to olfaction and obesity.

Heart disease in a mutant mouse model of spontaneous eosinophilic myocarditis maps to three loci

BackgroundHeart disease (HD) is the major cause of morbidity and mortality in patients with hypereosinophilic diseases. Due to a lack of adequate animal models, our understanding of the pathophysiology of eosinophil-mediated diseases with heart complications is limited. We have discovered a mouse mutant, now maintained on an A/J inbred background, that spontaneously develops hypereosinophilia in multiple organs. Cellular infiltration into the heart causes an eosinophilic myocarditis, with affected mice of the mutant line (i.e., A/JHD) demonstrating extensive myocardial damage and remodeling that leads to HD and premature death, usually by 15-weeks old.ResultsMaintaining the A/JHD line for many generations established that the HD trait was heritable and implied the mode of inheritance was not too complex. Backcross and intercross populations generated from mating A/JHD males with females from four different inbred strains produced recombinant populations with highly variable rates of affected offspring, ranging from none in C57BL/6 J intercrosses, to a few mice with HD using 129S1/SvImJ intercrosses and C57BL/6 J backcrosses, but nearly 8% of intercrosses and > 17% of backcrosses from SJL/J related populations developed HD. Linkage analyses of these SJL/J derived recombinants identified three highly significant loci: a recessive locus mapping to distal chromosome 5 (LOD = 4.88; named Emhd1 for eosinophilic myocarditis to heart disease-1); and two dominant variants mapping to chromosome 17, one (Emhd2; LOD = 7.51) proximal to the major histocompatibility complex, and a second (Emhd3; LOD = 6.89) that includes the major histocompatibility region. Haplotype analysis identified the specific crossovers that defined the Emhd1 (2.65 Mb), Emhd2 (8.46 Mb) and Emhd3 (14.59 Mb) intervals.ConclusionsThese results indicate the HD trait in this mutant mouse model of eosinophilic myocarditis is oligogenic with variable penetrance, due to multiple segregating variants and possibly additional genetic or nongenetic factors. The A/JHD mouse model represents a unique and valuable resource to understand the interplay of causal factors that underlie the pathology of this newly discovered eosinophil-associated disease with cardiac complications.

M88 - ASSOCIATION OF GENETIC RISK SCORES FOR SCHIZOPHRENIA WITH LYMPHOBLAST AND CORTICAL GENE EXPRESSION NETWORKS

Background Schizophrenia is a highly heritable disorder with complex etiology. Genetic risk scores provide an index of an individual's liability for schizophrenia, and may shed light on its biological underpinnings. Methods We investigated the association of genetic risk scores for schizophrenia using transcriptomic and genome-wide genotyping data from Lymphoblastoid Cells (LCLs) and postmortem brain. We removed the major histocompatibility region from our data and calculated genetic risk scores using linkage-independent risk markers for schizophrenia. Linear models were used to test the association of diagnosis or genetic risk scores with expression levels of gene networks in LCLs and brain, in addition to exon networks derived from brain. We specified covariates in our regression models to control for population stratification along with biological and technical variation. Results We identified gene networks whose expression was significantly associated with schizophrenia genetic risk scores in LCLs and brain. Pathways involving cell growth, apoptosis, and immunity were enriched in modules of interest, in addition to astrocyte-specific markers. Discussion Converging evidence shows that schizophrenia polygenes represent multiple biological pathways and processes. We identified relationships between schizophrenia polygenes and the expression of genes in pathways related to cell development and immunity, which recapitulates evidence from genetic, transcriptomic, epigenetic, and epidemiologic studies. Despite practical limitations, our study provides key insights into the role of schizophrenia polygenes in gene expression and splicing regulation.

Immuno-related polymorphisms and cervical cancer risk: The IARC multicentric case-control study.

A small proportion of women who are exposed to infection with human-papillomavirus (HPV) develop cervical cancer (CC). Genetic factors may affect the risk of progression from HPV infection to cervical precancer and cancer. We used samples from the International Agency for Research on Cancer (IARC) multicentric case-control study to evaluate the association of selected genetic variants with CC. Overall, 790 CC cases and 717 controls from Algeria, Morocco, India and Thailand were included. Cervical exfoliated cells were obtained from control women and cervical exfoliated cells or biopsy specimens from cases. HPV-positivity was determined using a general primer GP5+/6+ mediated PCR. Unconditional logistic regression was used to estimate odds ratios (OR) and corresponding 95% confidence intervals (CI) of host genotypes with CC risk, using the homozygous wild type genotype as the referent category and adjusting by age and study centre. The association of polymorphisms with the risk of high-risk HPV-positivity among controls was also evaluated. A statistically significant association was observed between single nucleotide polymorphism (SNP) CHR6 rs2844511 and CC risk: the OR for carriers of the GA or GG genotypes was 0.70 (95% CI: 0.43–1.14) and 0.61 (95% CI: 0.38–0.98), respectively, relative to carriers of AA genotype (p-value for trend 0.03). We also observed associations of borderline significance with the TIPARP rs2665390 polymorphism, which was previously found to be associated with ovarian and breast cancer, and with the EXOC1 rs13117307 polymorphism, which has been linked to cervical cancer in a large study in a Chinese population. We confirmed the association between CC and the rs2844511 polymorphism previously identified in a GWAS study in a Swedish population. The major histocompatibility region of chromosome 6, or perhaps other SNPs in linkage disequilibrium, may be involved in CC onset.

Molecular genetic contributions to self-rated health.

Background: Poorer self-rated health (SRH) predicts worse health outcomes, even when adjusted for objective measures of disease at time of rating. Twin studies indicate SRH has a heritability of up to 60% and that its genetic architecture may overlap with that of personality and cognition. Methods: We carried out a genome-wide association study (GWAS) of SRH on 111 749 members of the UK Biobank sample. Univariate genome-wide complex trait analysis (GCTA)-GREML analyses were used to estimate the proportion of variance explained by all common autosomal single nucleotide polymorphisms (SNPs) for SRH. Linkage disequilibrium (LD) score regression and polygenic risk scoring, two complementary methods, were used to investigate pleiotropy between SRH in the UK Biobank and up to 21 health-related and personality and cognitive traits from published GWAS consortia. Results: The GWAS identified 13 independent signals associated with SRH, including several in regions previously associated with diseases or disease-related traits. The strongest signal was on chromosome 2 (rs2360675, P = 1.77 x 10-10) close to KLF7. A second strong peak was identified on chromosome 6 in the major histocompatibility region (rs76380179, P = 6.15 x 10-10). The proportion of variance in SRH that was explained by all common genetic variants was 13%. Polygenic scores for the following traits and disorders were associated with SRH: cognitive ability, education, neuroticism, body mass index (BMI), longevity, attention-deficit hyperactivity disorder (ADHD), major depressive disorder, schizophrenia, lung function, blood pressure, coronary artery disease, large vessel disease stroke and type 2 diabetes. Conclusions: Individual differences in how people respond to a single item on SRH are partly explained by their genetic propensity to many common psychiatric and physical disorders and psychological traits.

The Receptor for Advanced Glycation End Products Activates the AIM2 Inflammasome in Acute Pancreatitis.

Severe acute pancreatitis (AP) is responsible for significant human morbidity and mortality worldwide. Currently, no specific treatments for AP exist, primarily due to the lack of a mechanistic understanding of sterile inflammation and the resultant multisystem organ dysfunction, the pathologic response of AP linked to early death. In this study, we demonstrate that the class III major histocompatibility region III receptor for advanced glycation end products (RAGE) contributes to AP by modulating inflammasome activation in macrophages. RAGE mediated nucleosome-induced absent in melanoma 2 (but not NLRP3) inflammasome activation by modulating dsRNA-dependent protein kinase phosphorylation in macrophages. Pharmacological and genetic inhibition of the RAGE-dsRNA-dependent protein kinase pathway attenuated the release of inflammasome-dependent exosomal leaderless cytokines (e.g., IL-1β and high-mobility group box 1) in vitro. RAGE or absent in melanoma 2 depletion in mice limited tissue injury, reduced systemic inflammation, and protected against AP induced by l-arginine or cerulein in experimental animal models. These findings define a novel role for RAGE in the propagation of the innate immune response with activation of the nucleosome-mediated inflammasome and will help guide future development of therapeutic strategies to treat AP.

Maternal Infection, Later Childhood Infection Linked to Psychosis in Offspring

Back to table of contents Previous article Next article Clinical and Research NewsFull AccessMaternal Infection, Later Childhood Infection Linked to Psychosis in OffspringMark MoranMark MoranSearch for more papers by this authorPublished Online:4 Feb 2016https://doi.org/10.1176/appi.pn.2016.1b13AbstractMaternal infection during pregnancy did not increase risk for psychosis in offspring when adjusted for confounding variables, but among mothers with psychiatric illness, maternal infection and later childhood infection did increase risk.Maternal psychiatric disorders and maternal infection during pregnancy appear to act synergistically with exposure to later childhood infection in offspring by increasing the risk of psychosis in those offspring, according to a report in the January Schizophrenia Bulletin. The study from a large Swedish birth cohort found that maternal infection alone during pregnancy was not statistically significantly linked to psychosis in offspring. But among mothers with a history of psychiatric illness, infection during pregnancy appeared to contribute to the risk of later childhood infections in offspring and to higher risk of psychosis in those offspring, according to the report.“A genetic predisposition to psychosis in conjunction with one or more environmental insults has been proposed in the etiology of psychosis,” wrote researchers from the Karolinska Institute in Stockholm. “We found evidence for synergism between maternal psychiatric disorder (a proxy marker of genetic predisposition in the mother as well as the child) and infection during pregnancy on psychosis risk in the offspring, which is in agreement with previous observations. … Importantly, exposure to maternal infection did not appear to interact with paternal psychiatric disorder (a proxy for genetic predisposition in the father as well as the child). … These results indicate an effect of acute infections during pregnancy specific to vulnerable mothers on the risk for the offspring to later develop nonaffective psychosis.”The study drew on data from several national registries uniquely accessible in Sweden. These include Psychiatry Sweden, which links several health and population registers created for studies of the etiology of psychiatric disorders; the National Patient Register, which was used for identification of infection and nonaffective psychoses and includes virtually all inpatient care in Sweden since 1973 and psychiatric outpatient visits since 2001; and the Medical Birth Register, which includes data from the prenatal, delivery, and neonatal periods from almost all deliveries in Sweden. The researchers used statistical analysis to examine several different possible associations with psychosis in offspring whose parents did or did not have psychiatric illness—the link between exposure to maternal infection during pregnancy and psychosis, between exposure to maternal infection and later childhood infection, and between combined exposure to maternal infection during pregnancy and later childhood infection and risk for psychosis. In the total population, there was a small but significantly increased risk of developing nonaffective psychosis among children whose mothers were hospitalized for infection during pregnancy, but this association disappeared when adjusted for confounding variables. In contrast, among individuals whose parents were diagnosed with a psychiatric disorder, exposure to maternal infection during pregnancy was significantly associated with psychosis; further, there was an interaction between maternal infection during pregnancy and childhood infection in terms of the risk of nonaffective psychosis.Research interest in a possible link between schizophrenia and viruses and infection, once strictly outside the mainstream, has become an important and seriously regarded line of inquiry. The January issue of Schizophenia Bulletin also has two other articles studying the relationship between infection and schizophrenia. The authors of the current paper noted that many of the genetic loci that so far have been associated with schizophrenia are located within the major histocompatibility (MHC) region on chromosome 6, a region dense with genes linked to both immunity and brain development. “Interestingly, genetic risk for schizophrenia, both within and outside the MHC region, appears to overlap with risk for other psychiatric diagnoses, which suggests that genetic variation in many regions, including the MHC region, may explain some of the interaction between maternal psychiatric disease and infection.”They added that brain development proceeds through early adulthood and is therefore potentially continuously vulnerable to disruptive influences that may be more likely to occur in individuals with immune deficits. “Here we observed that individuals whose mothers were exposed to infections before and, particularly, during pregnancy were themselves more likely to be hospitalized for infections during childhood,” they stated. “Importantly, exposure to maternal infection during … pregnancy and to a subsequent childhood infection acted synergistically on future psychosis risk. These observations indicate that maternal infection during pregnancy can modify not only the future risk of the offspring to be hospitalized for infection, but also the long-term outcomes of such infections.” ■“Associations Between Maternal Infection During Pregnancy, Childhood Infections, and the Risk of Subsequent Psychotic Disorder—A Swedish Cohort Study of Nearly 2 Million Individuals” can be accessed here. ISSUES NewArchived

MicroRNA-derived network analysis of differentially methylated genes in schizophrenia, implicating GABA receptor B1 [GABBR1] and protein kinase B [AKT1

BackgroundWhile hundreds of genes have been implicated already in the etiology of schizophrenia, the exact cause is not known or the disease is considered multigenic in origin. Recent discoveries of new types of RNAs and the gradual elimination of the “junk DNA” hypothesis refocused the attention on the noncoding part of the human genome. Here we re-analyzed a recent dataset of differentially methylated genes from schizophrenic patients and cross-tabulated them with cis regulatory and repetitive elements and microRNAs known to be involved in schizophrenia.ResultsWe found that the number of schizophrenia-related (SZ) microRNA targets follows a scale-free distribution with several microRNA hubs and that schizophrenia-related microRNAs with shared targets form a small-world network. The top ten microRNAs with the highest number of SZ gene targets regulate approximately 80 % of all microRNA-regulated genes whereas the top two microRNAs regulate 40–52 % of all such genes. We also found that genes that are regulated by the same microRNAs tend to have more protein-protein interactions than randomly selected schizophrenia genes. This highlights the role microRNAs possibly play in coordinating the abundance of interacting proteins, an important function that has not been sufficiently explored before. The analysis revealed that GABBR1 is regulated by both of the top two microRNAs and acts as a hub by interacting with many schizophrenia-related genes and sharing several types of transcription-binding sites with its interactors. We also found that differentially methylated repetitive elements are significantly more methylated in schizophrenia, pointing out their potential role in the disease.ConclusionsWe find that GABBR1 has a central importance in schizophrenia, even if no direct cause and effect have been shown for it for the time. In addition to being a hub in microRNA-derived regulatory pathways and protein-protein interactions, its centrality is also supported by the high number of cis regulatory elements and transcription factor-binding sites that regulate its transcription. These findings are in line with several genome-wide association studies that repeatedly find the major histocompatibility region (where GABBR1 is located) to have the highest number of single nucleotide polymorphisms in schizophrenics. Our model also offers an explanation for the downregulation of protein kinase B, another consistent finding in schizophrenic patients. Our observations support the notion that microRNAs fine-tune the amount of proteins acting in the same biological pathways in schizophrenia, giving further support to the emerging theory of competing endogenous RNAs.Open Peer ReviewThe manuscript was reviewed by Jaap Heringa, Sandor Pongor and Zoltan Gaspari.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-015-0089-y) contains supplementary material, which is available to authorized users.

Genome-Wide Assessment of Differential DNA Methylation Associated with Autoantibody Production in Systemic Lupus Erythematosus.

Systemic lupus erythematosus (SLE) is characterized by the development of autoantibodies associated with specific clinical manifestations. Previous studies have shown an association between differential DNA methylation and SLE susceptibility, but have not investigated SLE-related autoantibodies. Our goal was to determine whether DNA methylation is associated with production of clinically relevant SLE-related autoantibodies, with an emphasis on the anti-dsDNA autoantibody. In this study, we characterized the methylation status of 467,314 CpG sites in 326 women with SLE. Using a discovery and replication study design, we identified and replicated significant associations between anti-dsDNA autoantibody production and the methylation status of 16 CpG sites (pdiscovery<1.07E-07 and preplication<0.0029) in 11 genes. Associations were further investigated using multivariable regression to adjust for estimated leukocyte cell proportions and population substructure. The adjusted mean DNA methylation difference between anti-dsDNA positive and negative cases ranged from 1.2% to 19%, and the adjusted odds ratio for anti-dsDNA autoantibody production comparing the lowest and highest methylation tertiles ranged from 6.8 to 18.2. Differential methylation for these CpG sites was also associated with anti-SSA, anti-Sm, and anti-RNP autoantibody production. Overall, associated CpG sites were hypomethylated in autoantibody positive compared to autoantibody negative cases. Differential methylation of CpG sites within the major histocompatibility region was not strongly associated with autoantibody production. Genes with differentially methylated CpG sites represent multiple biologic pathways, and have not been associated with autoantibody production in genetic association studies. In conclusion, hypomethylation of CpG sites within genes from different pathways is associated with anti-dsDNA, anti-SSA, anti-Sm, and anti-RNP production in SLE, and these associations are not explained by genetic variation. Thus, studies of epigenetic mechanisms such as DNA methylation represent a complementary method to genetic association studies to identify biologic pathways that may contribute to the clinical heterogeneity of autoimmune diseases.

Imputation of class I and II HLA loci using high-density SNPs from ImmunoChip and their associations with Kawasaki disease in family-based study.

Kawasaki disease (KD) is the leading cause of acquired heart disease in children in most developed countries including the United States. The etiology of KD is not known; however, epidemiological and immunological data suggest infectious or immune-related factors in the manifestation of the disease. Further, KD has several hereditary features that strongly suggest a genetic component to disease pathogenesis. Human leucocyte antigen (HLA) loci have also been reported to be associated with KD, but results have been inconsistent, in part, because of small study samples and varying linkage disequilibrium (LD) patterns observed across different ethnic groups. To maximize the informativeness of single nucleotide polymorphism (SNP) genotypes in the major histocompatibility (MHC) region, we imputed classical HLA I (A, B, C) and HLA II (DRB1, DQA1, DQB1) alleles using SNP2HLA method from genotypes of 6700 SNPs within the extended MHC region contained in the ImmunoChip among 112 White patients with KD and their biological parents from North America and tested their association with KD susceptibility using the transmission disequilibrium test. Mendelian consistency in the trios suggested high accuracy and reliability of the imputed alleles (class I = 97.5%, class II = 96.6%). While several SNPs in the MHC region were individually associated with KD susceptibility, we report over-transmission of HLA-C*15 (z = +2.19, P = 0.03) and under-transmission of HLA-B*44 (z = -2.49, P = 0.01) alleles from parents to patients with KD. HLA-B*44 has been associated with KD in other smaller studies, and both HLA-C*15 and HLA-B*44 have biological mechanisms that could potentially be involved in KD pathogenesis. Overall, inferring HLA loci within the same ethnic group, using family-based information is a powerful approach. However, studies with larger sample sizes are warranted to evaluate the correlations of the strength and directions between the SNPs in MHC region and the imputed HLA alleles with KD.

Modeling HLA associations with EBV-positive and -negative Hodgkin lymphoma suggests distinct mechanisms in disease pathogenesis.

HLA genotyping and genome wide association studies provide strong evidence for associations between Human Leukocyte Antigen (HLA) alleles and classical Hodgkin lymphoma (cHL). Analysis of these associations is complicated by the extensive linkage disequilibrium within the major histocompatibility region and recent data suggesting that associations with EBV‐positive and EBV‐negative cHL are largely distinct. To distinguish independent and therefore potentially causal associations from associations confounded by linkage disequilibrium, we applied a variable selection regression modeling procedure to directly typed HLA class I and II genes and selected SNPs from EBV‐stratified patient subgroups. In final models, HLA‐A*01:01 and B*37:01 were associated with an increased risk of EBV‐positive cHL whereas DRB1*15:01 and DPB1*01:01 were associated with decreased risk. Effects were independent of a prior history of infectious mononucleosis. For EBV‐negative cHL the class II SNP rs6903608 remained the strongest predictor of disease risk after adjusting for the effects of common HLA alleles. Associations with “all cHL” and differences by case EBV status reflected the subgroup analysis. In conclusion, this study extends previous findings by identifying novel HLA associations with EBV‐stratified subgroups of cHL, highlighting those alleles likely to be biologically relevant and strengthening evidence implicating genetic variation associated with the SNP rs6903608.

Variants in PVT1 are Associated with Susceptibility for Hodgkin Lymphoma in Children and Adolescents: A Children’s Oncology Group Study

Few studies have investigated the etiology of pediatric and adolescent Hodgkin lymphoma (HL), the 8th most common cancer in U.S. children aged <15 years. In economically developed countries, HL in children has distinct demographic and clinical characteristics and risk factor profile from HL in older adolescents and young adults (15-39 years), implying a unique etiology. Established HL risk factors include congenital and acquired immunodeficiency, Epstein-Barr virus (EBV) infection, and family history of hematological cancer. The latter strongly supports a genetic component to HL etiology, although few susceptibility variants have been consistently identified. Linkage studies and genome-wide association studies (GWAS) in adult HL have implicated the major histocompatibility (MHC) region in susceptibility; however, these associations are thought to be insufficient to fully explain the strong familial clustering observed. Single nucleotide variants (SNVs) in PVT1, REL, GATA3, and EOMES have also been identified via GWAS. We hypothesized that these same SNVs would also be associated with risk for pediatric/adolescent HL.HL cases (n=160) diagnosed in 1989-2003 at 3-17 years of age were enrolled through North American Children’s Oncology Group institutions and genotyped via the Illumina HumanCoreExome array. These data were merged with a convenience control sample of unrelated parents of pediatric/adolescent germ cell tumor cases genotyped using the same array. Genotype clusters were called together and manually reviewed for all SNVs of interest using GenomeStudio. Race/ethnicity was jointly determined by principal components analysis (PCA) using the EIGENSOFT package and HapMap2 and 1000 Genomes Project samples as anchors. Primary analyses were restricted to Hispanic and non-Hispanic white individuals (128 cases and 746 controls). Case genotypes were compared to controls for 18 SNVs previously identified in adult HL GWAS via unconditional logistic regression using an additive model and adjusting for sex and the first two principal components for race/ethnicity, resulting in odds ratios (ORs) and 95% confidence intervals (CIs) to estimate the risk per additional copy of the variant allele. A second control sample pulled from three Minnesota Center for Twin and Family Research studies was also used for comparison. Different arrays were used (Illumina 660W-Quad, HumanExome12 v1.0), so separate PCAs were performed to select only non-Hispanic white case and control samples (95 cases and 3,124 unrelated controls). These analyses were also performed using an additive logistic regression model adjusted only for sex.The primary analyses revealed significant associations (Bonferroni alpha<0.003) with SNVs in/near PVT1 on chromosome 8 (rs2608053: OR=0.56, 95% CI: 0.41-0.75, P=0.0001; rs2019960: OR=1.49, 95% CI: 1.10-1.99, P=0.008). Comparable ORs were observed for the 3-9 and 10-17 year age groups examined separately. Restricting to non-Hispanic white individuals produced similar results (twin studies controls: rs2608053: OR=0.59, 95% CI: 0.44-0.80, P=0.0007; rs2019960: OR=1.71, 95% CI: 1.26-2.33, P=0.0007), indicating the observation is not attributable to population stratification. PVT1, a non-protein coding oncogene adjacent to and interacting with MYC, is a compelling candidate for further exploration, given that its transcripts are important in the generation of murine T-lineage lymphomas. Additionally, reciprocal translocations involving PVT1 are observed in variant Burkitt lymphoma.SNVs in the MHC region, including rs6903608, rs204999, and rs2248462, trended toward significance (P<0.05), suggesting that MHC variants are likely associated with pediatric/adolescent HL risk. Unfortunately, we lacked sufficient statistical power to achieve significance for any single marker examined in this region. Importantly, rs204999 has been specifically associated with EBV EBNA-1 antibody levels, supporting a role for MHC variants to impact lymphocyte responses to EBV infection.We found that some of the SNVs identified in adult HL GWAS are also associated with pediatric/adolescent HL. Additional strategies are needed to identify etiologically relevant variants to uncover the “missing heritability” of this unique malignancy and to understand the significance of MHC variants in imparting susceptibility. DisclosuresNo relevant conflicts of interest to declare.

Strategies for evaluating idiopathic inflammatory myopathy disease susceptibility genes.

This review outlines the progress that has been made in understanding the genetics of the idiopathic inflammatory myopathies in the previous 2 years, with a particular focus on dermatomyositis and polymyositis. A recent genome-wide association study in dermatomyositis has confirmed the importance of the major histocompatibility region in this disease, and has suggested a shared genetic etiology with other autoimmune disorders. This has led to an ongoing study of additional immune-related loci using the Immunochip array. Candidate gene studies have identified novel risk associations in non-Europeans, such as STAT4 and HLA-DRB1 in the Japanese population. Evidence for gene-environment interactions has come from two recent studies implicating smoking status and statin use with HLA alleles. This review also touches on future approaches to genetic research in myositis, including bioinformatics tools to identify causal variants, HLA imputation from existing genetic data and statistical methods to investigate shared effects between subgroups of myositis.

Immunoglobulin heavy chain variable region and major histocompatibility region genes are linked to induced graves' disease in females from two very large families of recombinant inbred mice.

Graves' hyperthyroidism is caused by antibodies to the TSH receptor (TSHR) that mimic thyroid stimulation by TSH. Stimulating TSHR antibodies and hyperthyroidism can be induced by immunizing mice with adenovirus expressing the human TSHR A-subunit. Prior analysis of induced Graves' disease in small families of recombinant inbred (RI) female mice demonstrated strong genetic control but did not resolve trait loci for TSHR antibodies or elevated serum T4. We investigated the genetic basis for induced Graves' disease in female mice of two large RI families and combined data with earlier findings to provide phenotypes for 178 genotypes. TSHR antibodies measured by inhibition of TSH binding to its receptor were highly significantly linked in the BXD set to the major histocompatibility region (chromosome 17), consistent with observations in 3 other RI families. In the LXS family, we detected linkage between T4 levels after TSHR-adenovirus immunization and the Ig heavy chain variable region (Igvh, chromosome 12). This observation is a key finding because components of the antigen binding region of Igs determine antibody specificity and have been previously linked to induced thyroid-stimulating antibodies. Data from the LXS family provide the first evidence in mice of a direct link between induced hyperthyroidism and Igvh genes. A role for major histocompatibility genes has now been established for genetic susceptibility to Graves' disease in both humans and mice. Future studies using arrays incorporating variation in the complex human Ig gene locus will be necessary to determine whether Igvh genes are also linked to Graves' disease in humans.

Whole Exome Sequencing To Estimate Alloreactivity Potential Between Donors and Recipients In Stem Cell Transplantation

Graft versus host disease (GVHD) continues to afflict allogeneic hematopoietic stem cell transplant (SCT) recipients despite HLA matching at the molecular level. This is largely a consequence of minor histocompatibility antigen (mHA) variation between the donors and recipients resulting in alloreactivity. To determine the extent of potential antigenic variation at a molecular level, whole exome sequencing (WES) was performed on DNA samples from nine HLA-matched donor-recipient (D-R) pairs to catalogue the sequence variation. TruSeq exome enriched libraries were prepared using Illumina HiSeq 2000 platform. All exomes had at least 28X coverage; single nucleotide polymorphism (SNP) calling was performed using Genome Analysis Toolkit v1.6. Donor and recipient samples were compared with each other and reference human genome using ANNOVAR. SNP between donors and recipients were coded as either synonymous (S) or nonsynonymous (NS); and either NS conservative (NSc), or non-conservative (NSnc). Further, SNPs were analyzed with respect to graft versus host (GVH) or host vs. graft (HVG) vector. First, the recipient exomes were compared with the actual HLA matched and ‘simulated' non-HLA matched donors; in this analysis, the major histocompatibility region demonstrated a 4-10 fold difference between the actual and simulated D-R pairs, unlike the whole exome, where similar sequence variation was observed between individuals regardless of HLA matching. For the actual D-R pairs the mean difference across the exome was 13,423 SNP, of which an average 6,445 were NS. Normalized for the number of nucleotide positions sequenced in the whole exome, the S- and NS-SNP scores were approximately equal, and NSnc-SNP were consistently > NSc-SNP (Figure 1). Further, in unrelated donor (URD) SCT, difference scores were approximately twice as large as in matched related donor recipients. GVHD was seen in 3/5 URD SCT with an alloreactivity score >0.1 NSnc-SNP/kilobase pair (Figure 1). Importantly the SNPs were equally distributed in GVH or HVG direction across the whole exome and the MHC locus in HLA matched pairs. When the location of the SNP was mapped onto the individual chromosomes, these were distributed across the entire genome with a small number of genes demonstrating frequent variation and others with a diminishing frequency. T cell receptor b sequencing was performed to determine T cell repertoire in donors, and recipients following SCT. Comparison of exome sequence variation between donor-recipient pairs and the proportion of unique to shared T cell clones and their frequency in recipients, suggested that post-transplant T cell repertoire reconstitution in the recipient may be influenced by exome sequence variation (Figure 2). In conclusion, WES reveals extensive nucleotide sequence variation in the exomes of HLA-matched donors and recipients indicating a large potential for alloreactivity in stem cell transplantation. By directly measuring this alloreactivity potential, in the future whole exome sequencing may aid in determining GVHD risk in HLA matched and mismatched D-R pairs. [Display omitted] [Display omitted] Disclosures:No relevant conflicts of interest to declare.

Human Leukocyte Antigens and Epstein–Barr Virus-Associated Nasopharyngeal Carcinoma: Old Associations Offer New Clues into the Role of Immunity in Infection-Associated Cancers

Nasopharyngeal carcinoma (NPC) is an Epstein–Barr virus (EBV) associated tumor. In addition to EBV, host genetic factors are believed to be important determinants of NPC risk. Of all genes studies to date, human leukocyte antigen (HLA) genes have shown the most consistent evidence for association with NPC, both from candidate-gene studies and genome-wide association studies (GWAS). In this report we summarize results from recent studies that evaluated the association between HLA and NPC, and discuss whether findings reflect direct causal associations for HLA genes and/or indirect associations that mark causal associations with other genes in the gene-dense major histocompatibility (MHC) region where HLA resides. We also compare GWAS results across cancer sites for which strong hits in the MHC region were observed to generate new hypotheses regarding the role of HLA genes in the development of EBV-associated cancers such as NPC. Of note, we report that MHC associations for EBV-associated cancers (NPC, EBV+ Hodgkin lymphoma) are driven by HLA class I genes. In contrast, MHC associations for other viral-associated cancers (cervical cancer, hepatocellular carcinoma) or other hematopoetic cancers (EBV− Hodgkin lymphoma, leukemia, non-Hodgkin lymphomas) are driven by HLA class II genes, and those for other solid tumors with less clear links to infections (lung, testicular, prostate cancers) are driven by non-HLA genes in the MHC region. Future studies should aim to better understand these patterns.

Improved Heritability Estimation from Genome-wide SNPs

Estimation of narrow-sense heritability, h(2), from genome-wide SNPs genotyped in unrelated individuals has recently attracted interest and offers several advantages over traditional pedigree-based methods. With the use of this approach, it has been estimated that over half the heritability of human height can be attributed to the ~300,000 SNPs on a genome-wide genotyping array. In comparison, only 5%-10% can be explained by SNPs reaching genome-wide significance. We investigated via simulation the validity of several key assumptions underpinning the mixed-model analysis used in SNP-based h(2) estimation. Although we found that the method is reasonably robust to violations of four key assumptions, it can be highly sensitive to uneven linkage disequilibrium (LD) between SNPs: contributions to h(2) are overestimated from causal variants in regions of high LD and are underestimated in regions of low LD. The overall direction of the bias can be up or down depending on the genetic architecture of the trait, but it can be substantial in realistic scenarios. We propose a modified kinship matrix in which SNPs are weighted according to local LD. We show that this correction greatly reduces the bias and increases the precision of h(2) estimates. We demonstrate the impact of our method on the first seven diseases studied by the Wellcome Trust Case Control Consortium. Our LD adjustment revises downward the h(2) estimate for immune-related diseases, as expected because of high LD in the major-histocompatibility region, but increases it for some nonimmune diseases. To calculate our revised kinship matrix, we developed LDAK, software for computing LD-adjusted kinships.

A Gene Co-Expression Network in Whole Blood of Schizophrenia Patients Is Independent of Antipsychotic-Use and Enriched for Brain-Expressed Genes

Despite large-scale genome-wide association studies (GWAS), the underlying genes for schizophrenia are largely unknown. Additional approaches are therefore required to identify the genetic background of this disorder. Here we report findings from a large gene expression study in peripheral blood of schizophrenia patients and controls. We applied a systems biology approach to genome-wide expression data from whole blood of 92 medicated and 29 antipsychotic-free schizophrenia patients and 118 healthy controls. We show that gene expression profiling in whole blood can identify twelve large gene co-expression modules associated with schizophrenia. Several of these disease related modules are likely to reflect expression changes due to antipsychotic medication. However, two of the disease modules could be replicated in an independent second data set involving antipsychotic-free patients and controls. One of these robustly defined disease modules is significantly enriched with brain-expressed genes and with genetic variants that were implicated in a GWAS study, which could imply a causal role in schizophrenia etiology. The most highly connected intramodular hub gene in this module (ABCF1), is located in, and regulated by the major histocompatibility (MHC) complex, which is intriguing in light of the fact that common allelic variants from the MHC region have been implicated in schizophrenia. This suggests that the MHC increases schizophrenia susceptibility via altered gene expression of regulatory genes in this network.