MHC Region Research Articles

GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database.

We created a deeply extracted and annotated database of genome-wide association studies (GWAS) results. GRASP v1.0 contains >6.2 million SNP-phenotype association from among 1390 GWAS studies. We re-annotated GWAS results with 16 annotation sources including some rarely compared to GWAS results (e.g. RNAediting sites, lincRNAs, PTMs). To create a high-quality resource to facilitate further use and interpretation of human GWAS results in order to address important scientific questions. GWAS have grown exponentially, with increases in sample sizes and markers tested, and continuing bias toward European ancestry samples. GRASP contains >100 000 phenotypes, roughly: eQTLs (71.5%), metabolite QTLs (21.2%), methylation QTLs (4.4%) and diseases, biomarkers and other traits (2.8%). cis-eQTLs, meQTLs, mQTLs and MHC region SNPs are highly enriched among significant results. After removing these categories, GRASP still contains a greater proportion of studies and results than comparable GWAS catalogs. Cardiovascular disease and related risk factors pre-dominate remaining GWAS results, followed by immunological, neurological and cancer traits. Significant results in GWAS display a highly gene-centric tendency. Sex chromosome X (OR = 0.18[0.16-0.20]) and Y (OR = 0.003[0.001-0.01]) genes are depleted for GWAS results. Gene length is correlated with GWAS results at nominal significance (P ≤ 0.05) levels. We show this gene-length correlation decays at increasingly more stringent P-value thresholds. Potential pleotropic genes and SNPs enriched for multi-phenotype association in GWAS are identified. However, we note possible population stratification at some of these loci. Finally, via re-annotation we identify compelling functional hypotheses at GWAS loci, in some cases unrealized in studies to date. Pooling summary-level GWAS results and re-annotating with bioinformatics predictions and molecular features provides a good platform for new insights. The GRASP database is available at http://apps.nhlbi.nih.gov/grasp.

OP0235 Genetic Risk Factors in Idiopathic Inflammatory Myopathies Are Shared with Other Autoimmune Disorders in European Populations

BackgroundIdiopathic inflammatory myopathies (IIM) may present as a primary disorder, or may overlap with connective tissue diseases such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) or systemic sclerosis. The...

OC-004 Thiopurine Induced Pancreatitis In Inflammatory Bowel Disease: Clinical Features And Genetic Determinants

IntroductionPancreatitis is a rare, but important complication of thiopurine treatment. The aims of this project were to a) characterise the clinical features of thiopurine-induced pancreatitis and b) identify clinical useful...

Systematic validation of hypothesis-driven candidate genes for cervical cancer in a genome-wide association study.

A large number of genetic associations with cervical cancer have been reported in hypothesis-driven candidate gene studies, but most studies have not included an independent replication or the results have been inconsistent between studies. In order to independently validate these associations, we reexamined 58 candidate gene/regions previously reported to be associated with cervical cancer using the gene-based Adaptive Rank Truncated Product test in a genome-wide association study (GWAS) of 1034 cervical cancer patients and 3948 controls from the Swedish population. Of the 58 gene/regions, 8 had a nominal P value < 0.05 [tumor necrosis factor (TNF), P = 5.0 × 10(-4); DEAD (Asp-Glu-Ala-Asp) box helicase 1 [DDX1], P = 2.2 × 10(-3); exonuclease 1 [EXO1], P = 4.7 × 10(-3); excision repair cross-complementing rodent repair deficiency, complementation group 1 [ERCC1], P = 0.020; transmembrane channel-like 6 and 8 genes [TMC6-TMC8], P = 0.023; secreted phosphoprotein 1 [SPP1], P = 0.028; v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 [ERBB2], P = 0.033 and chloride channel, voltage-sensitive 7 [CLCN7], P = 0.047). After correction for multiple testing, only TNF remained statistically significant (P = 0.028). Two single-nucleotide polymorphisms that are in nearly perfect linkage disequilibrium (rs2857602 and rs2844484) contributed most to the association with TNF. However, they are not independent from the previously reported associations within the MHC region. The very low number of previously reported associations with cervical cancer that replicate in the Swedish population underscore the need to apply more stringent criteria when reporting associations, including the prerequisite of replicating the association as part of the original study.

Replication and cross-phenotype study based upon schizophrenia GWASs data in the Japanese population: support for association of MHC region with psychosis.

Recent genome-wide association studies (GWASs) of schizophrenia (SCZ) identified several susceptibility genes and suggested shared genetic components between SCZ and bipolar disorder (BD). We conducted a genetic association study of single nucleotide polymorphisms (SNPs) selected according to previous SCZ GWAS targeting psychotic disorders (SCZ and BD) in the Japanese population. Fifty-one SNPs were analyzed in a two-stage design using first-set screening samples (all SNPs: 1,032 SCZ, 1,012 BD, and 993 controls) and second-set replication samples ("significant" SNPs in the first-set screening analysis: 1,808 SCZ, 821 BD, and 2,321 controls). We assessed allelic associations between the selected SNPs and the three phenotypes (SCZ, BD, and "psychosis" [SCZ + BD]). Nine SNPs revealed nominal association signals for all comparisons (P(uncorrected) < 0.05), of which two SNPs located in the major histocompatibility complex region (rs7759855 in zinc finger and SCAN domain containing 31 [ZSCAN31] and rs1736913 in HLA-F antisense RNA1 [HLA-F-AS1]) were further assessed in the second-set replication samples. The associations were confirmed for rs7759855 (P(corrected) = 0.026 for psychosis; P(corrected) = 0.032 for SCZ), although the direction of effect was opposite to that in the original GWAS of the Chinese population. Finally, a meta-analysis was conducted using our two samples and using our data and data from Psychiatric GWAS Consortium (PGC), which have shown the same direction of effect. SNP in ZSCAN31 (rs7759855) had the strongest association with the phenotypes (best P = 6.8 × 10(-5) for psychosis: present plus PGC results). These data support shared risk SNPs between SCZ and BD in the Japanese population and association between MHC and psychosis.

HLA-B*51 the primary risk in Behçet disease.

Behcet disease (BD) is a multisystem autoinflammatory condition characterized by mucosal ulceration and predominantly neutropilic inflammation of immune privileged sites including the eye, brain, and synovial joint (1). In PNAS, Ombrello et al. analyze a combination of directly ascertained and imputated single nucleotide polymorphisms (SNPs) in the HLA-B region in Turkish patients with BD (2). HLA-B*51 was the largest single risk factor for BD, with smaller, independent effects of HLA-B*15 and HLA-B*27. HLA-B*15 was also significantly associated in HLA-B*51−ve patients. Analysis of 32,869 SNPs across the MHC region identified HLA and MHC class I polypeptide-related sequence A (MICA) as the strongest association. Conditioning on HLA-B*51 and rs79556279, the strongest associated SNPs, 4.5 kb upstream of HLA-B loci showed no other significant SNPs. Moreover HLA-B*51 and rs79556279 are in strong linkage disequilibrium. Two other regions, one tetrameric to HLA-C and the second in a region that includes HLA-A, were associated with BD, but the former was lost on conditioning for rs79556279. Associations with HLA-A, particularly HLA-A26, have been previously reported, particularly in Japanese patients with BD.

6 Thiopurine Induced Pancreatitis in Inflammatory Bowel Disease: Clinical Features and Genetic Determinants

Introduction Pancreatitis is a rare, but important complication of thiopurine treatment. The aims of this project were to a) characterise the clinical features of thiopurine-induced pancreatitis and b) identify clinical useful genetic markers that might predict development of this serious adverse drug reaction. Methods Patients were identified and recruited from 172 sites (128 UK). Inclusion criteria included a) onset of acute severe abdominal pain within three months of starting thiopurine treatment b) ≥ two-fold rise in amylase or lipase c) medical opinion implicating thiopurine therapy and drug withdrawal. Results We recruited 303 patients. Following adjudication 48 cases classified as definite (recurrent pancreatitis on rechallenge) and 195 cases classified as probable (temporal relationship and no other cause for pancreatitis) were taken forward for analyses. 46% of patients were smokers at the time of development of pancreatitis. Patients were treated with a thiopurine for a median of 19 days (95% CI: 17 – 21) before development of pancreatitis. Most cases were mild, with only 5 cases developing single organ dysfunction. 70% of patients were hospitalised with a median length of stay of 4 days (95% CI: 3.2 – 4.8). Neither age (p = 0.08), drug dose (p = 0.11), BMI (p = 0.73) nor smoking (p = 0.59) predicted length of hospital stay or severity of pancreatitis in multivariate analysis. Using a control cohort of 4,109 Crohn’s disease and ulcerative colitis cases we conducted a genome wide association study with these 239 patients. A significant variant was identified in the Class II MHC region (Odds ratio 3.03, p = 2.63 × 10–20). Dedicated HLA and 1000 genome project imputation refined the association within the MHC (R squared > 0.8 and MAF > 0.01). This association was robust to principle component correction. TPMT genotype was not associated with pancreatitis development (p = 0.99). A second cohort of 100 cases and 500 independent disease controls treated with thiopurines but screened for pancreatitis has been generated to confirm the association. Conclusion We describe the largest clinical characterisation of thiopurine-induced pancreatitis to date and use this cohort to undertake a pharmacogenetics genome wide association study that has identified a significant association within the Class II MHC region. Disclosure of Interest None Declared.

Intertypic modular exchanges of genomic segments by homologous recombination at universally conserved segments in human adenovirus species D.

Human adenovirus species D (HAdV-D), which is composed of clinically and epidemiologically important pathogens worldwide, contains more taxonomic "types" than any other species of the genus Mastadenovirus, although the mechanisms accounting for the high level of diversity remain to be disclosed. Recent studies of known and new types of HAdV-D have indicated that intertypic recombination between distant types contributes to the increasing diversity of the species. However, such findings raise the question as to how homologous recombination events occur between diversified types since homologous recombination is suppressed as nucleotide sequences diverge. In order to address this question, we investigated the distribution of the recombination boundaries in comparison with the landscape of intergenomic sequence conservation assessed according to the synonymous substitution rate (dS). The results revealed that specific genomic segments are conserved between even the most distantly related genomes; we call these segments "universally conserved segments" (UCSs). These findings suggest that UCSs facilitate homologous recombination, resulting in intergenomic segmental exchanges of UCS-flanking genomic regions as recombination modules. With the aid of such a mechanism, the haploid genomes of HAdV-Ds may have been reshuffled, resulting in chimeric genomes out of diversified repertoires in the HAdV-D population analogous to the MHC region reshuffled via crossing over in vertebrates. In addition, some HAdVs with chimeric genomes may have had the opportunity to avoid host immune responses thereby causing epidemics.

Genomic Sequence Analysis of the MHC Class I G/F Segment in Common Marmoset (Callithrix jacchus)

The common marmoset (Callithrix jacchus) is a New World monkey that is used frequently as a model for various human diseases. However, detailed knowledge about the MHC is still lacking. In this study, we sequenced and annotated a total of 854 kb of the common marmoset MHC region that corresponds to the HLA-A/G/F segment (Caja-G/F) between the Caja-G1 and RNF39 genes. The sequenced region contains 19 MHC class I genes, of which 14 are of the MHC-G (Caja-G) type, and 5 are of the MHC-F (Caja-F) type. Six putatively functional Caja-G and Caja-F genes (Caja-G1, Caja-G3, Caja-G7, Caja-G12, Caja-G13, and Caja-F4), 13 pseudogenes related either to Caja-G or Caja-F, three non-MHC genes (ZNRD1, PPPIR11, and RNF39), two miscRNA genes (ZNRD1-AS1 and HCG8), and one non-MHC pseudogene (ETF1P1) were identified. Phylogenetic analysis suggests segmental duplications of units consisting of basically five (four Caja-G and one Caja-F) MHC class I genes, with subsequent expansion/deletion of genes. A similar genomic organization of the Caja-G/F segment has not been observed in catarrhine primates, indicating that this genomic segment was formed in New World monkeys after the split of New World and Old World monkeys.

Etiological factors of nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is a common disease among southern Chinese. The major etiological factors proposed for NPC pathogenesis include genetic susceptibility, environment factors and EBV infection. In the high risk population, genetic susceptibility to NPC has been mapped to the HLA loci and adjacent genes in MHC region on chromosome 6p21. Consumption of preserved food including salted fish has been implicated in its etiology in earlier studies. Its contribution to pathogenesis of NPC remains to be determined. A decreasing trend of NPC incidence was observed in Hong Kong, Taiwan and Singapore in recent years which may be accounted by a change of dietary habits. A comprehensive epidemiological study will help to elucidate the relative importance of various risk factors in the pathogenesis of NPC. Despite the close association of EBV infection with NPC, the etiological role of EBV in NPC pathogenesis remains enigmatic. EBV infection in primary nasopharyngeal epithelial cells is uncommon and difficult to achieve. EBV does not transform primary nasopharyngeal epithelial cells into proliferative clones, which contrasts greatly with the well-documented ability of EBV to transform and immortalize primary B cells. Genetic alterations identified in premalignant nasopharyngeal epithelium may play crucial roles to support stable EBV infection. Subsequently, latent and lytic EBV gene products may drive clonal expansion and transformation of premalignant nasopharyngeal epithelial cells into cancer cells. Stromal inflammation in nasopharyngeal mucosa is believed to play an important role in modulating the growth and possibly drive the malignant transformation of EBV-infected nasopharyngeal epithelial cells. Furthermore, there are increasing evidences supporting a role of EBV infection to evade host immune surveillance. EBV-infected cells may have selective growth advantages in vivo by acquiring a stress-resistance phenotype. Understanding the etiological factors and pathogenesis of NPC will contribute effectively to the prevention and treatment of this disease.

DOP011 A genome wide association study identifying association of the MHC region with 5-aminosalicylate (5-ASA) induced nephrotoxicity in inflammatory bowel disease

DOP011 A genome wide association study identifying association of the MHC region with 5-aminosalicylate (5-ASA) induced nephrotoxicity in inflammatory bowel disease

The Relevance ofHLASequencing in Population Genetics Studies

Next generation sequencing (NGS) is currently being adapted by different biotechnological platforms to the standard typing method for HLA polymorphism, the huge diversity of which makes this initiative particularly challenging. Boosting the molecular characterization of the HLA genes through efficient, rapid, and low-cost technologies is expected to amplify the success of tissue transplantation by enabling us to find donor-recipient matching for rare phenotypes. But the application of NGS technologies to the molecular mapping of the MHC region also anticipates essential changes in population genetic studies. Huge amounts of HLA sequence data will be available in the next years for different populations, with the potential to change our understanding of HLA variation in humans. In this review, we first explain how HLA sequencing allows a better assessment of the HLA diversity in human populations, taking also into account the methodological difficulties it introduces at the statistical level; secondly, we show how analyzing HLA sequence variation may improve our comprehension of population genetic relationships by facilitating the identification of demographic events that marked human evolution; finally, we discuss the interest of both HLA and genome-wide sequencing and genotyping in detecting functionally significant SNPs in the MHC region, the latter having also contributed to the makeup of the HLA molecular diversity observed today.

Contribution of genetic variation to transgenerational inheritance of DNA methylation.

BackgroundDespite the important role DNA methylation plays in transcriptional regulation, the transgenerational inheritance of DNA methylation is not well understood. The genetic heritability of DNA methylation has been estimated using twin pairs, although concern has been expressed whether the underlying assumption of equal common environmental effects are applicable due to intrauterine differences between monozygotic and dizygotic twins. We estimate the heritability of DNA methylation on peripheral blood leukocytes using Illumina HumanMethylation450 array using a family based sample of 614 people from 117 families, allowing comparison both within and across generations.ResultsThe correlations from the various available relative pairs indicate that on average the similarity in DNA methylation between relatives is predominantly due to genetic effects with any common environmental or zygotic effects being limited. The average heritability of DNA methylation measured at probes with no known SNPs is estimated as 0.187. The ten most heritable methylation probes were investigated with a genome-wide association study, all showing highly statistically significant cis mQTLs. Further investigation of one of these cis mQTL, found in the MHC region of chromosome 6, showed the most significantly associated SNP was also associated with over 200 other DNA methylation probes in this region and the gene expression level of 9 genes.ConclusionsThe majority of transgenerational similarity in DNA methylation is attributable to genetic effects, and approximately 20% of individual differences in DNA methylation in the population are caused by DNA sequence variation that is not located within CpG sites.

Symposium 2-1The autoimmunome: Similarities and differences among genetic susceptibility to common immune-related diseases.

Autoimmune disorders arise when physiological tolerance to "self" antigens is lost. Although several mechanisms may be involved in this pathogenic process, dysregulation of T-cell and B-cell activation and of pathways leading to inflammation are logical candidates. Susceptibility to autoimmune diseases has been associated with multiple factors including genetics, epigenetics, and the environment. While the modest concordance rate in monozygotic twins suggests that environmental factors are major players in most autoimmune diseases, increased heritability within families and the decrease in risk with the degree of relatedness all argue in favor of genetic factors. With the advent of high-throughput genomics, massive amounts of genetic data are being produced and reported on a monthly basis. Although considerable insight has been gained from each of these individual studies, a detailed comparative analysis will likely identify both unique and common pathways operating in autoimmunity.More than 40 genome-wide association studies (GWAS) have been published to date in several autoimmune diseases (AID) and hundreds of common variants have been identified that confer risk or protection. While statistical adjustments are essential to refine the list of potential associations with each disease, valuable information can be extracted by the systematic collection of moderately significant variants present in more than one trait. While involvement of the MHC region in chromosome 6p21 is not in question for most AID, the complex genetic architecture of this locus poses a significant analytical challenge. On the other hand, by considering the contribution of non-MHC-related genes, similarities and differences among AID can be readily computed thus gaining insights into possible pathogenic mechanisms. For example, statistically significant excess sharing of non-MHC genes was found between type I diabetes (T1D) and all other AID studied, a result also seen for RA. A smaller but significant degree of sharing was observed for multiple sclerosis (MS), Celiac disease (CeD) and Crohn's disease (CD). We have developed a bioinformatics tool called iCTNet (integrated Complex Traits networks), that enables downloading and visualization of large volumes of data and the relationships among the different data types, information that is not typically available for the general user. The most recent version of iCNet (scheduled to be released in Spring 2014) includes data from genome-wide association studies, OMIM, protein interactions, tissue expression, drug targets, drug side effects, and miRNA targets among other data types. During my presentation I will describe practical examples of how this tools may facilitate the biological interpretation of large throughput data in human immune-related diseases and how this can help to generate new hypotheses for drug repositioning strategies. Using this class of approaches the unique genetic landscape for each autoimmune disease can start to be defined. Furthermore, this kind of analysis may set the basis for more targeted and rational therapeutic approaches.

A 20 year history of clinical and genetic study of thyroid autoimmunity in a Tunisian multigenerational family: Evidence for gene interaction

Autoimmune thyroid diseases (AITD), which include Hashimoto thyroiditis (HT), Graves' disease (GD) and primary idiopathic myxoedema (PIM), are recognized by their clinical and genetic heterogeneity. In this study, we have carried on a global approach gathering 20year genetic and clinical data on a Tunisian multigenerational family (Akr). Our purpose was search for a combined genotype involved in AITD susceptibility using 33 gene polymorphisms. The Akr pedigree is composed of more than 400 members distributed on 10 generations. Clinical follow-up was performed by appreciation of the thyroid gland and measurement of both thyroid hormone and auto antibody levels. We used FBAT software to test for association between gene polymorphisms and AITDs. Clinical follow-up has showed that the number of AITD patients has increased from 25 to 78 subjects subdivided on 51 cases of GD, 22 PIM and 5 HT. Concerning genetic analysis, our study has revealed new gene association when compared with our previous analysis (considering single genes). Thus, PTPN22, TG and VDR gene polymorphisms have became associated with p-values ranging from 4.610−2 to 410−3 when considered with other genes on the same chromosome; giving evidence for gene interaction. The most significant association was found with the MHC region (p=7.1510−4). Moreover, and among gene polymorphisms explored, our analysis has identified some of them as AITD biomarkers. Indeed, PDS gene polymorphisms were associated with either exophthalmia or goiter (p-values from 10−2 to 10−3). In conclusion, our study gives evidence for gene interaction in AITD development confirming genetic complexity of these diseases.

Quantifying Missing Heritability at Known GWAS Loci

Recent work has shown that much of the missing heritability of complex traits can be resolved by estimates of heritability explained by all genotyped SNPs. However, it is currently unknown how much heritability is missing due to poor tagging or additional causal variants at known GWAS loci. Here, we use variance components to quantify the heritability explained by all SNPs at known GWAS loci in nine diseases from WTCCC1 and WTCCC2. After accounting for expectation, we observed all SNPs at known GWAS loci to explain more heritability than GWAS-associated SNPs on average (). For some diseases, this increase was individually significant: for Multiple Sclerosis (MS) () and for Crohn's Disease (CD) (); all analyses of autoimmune diseases excluded the well-studied MHC region. Additionally, we found that GWAS loci from other related traits also explained significant heritability. The union of all autoimmune disease loci explained more MS heritability than known MS SNPs () and more CD heritability than known CD SNPs (), with an analogous increase for all autoimmune diseases analyzed. We also observed significant increases in an analysis of Rheumatoid Arthritis (RA) samples typed on ImmunoChip, with more heritability from all SNPs at GWAS loci () and more heritability from all autoimmune disease loci () compared to known RA SNPs (including those identified in this cohort). Our methods adjust for LD between SNPs, which can bias standard estimates of heritability from SNPs even if all causal variants are typed. By comparing adjusted estimates, we hypothesize that the genome-wide distribution of causal variants is enriched for low-frequency alleles, but that causal variants at known GWAS loci are skewed towards common alleles. These findings have important ramifications for fine-mapping study design and our understanding of complex disease architecture.

Protein-interaction-network-based analysis for genome-wide association analysis of schizophrenia in Han Chinese population

Schizophrenia is a severe neuropsychiatric disorder with a strong and complex genetic background. Recent genome-wide association studies (GWAS) have successfully identified several susceptibility loci of schizophrenia. In order to interpret the functional role of the genetic variants and detect the combined effects of some of these genes on schizophrenia, protein-interaction-network-based analysis (PINBA) has emerged as an effective approach. In the current study, we conducted a PINBA of our previous GWAS data taken from the Han Chinese population. In order to do so, we used dense module search (DMS), a method that locates densely connected modules for complex diseases by integrating the association signal from GWAS datasets into the human protein–protein interaction (PPI) network. As a result, we identified one gene set with a joint effect significantly associated with schizophrenia and gene expression profiling analysis suggested that they were mainly neuro- and immune-related genes, such as glutamatergic gene (GRM5), GABAergic genes (GABRB1, GABARAP) and genes located in the MHC region (HLA-C, TAP2, HIST1H1B). Further pathway enrichment analysis suggested that these genes are involved in processes related to neuronal and immune systems, such as the Adherens junction pathway, the Neurotrophin signaling pathway and the Toll-like receptor signaling pathway. In our study, we identified a set of susceptibility genes that had been missed in single-marker GWAS, and our findings could promote the study of the genetic mechanisms in schizophrenia.

PReS-FINAL-2135: Analysis of the HLA region in a large cohort of juvenile idiopathic arthritis cases identifies independent effects at HLA-DRB1

Juvenile idiopathic arthritis (JIA) is the most common arthritic disease of childhood and is caused by a combination of genes and environment. In the last few years great advances have been made in dissecting the genetic basis of JIA with now 17 confirmed susceptibility loci identified. One of these loci, the MHC region, has been established for many years but the complexity and the broad linkage disequilibrium (LD) across the region has rendered fine-mapping associations challenging. Novel imputation strategies can now be utilized to impute HLA classical alleles and amino acids across the region.

Diversity of Extended HLA-DRB1 Haplotypes in the Finnish Population

The Major Histocompatibility Complex (MHC, 6p21) codes for traditional HLA and other host response related genes. The polymorphic HLA-DRB1 gene in MHC Class II has been associated with several complex diseases. In this study we focus on MHC haplotype structures in the Finnish population. We explore the variability of extended HLA-DRB1 haplotypes in relation to the other traditional HLA genes and a selected group of MHC class III genes. A total of 150 healthy Finnish individuals were included in the study. Subjects were genotyped for HLA alleles (HLA-A, -B, -DRB1, -DQB1, and -DPB1). The polymorphism of TNF, LTA, C4, BTNL2 and HLA-DRA genes was studied with 74 SNPs (single nucleotide polymorphism). The C4A and C4B gene copy numbers and a 2-bp silencing insertion at exon 29 in C4A gene were analysed with quantitative genomic realtime-PCR. The allele frequencies for each locus were calculated and haplotypes were constructed using both the traditional HLA alleles and SNP blocks. The most frequent Finnish A∼B∼DR -haplotype, uncommon in elsewhere in Europe, was A*03∼B*35∼DRB1*01∶01. The second most common haplotype was a common European ancestral haplotype AH 8.1 (A*01∼B*08∼DRB1*03∶01). Extended haplotypes containing HLA-B, TNF block, C4 and HLA-DPB1 strongly increased the number of HLA-DRB1 haplotypes showing variability in the extended HLA-DRB1 haplotype structures. On the contrary, BTNL2 block and HLA-DQB1 were more conserved showing linkage with the HLA-DRB1 alleles. We show that the use of HLA-DRB1 haplotypes rather than single HLA-DRB1 alleles is advantageous when studying the polymorphisms and LD patters of the MHC region. For disease association studies the HLA-DRB1 haplotypes with various MHC markers allows us to cluster haplotypes with functionally important gene variants such as C4 deficiency and cytokines TNF and LTA, and provides hypotheses for further assessment. Our study corroborates the importance of studying population-specific MHC haplotypes.

48-OR

Aim Capture and sequence by NGS the 4Mb of the MHC and derive genotypes of 33 MHC genes (HLA and non-HLAs) using Omixon Target HLA Typing software. Methods We applied our Region Specific Extraction method to target and capture 4Mb of the MHC region with custom designed capture oligos on 7 samples having known HLA genotypes: 5 homozygous cell lines (COX, DBB, JVM, PGF, and QBL) and 2 heterozygous samples (mixture of PGF and COX DNA, and a standard lab control). Each sample was whole-genome amplified, prepared for sequencing using Illumina TruSeq DNA sample prep kit and size selected for DNA fragments ranging from 300-400 bp. Paired-end 2x100bp sequencing was performed on the Illumina HiSeq. Each sample was genotyped for 33 genes within the MHC by Omixon Target using all paired-end reads. Derived genotypes were compared to known genotypes from the IMGT/HLA database for the cell lines and Sanger sequencing for the heterozygous control sample. Results We sequenced 7 samples throughout the 4Mb of the MHC region. On average, each sample had 284 million reads which were analyzed with Omixon Target. The 33 genes examined were Class I HLA-A, B, C, E, F, G, H, J, K, L, and V, Class II genes HLA-DMA, DMB, DOA, DOB, DPA1, DPB1, DQA1, DQB1, DRA, DRB1, DRB3, DRB4, DRB5, Class II pseudogenes HLA-DRB2, DRB6, DRB7, DRB8, DRB9, and MHC related genes MICA, MICB, TAP1, and TAP2. Omixon Target provided genotypes for 90% of the possible alleles; the remaining 10% of alleles (no genotype) were Class II pseudogenes. The average depth across the alleles ranged from 50–3000, a small percentage of the overall reads per sample. In the cases where the true HLA genotype was known, we determined the correct allele with 93% accuracy. Conclusions Our method of capturing and sequencing the MHC coupled with Omixon Target has yielded highly accurate genotypes for 33 HLA and non-HLA, MHC genes. This work sets the stage for further detailed characterization of the MHC and derivation of clinically relevant HLA typing from MHC NGS data. Major: Omixon, Inc.: Other: Contractor. Hague: Omixon, Inc.: Other: Contractor. Berces: Omixon, Inc.: Employee; Stockholder.