The impact of next-generation sequencing technologies on HLA research

Hosomichi, Kazuyoshi; Shiina, Takashi; Tajima, Atsushi; Inoue, Ituro

doi:10.1038/jhg.2015.102

Cited by 145 publications

(131 citation statements)

References 59 publications

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“…However these methods are very time consuming and not practical for large cohorts of individuals. One new emerging technology that can be applied to achieve HLA typing is next generation sequencing (NGS) [12], [49], [50]. Such technologies enabling single molecule sequencing in high throughput are becoming more widely available for HLA typing with more accurate computational tools [51] and implementation in clinical HLA laboratories [52], [53].…”

Section: Discussionmentioning

confidence: 99%

High resolution HLA haplotyping by imputation for a British population bioresource

et al. 2017

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This study aimed to establish the occurrence and frequency of HLA alleles and haplotypes for a healthy British Caucasian population bioresource from Oxfordshire. We present the results of imputation from HLA SNP genotyping data using SNP2HLA for 5553 individuals from Oxford Biobank, defining one- and two-field alleles together with amino acid polymorphisms. We show that this achieves a high level of accuracy with validation using sequence-specific primer amplification PCR. We define six- and eight-locus HLA haplotypes for this population by Bayesian methods implemented using PHASE. We determine patterns of linkage disequilibrium and recombination for these individuals involving classical HLA loci and show how analysis within a haplotype block structure may be more tractable for imputed data. Our findings contribute to knowledge of HLA diversity in healthy populations and further validate future large-scale use of HLA imputation as an informative approach in population bioresources.

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Section: Discussionmentioning

confidence: 99%

High resolution HLA haplotyping by imputation for a British population bioresource

et al. 2017

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“…Based on chromatin immunoprecipitation sequencing and DNaseI-seq peak data (ENCODE project), this SNP was shown to be located within regulatory regions. 26 …”

Section: Methodsmentioning

confidence: 99%

Pooled analysis of the HLA‐DRB1 by smoking interaction in Parkinson disease

Chuang

Lee

Vlaar

et al. 2017

Annals of Neurology

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Objective Inflammatory response plays an important role in Parkinson’s disease (PD). Previous studies have reported an association between human leukocyte antigen (HLA)-DRB1 and the risk of PD. There has also been growing interest in investigating whether inflammation-related genes interact with environmental factors such as smoking to influence PD risk. We performed a pooled analysis of the interaction between HLA-DRB1 and smoking in PD in three population-based case-control studies from Denmark and France. Methods We included 2,056 cases and 2,723 controls from three PD studies (Denmark, France) that obtained information on smoking through interviews. Genotyping of the rs660895 polymorphism in the HLA-DRB1 region was based on saliva or blood DNA samples. To assess interactions, we used logistic regression with product terms between rs660895 and smoking. We performed random-effects meta-analysis of marginal associations and interactions. Results Both carrying rs660895-G (AG vs. AA: OR= 0.81; GG vs. AA: OR= 0.56; p-trend=0.003) and ever smoking (OR=0.56, p<0.001) were inversely associated with PD. A multiplicative interaction was observed between rs660895 and smoking using codominant, additive (interaction parameter=1.37, p=0.005), and dominant (interaction parameter=1.54, p=0.001) genetic models without any heterogeneity (I2=0.0%): the inverse association of rs660895-(AG+GG) with PD seen in never smokers (OR=0.64, p<0.001) disappeared among ever smokers (OR=1.00, p=0.99). Similar interactions were observed when we investigated light and heavy smokers separately. Interpretation Our study provides the first evidence that smoking modifies the previously reported inverse association of rs660895-G with PD, and suggests that smoking and HLA-DRB1 are involved in common pathways, possibly related to neuroinflammation.

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“…The HLA region that encodes these molecules is considered to be the most polymorphic region in the genome, and has been associated with > 100 diseases, which are predominantly autoimmune [12]. The classical HLA alleles have also been an important focus in TAK, for which Naito et al reported the HLA-B5 serotype as the first genetic association with the disease in 1977 (table I) [13].…”

Section: Hla Genesmentioning

confidence: 99%

The genetics of Takayasu arteritis

Renauer

Sawalha

2017

La Presse Médicale

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Summary Takayasu arteritis (TAK) is a rare systemic vasculitis that is characterized by granulomatous inflammation of the aorta and its major branches. The cellular and biochemical processes involved in the pathogenesis of TAK are beginning to be elucidated, and implicate both cell and antibody-mediated autoimmune mechanisms. In addition, the underlying etiology to TAK may be explained, at least in part, by a complex genetic contribution. The most well-recognized genetic susceptibility locus for the disease is the classical HLA allele, HLA-B*52, which has been confirmed in several ethnicities. The genetic susceptibility with HLA-B*52, as well as additional classical alleles and loci, implicate both HLA class I and class II involvement in TAK. Furthermore, genetic associations with genes encoding immune response regulators, pro-inflammatory cytokines and mediators of humoral immunity may directly relate to disease mechanisms. Non-HLA susceptibility loci that have been recently established for TAK with a genome-wide level of significance include FCGR2A/FCGR3A, IL12B, IL6, RPS9/LILRB3, and a locus on chromosome 21 near PSMG1. In this review, we present the complex genetic predisposition to TAK and discuss how recent findings identified potential targets in the pathogenesis and treatment of the disease.

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The impact of next-generation sequencing technologies on HLA research

Cited by 145 publications

References 59 publications

High resolution HLA haplotyping by imputation for a British population bioresource

High resolution HLA haplotyping by imputation for a British population bioresource

Pooled analysis of the HLA‐DRB1 by smoking interaction in Parkinson disease

The genetics of Takayasu arteritis

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