Advances in DNA sequencing technologies for high resolution HLA typing

Cereb, Nezih; Kim, Hwa Ran; Ryu, Jae Jun; Yang, Soo Young

doi:10.1016/j.humimm.2015.09.015

Cited by 91 publications

(84 citation statements)

References 13 publications

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“…63 implemented a population reference graph to infer MHC sequence, taking into account the extended MHC haplotypes from the MHC haplotype project 64 and the HLA alleles reported in the IMGT/HLA database 65 . As sequence reads increase in length, many of the challenges with targeting HLA genes and read-mapping assembly are becoming more tractable 66 .…”

Section: Genetic Factors Associated With Autoimmunitymentioning

confidence: 99%

Autoimmune diseases — connecting risk alleles with molecular traits of the immune system

2016

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Genome-wide strategies have driven the discovery of more than 300 susceptibility loci for autoimmune diseases. However, for almost all loci, understanding of the mechanisms leading to autoimmunity remains limited, and most variants that are likely to be causal are in non-coding regions of the genome. A critical next step will be to identify the in vivo and ex vivo immunophenotypes that are affected by risk variants. To do this, key cell types and cell states that are implicated in autoimmune diseases will need to be defined. Functional genomic annotations from these cell types and states can then be used to resolve candidate genes and causal variants. Together with longitudinal studies, this approach may yield pivotal insights into how autoimmunity is triggered.

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Section: Genetic Factors Associated With Autoimmunitymentioning

confidence: 99%

Autoimmune diseases — connecting risk alleles with molecular traits of the immune system

2016

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“…1,2 The number of known HLA alleles is still growing and this trend will become even more pronounced with the wider use of high throughput sequencing methods 3 in clinical laboratories that perform histocompatibility testing. Allorecognition of HLA allelic differences by T lymphocytes confers a higher risk of acute graft-versus-host disease (GVHD) and mortality.…”

Section: Introductionmentioning

confidence: 99%

How to select the best available related or unrelated donor of hematopoietic stem cells?

2016

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“…These include high resolution HLA haplotype frequencies in US populations for the entire US donor registry [7] and large scale data for German donors [8], [9] while databases of allelic reference sequences and nomenclature are maintained by IPD-IMGT/HLA (http://www.ebi.ac.uk/imgt/hla) [10]. There are a range of methods for direct HLA typing including serological testing, use of sequence-specific amplification primers (SSP) or probes (SSO), Sanger sequencing and next generation sequencing based typing [11], [12]. Imputation of HLA alleles from SNP genotyping [13], [14], [15], [16], [17] provides a further complementary approach of significant interest given the low cost and broad availability of accurate high throughput genotyping through genome-wide association studies and other initiatives.…”

Section: Introductionmentioning

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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Advances in DNA sequencing technologies for high resolution HLA typing

Cited by 91 publications

References 13 publications

Autoimmune diseases — connecting risk alleles with molecular traits of the immune system

Autoimmune diseases — connecting risk alleles with molecular traits of the immune system

How to select the best available related or unrelated donor of hematopoietic stem cells?

High resolution HLA haplotyping by imputation for a British population bioresource

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