Comparative analysis of NGS and Sanger sequencing methods for HLA typing at a Russian university clinic

Glotov, Oleg S.; Романова, О. В.; Eismont, Yuri A.; Sarana, Andrey М.; Scherbak, Sergey G.; Кузьмич, Е В; Alyanskiy, Alexander L.; Ivanova, Natalya E.; Teplyashina, Vera V.; Serov, Yury A.; Zubarovskaya, Ludmila; Afanasyev, Boris

doi:10.18620/ctt-1866-8836-2018-7-4-72-82

Cited by 2 publications

(2 citation statements)

References 6 publications

(8 reference statements)

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“…Besides, it is reported that the concordance of HLA typing by the current gold standard methods (PCR-based) is only 84%, reflecting the inaccuracy of the laboratory methods as well as inter-laboratory variability ( 26 ). We used NGSgo-AmpX as our benchmarked assay, which is a Research Use Only (RUO) and the only one CE-marked IVD product when our study started, and yielded almost 100% homology results compared to Sanger sequencing ( 38 ). In addition, seq2HLA and HLAforest are originally used for RNA-seq based HLA typing, they perform best on RNAseq data as the datatype they were designed for, whereas the performance in WES/WGS data decreased significantly ( 26 ).…”

Section: Discussionmentioning

confidence: 99%

Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms

et al. 2021

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With the great progress made recently in next generation sequencing (NGS) technology, sequencing accuracy and throughput have increased, while the cost for data has decreased. Various human leukocyte antigen (HLA) typing algorithms and assays have been developed and have begun to be used in clinical practice. In this study, we compared the HLA typing performance of three HLA assays and seven NGS-based HLA algorithms and assessed the impact of sequencing depth and length on HLA typing accuracy based on 24 benchmarked samples. The algorithms HISAT-genotype and HLA-HD showed the highest accuracy at both the first field and the second field resolution, followed by HLAscan. Our internal capture-based HLA assay showed comparable performance with whole exome sequencing (WES). We found that the minimal depth was 100X for HISAT-genotype and HLA-HD to obtain more than 90% accuracy at the third field level. The top three algorithms were quite robust to the change of read length. Thus, we recommend using HISAT-genotype and HLA-HD for NGS-based HLA genotyping because of their higher accuracy and robustness to read length. We propose that a minimal sequence depth for obtaining more than 90% HLA typing accuracy at the third field level is 100X. Besides, targeting capture-based NGS HLA typing may be more suitable than WES in clinical practice due to its lower sequencing cost and higher HLA sequencing depth.

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Section: Discussionmentioning

confidence: 99%

Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms

et al. 2021

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“…Since the 1970's, the high-throughput and precise techniques of HLA-typing were introduced for allogeneic transplantation of hematopoietic cells (HSCT). More than 30.000 HLA variations of HLA proteins are registered and DNA-sequenced by the classical Sanger technique or NGS approach which is implemented for HLA typing worldwide [1]. The resulting databases contain quite extensive data on HLA polymorphic regions and provide excellent opportunities for in silico modeling of best matches between HLA and any foreign proteins, including fragments of viral antigens.…”

Section: Introductionmentioning

confidence: 99%

Immunoinformatics in COVID-19 Vaccine Development: The Role of HLA System

Anisenkova¹,

Vologzhanin²,

Kamilova³

et al. 2021

CTT

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Individual genetic variation may help to explain different immune responses to a coronavirus SARS-CoV-2 across a population. The in silico computer simulation methodology provides the experimental community with a more complete list of SARS-CoV-2 immunogenic peptides presented by the antigens of the HLA system. This review considers an array of computationally predicted immunogenic peptides from SARS-CoV-2 for in vitro functional validation and potential vaccine developments. Several independent studies conducted with different approaches showed a high degree of confidence and reproducibility of the results. Computer-assisted prediction is instrumental for a quick and cost-effective solution to prevent the spread and ultimately eliminate the infection.Most efforts to develop vaccines and drugs against SARS-CoV-2 target the spike glycoprotein (protein S), the major inducer of neutralizing antibodies. Several candidates have been shown to be effective in in vitro studies and have progressed to randomized trials in animals or humans against COVID-19 infection. This article highlights current advances in the development of subunit vaccines to combat COVID-19 that are reducing the time and costs of vaccine development.

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Comparative analysis of NGS and Sanger sequencing methods for HLA typing at a Russian university clinic

Cited by 2 publications

References 6 publications

Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms

Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms

Immunoinformatics in COVID-19 Vaccine Development: The Role of HLA System

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