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

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...

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Autores principales: Liu, Ping, Yao, Minya, Gong, Yu, Song, Yunjie, Chen, Yanan, Ye, Yizhou, Liu, Xiao, Li, Fugen, Dong, Hua, Meng, Rui, Chen, Hao, Zheng, Aiwen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8045758/
https://www.ncbi.nlm.nih.gov/pubmed/33868290
http://dx.doi.org/10.3389/fimmu.2021.652258
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author Liu, Ping
Yao, Minya
Gong, Yu
Song, Yunjie
Chen, Yanan
Ye, Yizhou
Liu, Xiao
Li, Fugen
Dong, Hua
Meng, Rui
Chen, Hao
Zheng, Aiwen
author_facet Liu, Ping
Yao, Minya
Gong, Yu
Song, Yunjie
Chen, Yanan
Ye, Yizhou
Liu, Xiao
Li, Fugen
Dong, Hua
Meng, Rui
Chen, Hao
Zheng, Aiwen
author_sort Liu, Ping
collection PubMed
description 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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spelling pubmed-80457582021-04-15 Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms Liu, Ping Yao, Minya Gong, Yu Song, Yunjie Chen, Yanan Ye, Yizhou Liu, Xiao Li, Fugen Dong, Hua Meng, Rui Chen, Hao Zheng, Aiwen Front Immunol Immunology 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. Frontiers Media S.A. 2021-03-31 /pmc/articles/PMC8045758/ /pubmed/33868290 http://dx.doi.org/10.3389/fimmu.2021.652258 Text en Copyright © 2021 Liu, Yao, Gong, Song, Chen, Ye, Liu, Li, Dong, Meng, Chen and Zheng https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Immunology
Liu, Ping
Yao, Minya
Gong, Yu
Song, Yunjie
Chen, Yanan
Ye, Yizhou
Liu, Xiao
Li, Fugen
Dong, Hua
Meng, Rui
Chen, Hao
Zheng, Aiwen
Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms
title Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms
title_full Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms
title_fullStr Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms
title_full_unstemmed Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms
title_short Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms
title_sort benchmarking the human leukocyte antigen typing performance of three assays and seven next-generation sequencing-based algorithms
topic Immunology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8045758/
https://www.ncbi.nlm.nih.gov/pubmed/33868290
http://dx.doi.org/10.3389/fimmu.2021.652258
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