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

doi:10.3389/fimmu.2021.652258

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	Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms
	Liu, Ping 1; Yao, Minya 2; Gong, Yu 3; Song, Yunjie 4; Chen, Yanan 4; Ye, Yizhou 4; Liu, Xiao4 ; Li, Fugen 4; Dong, Hua 4; Meng, Rui 5; Chen, Hao 4; Zheng, Aiwen 6,7
	2021-03-31
发表期刊	FRONTIERS IN IMMUNOLOGY
ISSN	1664-3224
通讯作者	Meng, Rui(mengruivip@163.com) ; Chen, Hao(hao.chen1@3dmedcare.com) ; Zheng, Aiwen(zhengaw@zjcc.org.cn)
摘要	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.
关键词	human leukocyte antigen accuracy next-generation sequencing algorithms benchmark
DOI	10.3389/fimmu.2021.652258
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2017YFC0908500]
项目资助者	National Key Research and Development Program of China
WOS研究方向	Immunology
WOS类目	Immunology
WOS记录号	WOS:000639982200001
出版者	FRONTIERS MEDIA SA
引用统计	被引频次：11[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.hfcas.ac.cn:8080/handle/334002/121745
专题	中国科学院合肥物质科学研究院
通讯作者	Meng, Rui; Chen, Hao; Zheng, Aiwen
作者单位	1.Cent South Univ, Xiangya Hosp 2, Dept Oncol, Changsha, Peoples R China 2.Zhejiang Univ, Sch Med, Affiliated Hosp 1, Hangzhou, Peoples R China 3.Zhejiang Univ, Affiliated Hosp 2, Dept Urol, Coll Med, Hangzhou, Peoples R China 4.3DMed Inc, Bioinformat Dept, Shanghai, Peoples R China 5.Huazhong Univ Sci & Technol, Tongji Med Coll, Wuhan, Peoples R China 6.Univ Chinese Acad Sci, Canc Hosp, Zhejiang Canc Hosp, Hangzhou, Peoples R China 7.Chinese Acad Sci, Inst Canc & Basic Med IBMC, Hangzhou, Peoples R China
推荐引用方式 GB/T 7714	Liu, Ping,Yao, Minya,Gong, Yu,et al. Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms[J]. FRONTIERS IN IMMUNOLOGY,2021,12.
APA	Liu, Ping.,Yao, Minya.,Gong, Yu.,Song, Yunjie.,Chen, Yanan.,...&Zheng, Aiwen.(2021).Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms.FRONTIERS IN IMMUNOLOGY,12.
MLA	Liu, Ping,et al."Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms".FRONTIERS IN IMMUNOLOGY 12(2021).