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

文献类型：期刊论文

作者Liu, Ping3; Yao, Minya4; Gong, Yu6; Song, Yunjie1; Chen, Yanan1; Ye, Yizhou1; Liu, Xiao1; Li, Fugen1; Dong, Hua1; Meng, Rui5
刊名FRONTIERS IN IMMUNOLOGY
出版日期2021-03-31
卷号12
ISSN号1664-3224
关键词human leukocyte antigen accuracy next-generation sequencing algorithms benchmark
DOI10.3389/fimmu.2021.652258
通讯作者Meng, Rui(mengruivip@163.com) ; Chen, Hao(hao.chen1@3dmedcare.com) ; Zheng, Aiwen(zhengaw@zjcc.org.cn)
英文摘要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.
资助项目National Key Research and Development Program of China[2017YFC0908500]
WOS研究方向Immunology
语种英语
出版者FRONTIERS MEDIA SA
WOS记录号WOS:000639982200001
资助机构National Key Research and Development Program of China
源URL[http://ir.hfcas.ac.cn:8080/handle/334002/121744]  
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1.3DMed Inc, Bioinformat Dept, Shanghai, Peoples R China
2.Univ Chinese Acad Sci, Canc Hosp, Zhejiang Canc Hosp, Hangzhou, Peoples R China
3.Cent South Univ, Xiangya Hosp 2, Dept Oncol, Changsha, Peoples R China
4.Zhejiang Univ, Sch Med, Affiliated Hosp 1, Hangzhou, Peoples R China
5.Huazhong Univ Sci & Technol, Tongji Med Coll, Wuhan, Peoples R China
6.Zhejiang Univ, Affiliated Hosp 2, Dept Urol, Coll Med, 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).

入库方式： OAI收割

来源：合肥物质科学研究院

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