Robust Benchmark Structural Variant Calls of An Asian Using State-of-the-art Long-read Sequencing Technologies
Robust Benchmark Structural Variant Calls of An Asian Using State-of-the-art Long-read Sequencing Technologies作者机构：National Institutes for food and drug Control(NIFDC)Beijing 10050China BGI-QingdaoBGI-ShenzhenQingdao 266555China GrandOmics BiosciencesBeijing 102200China Annoroad Gene Technology(Beijing)Co.Ltd.Beijing 102200China BGI-ShenzhenShenzhen 518083China MGIBGI-ShenzhenShenzhen 518083China State Key Laboratory of Agricultural GenomicsBGI-ShenzhenShenzhen 518083China China National GeneBankBGI-ShenzhenShenzhen 518120China
出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)
年 卷 期：2022年第20卷第1期
页 面：192-204页
核心收录：
学科分类：0710[理学-生物学] 07[理学] 071007[理学-遗传学]
基 金：supported by grants from the National Key R&D Program of China(Grant No.2017YFC0906501)
主 题：Asian benchmark Reference material Structural variation Haplotype-resolved Sanger validation
摘 要：The importance of structural variants(SVs)for human phenotypes and diseases is now *** a variety of SV detection platforms and strategies that vary in sensitivity and specificity have been developed,few benchmarking procedures are available to confidently assess their performances in biological and clinical *** facilitate the validation and application of these SV detection approaches,we established an Asian reference material by characterizing the genome of an Epstein-Barr virus(EBV)-immortalized B lymphocyte line along with identified benchmark regions and high-confidence SV *** established a high-confidence SV callset with 8938 SVs by integrating four alignment-based SV callers,including 109×Pacific Bio sciences(PacBio)continuous long reads(CLRs),22×PacBio circular consensus sequencing(CCS)reads,104×Oxford Nanopore Technologies(ONT)long reads,and 114×Bionano optical mapping platform,and one de novo assembly-based SV caller using CCS reads.A total of 544 randomly selected SVs were validated by PCR amplification and Sanger sequencing,demonstrating the robustness of our SV *** trio-binning-based haplotype assemblies,we established an SV benchmark for identifying false negatives and false positives by constructing the continuous high-confidence regions(CHCRs),which covered 1.46 gigabase pairs(Gb)and 6882 SVs supported by at least one diploid haplotype *** high-confidence SV calls for a benchmark sample that has been characterized by multiple technologies provides a valuable resource for investigating SVs in human biology,disease,and clinical research.
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