A new massively parallel nanoball sequencing platform for whole exome research

Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-500 is a recently established next-generation sequencing platform. However, the performance of BGISEQ-500 on WES is not well studied. In this study, we evaluated the performance of BGISEQ-500 on WES by side-to-side...

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Bibliographic Details
Published in:BMC bioinformatics 2019-03, Vol.20 (1), p.153-153, Article 153
Main Authors: Xu, Yu, Lin, Zhe, Tang, Chong, Tang, Yujing, Cai, Yue, Zhong, Hongbin, Wang, Xuebin, Zhang, Wenwei, Xu, Chongjun, Wang, Jingjing, Wang, Jian, Yang, Huanming, Yang, Linfeng, Gao, Qiang
Format: Article
Language:English
Subjects:
Benchmarking
BGISEQ-500
Bioinformatics
Datasets
Deoxyribonucleic acid
DNA
DNA sequencing
Genetic research
Genetic Variation
Genetics
Genome, Human
Genomes
Genomics
High-Throughput Nucleotide Sequencing - methods
Humans
INDEL Mutation
Methodology
Methods
Multiprocessing
Next-generation sequencing
Proteins
Reproducibility
Reproducibility of Results
Researchers
Scientific software
Sensitivity
Sensitivity analysis
Sensitivity and Specificity
Technology application
Variation detection
Whole exome sequencing
Whole Exome Sequencing - methods
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Summary:Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-500 is a recently established next-generation sequencing platform. However, the performance of BGISEQ-500 on WES is not well studied. In this study, we evaluated the performance of BGISEQ-500 on WES by side-to-side comparison with Hiseq4000, on well-characterized human sample NA12878. BGISEQ demonstrated similarly high reproducibility as Hiseq for variation detection. Also, the SNVs from BGISEQ data is highly consistent with Hiseq results (concordance 96.5%~ 97%). Variation detection accuracy was subsequently evaluated with data from the genome in a bottle project as the benchmark. Both platforms showed similar sensitivity and precision in SNV detection. While in indel detection, BGISEQ showed slightly higher sensitivity and lower precision. The impact of sequence depth and read length on variation detection accuracy was further analyzed, and showed that variation detection sensitivity still increasing when the sequence depth is larger than 100x, and the impact of read length is minor when using 100x data. This study suggested that BGISEQ-500 is a qualified sequencing platform for WES.
ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-019-2751-3