Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing

Ann Marie Patch, Katia Nones, Stephen H. Kazakoff, Felicity Newell, Scott Wood, Conrad Leonard, Oliver Holmes, Qinying Xu, Venkateswar Addala, Jenette Creaney, Bruce W. Robinson, Shujin Fu, Chunyu Geng, Tong Li, Wenwei Zhang, Xinming Liang, Junhua Rao, Jiahao Wang, Mingyu Tian, Yonggang ZhaoFei Teng, Honglan Gou, Bicheng Yang, Hui Jiang, Feng Mu, John V. Pearson, Nicola Waddell

Research output: Contribution to journalArticlepeer-review

43 Citations (Scopus)


Technological innovation and increased affordability have contributed to the widespread adoption of genome sequencing technologies in biomedical research. In particular large cancer research consortia have embraced next generation sequencing, and have used the technology to define the somatic mutation landscape of multiple cancer types. These studies have primarily utilised the Illumina HiSeq platforms. In this study we performed whole genome sequencing of three malignant pleural mesothelioma and matched normal samples using a new platform, the BGISEQ-500, and compared the results obtained with Illumina HiSeq X Ten. Germline and somatic, single nucleotide variants and small insertions or deletions were independently identified from data aligned human genome reference. The BGI-SEQ-500 and HiSeq X Ten platforms showed high concordance for germline calls with genotypes from SNP arrays (>99%). The germline and somatic single nucleotide variants identified in both sequencing platforms were highly concordant (86% and 72% respectively). These results indicate the potential applicability of the BGISEQ-500 platform for the identification of somatic and germline single nucleotide variants by whole genome sequencing. The BGISEQ-500 datasets described here represent the first publicly-available cancer genome sequencing performed using this platform.

Original languageEnglish
Article numbere0190264
Number of pages12
JournalPLoS One
Issue number1
Publication statusPublished - 10 Jan 2018


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