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 Zhao & 7 others Fei Teng, Honglan Gou, Bicheng Yang, Hui Jiang, Feng Mu, John V. Pearson, Nicola Waddell

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

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
JournalPLoS One
Volume13
Issue number1
DOIs
Publication statusPublished - 10 Jan 2018

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germ cells
Genes
Genome
genome
Nucleotides
nucleotides
neoplasms
Inventions
Technology
Neoplasms
affordability
mesothelioma
Human Genome
somatic mutation
Single Nucleotide Polymorphism
biomedical research
Biomedical Research
Genotype
Mutation
Innovation

Cite this

Patch, A. M., Nones, K., Kazakoff, S. H., Newell, F., Wood, S., Leonard, C., ... Waddell, N. (2018). Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing. PLoS One, 13(1), [e0190264]. https://doi.org/10.1371/journal.pone.0190264
Patch, Ann Marie ; Nones, Katia ; Kazakoff, Stephen H. ; Newell, Felicity ; Wood, Scott ; Leonard, Conrad ; Holmes, Oliver ; Xu, Qinying ; Addala, Venkateswar ; Creaney, Jenette ; Robinson, Bruce W. ; Fu, Shujin ; Geng, Chunyu ; Li, Tong ; Zhang, Wenwei ; Liang, Xinming ; Rao, Junhua ; Wang, Jiahao ; Tian, Mingyu ; Zhao, Yonggang ; Teng, Fei ; Gou, Honglan ; Yang, Bicheng ; Jiang, Hui ; Mu, Feng ; Pearson, John V. ; Waddell, Nicola. / Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing. In: PLoS One. 2018 ; Vol. 13, No. 1.
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Patch, AM, Nones, K, Kazakoff, SH, Newell, F, Wood, S, Leonard, C, Holmes, O, Xu, Q, Addala, V, Creaney, J, Robinson, BW, Fu, S, Geng, C, Li, T, Zhang, W, Liang, X, Rao, J, Wang, J, Tian, M, Zhao, Y, Teng, F, Gou, H, Yang, B, Jiang, H, Mu, F, Pearson, JV & Waddell, N 2018, 'Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing' PLoS One, vol. 13, no. 1, e0190264. https://doi.org/10.1371/journal.pone.0190264

Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing. / Patch, Ann Marie; Nones, Katia; Kazakoff, Stephen H.; Newell, Felicity; Wood, Scott; Leonard, Conrad; Holmes, Oliver; Xu, Qinying; Addala, Venkateswar; Creaney, Jenette; Robinson, Bruce W.; Fu, Shujin; Geng, Chunyu; Li, Tong; Zhang, Wenwei; Liang, Xinming; Rao, Junhua; Wang, Jiahao; Tian, Mingyu; Zhao, Yonggang; Teng, Fei; Gou, Honglan; Yang, Bicheng; Jiang, Hui; Mu, Feng; Pearson, John V.; Waddell, Nicola.

In: PLoS One, Vol. 13, No. 1, e0190264, 10.01.2018.

Research output: Contribution to journalArticle

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T1 - Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing

AU - Patch, Ann Marie

AU - Nones, Katia

AU - Kazakoff, Stephen H.

AU - Newell, Felicity

AU - Wood, Scott

AU - Leonard, Conrad

AU - Holmes, Oliver

AU - Xu, Qinying

AU - Addala, Venkateswar

AU - Creaney, Jenette

AU - Robinson, Bruce W.

AU - Fu, Shujin

AU - Geng, Chunyu

AU - Li, Tong

AU - Zhang, Wenwei

AU - Liang, Xinming

AU - Rao, Junhua

AU - Wang, Jiahao

AU - Tian, Mingyu

AU - Zhao, Yonggang

AU - Teng, Fei

AU - Gou, Honglan

AU - Yang, Bicheng

AU - Jiang, Hui

AU - Mu, Feng

AU - Pearson, John V.

AU - Waddell, Nicola

PY - 2018/1/10

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N2 - 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.

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