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

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

doi:10.1371/journal.pone.0190264

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 BGISEQ-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.

Highlights

The human genome project was an important achievement in life sciences and paved the way for major technology developments in DNA sequencing
The sequence data generated on the BGISEQ-500 and the HiSeq X Ten platforms showed a >99% concordance with the genotypes obtained from the Illumina SNP arrays (Table 1), indicating that both platforms were able to accurately detect common germline substitution variants (SNV) assayed by the SNP arrays
Across the genome the BGISEQ-500 and HiSeq X Ten platforms called an average of 3,562,321 germline SNV in each patient

Summary

Introduction

The human genome project was an important achievement in life sciences and paved the way for major technology developments in DNA sequencing. The Cancer Genome Atlas (TCGA) [3] and the International Cancer Genome Consortium (ICGC) [4], have sequenced thousands of tumours from over 50 cancer types. These two consortia have been instrumental in increasing our knowledge of cancer genomics and have identified significantly mutated genes, candidate actionable mutations and mutational processes [5] that occur during tumour development

Methods

Results

Conclusion