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使用BGISEQ-500和HiSeq X Ten全基因组测序进行种系和体细胞变异鉴定。

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

作者信息

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

机构信息

Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.

National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia.

出版信息

PLoS One. 2018 Jan 10;13(1):e0190264. doi: 10.1371/journal.pone.0190264. eCollection 2018.

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.

摘要

技术创新和可承受性的提高推动了基因组测序技术在生物医学研究中的广泛应用。特别是大型癌症研究联盟已经采用了下一代测序技术,并利用该技术确定了多种癌症类型的体细胞突变图谱。这些研究主要使用了Illumina HiSeq平台。在本研究中,我们使用新平台BGISEQ-500对三个恶性胸膜间皮瘤及其匹配的正常样本进行了全基因组测序,并将所得结果与Illumina HiSeq X Ten进行了比较。从比对到人类基因组参考的数据中独立鉴定出种系和体细胞单核苷酸变异以及小插入或缺失。BGISEQ-500和HiSeq X Ten平台在种系检测方面与SNP阵列的基因型具有高度一致性(>99%)。在两个测序平台中鉴定出的种系和体细胞单核苷酸变异高度一致(分别为86%和72%)。这些结果表明BGISEQ-500平台通过全基因组测序鉴定体细胞和种系单核苷酸变异具有潜在的适用性。这里描述的BGISEQ-500数据集代表了首次使用该平台进行的公开可用的癌症基因组测序。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9c23/5761881/1aa0c705f044/pone.0190264.g001.jpg

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