用于配对肿瘤-正常样本二代测序（NGS）实验的全面质量控制工作流程。

A comprehensive quality control workflow for paired tumor-normal NGS experiments.

作者信息

Schroeder Christopher M, Hilke Franz J, Löffler Markus W, Bitzer Michael, Lenz Florian, Sturm Marc

机构信息

Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.

Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany.

出版信息

Bioinformatics. 2017 Jun 1;33(11):1721-1722. doi: 10.1093/bioinformatics/btx032.

DOI:10.1093/bioinformatics/btx032

PMID:28130233

Abstract

SUMMARY

Quality control (QC) is an important part of all NGS data analysis stages. Many available tools calculate QC metrics from different analysis steps of single sample experiments (raw reads, mapped reads and variant lists). Multi-sample experiments, as sequencing of tumor-normal pairs, require additional QC metrics to ensure validity of results. These multi-sample QC metrics still lack standardization. We therefore suggest a new workflow for QC of DNA sequencing of tumor-normal pairs. With this workflow well-known single-sample QC metrics and additional metrics specific for tumor-normal pairs can be calculated. The segmentation into different tools offers a high flexibility and allows reuse for other purposes. All tools produce qcML, a generic XML format for QC of -omics experiments. qcML uses quality metrics defined in an ontology, which was adapted for NGS.

AVAILABILITY AND IMPLEMENTATION

All QC tools are implemented in C ++ and run both under Linux and Windows. Plotting requires python 2.7 and matplotlib. The software is available under the 'GNU General Public License version 2' as part of the ngs-bits project: https://github.com/imgag/ngs-bits.

CONTACT

christopher.schroeder@med.uni-tuebingen.de.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

质量控制（QC）是所有二代测序（NGS）数据分析阶段的重要组成部分。许多现有工具可从单样本实验的不同分析步骤（原始读数、比对读数和变异列表）计算QC指标。多样本实验，如肿瘤-正常样本对的测序，需要额外的QC指标来确保结果的有效性。这些多样本QC指标仍缺乏标准化。因此，我们提出了一种用于肿瘤-正常样本对DNA测序QC的新工作流程。通过此工作流程，可以计算出众所周知的单样本QC指标以及特定于肿瘤-正常样本对的其他指标。划分为不同工具提供了高度的灵活性，并允许用于其他目的。所有工具都会生成qcML，这是一种用于-组学实验QC的通用XML格式。qcML使用在本体中定义的质量指标，该本体已针对NGS进行了调整。