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Related Experiment Video

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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
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A comprehensive quality control workflow for paired tumor-normal NGS experiments.

Christopher M Schroeder1, Franz J Hilke1, Markus W Löffler2,3

  • 1Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.

Bioinformatics (Oxford, England)
|January 29, 2017
PubMed
Summary

A new workflow standardizes quality control (QC) for next-generation sequencing (NGS) tumor-normal pairs. This approach integrates single-sample metrics with novel multi-sample QC metrics for improved data validity.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Quality control (QC) is crucial for next-generation sequencing (NGS) data analysis.
  • Existing tools primarily focus on single-sample QC metrics.
  • Multi-sample experiments, like tumor-normal sequencing, require specialized QC metrics that currently lack standardization.

Purpose of the Study:

  • To propose a novel workflow for the quality control of DNA sequencing in tumor-normal pairs.
  • To introduce standardized multi-sample QC metrics for tumor-normal sequencing data.
  • To enhance the flexibility and reusability of QC tools.

Main Methods:

  • Development of a flexible workflow integrating well-known single-sample QC metrics.
  • Inclusion of additional QC metrics specifically designed for tumor-normal pairs.
  • All tools are implemented in C++ and produce output in qcML format, a generic XML standard for -omics data QC.

Main Results:

  • The proposed workflow enables calculation of both single-sample and multi-sample specific QC metrics.
  • The modular design allows for high flexibility and potential reuse of individual tools.
  • Standardized QC metrics are generated in the qcML format, utilizing an ontology adapted for NGS.

Conclusions:

  • The developed workflow provides a standardized approach to QC for tumor-normal DNA sequencing.
  • This standardization is essential for ensuring the validity and reliability of results from multi-sample NGS experiments.
  • The use of qcML and an adapted ontology promotes interoperability and consistency in QC reporting.