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Evaluation of Commercial Next-Generation Sequencing Bioinformatics Software Solutions
1Departments of Pathology and Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico.
The Journal of Molecular Diagnostics : JMD
|November 22, 2019
Summary
Commercial next-generation sequencing (NGS) bioinformatics software can overcome clinical lab challenges. This evaluation provides a roadmap for selecting the best NGS solutions for diagnostic and therapeutic assessments.
Area of Science:
- Clinical diagnostics
- Bioinformatics
- Molecular pathology
Background:
- Next-generation sequencing (NGS) is expanding in clinical medicine for molecular biomarker assessment.
- Falling sequencing costs drive NGS adoption, but bioinformatics analysis poses challenges for clinical labs.
- Shortages of bioinformatics personnel and software scalability issues hinder clinical NGS implementation.
Purpose of the Study:
- To systematically evaluate commercial next-generation sequencing (NGS) bioinformatics solutions.
- To provide a roadmap for small- to mid-size clinical laboratories seeking to implement NGS.
- To detail key lessons learned during the vendor evaluation process.
Main Methods:
- Systematic, end-to-end evaluation of six commercial NGS bioinformatics software solutions.
- Development and application of key metrics for robust software assessment.
- Feedback collection from a molecular pathology team at TriCore Reference Laboratories.
Main Results:
- Six commercial NGS bioinformatics solutions were systematically assessed.
- Key evaluation metrics for NGS software were defined.
- Comprehensive feedback guided the final vendor selection process.
Conclusions:
- Commercial NGS bioinformatics solutions can address clinical laboratory challenges.
- A systematic evaluation process is crucial for selecting appropriate software.
- This article offers a practical roadmap for laboratories navigating NGS software options.
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