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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
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Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors
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Next-Generation Sequencing Somatic and Germline Assay Troubleshooting Guide Derived From Proficiency Testing Data.

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Summary

Next-generation sequencing (NGS) assays show excellent performance in detecting somatic and germline variants. Common errors involve difficult genomic regions, homopolymers, pseudogenes, and annotation issues, but remedies exist to improve accuracy.

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Area of Science:

  • Clinical Molecular Diagnostics
  • Genomics
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) is crucial for detecting somatic and constitutional variants in clinical molecular laboratories.
  • Proficiency testing (PT) data offer insights into assay performance challenges.

Purpose of the Study:

  • To identify common causes of unacceptable results in NGS-based PT surveys for hematologic malignancies, solid tumors, and germline variants.
  • To provide recommendations for improving laboratory performance in NGS variant detection.

Main Methods:

  • Analysis of College of American Pathologists (CAP) NGS PT survey data from 2016-2019.
  • Identification of recurrent errors in variant detection and annotation.

Main Results:

  • High overall accuracy (95.9% somatic, 97.8% germline) was observed.
  • Frequent causes of errors included false negatives in high GC regions, false positives in homopolymers/pseudogenes, and annotation errors (transcript selection, nomenclature).
  • Minor preanalytic/postanalytic errors involved specimen swaps and transcription mistakes.

Conclusions:

  • Laboratories exhibit strong performance in NGS variant detection.
  • Recurrent analytic and nonanalytic challenges in NGS assays are identifiable and addressable.
  • PT data are valuable for guiding improvements in NGS assay performance.