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Related Concept Videos

Genetic Screens02:46

Genetic Screens

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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
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Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors
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Tumor mutation burden derived from small next generation sequencing targeted gene panel as an initial screening

Yuan Tang1, Yuli Li1, Weiya Wang1

  • 1Department of Pathology, West China Hospital, Chengdu 610041, China.

Translational Lung Cancer Research
|March 25, 2020
PubMed
Summary

A small 56-gene panel can effectively screen for low tumor mutation burden (TMB) in non-small cell lung cancer patients. This cost-effective approach identifies patients unlikely to benefit from immune checkpoint inhibitors, guiding further testing.

Keywords:
Non-small cell lung cancer (NSCLC)TMB in NSCLCsmall gene paneltumor mutation burden (TMB)

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Area of Science:

  • Oncology
  • Genomics
  • Biomarker Discovery

Background:

  • Immune checkpoint inhibitors (ICIs) are increasingly used in cancer therapy.
  • Tumor mutation burden (TMB) assessment is crucial for predicting ICI response.
  • Large gene panels for TMB assessment are not always necessary for all patients.

Purpose of the Study:

  • To evaluate the feasibility of a small 56-gene panel for predicting TMB.
  • To establish a reliable TMB screening method using a cost-effective approach.

Main Methods:

  • TMB was estimated for 406 non-small cell lung cancer (NSCLC) patients using a large 520-gene panel, simulating results from a small 56-gene panel.
  • An optimal cut-off value for TMB prediction was determined.
  • An independent cohort of 30 NSCLC patients was sequenced using both panels to validate the cut-off.

Main Results:

  • A cut-off of 10 mutations/megabase demonstrated 81.4% specificity and 83.6% sensitivity in the initial cohort.
  • Validation in an independent cohort showed 95.7% sensitivity and 71.4% specificity.
  • The small panel reliably stratified patients into low (<10) and high (≥10) TMB groups, with a low likelihood of false positives.

Conclusions:

  • A small 56-gene panel serves as a cost-effective screening tool for identifying patients with low TMB.
  • Patients identified with TMB ≥10 by the small panel require further validation with larger gene panels.
  • This approach optimizes TMB assessment, potentially reducing healthcare costs.