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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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Analysis of somatic microsatellite indels identifies driver events in human tumors

Yosef E Maruvka1,2, Kent W Mouw3,4, Rosa Karlic5

  • 1Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts, USA.

Nature Biotechnology
|September 12, 2017
PubMed

Insights

New tools accurately detect microsatellite (MS) indel mutations in cancer, revealing over 1,000 new mutations in cancer genes. These findings aid in distinguishing tumor types and identifying novel cancer drivers.

Area of Science:

  • Genomics and Cancer Research
  • Bioinformatics and Computational Biology

Background:

  • Microsatellites (MSs) are repetitive DNA sequences prone to insertions/deletions (indels).
  • Somatic MS indels' role in cancer is understudied due to detection challenges in short-read sequencing data.

Purpose of the Study:

  • To develop accurate tools for detecting somatic MS indels in cancer.
  • To identify genes with significantly frequent MS indels.
  • To explore the utility of MS indels in tumor classification and driver identification.

Main Methods:

  • Development of MSMuTect for somatic MS indel detection.
  • Development of MSMutSig for identifying cancer genes with frequent MS indels.
  • Application of MSMuTect to whole-exome sequencing data from 6,747 human tumors across 20 types.

Main Results:

  • Identification of over 1,000 previously undescribed MS indels in cancer genes.
  • Demonstration that MS indel patterns can distinguish microsatellite-stable from microsatellite-unstable tumors.
  • Discovery of seven MS indel driver hotspots, including novel cancer drivers (ESRP1, PRDM2, DOCK3).

Conclusions:

  • The developed tools enable accurate detection and analysis of somatic MS indels in cancer.
  • MS indel analysis can improve tumor classification and identify novel cancer drivers.
  • Somatic MS indels represent a significant, previously underappreciated factor in cancer development.

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