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Related Experiment Video

Updated: May 16, 2026

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
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Genomics of MTAP Loss in >500,000 Solid Tumor Specimens Profiled Using Comprehensive Genomic Profiling Platforms.

Dean C Pavlick1, Shruthi Rengarajan1, Jessica K Lee2

  • 1Department of Computational Discovery, Foundation Medicine, Inc, Boston, MA.

JCO Precision Oncology
|May 14, 2026
PubMed
Summary

Methylthioadenosine phosphorylase (MTAP) loss is a common cancer alteration, indicating potential sensitivity to specific inhibitors. Further research is needed for partial MTAP loss cases to clarify clinical benefit.

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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 for the Detection of Actionable Mutations in Solid and Liquid Tumors

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Area of Science:

  • Oncology
  • Genomics
  • Biomarker Discovery

Background:

  • Methylthioadenosine phosphorylase (MTAP) genomic loss is an emerging biomarker for PRMT5 and MAT2A inhibitors.
  • The MTAP gene is located on chromosome 9p21.3 near CDKN2A/B.

Purpose of the Study:

  • Assess MTAP homozygous loss across tumor types, specific exons lost, MTAP expression, and associated co-alterations.
  • Evaluate MTAP loss as a predictive biomarker for targeted therapies.

Main Methods:

  • Sequenced 409,755 tissue biopsies and 85,801 liquid biopsies using hybrid capture-based NGS.
  • Analyzed genomic alterations, ctDNA tumor fraction, and MTAP gene expression via RNA and DNA sequencing.

Main Results:

  • Pan-tumor MTAP loss prevalence was 11.4%, highest in mesothelioma (32.8%), glioma (32.7%), pancreatic (28.9%), and bladder cancers (26.4%).
  • Liquid biopsy detection approximated tissue biopsy results with ctDNA TF ≥20%.
  • CDKN2A loss was not a reliable proxy for MTAP loss; 33.7% of CDKN2A loss cases lacked MTAP loss.

Conclusions:

  • MTAP loss is a frequent pan-tumor alteration predicting potential sensitivity to PRMT5 or MAT2A inhibitors.
  • Complete MTAP loss was observed in 82.9%, while 16.5% had partial loss with uncertain clinical benefit.
  • The identified co-alteration landscape can inform future clinical trials for MTAP-targeted therapies.