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Mutation Yield of a Custom 212-Gene Next-Generation Sequencing Panel for Solid Tumors: Clinical Experience of the First 260 Cases Tested Using the JAX ActionSeq™ Assay

  • Pavalan Selvam
  • Meng-Chang Hsiao
  • Gregory Omerza
  • Daniel Bergeron
  • Shannon Rowe
  • Jasmina Uvalic
  • Melissa Soucy
  • Michael Peracchio
  • Shelbi Burns
  • Bridgette Meyers
  • Matthew Prego
  • Qian Nie
  • Guruprasad Ananda
  • Harshpreet Chandok
  • Kevin Kelly
  • Andrew Hesse
  • Honey V. ReddiEmail author
Original Research Article

Abstract

Objective

The study aimed to retrospectively evaluate the positive yield rate of a custom 212-gene next-generation sequencing (NGS) panel, the JAX ActionSeq™ assay, used in molecular profiling of solid tumors for precision medicine.

Methods

We evaluated 261 cases tested over a 24-month period including cancers across 24 primary tissue types and report on the mutation yield in these cases.

Results

Thirty-three of the 261 cases (13%) had no detectable clinically significant variants. In the remaining 228 cases (87%), we identified 550 clinically significant variants in 88 of the 212 genes, with four of fewer clinically significant variants being detected in 62 of 88 genes (70%). TP53 had the highest number of variants (125), followed by APC (47), KRAS (47), ARID1A (20), PIK3CA (20) and EGFR (18). There were 38 tier I and 512 tier II variants, with two genes having only a tier I variant, seven genes having both a tier I and tier II variant, and 79 genes having at least one tier II variant. Overall, the ActionSeq™ assay detected clinically significant variants in 42% of the genes included in the panel (88/212), 68% of which (60/88) were detected in more than one tumor type.

Conclusions

This study demonstrates that of the genes with documented involvement in cancer, only a limited number are currently clinically significant from a therapeutic, diagnostic and/or prognostic perspective.

Notes

Compliance with Ethical Standards

Funding

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Conflict of Interest

The authors, Pavalan Selvam, Meng-Chang Hsiao, Gregory Omerza, Daniel Bergeron, Shannon Rowe, Jasmina Uvalic, Melissa Soucy, Michael Peracchio, Shelbi Burns, Bridgette Meyers, Matthew Prego, Qian Nie, Guruprasad Ananda, Harshpreet Chandok, Kevin Kelly, Andrew Hesse, and Honey V. Reddi, declare no relevant conflicts of interest.

Ethical Approval and Informed Consent

Review by institutional review committee was deemed not necessary because only data collected during regular patient testing were used.

Supplementary material

40291_2019_435_MOESM1_ESM.pdf (432 kb)
Supplementary material 1 (PDF 431 kb)

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Pavalan Selvam
    • 1
  • Meng-Chang Hsiao
    • 1
  • Gregory Omerza
    • 1
  • Daniel Bergeron
    • 1
  • Shannon Rowe
    • 1
  • Jasmina Uvalic
    • 1
  • Melissa Soucy
    • 1
  • Michael Peracchio
    • 1
  • Shelbi Burns
    • 1
  • Bridgette Meyers
    • 1
  • Matthew Prego
    • 1
  • Qian Nie
    • 1
  • Guruprasad Ananda
    • 1
  • Harshpreet Chandok
    • 1
  • Kevin Kelly
    • 1
  • Andrew Hesse
    • 1
  • Honey V. Reddi
    • 1
    Email author
  1. 1.FarmingtonUSA

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