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.

Selvam P1, Hsiao MC1, Omerza G1, Bergeron D1, Rowe S1, Uvalic J1, Soucy M1, Peracchio M1, Burns S1, Meyers B1, Prego M1, Nie Q1, Ananda G1, Chandok H1, Kelly K1, Hesse A1, Reddi HV2.

Author information

1: , 10 Discovery Drive, Farmington, CT, 06032, USA.
2: , 10 Discovery Drive, Farmington, CT, 06032, USA. honey.reddi@jax.org.

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.