Analytic validation and clinical utilization of the comprehensive genomic profiling test, GEM ExTra®

Abstract

We developed and analytically validated a comprehensive genomic profiling (CGP) assay, GEM ExTra, for patients with advanced solid tumors that uses Next Generation Sequencing (NGS) to characterize whole exomes employing a paired tumor-normal subtraction methodology. The assay detects single nucleotide variants (SNV), indels, focal copy number alterations (CNA), TERT promoter region, as well as tumor mutation burden (TMB) and microsatellite instability (MSI) status. Additionally, the assay incorporates whole transcriptome sequencing of the tumor sample that allows for the detection of gene fusions and select special transcripts, including AR-V7, EGFR vIII, EGFRvIV, and MET exon 14 skipping events. The assay has a mean target coverage of 180X for the normal (germline) and 400X for tumor DNA including enhanced probe design to facilitate the sequencing of difficult regions. Proprietary bioinformatics, paired with comprehensive clinical curation results in reporting that defines clinically actionable, FDA-approved, and clinical trial drug options for the management of the patient’s cancer. GEM ExTra demonstrated analytic specificity (PPV) of > 99.9% and analytic sensitivity of 98.8%. Application of GEM ExTra to 1,435 patient samples revealed clinically actionable alterations in 83.9% of reports, including 31 (2.5%) where therapeutic recommendations were based on RNA fusion findings only.

The value of comprehensive genomic sequencing to maximize the identification of clinically actionable alterations in advanced cancer patients: a case series

“…This mutation is present on exon 4 and according to NCCN Guidelines for CRC, patients with any known KRAS or NRAS mutation in exon 2, 3, 4 should not be treated with EGFR targeted monoclonal antibodies (cetuximab and panitumumab) (NCCN Guidelines, 2021). Based on current evidence, the KRAS (A146T) mutation is likely an intrinsic resistance mutation and may have been detected in the original sample if exon 4 was tested [ 21 ]. Earlier identification of this KRAS (A146T) mutation could have avoided the use of cetuximab and the associated toxicity the patient endured with no anticipated benefit.…”

“…The test also detects tumor mutational burden (TMB) and microsatellite instability (MSI) to predict clinical benefit of immunotherapy [ 20 ]. The test has been validated to detect point mutations at greater than equal to 5% mutant allele frequency (MAF) (MAF greater than equal to 1% at hot spots) with an overall sensitivity of > 98%, specificity of > 99% and PPV of 100% for the detection of select single nucleotide variants (SNVs), insertion/deletion (Indels), copy number variations (CNVs), and fusions [ 21 ]. Turnaround time is within 14 calendar days from sample receipt.…”

Comprehensive Genomic Profiling of High-Risk Pediatric Cancer Patients Has a Measurable Impact on Clinical Care

“…Genomic profiling with germline subtraction was performed via the GEM ExTra assay in a College of American Pathologists-accredited, Clinical Laboratory Improvement Amendments (CLIA)–certified laboratory through Ashion Analytics and included DNA (paired tumor-germline WES) and RNA (tumor whole-transcriptome sequencing) sequencing (Data Supplement). 26 Peripheral blood (STs and BTs) or saliva (leukemias) samples were obtained for germline DNA WES. GEM ExTra reports somatic variants, copy-number alterations, and structural rearrangements including gene fusions.…”

Genomic Markers of CDK 4/6 Inhibitor Resistance in Hormone Receptor Positive Metastatic Breast Cancer

“…A total of 22 (15%) of these samples were sequenced using HopeSeq platform, including 89 "hot-spot" genes [27]. An additional 9 (6%) patient samples were sequenced using GEM ExTra ® , which covers all protein coding regions [28]. To study the associations of PFS and genomic alterations, we evaluated the hazard ratio (HR) for each gene associated with PFS using a Cox proportional hazard model.…”