Clinical Application of a Cancer Genomic Profiling Assay to Guide Precision Medicine Decisions

Abstract

Aim:Develop and apply a comprehensive and accurate next-generation sequencing based assay to help clinicians to match oncology patients to therapies.Materials & methods:The performance of the CANCERPLEX® assay was assessed using DNA from well-characterized routine clinical formalin-fixed paraffin-embedded (FFPE) specimens and cell lines.Results:The maximum sensitivity of the assay is 99.5% and its accuracy is virtually 100% for detecting somatic alterations with an allele fraction of as low as 10%. Clinically actionable variants were identified in 93% of patients (930 of 1000) who underwent testing.Conclusion:The test's capacity to determine all of the critical genetic changes, tumor mutation burden, microsatellite instability status and viral associations has important ramifications on clinical decision support strategies, including identification of patients who are likely to benefit from immune checkpoint blockage therapies.

XCL1 expression correlates with CD8-positive T cells infiltration and PD-L1 expression in squamous cell carcinoma arising from mature cystic teratoma of the ovary

“…To increase the number of samples, we tried to sequence six formalin-fixed paraffin-embedded (FFPE) MCT-SCC samples using a gene panel containing 435 cancerassociated genes (CANCERPLEX®) [23]. After a quality control check, we analyzed target-gene panel data in three samples.…”

Dual MAPK Inhibition Is an Effective Therapeutic Strategy for a Subset of Class II BRAF Mutant Melanomas

“…A next-generation sequencing-based test was performed by the CANCERPLEX assay (18). The CANCERPLEX data analysis pipeline was applied to report single-nucleotide variants, insertions, deletions, structural variants, and copy-number variations.…”

Next generation sequencing‐based gene panel tests for the management of solid tumors

“…The mutation burden can be defined as the rate of peptide‐changing single‐nucleotide variants per million base pairs . To estimate the mutation burden, single‐nucleotide variants with a mutation allelic fraction of at least 0.1 after standard filtering were retained .…”

“…The mutation burden can be defined as the rate of peptide‐changing single‐nucleotide variants per million base pairs . To estimate the mutation burden, single‐nucleotide variants with a mutation allelic fraction of at least 0.1 after standard filtering were retained . We have previously reported that a panel test with 400 genes (roughly 1/2000th of the genome) is comparable to WES in generating mutation rates and to distinguish hypermutated and nonhypermutated tumors, although the average mutation rate detected by the panel test was higher than that detected by WES, reflecting the fact that the panel content includes genes that are more frequently mutated in cancer.…”

“…The mutation burden can be defined as the rate of peptidechanging single-nucleotide variants per million base pairs. 56 To estimate the mutation burden, single-nucleotide variants with a mutation allelic fraction of at least 0.1 after standard filtering were retained. 56 We have previously reported that a panel test with 400 genes (roughly Detection of MSI is now considered important for the estimation of hypermutation, especially in colorectal and gastric cancer.…”