P2.02-052 A Clinically-Validated Universal Companion Diagnostic Platform for Cancer Patient Care


      The increase in targeted therapies and associated companion diagnostics (CDx) has led to the need for efficient determination of therapeutic eligibility from a single assay. Comprehensive genomic profiling (CGP) provides a solution, but due to the complexity and number of assays available today, standardization of validation has become critically important. We present here the first NGS-based universal CDx platform developed and performed in compliance with FDA 21 CFR part 820. The assay interrogates 324 genes, and is anticipated initially to have eight CDx indications (Table 1). The versatile assay design will facilitate streamlined development of future CDx indications.


      DNA extracted from FFPE tumor tissue underwent whole-genome shotgun library construction and hybridization-based capture, followed by sequencing using Illumina HiSeq 4000. Sequence data were processed using a proprietary analysis pipeline designed to detect base substitutions, indels, copy number alterations, genomic rearrangements, microsatellite instability (MSI), and tumor mutational burden (TMB).


      Concordance with FDA-approved CDx are shown in Table 1. Clinical validity was established such that the concordance between CGP and approved CDx were statistically non-inferior to that of two runs of approved CDx. For analytical validity, limit of detection (LoD) was at allele frequency 4% for known substitutions and indels. LoD was 16% tumor content for copy number amplifications, 30% for homozygous deletions, 11% for genomic rearrangements, 12% for MSI, and estimated 20% for TMB. Positive percent agreement (PPA) with an orthogonal NGS platform was 95.8% in substitutions and indels. PPA with FoundationOne was 98.3% across all variant types. Within-assay reproducibility was measured with PPA 99.4%.


      Rapid expansion of targeted therapies and CDx has necessitated a new approach and urgency to defining performance standards. We developed a universal CDx assay and established a robust approach for demonstrating clinical and analytical validity to support and accelerate the use of CGP for routine clinical care.


      Tabled 1
      Companion diagnosticIndicated usePPAComparator CDx assay
      EGFR exon 19 deletions and L858Rerlotinib, afatinib or gefitinib in NSCLC98.1% (106/108)cobas® EGFR Mutation Test v2
      EGFR T790Mosimertinib in NSCLC98.9% (87/88)cobas® EGFR Mutation Test v2
      ALK rearrangementscrizotinib in NSCLC92.9% (78/84)Ventana ALK (D5F3) CDx Assay Vysis ALK Break-Apart FISH
      KRAScetuximab or panitumumab in CRC100% (173/173)therascreen® KRAS PCR
      ERBB2 (HER2) Amplificationstrastuzumab, pertuzumab and ado-trastuzumab-emtansine in breast and gastric cancer89.4% (101/113)Dako HER2 FISH PharmDx®
      BRAF V600E/Kvemurafenib, dabrafenib, trametinib in melanoma99.4% (166/167)cobas® BRAF V600 PCR
      BRCA1/2rucaparib in ovarian cancerN/AN/A: Novel CDx that was previously validated in PMA P160018