The Oncomine™ Comprehensive DNA Assay
This is a targeted, multi-biomarker assay that enables simultaneous detection of thousands of variants across 148 genes relevant to solid tumours using DNA sequencing. The Oncomine™ Comprehensive RNA Assay (OCP22) uses RNA sequencing to detect gene fusions in 22 genes.
The panel has been designed for translational and clinical research and diagnostic testing and this assay includes solid tumour genes targeted by on-market oncology drugs and published evidence. The relevant solid tumour somatic genome variants (gain-of-function or loss-of-function mutations, highlevel copy number alterations, and gene fusions) were identified through comprehensive bioinformatics analysis of >700,000 samples . The OCP148 and OCP22 have been validated using molecular standards and more than 300 FFPE tumour samples. 6% to 42% of profiled samples (depending on cancer type) harboured alterations beyond routine molecular testing that were associated with approved or guideline-referenced therapies . The assay enables the identification of DNA mutations and RNA gene fusions in a single workflow.
The panel includes copy number analysis for the CD274 and PDCD1LG2 genes which encode the PDL1 and PDL2 proteins, respectively.
Programmed cell death-1 (PD-1) and the programmed death ligands (PDLs), PDL1 and PDL2, form a signalling network that limits T-cell immunity during chronic viral infection and during pregnancy . A subset of malignant tumours co-opts the PD-1 signalling axis to evade immune surveillance . Targeting PD-1 signalling with inhibitory antibodies can relieve the block in antitumour immunity and achieve durable clinical responses in a subset of patients with solid tumours .
Amplification of chromosome 9p24 occurs in a number of tumour types with co-amplification of CD274 and PDCD1LG2. In small cell lung cancer, amplification of CD274 can occur with co-amplification of the neighbouring gene PDCD1LG2, encoding another PD-1 ligand, PDL2, however, this did not lead to strong upregulation of the corresponding PDL2 transcript levels as observed for CD274 . Therefore, PDL1, rather than PDL2, seems to play a major role in suppressing immune responses in 9p24 amplified small cell lung cancer tumours .
In triple-negative breast cancer, samples with PD-L1 strong expression are associated with a CD274 gene copy number gain .
Tumour CD274 copy number status is more consistent and reproducible than tumour PDL1 protein expression detected by immunohistochemistry when primary tumours and synchronous regional lymph node metastases have been comparatively analysed [5, 6].
CD274 copy number alterations correlate significantly with PDL1 mRNA expression changes in many cancer types, and tumours with CD274 gains harbour a significantly higher mutational load compared to nonamplified cases (median: 78 non-synonymous mutations vs. 40) . In general, both CD274 amplifications and deletions are associated with a dismal prognosis .