Up to 12 ng/μl DNA was plated at 6.6 μl per well (maximum of 79.2 ng DNA per well) into MicroAmp Optical 96-well reaction plates (Life Technologies), which were either used immediately or frozen at −20 °C until needed.
The OncoScan assay utilises molecular inversion probe (MIP) technology,20 (link) for the identification of CN alterations, loss of heterozygosity (LOH) and recurrent clinically actionable somatic mutations (SMs). MIP probes in this assay enable the capture of the alleles of over 220 000 SNPs distributed across the whole genome, with increased probe density within ~900 cancer genes. They also enable detection of 74 frequently tested somatic mutations in BRAF, KRAS, EGFR, IDH1, IDH2, PTEN, PIK3CA, NRAS and TP53. The assay was undertaken following the recommended OncoScan protocol as previously described.21 (link)OSCHP files were generated by the OncoScan Console software (Affymetrix), using data from fluorescence intensity (CEL) files generated during scanning of OncoScan chips. OSCHP files were used as inputs for the SM Viewer Software v1.01.16304 (Affymetrix) for the detection of SMs in each sample and Nexus Express for OncoScan 3.0.1 (BioDiscovery, Hawthorne CA, USA) for the analysis of CN aberrations and LOH.
The OncoScan assay utilises molecular inversion probe (MIP) technology,20 (link) for the identification of CN alterations, loss of heterozygosity (LOH) and recurrent clinically actionable somatic mutations (SMs). MIP probes in this assay enable the capture of the alleles of over 220 000 SNPs distributed across the whole genome, with increased probe density within ~900 cancer genes. They also enable detection of 74 frequently tested somatic mutations in BRAF, KRAS, EGFR, IDH1, IDH2, PTEN, PIK3CA, NRAS and TP53. The assay was undertaken following the recommended OncoScan protocol as previously described.21 (link)OSCHP files were generated by the OncoScan Console software (Affymetrix), using data from fluorescence intensity (CEL) files generated during scanning of OncoScan chips. OSCHP files were used as inputs for the SM Viewer Software v1.01.16304 (Affymetrix) for the detection of SMs in each sample and Nexus Express for OncoScan 3.0.1 (BioDiscovery, Hawthorne CA, USA) for the analysis of CN aberrations and LOH.
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