Oncomine™ comprehensive assay (TMO comprehensive assay, Thermo Fisher Scientific, Waltham, MA) was used to profile thousands of variants across 161 cancer-relevant genes using FFPE tissues (17 (link)). Analyses of TMO comprehensive assay included identification of genes and detection of mutation types such as frameshift, missense, synonymous, single nucleotide variation (SNV), insertion/deletion (Indel), and copy number variation (CNV) observed in individual subject.
Amplicon libraries were constructed with multiplex polymerase chain reaction (PCR) primers for preparation of DNA and RNA (for fusion genes) from FFPE samples. Sequencing was performed with the Ion Gene Studio S5 System and Ion 540 Chips. Raw data process, alignment, and variant calling were performed with Torrent Suite™ Software, with variant calling using the Torrent Variant Caller plug-in. Further management was proceeded by Ion Reporter™ Software with workflow “Oncomine Comprehensive v3 - w3.2 - DNA and Fusions - Single Sample” version 5.10 selected and filter chain “Oncomine Variants” version 5.10 applied. Reference genome was hg19.
Amplicon libraries were constructed with multiplex polymerase chain reaction (PCR) primers for preparation of DNA and RNA (for fusion genes) from FFPE samples. Sequencing was performed with the Ion Gene Studio S5 System and Ion 540 Chips. Raw data process, alignment, and variant calling were performed with Torrent Suite™ Software, with variant calling using the Torrent Variant Caller plug-in. Further management was proceeded by Ion Reporter™ Software with workflow “Oncomine Comprehensive v3 - w3.2 - DNA and Fusions - Single Sample” version 5.10 selected and filter chain “Oncomine Variants” version 5.10 applied. Reference genome was hg19.
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