Oncomine™ Childhood Cancer Research Assay，Chef-Ready

This panel is compatible with as little as 10 ng per pool input DNA or RNA, per library, from blood, bone marrow, fresh/frozen tissue or FFPE samples. Chef-ready RNA library preparation requires 10 ng of DNase-treated total RNA (≥0.8 ng/µL) for each sample. Chef-ready DNA library preparation requires 10 ng (≥0.67 ng/µL) of gDNA in total.

There are 4 primer pools in total, two DNA and two RNA pools across 202 genes. This assay allows concurrent analysis of DNA and RNA to simultaneously detect multiple types of variants, including hotspots, single nucleotide variants (SNVs), indels, copy number variants (CNVs), and gene fusions, in a single workflow.

The panel comprises 203 unique genes: 130 key DNA genes, 28 copy number variant targets, an expansive fusion panel of 90 driver genes with multiple partners, and 9 expression genes and controls. The panel also includes the Ion AmpliSeq Sample ID Panel primers to prevent research sample misidentification and provide gender assignment of the research sample. Please see this flyer: https://assets.thermofisher.com/TFS-Assets/CSD/Flyers/oncomine-childhood-cancer-assay-flyer.pdf

The recommended controls are:
-Acrometrix Oncology Hotspot Control, Cat. No. 969056 (https://www.thermofisher.com/order/catalog/product/969056)
-Seraseq FFPE Tumor Fusion RNA Reference Material v2, Cat. No. 0710-0129 (https://www.seracare.com/Seraseq-FFPE-Tumor-Fusion-RNA-Reference-Material-v2-0710-0129/)

We have validated 8 samples on an Ion 540 chip: 7 DNA samples plus one negative control PLUS 7 RNA samples plus one negative control per chip; RNA and DNA from the same sample; 16 barcodes on each chip (8 barcodes for DNA and 8 barcodes for RNA).