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View additional product information for Oncomine™ Childhood Cancer Research Assay, Chef-Ready - FAQs (A36486)
8 product FAQs found
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).
For automated library preparation using the Ion Chef System, we offer the Oncomine Childhood Cancer Research Assay, Chef-Ready (Cat. No. A36486).
The Oncomine Childhood Cancer Research Assay, Chef-Ready (Cat. No. A36486) consists of the DNA Oncomine Childhood Cancer Research Panel (2-pools) and RNA Oncomine Childhood Cancer Research Panel (2-pools) at 2X concentration, pre-measured in barcoded Primer Pool tubes ready to load into an Ion AmpliSeq Chef Reagents DL8 cartridge. Sufficient reagents are provided for the rapid preparation of 32 uniquely barcoded DNA-libraries and 32 uniquely barcoded RNA-libraries from 32 research samples. Equalizer and barcodes (ioncodes) are included.
The Oncomine Childhood Cancer Research Assay is a unique next-generation sequencing (NGS)-based assay designed for comprehensive genomic profiling of cancers affecting children and young adults. It consists of four pools of Ion AmpliSeq oligonucleotide primers and associated reagents to generate amplicon libraries for next-generation sequencing on the Ion GeneStudio S5 platforms. Since the driving genetic aberrations of these malignancies are different than those affecting adults, a specific and comprehensive panel is needed to advance research. The Oncomine Childhood Cancer Research Assay (Cat. No. A36485) is for manual library preparation where barcodes are not included, and the Oncomine Childhood Cancer Research Assay, Chef-Ready (Cat. No. A36486) is for automated library preparation using the Ion Chef System.