Analytical validation and implementation of a pan cancer next-generation sequencing panel, CANSeqTMKids for molecular profiling of childhood malignancies. Front Genet 2023;14:1067457
Date
02/28/2023Pubmed ID
36845394Pubmed Central ID
PMC9947346DOI
10.3389/fgene.2023.1067457Scopus ID
2-s2.0-85148574125 (requires institutional sign-in at Scopus site) 2 CitationsAbstract
Next-Generation Sequencing (NGS) allows rapid analysis of multiple genes for the detection of clinically actionable variants. This study reports the analytical validation of a targeted pan cancer NGS panel CANSeqTMKids for molecular profiling of childhood malignancies. Analytical validation included DNA and RNA extracted from de-identified clinical specimens including formalin fixed paraffin embedded (FFPE) tissue, bone marrow and whole blood as well as commercially available reference materials. The DNA component of the panel evaluates 130 genes for the detection of single nucleotide variants (SNVs), Insertion and Deletions (INDELs), and 91 genes for fusion variants associated with childhood malignancies. Conditions were optimized to use as low as 20% neoplastic content with 5 ng of nucleic acid input. Evaluation of the data determined greater than 99% accuracy, sensitivity, repeatability, and reproducibility. The limit of detection was established to be 5% allele fraction for SNVs and INDELs, 5 copies for gene amplifications and 1,100 reads for gene fusions. Assay efficiency was improved by automation of library preparation. In conclusion, the CANSeqTMKids allows for the comprehensive molecular profiling of childhood malignancies from different specimen sources with high quality and fast turnaround time.
Author List
Schilter KF, Smith BA, Nie Q, Stoll K, Felix JC, Jarzembowski JA, Reddi HVAuthors
Juan Felix MD Vice Chair, Director, Professor in the Pathology department at Medical College of WisconsinJason A. Jarzembowski MD, PhD Sr Associate Dean, CEO CSG, Professor in the Pathology department at Medical College of Wisconsin
Kala Schilter in the CTSI department at Medical College of Wisconsin - CTSI
