New Optimized Workflow Offers Comprehensive Characterization of Childhood Cancers

Genomic studies of childhood and rare cancers got a major boost, as a new optimized workflow for managing these data was recently reported in Nature Communications by Dr. Andrew Kung, senior study author and Chair of the Department of Pediatrics at Memorial Sloan Kettering Cancer Center. And, thanks to funding by NCI’s Childhood Cancer Data Initiative (CCDI), it’s easier and faster to share those data with the cancer research community.

Using an end-to-end pipeline for cancer whole genome and transcriptome sequencing (or cWGTS), scientists analyzed samples from 114 pediatric, adolescent, and young adult patients. The new workflow was able to capture the full spectrum of cancer-associated genomic alterations in about 9 days, which is a significant improvement over earlier turnaround times of 2–4 weeks. With costs for such testing becoming more manageable, and with this reduced timeframe for generating results, cWGTS offers a promising tool for routine clinical oncology practice for pediatric patients.

The researchers corroborated findings from DNA with evidence from RNA to detect, annotate, and prioritize variants. The integrative assay detected germline, somatic mutation, and fusion genes, which are typically captured using targeted gene-panel assays in adults. However, these tests haven’t been optimized for patients with pediatric or rare cancers, which are driven by distinct molecular features.

The raw whole genome and RNA-sequencing data are available for researchers for further analysis through NCI’s Cancer Data Service (CDS). According to Dr. Subhashini Jagu, a CCDI Data Platform Working Group member, “These data and accompanying analytical workflows have the sensitivity to capture a range of genomic alterations that will help inform the function of genes and post-transcriptional modifications and enable the development of new or more effective therapies for these rare cancers.”

Data scientists interested in accessing the data for this study can submit a request to the database of Genotypes and Phenotypes (dbGaP). The data are under controlled-access due to privacy concerns. Requests are managed by NCI’s Data Access Committee and take less than 2 days for approval, with access granted for up to 12 months. Code for reproducing the findings from this article can be found in the GitHub repository. A copy of the processed data is available at the cbioPortal study-specific site.

“The pediatric cancer community understands the importance of sharing data to empower research into these rare cancers,” said Dr. Kung. “I’m grateful to CCDI for establishing the framework for immediately sharing these large data sets and am proud to also be a part of CCDI’s efforts to transform what we learn from patients into more effective treatments for childhood and rare cancers.”

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