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Study Description
Comprehensive Whole Genome Sequencing and Whole Transcriptome (RNASeq) analyses from 114 pediatric patients at Memorial Sloan Kettering. This dataset was used as a prospective clinical utility and feasibility study. By using our Isabl infrastructure for precision medicine, we developed a 2-week end-to-end pipeline to analyze cfDNA, WGS and WTS, which we refer to as cWGTS.
Authorized Access
Publicly Available Data (Public ftp)
Study Inclusion/Exclusion Criteria

Pediatric patients diagnosed with solid/CNS tumors, as well as adults under the age of 40, with pediatric-type solid/CNS tumors were eligible to enroll. Patients were eligible to enroll at any point during their disease course (i.e., newly diagnosed, on therapy, or relapsed disease). All participating patients enrolled in to an institutional prospective tumor/germline sequencing protocol (ClinicalTrials.gov NCT01775072) with informed consent. Patients were required to have adequate tissue for both targeted NGS sequencing and whole genome sequencing, with at least 20% tumor purity for inclusion onto the study.


Selected publications
Diseases/Traits Related to Study (MeSH terms)
Links to Related Resources
Authorized Data Access Requests
Study Attribution
  • First Author Investigator
    • Neerav Shukla. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Max Levine. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Gunes Gundem. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
  • Co-Investigators
    • Dylan Domenico. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Barbara Spitzer. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Nancy Bouvier. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Juan E. Arango Ossa. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Dominik Glodzik. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Juan Medina-Martinez. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Jesus Gutierrez-Abril. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Umeshkumar Bhanot. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Yangyu Zhou. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Elise Fiala. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Emily Stockfisch. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Maria Irene Rodriguez-Sanchez. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Tara O'Donohue. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Ahmet Zehir. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Agnes Viale. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Cassidy Cobbs. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • MH Roerhl. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Jamal Benhamida. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Fiorella Iglesias Cardenas. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Michael Ortiz. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Michael Kinnaman. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Stephen Roberts. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Marc Ladanyi. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Sameer Farouk-Sait. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Shakeel Modak. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Filemon S. Dela Cruz. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Emily K Slotkin. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Matthias A. Karajannis. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Julia Lynne Glade Bender. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Michael Francis Walsh. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
  • Principal Investigators
    • Elli Papaemmanuil. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
    • Andrew Kung. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
  • Funding Source
    • The Scarlett Fund. Olayan Fund for Precision Pediatric Cancer Medicine.. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
  • Sequencing Center
    • Integrated Genomics Operation. Memorial Sloan Kettering Cancer Center, New York, NY, USA.
  • Project Coordinator
    • Pediatrics Translation Medicine Program at MSK Kids. Memorial Sloan Kettering Cancer Center, New York, NY, USA.