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Shukla N, Levine MF, Gundem G, Domenico D, Spitzer B, Bouvier N, Arango-Ossa JE, Glodzik D, Medina-Martínez JS, Bhanot U, Gutiérrez-Abril J, Zhou Y, Fiala E, Stockfisch E, Li S, Rodriguez-Sanchez MI, O'Donohue T, Cobbs C, Roehrl MHA, Benhamida J, Iglesias Cardenas F, Ortiz M, Kinnaman M, Roberts S, Ladanyi M, Modak S, Farouk-Sait S, Slotkin E, Karajannis MA, Dela Cruz F, Glade Bender J, Zehir A, Viale A, Walsh MF, Kung AL, Papaemmanuil E. Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers. Nat Commun 2022; 13:2485. [PMID: 35585047 PMCID: PMC9117241 DOI: 10.1038/s41467-022-30233-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/21/2022] [Indexed: 02/07/2023] Open
Abstract
The utility of cancer whole genome and transcriptome sequencing (cWGTS) in oncology is increasingly recognized. However, implementation of cWGTS is challenged by the need to deliver results within clinically relevant timeframes, concerns about assay sensitivity, reporting and prioritization of findings. In a prospective research study we develop a workflow that reports comprehensive cWGTS results in 9 days. Comparison of cWGTS to diagnostic panel assays demonstrates the potential of cWGTS to capture all clinically reported mutations with comparable sensitivity in a single workflow. Benchmarking identifies a minimum of 80× as optimal depth for clinical WGS sequencing. Integration of germline, somatic DNA and RNA-seq data enable data-driven variant prioritization and reporting, with oncogenic findings reported in 54% more patients than standard of care. These results establish key technical considerations for the implementation of cWGTS as an integrated test in clinical oncology. Cancer whole-genome and transcriptome sequencing (cWGTS) has been challenging to implement in clinical settings. Here, the authors develop a workflow to deliver robust cWGTS analyses and reports within clinically-relevant timeframes for paediatric, adolescent and young adult solid tumour patients.
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Affiliation(s)
- N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M F Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - G Gundem
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D Domenico
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - B Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J E Arango-Ossa
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D Glodzik
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J S Medina-Martínez
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - U Bhanot
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Gutiérrez-Abril
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Y Zhou
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Fiala
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Stockfisch
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Li
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - T O'Donohue
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - C Cobbs
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M H A Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - F Iglesias Cardenas
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Kinnaman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Farouk-Sait
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M A Karajannis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - F Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Glade Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Viale
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M F Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - E Papaemmanuil
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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