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Bayesian approach to interpreting somatic cancer sequencing data: a case in point
  1. Ju-Yoon Yoon1,
  2. Jason N Rosenbaum1,2,
  3. Norge Vergara1,
  4. Roger B Cohen3,
  5. Robert B Wilson4
  1. 1Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
  2. 2Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
  3. 3Division of Hematology Oncology, Department of Medicine, Perelman Center for Advanced Medicine, Philadelphia, Pennsylvania, USA
  4. 4Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
  1. Correspondence to Dr Robert B Wilson, Department of Pathology and Laboratory Medicine; Division of Pathology Informatics, Perelman School of Medicine at the University of Pennsylvania, 3501 Civic Center Blvd., CTRB 6024, Philadelphia, PA 19104, Pennsylvania, USA; wilsonr{at}pennmedicine.upenn.edu

Abstract

Cancer lineage/tissue-of-origin assignment in cancers of unknown primary remains a challenge even when aided by massively parallel sequencing. The stakes are high for patients as many contemporary therapeutic strategies are disease-specific, and the biological differences can influence the patients’ responses. Herein, we provide an example of how Bayesian analysis can be used to merge data from clinical history, histology, immunohistochemistry (IHC) and cancer DNA sequencing to assist in tissue-of-origin assignment. Iterative Bayesian analysis is performed through a set of simple calculations to calculate the OR between the differential diagnoses. We illustrate a clinical case, where the distinction between a primary lung versus metastatic bladder cancer was aided meaningfully by iterative Bayesian analyses, incorporating IHC and sequencing data.

  • biomarkers
  • tumour
  • diagnosis
  • genetics
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Footnotes

  • Handling editor Runjan Chetty.

  • Twitter @MoPathGuy

  • Contributors J-YY and RBW performed the Bayesian analysis. JNR analysed the sequencing data. NV analysed the cytology and immunohistochemistry data. RBC clinically managed the patient. All authors contributed to manuscript writing.

  • Funding The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.

  • Competing interests None declared.

  • Patient consent for publication Not required.

  • Provenance and peer review Not commissioned; externally peer reviewed.

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