Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors.
As our understanding of the driver mutations necessary for initiation and progression of cancers improves, we gain critical information on how specific molecular profiles of a tumor may predict responsiveness to therapeutic agents or provide knowledge about prognosis. At our institution a tumor genotyping program was established as part of routine clinical care, screening both hematologic and solid tumors for a wide spectrum of mutations using two next-generation sequencing (NGS) panels: a custom, 33 gene hematological malignancies panel for use with peripheral blood and bone marrow, and a commercially produced solid tumor panel for use with formalin-fixed paraffin-embedded tissue that targets 47 genes commonly mutated in cancer. Our workflow includes a pathologist review of the biopsy to ensure there is adequate amount of tumor for the assay followed by customized DNA extraction is performed on the specimen. Quality control of the specimen includes steps for quantity, quality and integrity and only after the extracted DNA passes these metrics an amplicon library is generated and sequenced. The resulting data is analyzed through an in-house bioinformatics pipeline and the variants are reviewed and interpreted for pathogenicity. Here we provide a snapshot of the utility of each panel using two clinical cases to provide insight into how a well-designed NGS workflow can contribute to optimizing clinical outcomes.
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania.
Alan J
AJ
Fox
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania.
Matthew C
MC
Hiemenz
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania.
David B
DB
Lieberman
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania.
Shrey
S
Sukhadia
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania.
Barnett
B
Li
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania.
Joseph
J
Grubb
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania.
Patrick
P
Candrea
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania.
Karthik
K
Ganapathy
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania.
Jianhua
J
Zhao
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania.
David
D
Roth
Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania; Abramson Cancer Center.
Evan
E
Alley
Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania; Abramson Cancer Center.
Alison
A
Loren
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania; Jennifer.Morrissette@uphs.upenn.edu.
Jennifer J D
JJ
Morrissette
D019295:Computational Biology / Q000379:methods; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*
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