Copy number variants in clinical next-generation sequencing data can define the relationship between simultaneous tumors in an individual patient

Targeted next-generation sequencing (NGS) cancer panels have become a popular method for the identification of clinically predictive mutations in cancer. Such methods typically detect single nucleotide variants (SNVs) and small insertions/deletions (indels) in known cancer genes and can provide furt...

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Bibliographic Details
Published in:Experimental and molecular pathology 2014-08, Vol.97 (1), p.69-73
Main Authors: Sehn, Jennifer K., Abel, Haley J., Duncavage, Eric J.
Format: Article
Language:English
Subjects:
Biopsy, Large-Core Needle
Cancer
Carcinoma, Neuroendocrine - genetics
Carcinoma, Neuroendocrine - pathology
Copy number change
Deep sequencing
Gene Dosage
High-Throughput Nucleotide Sequencing - methods
Humans
Liver Neoplasms - genetics
Liver Neoplasms - pathology
Metastasis
Molecular diagnostics
Neoplasms, Multiple Primary - genetics
Precision Medicine
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Summary:Targeted next-generation sequencing (NGS) cancer panels have become a popular method for the identification of clinically predictive mutations in cancer. Such methods typically detect single nucleotide variants (SNVs) and small insertions/deletions (indels) in known cancer genes and can provide further information regarding diagnosis in challenging surgical pathology cases, as well as identify therapeutic targets and prognostically significant mutations. However, in addition to SNVs and indels, other mutation classes, including copy number variants (CNVs) and translocations, can be simultaneously detected from targeted NGS data. Here, as proof of methods, we present clinical data which demonstrate that targeted NGS panels can separate synchronous liver tumors based on CNV status, in the absence of distinct SNVs and indels. Such CNV-based analysis can be performed without additional cost using existing targeted cancer panel data and publically available software. •Clinical NGS of cancer specimens can be used to identify somatic mutations.•Identified somatic mutations provide clinically relevant information.•Mutation profiles can differentiate multiple primary tumors from metastases.•Copy number variants can be the only mutations that distinguish two tumors.•Copy number analysis should be included in clinical NGS assays.
ISSN:0014-4800
1096-0945
DOI:10.1016/j.yexmp.2014.05.008