TumorNext: A comprehensive tumor profiling assay that incorporates high resolution copy number analysis and germline status to improve testing accuracy
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Phillip N. Gray1, Huy Vuong1, Pei Tsai1, Hsaio-Mei Lu1, Wenbo Mu1, Vickie Hsuan1, Jayne Hoo1, Swati Shah1, Lisa Uyeda1, Susanne Fox1, Harshil Patel1, Mike Janicek2, Sandra Brown3, Lavinia Dobrea3, Lawrence Wagman3, Elizabeth Plimack4, Ranee Mehra4, Erica A. Golemis4, Marijo Bilusic4, Matthew Zibelman4, Aaron Elliott1
1Ambry Genetics, Aliso Viejo, CA, 92656, USA
2Arizona Oncology, Scottsdale, AZ, 85258, USA
3St. Joseph Health, Orange, CA, 92868, USA
4Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
Phillip N. Gray, email: [email protected]
Keywords: tumor profiling, actionable mutations, next generation sequencing, copy number variants, germline mutations
Received: June 16, 2016 Accepted: August 26, 2016 Published: September 08, 2016
The development of targeted therapies for both germline and somatic DNA mutations has increased the need for molecular profiling assays to determine the mutational status of specific genes. Moreover, the potential of off-label prescription of targeted therapies favors classifying tumors based on DNA alterations rather than traditional tissue pathology. Here we describe the analytical validation of a custom probe-based NGS tumor panel, TumorNext, which can detect single nucleotide variants, small insertions and deletions in 142 genes that are frequently mutated in somatic and/or germline cancers. TumorNext also detects gene fusions and structural variants, such as tandem duplications and inversions, in 15 frequently disrupted oncogenes and tumor suppressors. The assay uses a matched control and custom bioinformatics pipeline to differentiate between somatic and germline mutations, allowing precise variant classification. We tested 170 previously characterized samples, of which > 95% were formalin-fixed paraffin embedded tissue from 8 different cancer types, and highlight examples where lack of germline status may have led to the inappropriate prescription of therapy. We also describe the validation of the Affymetrix OncoScan platform, an array technology for high resolution copy number variant detection for use in parallel with the NGS panel that can detect single copy amplifications and hemizygous deletions. We analyzed 80 previously characterized formalin-fixed paraffin-embedded specimens and provide examples of hemizygous deletion detection in samples with known pathogenic germline mutations. Thus, the TumorNext combined approach of NGS and OncoScan potentially allows for the identification of the “second hit” in hereditary cancer patients.
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