TumorNext: A comprehensive tumor profiling assay that incorporates high resolution copy number analysis and germline status to improve testing accuracy.
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.
Ambry Genetics, Aliso Viejo, CA, 92656, USA.
Phillip N
PN
Gray
Ambry Genetics, Aliso Viejo, CA, 92656, USA.
Huy
H
Vuong
Ambry Genetics, Aliso Viejo, CA, 92656, USA.
Pei
P
Tsai
Ambry Genetics, Aliso Viejo, CA, 92656, USA.
Hsaio-Mei
HM
Lu
Ambry Genetics, Aliso Viejo, CA, 92656, USA.
Wenbo
W
Mu
Ambry Genetics, Aliso Viejo, CA, 92656, USA.
Vickie
V
Hsuan
Ambry Genetics, Aliso Viejo, CA, 92656, USA.
Jayne
J
Hoo
Ambry Genetics, Aliso Viejo, CA, 92656, USA.
Swati
S
Shah
Ambry Genetics, Aliso Viejo, CA, 92656, USA.
Lisa
L
Uyeda
Ambry Genetics, Aliso Viejo, CA, 92656, USA.
Susanne
S
Fox
Ambry Genetics, Aliso Viejo, CA, 92656, USA.
Harshil
H
Patel
Arizona Oncology, Scottsdale, AZ, 85258, USA.
Mike
M
Janicek
St. Joseph Health, Orange, CA, 92868, USA.
Sandra
S
Brown
St. Joseph Health, Orange, CA, 92868, USA.
Lavinia
L
Dobrea
St. Joseph Health, Orange, CA, 92868, USA.
Lawrence
L
Wagman
Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
Elizabeth
E
Plimack
Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
Ranee
R
Mehra
Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
Erica A
EA
Golemis
Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
Marijo
M
Bilusic
Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
Matthew
M
Zibelman
Ambry Genetics, Aliso Viejo, CA, 92656, USA.
Aaron
A
Elliott
D019295:Computational Biology / Q000379:methods*; D056915:DNA Copy Number Variations; D004252:DNA Mutational Analysis / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology; D016612:Paraffin Embedding; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D016707:Tissue Fixation
actionable mutations; copy number variants; germline mutations; next generation sequencing; tumor profiling