Diagnosis; Mutation Confirmation; Prognostic; Therapeutic management

Identifying mutations and rearrangements that may support a diagnosis for patients with tumors of the central nervous system (CNS). Identifying mutations and rearrangements that may help determine prognosis for patients with tumors of the CNS. Identifying specific mutations and rearrangements within genes known to be associated with response or resistance … Identifying mutations and rearrangements that may support a diagnosis for patients with tumors of the central nervous system (CNS).   Identifying mutations and rearrangements that may help determine prognosis for patients with tumors of the CNS.   Identifying specific mutations and rearrangements within genes known to be associated with response or resistance to specific cancer therapies. View more

Is research allowed on the sample after clinical testing is complete? Help
Research testing is only performed under IRB approved protocol with an opt-out policy in place.

Next-generation sequencing (NGS) is performed to test for the presence of a mutation in approximately 95% of exonic regions and exon/intron boundaries of 118 targeted genes. NGS is performed to test for the presence of rearrangements in 81 genes, including 104 known gene fusions and 29 known abnormal gene transcript … Next-generation sequencing (NGS) is performed to test for the presence of a mutation in approximately 95% of exonic regions and exon/intron boundaries of 118 targeted genes. NGS is performed to test for the presence of rearrangements in 81 genes, including 104 known gene fusions and 29 known abnormal gene transcript variants. See Targeted DNA Gene Regions Interrogated by Neuro-Oncology Panel and RNA Targeted Gene Fusions and Abnormal Transcript Variants in Special Instructions for details regarding the targeted gene regions identified by this test.(Unpublished Mayo method) View more

Tests performed
Entire test performed in-house

The analytical sensitivity of this assay for sequence reportable alterations is 15% mutant allele frequency with a minimum coverage of 100x in a sample with 30% or greater tumor purity, and for rearrangements is a minimum coverage of 10 targeted fusion reads with 5 unique fusion molecules in a sample … The analytical sensitivity of this assay for sequence reportable alterations is 15% mutant allele frequency with a minimum coverage of 100x in a sample with 30% or greater tumor purity, and for rearrangements is a minimum coverage of 10 targeted fusion reads with 5 unique fusion molecules in a sample with 10% or greater tumor purity. Detection of somatic mutations (DNA): The DNA mutation portion of the assay has been shown to detect more than 97% of single base substitutions, insertions, and deletions within the reportable range of this assay. Detection of fusion transcripts (RNA): The RNA fusion portion of the test exhibited 94.2% sensitivity (49/52) in detecting fusion transcripts (confirmed detection by reverse transcriptase polymerase chain reaction or chromosomal microarray). No fusion transcripts were detected in 25 unique samples (100% specificity compared to chromosomal microarray) resulting in an overall concordance of 96.1%.This test does not detect large single or multiexon deletions or duplications or genomic copy number alterations. Rare polymorphisms may be present that could lead to false-negative or false-positive results. Test results should be interpreted in the context of clinical findings, tumor sampling, and other laboratory data. View more

This test is not designed to differentiate between somatic and germline alterations. Additional testing may be necessary to clarify the significance of results if there is a potential hereditary risk. DNA variants of uncertain significance may be identified. A negative (wild-type) result does not rule out the presence of a … This test is not designed to differentiate between somatic and germline alterations. Additional testing may be necessary to clarify the significance of results if there is a potential hereditary risk.   DNA variants of uncertain significance may be identified.   A negative (wild-type) result does not rule out the presence of a mutation or rearrangement that may be present but below the limits of detection of this assay. The analytical sensitivity of this assay for sequence reportable alterations is 15% mutant allele frequency with a minimum coverage of 100 times in a sample with 30% or greater tumor content, and for rearrangements is a minimum coverage of 10 targeted fusion reads with 5 unique fusion molecules in a sample with 10% or greater tumor content.    This test does not detect large single or multiexon deletions or duplications or genomic copy number alterations   Rare polymorphisms may be present that could lead to false-negative or false-positive results. Test results should be interpreted in the context of clinical findings, tumor sampling, and other laboratory data. If results obtained do not match other clinical or laboratory findings, contact the laboratory for discussion of the findings. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.   Genes may be added or removed based on updated clinical relevance. Please refer to the Targeted DNA Gene Regions Interrogated by Neuro-Oncology Panel in Special Instructions for the most up to date list of genes included in this test. View more

Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Formal PT program

PT Provider: Help
College of American Pathologists, CAP

Description of PT method: Help
CAP Vended/ Internal Blind

Software used to interpret novel variations Help
Variants may be analyzed using any combination of the following: Alamut, REVEL, Polyphen-2, SIFT, AGVGD, MutationTaster, SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, gene and somatic-specific online databases, ISCA, UCSC Genome Browser

Laboratory's policy on reporting novel variations Help
All novel alterations and copy number variants are evaluated for potential pathogenicity and included in the written report, accordingly.