BrainTumorNext

BrainTumorNext is a next generation sequencing panel that simultaneously analyzes 27 genes associated with increased risk for brain tumors and other cancers/tumors.

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Test Code 8847
Turnaround Time (TAT) 14-21 days
Number of Genes 27
Specimen Requirements Click here

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Why Is This Important?

  1. Ability to modify surveillance options and age of initial screening 
  2. Consideration of risk-reduction measures for your patient and/or their family members
  3. Referral to other specialists for screening/management of non-nervous system symptoms, as needed
  4. Availability of tailored treatment options (e.g. avoid radiation-based therapy for TP53 mutation carriers)
  5. Identification of at-risk family members

When To Consider Testing

  • Early-onset brain tumor(s) (diagnosed <50 years of age)
  • Multiple primary cancers in one person (e.g. brain tumor and colorectal cancer)
  • Multiple close relatives* with brain tumors
  • A family history of a mutation in a gene that predisposes to brain tumors

    * On the same side of the family

Mutation Detection Rate

BrainTumorNext can detect >99.9% of described mutations in the included genes, when present (analytic sensitivity).

Test Description

BrainTumorNext analyzes 27 genes (listed above). All genes are evaluated by next generation sequencing (NGS) or Sanger sequencing of all coding domains, and well into the flanking 5’ and 3’ ends of all the introns and untranslated regions. In addition, sequencing of the promoter region is performed for the following genes: PTEN (c.-1300 to c.-745), MLH1 (c.-337 to c.-194), and MSH2 (c.-318 to c.-65). The inversion of coding exons 1-7 of the MSH2 gene is detected by NGS and confirmed by PCR and agarose gel electrophoresis. For ALK, only variants located within the kinase domain (c.3286-c.4149) are reported. For PHOX2B, the polyalanine repeat region is excluded from analysis. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of unknown or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction. Additional Sanger sequencing is performed for any regions missing or with insufficient read depth coverage for reliable heterozygous variant detection.

Reportable small insertions and deletions, potentially homozygous variants, variants in regions complicated by pseudogene interference, and single nucleotide variant calls not satisfying 100x depth of coverage and 40% het ratio thresholds are verified by Sanger sequencing.1 Gross deletion/duplication analysis is performed for the covered exons and untranslated regions of all 27 genes using read-depth from NGS data with confirmatory multiplex ligation-dependent probe amplification (MLPA) and/or targeted chromosomal microarray. For APC, all promoter 1B gross deletions as well as single nucleotide substitutions within the promoter 1B YY1 binding motif are analyzed and reported. If a deletion is detected in exons 13, 14, or 15 of PMS2, double stranded sequencing of the appropriate exon(s) of the pseudogene, PMS2CL, will be performed to determine if the deletion is located in the PMS2 gene or pseudogene.

1. Mu W, et al. Sanger confirmation is required to achieve optimal sensitivity and specificity in next-generation sequencing panel testing. J Mol Diagn. 2016. 18(6):923-932

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