CancerNext-Expanded

CancerNext-Expanded is a next generation sequencing panel that simultaneously analyzes 67 genes associated with increased risks for brain, breast, colon, ovarian, pancreatic, prostate, renal, uterine, and many other cancers.

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Test Code 8874
Turnaround Time (TAT) 14-21 days
Number of Genes 67
Specimen Requirements Click here

Ordering Options

Why Is This Important?

  1. Option to modify frequency and initial age of mammogram/breast MRI, colonoscopy, prostate cancer screening, or other screening as appropriate
  2. Consideration of prophylactic mastectomy, colectomy, or other risk-reducing measures, as appropriate 
  3. Option to tailor chemotherapy strategies and/or determine eligibility for clinical trials 
  4. Identify at-risk family members 

When To Consider Testing

  • Multiple primary tumors in one person that are suspicious for a combination of hereditary breast, ovarian, colorectal, uterine cancers and/or melanoma in addition to hereditary brain tumors, kidney cancer, and/or PGL/PCC
  • 3 or more close family members with cancers that are suspicious for a combination of hereditary breast, ovarian, colorectal, uterine cancers and/or melanoma in addition to hereditary brain tumors, kidney cancer, and/or PGL/PCC
  • Previous genetic testing was uninformative (negative or variant of uncertain significance) for a combination of hereditary breast, ovarian, colorectal, uterine cancers and/or melanoma, in addition to hereditary brain tumors, kidney cancer, and/or PGL/PCC

Mutation Detection Rate

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

Test Description

CancerNext-Expanded analyzes 67 genes (listed above). 65 genes (excluding EPCAM and GREM1) 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). For POLD1 and POLE, missense variants located outside of the exonuclease domains (codons 311-541 and 269-485, respectively) are not routinely reported. For MITF, only the status of the c.952G>A (p.E318K) alteration is analyzed and reported. The inversion of coding exons 1-7 of the MSH2 gene and the BRCA2 Portuguese founder mutation, c.156_157insAlu (also known as 384insAlu) are 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 66 genes (excluding MITF) using read-depth from NGS data with confirmatory multiplex ligation-dependent probe amplification (MLPA) and/or targeted chromosomal microarray. For GREM1, only the status of the 40kb 5’ UTR gross duplication is analyzed and reported. 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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