For patients with a complex personal or family history of cancer, CustomNext-Cancer gives you the flexibility to choose from up to 81 genes to analyze so you can accurately diagnose, treat, and manage your patient’s cancer risks.

Quick Reference
Test Code 9510
Turnaround Time (TAT) 14-21 days
Number of Genes 81


Learn more about your patient’s breast or prostate cancer risk by adding AmbryScore to this test for eligible patients.

Learn more

Ordering Options

We now offer single site analysis (SSA) at no additional cost to family members

following single gene or panel testing* of the first family member (proband) within 90 days of the original Ambry report date.

Order Now

*excludes Secondary Findings and SNP Array tests

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

  • Your patient's complex personal and/or family history requires a unique panel of genes to assess (not found in an existing panel) 
  • You would like to assess more or fewer genes than those currently found on existing panels 

Mutation Detection Rates

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

Test Description

CustomNext-Cancer analyzes up to 81 genes (listed above) selected by the ordering healthcare provider. All selected 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, if selected: 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. For EGFR, only the status of the c.2369C>T (p.T790M) and c.2327G>A (p.R776H) alterations are analyzed and reported. For KIT and PDGFRA, missense variants which are not located at or near activation domains, may not be routinely reported. When applicable, 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 ordered genes (excluding CASR, CFTR, CPA1, CTRC, EGFR, MITF, PMS2, PRSS1, and SPINK1) 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, when applicable. For EPCAM, only gross deletions encompassing the 3’ end of the gene are reported. For NTHL1, only full-gene gross deletions and duplications are detected. For APC, all promoter 1B gross deletions as well as single nucleotide substitutions within the promoter 1B YY1 binding motif are analyzed and reported. For PMS2, gross deletion/duplication analysis is performed using MLPA kit P008-B1. 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.

View Full Menu

Search Results

Start your search...