CustomNext-Cancer ®

For patients with a complex personal or family history of cancer, CustomNext-Cancer gives you the flexibility to choose from up to 91 genes that fit the needs of your patient to enable more informed management of your patient’s cancer risks.

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Test Code 9510
Turnaround Time (TAT) 14-21 days
Number of Genes 91

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Ordering Options

We offer family variant testing at no additional cost

for all blood relatives of patients who undergo full single gene sequencing or multigene panel testing* at Ambry Genetics and are found to have a pathogenic or likely pathogenic variant. No-cost testing of blood relatives must be completed within 90 days of the original Ambry report date.

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*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 
  • You are interested in adding limited evidence genes only available via CustomNext-Cancer 
  • You would like to add the pancreatitis genes with other hereditary cancer genes 

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 91 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. For POLD1 and POLE, only missense and in-frame indel variants in the exonuclease domains (codons 311-541 and 269-485, respectively) are routinely reported. For HOXB13, only variants impacting codon 84 are routinely reported. For MITF, only the status of the variant c.952G>A (p.E318K) is analyzed and reported. For EGFR, only the status of the variants c.2369C>T (p.T790M) and c.2327G>A (p.R776H) are analyzed and reported. For EGLN1, only missense variants in the catalytic domain (codons 188-418) are routinely reported. For PALLD, only the p.P139S (c.451C>T) variant is routinely reported. For ABRAXAS1, only the p.R361Q (c.1082G>A) variant is routinely reported. For TERT, only the c.-57A>C variant is routinely reported. For RPS20, only exonic truncating variants are routinely reported. For RECQL, only missense variants in the helicase and RCQ domains (codons 63-592) and exonic truncating variants are routinely reported. For KIT, only missense and in-frame indel variants in select coding exons (8, 9, 11, 13, and 17) are routinely reported. For PDGFRA, only missense and in-frame indel variants in select coding exons (9, 11, 13, and 17) are 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 routinely reported. For PHOX2B and MSH3, the polyalanine repeat regions are 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. Potentially homozygous variants, variants in regions complicated by pseudogene interference, and variant calls not satisfying depth of coverage and variant allele frequency quality thresholds are verified by Sanger sequencing.  Gross deletion/duplication analysis is performed for the covered exons and untranslated regions of ordered genes (excluding ABRAXAS1CASR, CFTR, CPA1, CTRC, EGFREGLN1, HOXB13, KITMITFMLH3PALLDPDGFRA, POLD1, POLE,  PMS2, PRSS1RINT1, RPS20, SPINK1, and TERT) 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 (NM_001127511 c.-196_c.-186) are analyzed and reported. For PMS2, gross deletion/duplication analysis is performed using MLPA. 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. 

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