CancerNext-Expanded is intended to determine if a person has an inherited cancer predisposition condition. This is a broad test option which includes 77 genes that put individuals at increased risk for various cancers, such as breast, ovarian, uterine, colorectal, gastric, pancreatic, prostate, melanoma, kidney, central nervous system tumors, and pheochromocytoma/paraganglioma cancer predisposition conditions. CancerNext-Expanded should be considered in persons with suspicious personal and/or family histories. Certain hematologic malignancy predisposition genes are included on this panel. For certain patients, information about pancreatitis risk genes or genes which have only limited evidence of an association with cancer predisposition may be desired. These genes may be included by selecting the Pancreatitis add-on (5 genes—CFTR, CPA1, CTRC, PRSS1, SPINK1) and/or the Limited Evidence Genes add-on (8 genes—ATRIP, MLH3, PALLD, EGLN1, KIF1B, TERT, RNF43, RAD51B).
Genes included on the CancerNext-Expanded test are evaluated by next generation sequencing (NGS) of the coding exons and well into the flanking 5’ and 3’ ends of the introns and untranslated regions. Variants in regions complicated by pseudogene interference, variant calls not satisfying depth of coverage and variant allele frequency quality thresholds, and potentially homozygous variants are verified by Sanger sequencing. The MSH3 and PHOX2B polyalanine repeat regions are excluded from analysis. For MITF, only the c.952G>A (p.E318K) variant is reported. The inversion of coding exons 1-7 of the MSH2 gene is detected by NGS and confirmed by multiplex ligation-dependent probe amplification (MLPA) or PCR and agarose gel electrophoresis. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of uncertain or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction.
Gross deletion/duplication analysis is performed for CancerNext-Expanded genes (excluding ATRIP, AXIN2, CFTR, CPA1, CTNNA1, CTRC, DDX41, EGFR, EGLN1, HOXB13, KIT, MBD4, MITF, MLH3, MSH3, PALLD, PDGFRA, POLD1, POLE, PRSS1, RAD51B, RNF43, SPINK1, and TERT) using a customized pipeline using a combination of third-party coverage-based tools and custom methodologies with confirmatory MLPA and/or targeted chromosomal microarray. For GREM1, only the status of the 40kb 5’ UTR gross duplication is analyzed and reported. 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_-186) are analyzed and reported. Gross deletions and duplications of exons 11-15 of PMS2 are reflexed to long-range PCR and gel electrophoresis and/or sequencing to determine if the event occurs within PMS2 or pseudogene PMS2CL.
Test Description
Genes included on the CancerNext-Expanded test are evaluated by next generation sequencing (NGS) of the coding exons and well into the flanking 5’ and 3’ ends of the introns and untranslated regions. Variants in regions complicated by pseudogene interference, variant calls not satisfying depth of coverage and variant allele frequency quality thresholds, and potentially homozygous variants are verified by Sanger sequencing. The MSH3 and PHOX2B polyalanine repeat regions are excluded from analysis. For MITF, only the c.952G>A (p.E318K) variant is reported. The inversion of coding exons 1-7 of the MSH2 gene is detected by NGS and confirmed by multiplex ligation-dependent probe amplification (MLPA) or PCR and agarose gel electrophoresis. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of uncertain or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction.
Gross deletion/duplication analysis is performed for CancerNext-Expanded genes (excluding ATRIP, AXIN2, CFTR, CPA1, CTNNA1, CTRC, DDX41, EGFR, EGLN1, HOXB13, KIT, MBD4, MITF, MLH3, MSH3, PALLD, PDGFRA, POLD1, POLE, PRSS1, RAD51B, RNF43, SPINK1, and TERT) using a customized pipeline using a combination of third-party coverage-based tools and custom methodologies with confirmatory MLPA and/or targeted chromosomal microarray. For GREM1, only the status of the 40kb 5’ UTR gross duplication is analyzed and reported. 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_-186) are analyzed and reported. Gross deletions and duplications of exons 11-15 of PMS2 are reflexed to long-range PCR and gel electrophoresis and/or sequencing to determine if the event occurs within PMS2 or pseudogene PMS2CL.
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