ColonNext®

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ColonNext^® is a 20-gene guideline-based panel that help to identify patients with inherited risk for colorectal cancer and/or polyps.

Why Is This Important?

• Option to modify frequency and initial age of colonoscopy and other screening
• Consideration of prophylactic colectomy or other risk-reducing measures, as appropriate
• Option to tailor treatment and/or determine eligibility for clinical trials
• Identify at-risk family members 

When To Consider Testing?

• Early-onset colorectal cancer (diagnosed <50 years of age)
• Multiple primary cancers in one person (e.g. two primary colorectal cancers or colorectal and uterine cancer)
• 3 or more family members with colorectal, uterine, ovarian, and/or stomach cancer
• Multiple close family members, on the same side of the family, with colorectal and other cancers
• 10 or more GI polyps during one’s lifetime (adenomatous, hyperplastic, hamartomatous, and/or other types of polyps)

Test Method

ColonNext^® analyses 20 genes. These genes (excludingEPCAMandGREM1) 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. The inversion of coding exons 1-7 of theMSH2gene is detected by NGS and confirmed by MLPA. 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. The MSH3 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. 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 sequenced genes (excluding AXIN2, MSH3, POLD1, and POLE) plus EPCAM and GREM1 using read-depth from NGS data with confirmatory multiplex ligation-dependent probe amplification (MLPA) and/or targeted chromosomal microarray. ForGREM1, only the status of the 40kb 5’ UTR gross duplication is analyzed and reported. For NTHL1, only full-gene gross deletions and duplications are detected. For EPCAM, only gross deletions encompassing the 3’ end of the gene are reported. ForAPC,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. Gross deletion/duplication analysis of PMS2 is performed using MLPA. If a deletion is detected in exons 13, 14, or 15 ofPMS2, double stranded sequencing of the appropriate exon(s) of the pseudogene,PMS2CL, will be performed to determine if the deletion is located in thePMS2gene or pseudogene. 

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