ColoNext includes 20 genes associated with inherited risk for colorectal cancer, gastric cancer, &/or polyposis based on personal &/or family history.
For certain patients, information about genes which have only limited evidence of an association with cancer predisposition may be desired. These genes may be included by selecting the Limited Evidence Genes add-on option (6 genes—ATM, CHEK2, MLH3, RNF43, RPS20, CTNNA1).
| Test Code | 8821 |
| Turnaround Time (TAT) | 14-21 days |
| Number of Genes | 20 |
We offer family variant testing for all blood relatives of patients who undergo full single gene sequencing, multigene panel testing or exome sequencing at Ambry Genetics and are found to have a pathogenic or likely pathogenic variant. Testing must be completed within 90 days of the original report date. Whenever possible, more closely related relatives should be tested before more distant relatives. If you or a family member are interested in learning more about our family testing program or when family testing may be clinically indicated, please contact us or your provider for additional information. Note that Ambry can only provide such family testing services to patients receiving medical care in the U.S or US territories.
Order NowGenes included on the ColoNext 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 polyalanine repeat region is excluded from analysis. 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 ColoNext genes (excluding AXIN2, CTNNA1, MBD4, MLH3, MSH3, POLD1, POLE, RNF43, and RPS20) 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.