Polyposis Comprehensive

  • Test Description
  • CPT Codes
  • Gene Descriptions

Test Description

  • Sequencing (included)
  • Del/Dup (included)
  • Rush / STAT
  • Exclude VUS
2 - 3 weeks
Call for details
99% at 50x
Blood (two 4ml EDTA tubes, lavender top) or Extracted DNA (3ug in EB buffer) or Buccal Swab or Saliva (kits available upon request)
Test results and variant interpretation are based on the proper identification of the submitted specimen and use of correct human reference sequences at the queried loci. In very rare instances, errors may result due to mix-up or co-mingling of specimens. Positive results do not imply that there are no other contributions, genetic or otherwise, to the patient's phenotype, and negative results do not rule out a genetic cause for the indication for testing. Result interpretation is based on the collected information and Alamut annotation available at the time of reporting. This assay is not designed or validated for the detection of mosaicism. DNA alterations in regulatory regions or deep intronic regions (greater than 20bp from an exon) will not be detected by this test. There are technical limitations on the ability of DNA sequencing to detect small insertions and deletions. Our laboratory uses a sensitive detection algorithm, however these types of alterations are not detected as reliably as single nucleotide variants. Rarely, due to systematic chemical, computational, or human error, DNA variants may be missed. Although next generation sequencing technologies and our bioinformatics analysis significantly reduce the confounding contribution of pseudogene sequences or other highly-homologous sequences, sometimes these may still interfere with the technical ability of the assay to identify pathogenic variant alleles in both sequencing and deletion/duplication analyses. Deletion/duplication analysis can identify alterations of genomic regions which are a single exon in size. When novel DNA duplications are identified, it is not possible to discern the genomic location or orientation of the duplicated segment, hence the effect of the duplication cannot be predicted. Where deletions are detected, it is not always possible to determine whether the predicted product will remain in-frame or not. Unless otherwise indicated, in regions that have been sequenced by Sanger, deletion/duplication analysis has not been performed.

Patients with Bone Marrow Transplants:
DNA extracted from cultured fibroblasts should be submitted instead of blood/saliva/buccal samples from individuals who have undergone allogeneic bone marrow transplant and from patients with hematologic malignancy.

CPT Code

NOTE:  The CPT codes listed on the website are in accordance with Current Procedural Terminology, a publication of the American Medical Association. CPT codes are provided here for the convenience of our clients. Clients who bill for services should make the final decision on which codes to use.

Gene Descriptions

Gene Reason Reference
APC Heterozygous pathogenic variants in APC are associated with both classic and attenuated familial adenomatous polyposis (FAP), Gardner syndrome, Turcot syndrome, and Hereditary Desmoid disease. OMIM: 175100; PubMed: 1544113, 20301519
SMAD4 Heterozygous pathogenic variants in SMAD4 are associated with Juvenile Polyposis Syndrome (JPS). Biallelic pathogenic variants cause Hereditary Hemorrhagic Telangiectasia (HHT). PubMed: 19553198, 20301642; OMIM 174900
MSH3 Autosomal recessive variants in the MSH3 gene have been associated with attenuated familial adenomatous polyposis. MSH3 has also been implicated in autosomal dominant hereditary nonpolyposis colon cancer. MSH3 gene encodes the MSH3 protein which has downstream implications in the DNA mismatch repair (MMR) pathway. PubMed: 27476653, 35675019; OMIM: 600887
NTHL1 Biallelic mutations in the base excision repair gene NTHL1 have been associated with familial adenomatous polyposis-3 (FAP3) which is also referred to as NTHL1-associated polyposis (NAP). PubMed: 28331556, 26431160; OMIM: 602656