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Test ID APCZ APC Gene, Full Gene Analysis

Useful For

Confirmation of familial adenomatous polyposis (FAP) diagnosis for patients with clinical features

Additional Tests

Test ID Reporting Name Available Separately Always Performed
COLAB Hereditary Colon Cancer CGH Array Yes, (order FMTT) Yes

Testing Algorithm

When this test is ordered, comparative genomic hybridization will always be performed at an additional charge.

 

This test should be ordered only for individuals with symptoms suggestive of familial adenomatous polyposis (FAP). Asymptomatic patients with a family history of FAP should not be tested until a mutation has been identified in an affected family member.

 

See Colonic Polyposis Syndromes Testing Algorithm in Special Instructions.

Method Name

Custom Sequence Capture and Targeted Next Generation Sequencing

Reporting Name

APC Gene, Full Gene Analysis

Specimen Type

Varies

Specimen Type: Whole blood

Container/Tube:

Preferred: Lavender top (EDTA) or yellow top (ACD)

Acceptable: Any anticoagulant

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send specimen in original tube.

Additional Information: Specimen preferred to arrive within 96 hours of draw.

Forms:

1. New York Clients-Informed consent is required. Please document on the request form or electronic order that a copy is on file. An Informed Consent for Genetic Testing (T576) is available in Special Instructions.

2. Molecular Genetics: Inherited Cancer Syndromes Patient Information (T519) in Special Instructions

3. If not ordering electronically, complete, print, and send an Oncology Test Request Form (T729) with the specimen

(http://www.mayomedicallaboratories.com/it-mmfiles/oncology-request-form.pdf)

Specimen Minimum Volume

1 mL

Specimen Stability Information

Specimen Type Temperature Time
Varies Ambient (preferred)
  Frozen 
  Refrigerated 

Clinical Information

Familial adenomatous polyposis (FAP) is an autosomal dominant condition caused by mutations in the APC gene located on the long arm of chromosome 5 (5q21). Classic FAP is characterized by progressive development of hundreds to thousands of adenomatous colon polyps. Polyps may develop during the first decade of life and the majority of untreated FAP patients will develop colon cancer by age 40. Typically, there is a predominance of polyps on the left side of the colon, however, other areas of the colon may also be affected. The presence of extracolonic manifestations is variable and includes gastric and duodenal polyps, ampullary polyps, osteomas, dental abnormalities (unerupted teeth), congenital hypertrophy of the retinal pigment epithelium (CHRPE), benign cutaneous lesions, desmoids tumors, hepatoblastoma, and extracolonic cancers. Common constellations of colonic and extracolonic manifestations have resulted in the designation of 3 clinical variants: Gardner syndrome, Turcot syndrome, and hereditary desmoid disease.

 

Gardner syndrome is characterized by colonic polyps of classic FAP with epidermoid skin cysts and benign osteoid tumors of the mandible and long bones. Turcot syndrome is characterized by multiple colonic polyps and central nervous system (CNS) tumors.

 

Turcot syndrome is an unusual clinical variant of FAP, as it is also considered a clinical variant of hereditary nonpolyposis colorectal cancer (HNPCC). Individuals with Turcot syndrome have CNS tumors in addition to adenomatous polyps. The types of CNS tumor observed helps to distinguish Turcot-FAP variant patients from Turcot-HNPCC variant patients. The predominant CNS tumor associated with the Turcot-FAP variant is medulloblastoma, while glioblastoma is the predominant CNS tumor associated with Turcot-HNPCC.

 

Hereditary desmoid disease (HDD) is a variant of FAP with multiple desmoids tumors as the predominant feature. Many patients with HDD may not even show colonic manifestations of FAP. APC germline testing may assist clinicians in distinguishing a sporadic desmoid tumor, from that associated with FAP.

 

Attenuated FAP (AFAP) is characterized by later onset of disease and a milder phenotype (typically <100 adenomatous polyps and fewer extracolonic manifestations) than classic FAP. Typically individuals with AFAP develop symptoms of the disease at least 10 to 20 years later than classically affected individuals. Individuals with AFAP often lack a family history of colon cancer and/or multiple adenomatous polyps. Of note, clinical overlap is observed between AFAP and MYH-associated polyposis (MAP), an autosomal recessive polyposis syndrome typically associated with fewer than 100 polyps. Although the clinical phenotype of MAP remains somewhat undefined, extracolonic manifestations, including CHRPE have been described in affected patients. Given the phenotypic overlap of AFAP and MAP, these tests are commonly ordered together or in a reflex fashion.

 

See Colonic Polyposis Syndromes Testing Algorithm in Special Instructions for additional information. Also see Hereditary Colorectal Cancer: Adenomatous Polyposis Syndromes (September 2004 Communique) in publications for additional information.

Reference Values

An interpretive report will be provided.

Cautions

A small percentage of individuals who are carriers or have a diagnosis of familial adenomatous polyposis (FAP) may have a mutation that is not identified by this method (eg, promoter mutations, deep intronic alterations, biallelic mutations in MYH gene). The absence of a mutation, therefore, does not eliminate the possibility of positive carrier status or the diagnosis of FAP. For carrier testing, it is important to first document the presence of an APC gene mutation in an affected family member.

 

Rare polymorphisms exist that could lead to false-negative or false-positive results. If results obtained do not match the clinical findings, additional testing should be considered.

 

A previous bone marrow transplant from an allogenic donor will interfere with testing. Call Mayo Medical Laboratories for instructions for testing patients who have received a bone marrow transplant.

 

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Errors in our interpretation of results may occur if information given is inaccurate or incomplete.

 

We strongly recommend that patients undergoing predictive testing receive genetic counseling both prior to testing and after results are available.

 

Technical Limitations:

In some cases, DNA variants of undetermined significance may be identified. Due to the limitations of next generation sequencing, we can detect 90% of insertions and deletions up to 28 bases and 38 bases, respectively. If a diagnosis of one of the syndromes on this panel is still suspected, consider full gene sequencing using traditional Sanger methods. Single or multiexon deletions as well as whole gene deletions will be detected by array comparative genomic hybridization (aCGH). Rare polymorphisms exist that could lead to false-negative or false-positive results. If results obtained do not match the clinical findings, additional testing should be considered.

 

Evaluation Tools:

Multiple in-silico evaluation tools were used to assist in the interpretation of these results. These tools are updated regularly, therefore, changes to these algorithms may result in different predictions for a given alteration. Additionally, the predictability of these tools for the determination of pathogenicity is currently unvalidated.

 

Unless predicted to cause disease, alterations found deep in the intron or alterations that do not result in an amino acid substitution are not reported.

 

Reclassification of Variants-Policy: All detected alterations are evaluated according to American College of Medical Genetics and Genomics recommendations (2). Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance. At this time, it is not standard practice for the laboratory to systematically review likely deleterious alterations or variants of uncertain significance that are detected and reported. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time.

Day(s) Performed

Performed weekly; Varies

Report Available

14 days

Performing Laboratory

Mayo Medical Laboratories in Rochester

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the U.S. Food and Drug Administration.

CPT Code Information

81201-APC (adenomatous polyposis coli) (eg, familial adenomatosis polyposis [FAP], attenuated FAP) gene analysis; full gene sequence

81228-Cytogenomic constitutional (genome-wide) microarray analysis; interrogation of genomic regions for copy number variants (eg, bacterial artificial chromosome [BAC] or oligo-based comparative genomic hybridization [CGH] microarray analysis)

NY State Approved

Conditional