Unit Code 82582:
Familial Adenomatous Polyposis (FAP) Mutation Screen

Confirmation of FAP diagnosis for patients with clinical features  

This test should be ordered only for individuals with symptoms

suggestive of FAP. Asymptomatic patients with a family history

of FAP should not be tested until a mutation has been identified

in an affected family member.

APC gene sequence analysis for exons 1-14 and PTT for exon 15.

Changes identified in exon 15 via PTT are verified by DNA

sequencing. Gene dosage analysis by multiplex ligation probe

amplification (MLPA) is used to investigate for the presence of

large deletions and duplications.

When this test is ordered, #89850 "FAP Large Deletion/

Duplication, MLPA" will always be performed at an additional

charge.

82582: Polymerase Chain Reaction (PCR) followed by
DNA Sequence Analysis/Protein Truncation Test with
follow-up sequencing when appropriate (PCR is utilized
pursuant to a license agreement with Roche Molecular
Systems, Inc.)
89850: Gene Dosage Analysis by Multiplex
Ligation-Dependent Probe Amplification (MLPA).
(PCR is utilized pursuant to a license agreement
with Roche Molecular Systems, Inc.)
 
See "Colorectal Adenomatous Polyposis Algorithm" in
Special Instrucitons.

FAP Mutation Screen

FAPMS

Adenomatous Polyposis Coli (APC)

APC (Adenomatous Polyposis Coli)

FAP (Familial Adenomatous Polyposis)

Gardner's syndrome

Soft-FAPMS

"Molecular Genetics - Inherited Cancer Syndromes

Patient Information Sheet" (Supply T519 or see Special

Instructions) is required for all orders. If not ordering

electronically, please submit the above information sheet along

with a "Molecular Genetics Request Form" (Supply T245) with

the specimen. An "Informed Consent for DNA Testing"

(Supply T576) is available. See Special Instructions for a copy

of the form.

Specimen must arrive within 96 hours of draw.

Draw blood in a lavender-top (EDTA) tube or a yellow-top

(ACD) tube, and send 3 mL of EDTA or ACD whole blood in

original VACUTAINER. Invert several times to mix blood.

Forward unprocessed whole blood promptly at ambient

temperature.

3 mL

Ambient\Refrig OK\Frozen NO

Hemolysis:                                          No                         

Lipemia:                                               NA

Icteric:

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). The incidence of FAP may demonstrate ethnic

variability, however most reports estimate a panethnic incidence

somewhere between 1 in 6,000 to 1 in 18,000 individuals. Approximately

25% (1 in 4) of affected individuals are the de novo case in their family.

Therefore, FAP is inherited from an affected parent approximately 75%

of the time.

Classic FAP is clinically characterized by the progressive development

of hundreds to thousands of adenomatous colon polyps, some of which

inevitably progress to carcinoma if the colon is not surgically removed.

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 my also be affected. The presence of

extracolonic manifestations is variable and includes gastric and

duodenal polyps, ampullary polyps, congenital hypertrophy of the

retinal pigment epithelium (CHRPE), desmoids tumors, thyroid cancer,

hepatoblastoma (most commonly diagnosed before the age of 4 years),

and rarely jejunal, adrenal, pancreatic, and biliary tract malignancies.

Common constellations of colonic and extracolonic manifestations have

resulted in the designation of 3 clinical variants: Gardner syndrome,

Turcot syndrome, and hereditary desmoid disease.

In addition to the typical colonic manifestations of classic FAP, Gardner

syndrome is characterized by the presence of soft tissue tumors (thyroid),

osteomas (typically of mandible, but not always), tooth abnormalities

(supernumerary) and skin tumors (epidermoid cysts, lipomas, fibromas,

leiomyomas).

Individuals with Turcot syndrome show central nervous system (CNS)

tumors in addition to adenomatous polyps. Turcot syndrome is an

unusual clinical variant of FAP, as it is also considered a clinical variant

of hereditary nonpolyposis colorectal cancer (HNPCC). 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 where multiple

desmoids tumors is 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 extraclonic manifestations) than classic FAP (typically 100s to

1,000s of adenomatous polyps). 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 (example:  if MYH germline testing is negative,

proceed with APC germline testing). Mayo Medical Laboratories does

not offer a formal reflex test for FAP and MYH, however, reflex testing can

be arranged by contacting the on-call genetic counselor for the molecular

genetics laboratory at 800-533-1710.

The APC gene is quite large. It is composed of 15 exons and has an

8,538 bp reading frame. A variety of technologists must be employed

when analyzing each specimen to ensure accurate results within an

efficient, clinically helpful, turnaround time. The Mayo Molecular

Genetics Laboratory utilizes multiplex ligation probe amplification

(MLPA) to investigate for large genomic deletions/duplications within

the APC gene. In addition, DNA sequencing is performed to investigate

for mutations within exons 1-14. Protein truncation with follow-up

site-specific DNA sequencing is performed to investigate for mutations

within exon 15.

Detection of a disease causing mutation in the APC gene can be used to

confirm a diagnosis of FAP and to predict carrier status for at-risk family

members of an affected individual. Patients diagnosed with FAP benefit

from genetic counseling, prophylactic surgery, and cancer surveillance.

For at-risk individuals, molecular genetic studies can be useful to refine

risk estimates and to determine an appropriate cancer surveillance

regimen.

See "Colorectal Adenomatous Polyposis Algorithm" in Special Instructions

for additional information. Also see "Hereditary Colorectal Cancer:

Adenomatous Polyposis Syndromes" (September 2004 Communique')

in publications for additional information.

An interpretive report will be provided.

An interpretive report will include specimen information, pedigree

(when appropriate), assay information, and whether or not results

are consistent with a diagnosis of FAP, or indicate a risk to

develop FAP.

A small percentage of individuals who are carriers or have a diagnosis

of FAP may have a mutation that is not identified by this method (eg,

promoter mutations, deep intronic alterations). The absence of a

mutation(s), 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 a APC gene mutation in an affected

family member.

In some cases, DNA alterations of undetermined significance may be

identified.

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.

In addition to disease-related probes, the MLPA technique utilizes

probes localized to other chromosomal regions as internal controls. In

certain circumstances, these control probes may detect other

diseases or conditions for which this test was not specifically intended.

Results of the control probes are not normally reported. However, in

cases where clinically relevant information is identified, the ordering

physician will be informed of the result and provided with

recommendations for any appropriate follow-up testing.

1.   American Society of Clinical Oncology. American Society of

      Clinical Oncology policy statement update: genetic testing for

      cancer susceptibility Clin Oncol. 2003;21:2397-2406.

2.   Mandl M, Paffenholz R, Friedl E, et al:  Frequency of common

      and novel inactivation APC mutations in 202 families with

      adenomatous polyposis. Hum Molec Genet 1994;3:181-184

3.   Galiatsatos P, Foulkes WD:  Familial adenomatous polyposis.

      Am J Gastroenterol 2006;101:385-398

4.   Croner RS, Brueckl WM, Reingruber B, et al:  Age and manifestation

      related symptoms in familial adenomatous polyposis. BMC Cancer

      2005 Mar 2;5:24

DNA sequencing is used to detect mutations in exons 1-14 (segment 1)

and the 5' end of exon 15. The protein truncation test is used to

screen for mutations in exon 15 (segments 2-5) of the APC gene. If an

alteration is detected within exon 15, DNA sequencing will be performed

to characterize the alteration. Multiplex ligation probe amplification

(MLPA) is used to detect large deletions/duplications.

Specimens received by Saturday at 12 noon will be set up on

the next run. The FAP assay is run every other Monday and

requires 2 weeks to completion.

14 days

28 days

Positives: Indefinite; Negatives: 3 months

$1,300.00

The following test(s) will be added at an additional charge:

$273.00 for #89850 "FAP Large Deletion/Duplication, MLPA"

$1,573.00 = Total List Fee

This test was developed and its performance characteristics

determined by Laboratory Medicine and Pathology, Mayo Clinic.

This test has not been cleared or approved by the U.S. Food

and Drug Administration.

"Familial Adenomatous Polyposis (FAP) Mutation Screen"

DNA Sequence Analysis

83891/Isolation or extraction of highly purified nucleic acid

83892/x4 Enzymatic digestion

83894/x4 Separation by gel electrophoresis

83898/Amplification, target, each nucleic acid sequence

83900/x3 Amplification, target, multiplex, first 2 nucleic acid sequences

83901/x8 Amplification, target, multiplex, each additional nucleic acid

sequence beyond 2

83909/x30 Separation and identification by high-resolution technique

83912/Interpretation and report

Protein Truncation

83894/x4 Separation by gel electrophoresis

83898/x4 Amplification, target, each nucleic acid sequence

83905/x4 Mutation identification by allele-specific transcription,

single segment

83906/x4 Mutation identification by allele-specific translation, single

segment, each segment

"FAP Large Deletion/Duplication, MLPA"

Gene Dosage Analysis

83900/Amplification, target, multiplex, first 2 nucleic acid sequences

83909/Separation and identification by high-resolution technique

83914/x26 Mutation identification by enzymatic ligation or primer

extension, single segment, each segment