Familial Adenomatous Polyposis (FAP) via the APC Gene
Summary and Pricing 
Test Method
Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 3115 | APC | 81201 | 81201,81203 | $990 | Order Options and Pricing |
Pricing Comments
Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.
Turnaround Time
3 weeks on average for standard orders or 2 weeks on average for STAT orders.
Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.
Targeted Testing
For ordering sequencing of targeted known variants, go to our Targeted Variants page.
Clinical Features and Genetics
Clinical Features
Familial adenomatous polyposis (FAP) (OMIM 175100) is an inherited cancer syndrome characterized clinically by the development of hundreds to thousands of adenomatous polyps in the colon and rectum. If not treated, nearly all FAP patients will develop colorectal cancer (CRC) by age 40 (Fearnhead et al. Hum Mol Genet 10:721-733, 2001). In addition to CRC, FAP patients are also predisposed to desmoid tumors, small bowel cancer, thyroid cancer, hepatoblastoma, and medulloblastoma (Galiatsatos et al. Am J Gastroenterol 101:385-398, 2006). About 60% of families with FAP also display congenital hypertrophy of the retinal pigment epithelium (CHRPE), a condition that does not affect sight or have malignant potential but can be easily detected by ophthalmoscopy at any age. CHRPE is highly diagnostic of FAP and can be useful for identifying FAP patients and at-risk family members well before the appearance of polyps (Diaz-Llopis and Menezo Arch Ophthalmol 106:412-413, 1988).
Genetics
Familial adenomatous polyposis (FAP) is an autosomal dominant disorder caused by germline variants in the APC gene. More than 1200 variants have been reported in APC (Human Gene Mutation Database, www.hgmd.cf.ac.uk) and >90% are nonsense or frameshift variants that result in a dysfunctional truncated protein product (Nagase and Nakamura Hum Mut 2:425-434, 1993). Germline variants are spread throughout the coding region (Beroud and Soussi Nucleic Acids Res 24:121-124, 1996). Severe FAP (i.e. more than 1000 polyps) typically occurs in patients with variants between codons 1250 and 1464 (Caspari et al. Lancet 343:629-632, 1994). In contrast, patients with attenuated FAP (i.e. fewer than 100 colorectal polyps) usually have variants at the very 5’ and 3’ ends of the gene or in an alternatively spliced region of exon 9 (Young et al. Hum Mut 11:450-455, 1998; Soravia et al. Am J Hum Genet 62:1290-1301, 1998). Congenital hypertrophy of retinal pigment epithelium (CHRPE) is limited to patients with variants between codons 457 and 1444 (Caspari et al. Hum Mol Genet 4:337-340, 1995). Two missense variants, p.Ile1307Lys and p.Glu1317Lys (commonly found in Ashkenazi Jewish populations), predispose carriers to multiple colorectal adenomas (generally less than 100) and carcinoma, but with low and variable penetrance (Frayling et al. PNAS 95:10722-10727, 1998). Pathogenic variants in the exon 1B promoter of APC have also been associated with gastric adenocarcinoma and proximal polyposis of the stomach (Li et al. 2016).
Clinical Sensitivity - Sequencing with CNV PG-Select
This test is predicted to detect >90% of causative FAP variants (Laken et al. PNAS 96:2322-2326, 1999).
Gross deletions/duplications have been reported in up to 12% of APC patient samples (Jasperson and Burt. GeneReviews. 2011).
Testing Strategy
This test provides full coverage of all coding exons of the APC gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.
Indications for Test
Candidates for this test are FAP patients and relatives of patients with a known APC variant. This test is designed for heritable germline variants and is not appropriate for the detection of somatic variants in tumor tissue.
Candidates for this test are FAP patients and relatives of patients with a known APC variant. This test is designed for heritable germline variants and is not appropriate for the detection of somatic variants in tumor tissue.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| APC | 611731 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Adenomatous Polyposis Coli | AD | 175100 |
Citations
- Beroud C, Soussi T. 1996. APC gene: database of germline and somatic mutations in human tumors and cell lines. Nucleic acids research 24: 121-124. PubMed ID: 8594558
- Caspari R, Friedl W, Mandl M, Propping P, Möslein G, Kadmon M, Timmermanns G, Knapp M, Jacobasch KH, Ecker KW. 1994. Familial adenomatous polyposis: mutation at codon 1309 and early onset of colon cancer. The Lancet 343: 629–632. PubMed ID: 7906810
- Caspari R, Olschwang S, Friedl W, Mandl M, Boisson C, Böker T, Augustin A, Kadmon M, Möslein G, Thomas G. 1995. Familial adenomatous polyposis: desmoid tumours and lack of ophthalmic lesions (CHRPE) associated with APC mutations beyond codon 1444. Human molecular genetics 4: 337–340. PubMed ID: 7795585
- Díaz-Llopis M, Menezo JL. 1988. Congenital hypertrophy of the retinal pigment epithelium in familial adenomatous polyposis. Arch. Ophthalmol. 106: 412–413. PubMed ID: 2830869
- Fearnhead NS, Britton MP, Bodmer WF. 2001. The ABC of APC. Hum. Mol. Genet. 10: 721–733. PubMed ID: 11257105
- Frayling IM, Beck NE, Ilyas M, Dove-Edwin I, Goodman P, Pack K, Bell JA, Williams CB, Hodgson SV, Thomas HJ. 1998. The APC variants I1307K and E1317Q are associated with colorectal tumors, but not always with a family history. Proceedings of the National Academy of Sciences 95: 10722–10727. PubMed ID: 9724771
- Galiatsatos P, Foulkes WD. 2006. Familial Adenomatous Polyposis. The American Journal of Gastroenterology 101: 385–398. PubMed ID: 16454848
- Human Gene Mutation Database.
- Laken SJ, Papadopoulos N, Petersen GM, Gruber SB, Hamilton SR, Giardiello FM, Brensinger JD, Vogelstein B, Kinzler KW. 1999. Analysis of masked mutations in familial adenomatous polyposis. Proceedings of the National Academy of Sciences 96: 2322–2326. PubMed ID: 10051640
- Li J. et al. 2016. American Journal of Human Genetics. 98: 830-42. PubMed ID: 27087319
- Nagase H, Nakamura Y. 1993. Mutations of the APC adenomatous polyposis coli gene. Human Mutation 2: 425–434. PubMed ID: 8111410
- Soravia C, Berk T, Madlensky L, Mitri A, Cheng H, Gallinger S, Cohen Z, Bapat B. 1998. Genotype-phenotype correlations in attenuated adenomatous polyposis coli. The American Journal of Human Genetics 62: 1290–1301. PubMed ID: 9585611
- Young J, Simms LA, Tarish J, Buttenshaw R, Knight N, Anderson GJ, Bell A, Leggett B. 1998. A family with attenuated familial adenomatous polyposis due to a mutation in the alternatively spliced region of APC exon 9. Hum. Mutat. 11: 450–455. PubMed ID: 9603437
Ordering/Specimens
Ordering Options
We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.
myPrevent - Online Ordering
- The test can be added to your online orders in the Summary and Pricing section.
- Once the test has been added log in to myPrevent to fill out an online requisition form.
- PGnome sequencing panels can be ordered via the myPrevent portal only at this time.
Requisition Form
- A completed requisition form must accompany all specimens.
- Billing information along with specimen and shipping instructions are within the requisition form.
- All testing must be ordered by a qualified healthcare provider.
For Requisition Forms, visit our Forms page
If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.
Specimen Types
Specimen Requirements and Shipping Details
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ORDER OPTIONS
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