Clinical UM Guideline |
Subject: Genetic Testing for Lynch Syndrome, Familial Adenomatous Polyposis (FAP), Attenuated FAP and MYH-associated Polyposis | |
Guideline #: CG-GENE-15 | Publish Date: 09/27/2023 |
Status: Reviewed | Last Review Date: 11/10/2022 |
Description |
This document addresses genetic testing for the following types of hereditary colorectal cancer:
This document does not address panel testing for colorectal cancer susceptibility. Please refer to:
For additional information on genetic testing for malignant conditions, please refer to:
Note: Although immunohistochemistry (IHC) and microsatellite instability (MSI) are discussed in this document, this document is not meant to provide testing criteria for IHC or MSI.
Clinical Indications |
Medically Necessary:
Lynch Syndrome (Hereditary Non-Polyposis Colorectal Cancer [HNPCC])
Familial Adenomatous Polyposis (FAP) and Attenuated FAP (AFAP)
MYH (Human MutY homolog)-associated Polyposis (MAP)
Not Medically Necessary:
Genetic testing for HNPCC, FAP, AFAP or MAP is considered not medically necessary in individuals not meeting any of the criteria above.
Coding |
The following codes for treatments and procedures applicable to this guideline are included below for informational purposes. Inclusion or exclusion of a procedure, diagnosis or device code(s) does not constitute or imply member coverage or provider reimbursement policy. Please refer to the member's contract benefits in effect at the time of service to determine coverage or non-coverage of these services as it applies to an individual member.
Lynch Syndrome (Hereditary Non-Polyposis Colorectal Cancer [HNPCC])
When services may be Medically Necessary when criteria are met:
CPT |
| |
81288 | MLH1 (mutL homolog 1, colon cancer, nonpolyposis type 2) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; promoter methylation analysis | |
81292 | MLH1 (mutL homolog 1, colon cancer, nonpolyposis type 2) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; full sequence analysis | |
81293 | MLH1 (mutL homolog 1, colon cancer, nonpolyposis type 2) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; known familial variants | |
81294 | MLH1 (mutL homolog 1, colon cancer, nonpolyposis type 2) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; duplication/deletion variants | |
81295 | MSH2 (mutS homolog 2, colon cancer, nonpolyposis type 1) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; full sequence analysis | |
81296 | MSH2 (mutS homolog 2, colon cancer, nonpolyposis type 1) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; known familial variants | |
81297 | MSH2 (mutS homolog 2, colon cancer, nonpolyposis type 1) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; duplication/deletion variants | |
81298 | MSH6 (mutS homolog 6 [E. coli]) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; full sequence analysis | |
81299 | MSH6 (mutS homolog 6 [E. coli]) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; known familial variants | |
81300 | MSH6 (mutS homolog 6 [E. coli]) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; duplication/deletion variants | |
81317 | PMS2 (postmeiotic segregation increased 2 [S. cerevisiae]) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; full sequence analysis | |
81318 | PMS2 (postmeiotic segregation increased 2 [S. cerevisiae]) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; known familial variants | |
81319 | PMS2 (postmeiotic segregation increased 2 [S. cerevisiae]) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; duplication/deletion variants | |
81403 | Molecular pathology procedure, Level 4 (eg, analysis of single exon by DNA sequence analysis, analysis of >10 amplicons using multiplex PCR in 2 or more independent reactions, mutation scanning or duplication/deletion variants of 2-5 exons):
| |
|
| |
ICD-10 Diagnosis |
|
|
C16.0-C16.9 | Malignant neoplasm of stomach |
|
C17.0-C17.9 | Malignant neoplasm of small intestine |
|
C18.0-C20 | Malignant neoplasm of colon, rectosigmoid junction, rectum |
|
C23 | Malignant neoplasm of gallbladder |
|
C24.0-C24.9 | Malignant neoplasm of other and unspecified parts of biliary tract |
|
C25.0-C25.9 | Malignant neoplasm of pancreas |
|
C54.0-C54.9 | Malignant neoplasm of corpus uteri |
|
C56.1-C57.9 | Malignant neoplasm of ovary and other and unspecified female genital organs |
|
C65.1-C66.9 | Malignant neoplasm of renal pelvis, ureter |
|
C71.0-C71.9 | Malignant neoplasm of brain |
|
D23.0-D23.9 | Other benign neoplasms of skin [sebaceous glands] |
|
L85.8 | Other specified epidermal thickening [keratoacanthoma] |
|
Z80.0 | Family history of malignant neoplasm of digestive organs |
|
Z80.41 | Family history of malignant neoplasm of ovary |
|
Z80.49 | Family history of malignant neoplasm of other genital organs |
|
Z80.51 | Family history of malignant neoplasm of kidney |
|
Z80.59 | Family history of malignant neoplasm of other urinary tract organ |
|
Z80.8 | Family history of malignant neoplasm of other organs or systems |
|
Z85.038 | Personal history of other malignant neoplasm of large intestine |
|
Z85.048 | Personal history of other malignant neoplasm of rectum, rectosigmoid junction, and anus |
|
When services are Not Medically Necessary:
For the procedure and diagnosis codes listed above when criteria are not met or for all other diagnoses not listed.
Familial Adenomatous Polyposis (FAP), Attenuated FAP (AFAP) and MYH (Human MutY homolog)-associated Polyposis (MAP)
When services may be Medically Necessary when criteria are met:
CPT |
| |
81201 | APC (adenomatous polyposis coli) (eg, familial adenomatosis polyposis [FAP], attenuated FAP) gene analysis; full gene sequence | |
81202 | APC (adenomatous polyposis coli) (eg, familial adenomatosis polyposis [FAP], attenuated FAP) gene analysis; known familial variants | |
81203 | APC (adenomatous polyposis coli) (eg, familial adenomatosis polyposis [FAP], attenuated FAP) gene analysis; duplication/deletion variants | |
81401 | Molecular pathology procedure, Level 2 (eg, 2-10 SNPs, 1 methylated variant, or 1 somatic variant [typically using nonsequencing target variant analysis], or detection of a dynamic mutation disorder/triplet repeat) [when specified as the following]:
| |
81406 | Molecular pathology procedure, Level 7 (eg, analysis of 11-25 exons by DNA sequence analysis, mutation scanning or duplication/deletion variants of 26-50 exons, cytogenomic array analysis for neoplasia) [when specified as the following]:
| |
|
| |
ICD-10 Diagnosis |
|
|
D12.0-D12.8 | Benign neoplasm of colon, rectosigmoid junction, rectum |
|
D13.91 | Familial adenomatous polyposis |
|
D37.4-D37.5 | Neoplasm of uncertain behavior of colon, rectum [specified as colonic polyps] |
|
D48.110-D48.119 | Desmoid tumor |
|
D49.0 | Neoplasm of unspecified behavior of digestive system [specified as colonic polyps] |
|
Z83.710-Z83.719 | Family history of colonic polyps |
|
Z86.010 | Personal history of colonic polyps |
|
Z87.39 | Personal history of other diseases of the musculoskeletal system and connective tissue [desmoid tumor] |
|
When services are Not Medically Necessary:
For the procedure and diagnosis codes listed above when criteria are not met or for all other diagnoses not listed.
Discussion/General Information |
There are multiple well-defined types of hereditary colorectal cancer (CRC); three of the most common are familial adenomatous polyposis (FAP), hereditary nonpolyposis colorectal cancer (HNPCC), known as Lynch syndrome, and MYH-associated Polyposis (MAP). FAP can be clinically recognized by the presence of hundreds of colon polyps, typically apparent by age 10-20. If left untreated, affected individuals will go on to develop colorectal cancer. Individuals with HNPCC tend to have early-onset colorectal cancer, right-sided tumors and/or multiple synchronous or metachronous lesions. Extracolonic tumors may also be present. The lifetime risk of developing colorectal cancer in HPNCC is approximately 80%. Germline mutations have been associated with both FAP and HNPCC creating the option of genetic testing of both affected individuals (to establish the genetic basis of the tumor) and their family members (to determine whether an individual carries the same mutation as the affected relative). Subjects with germline mutations may undergo increased surveillance or may consider prophylactic colectomy.
Lynch Syndrome (Hereditary Non-Polyposis Colon Cancer [HNPCC])
Lynch syndrome is defined as a hereditary predisposition to CRC and other malignancies including endometrial and gastric cancer. Lynch syndrome is the most common form of genetically determined colon cancer and accounts for 1-3% of all newly diagnosed CRC cases and 3% of endometrial cancers. This predisposition is a result of a mismatch repair (MMR) germ-line (constitutional) gene mutation (MLH1, MSH2, MSH6, and PMS2) or epithelial cell adhesion molecule (EPCAM, which causes epigenetic silencing of MSH2). It has been estimated that over 70% of MMR mutations are located in the MLH1, MSH2 genes, or EPCAM in tumors with microsatellite instability (MSI)-high. Pathogenic genetic alterations might be frameshift, nonsense and splice site mutations that result in truncating or unstable proteins. Large deletions and rearrangements are also common. Therefore, full germline genetic testing including both DNA sequencing and large rearrangement analysis has been recommended (Stjepanovic, 2019).
EPCAM is not an MMR gene but can disrupt the MMR pathway. Large deletions of the EPCAM gene can lead to hypermethylation of the MSH2 promoter and subsequent MSH2 silencing. It has been estimated that EPCAM deletions may account for 20-25% of cases in which MSH2 protein is not detected by IHC but germline MSH2 mutations are not identified. The National Comprehensive Cancer Network (NCCN) guidelines for Genetic/Familial High Risk Assessment: Colorectal Cancer indicate that germline mutation testing of the EPCAM gene is appropriate when the tumor IHC stain is negative (absent) for both MSH2 and MSH6 and genetic testing for MSH2 is negative (Kempers, 2011; NCCN, 2021; Rumilla, 2011).
Identification of Lynch syndrome is important for individuals with cancer because of the increased risk for metachronous Lynch syndrome cancers, and for their relatives because of autosomal dominant inheritance and potentially high penetrance. Once Lynch syndrome has been identified, surveillance provides an opportunity for early detection and possibly the prevention of cancer among mutation carriers.
Two phenotypic tests performed on colon cancer tissue to identify individuals at risk for Lynch Syndrome are used by themselves or together as initial screening tests. These are used to screen individuals with colon cancer who have a clinical or family history suggesting Lynch Syndrome. The most widely used is a test which measures “microsatellite instability” or MSI. Microsatellites are repeated sequences of DNA which normally occur thousands of times across the genome. These sequences are made of repeating units of 1-6 base pairs in length. Each individual has microsatellites of a set length. MSI resulting from impaired DNA MMR occurs in 80%-90% of Lynch syndrome CRC tumors. MSI is a phenotypic expression of MMR gene mutations. The function of the MMR gene is to correct errors which spontaneously occur during DNA replication. The MMR gene products form a complex that binds to the mismatch, identifies the correct strand of DNA, then excises the error and repairs the mismatch. Cells carrying an MMR mutation can accumulate microsatellite replication errors resulting in novel repeated DNA sequences (microsatellites) or microsatellite instability. Five markers have been recommended by the National Cancer Institute to screen for MSI in HNPCC (Bethesda markers). MSI detection in two of these markers is considered a positive result or “high probability of MSI” (Sinn, 2009).
The second screening test for Lynch syndrome performed on colon cancer tissue involves IHC. IHC involves staining of tumor tissue for protein expression of the four mismatch genes associated with Lynch Syndrome (MLH1, MSH2, MSH6, and PMS2). If at least one of these four gene products is absent by IHC, the test is considered abnormal. Both MSI and IHC have a 5-15% false negative rate and are often used as preliminary screening tests to select individuals for gene mutation testing. MSI testing performance depends on the specific MMR mutation. For MLH1or MSH2 mutations, MSI has a sensitivity of 80-91% and specificity of 90% while for MSH6 or PMS2 the sensitivity is lower (55-77%) and the specificity is 90%. IHC testing, regardless of MMR gene mutation, has a sensitivity of 83% and specificity of 89% (EGAPP Working Group, 2009; NCCN, 2022).
Several criteria sets have been developed over the years to identify individuals who should be tested for possible Lynch Syndrome. The Amsterdam I criteria were proposed to identify individuals who were likely Lynch syndrome mutation carriers. These criteria require the presence of early onset CRC in addition to a family history which includes 3 CRCs involving two successive generations. The Amsterdam I criteria were later modified to include other Lynch syndrome-related malignancies. Based on the Amsterdam II criteria, Lynch syndrome should be suspected in individuals with 3 or more relatives with an HNPCC-related cancer in addition to all of the following:
Although the Amsterdam II criteria are considered by many to be very stringent, it has been estimated that these criteria may miss as many as 68% of individuals with Lynch syndrome. It has also been estimated that approximately 50% of the families fulfilling the Amsterdam II criteria have an MMR gene mutation.
The National Cancer Institute developed the “Revised Bethesda Guidelines” in 2004 to identify those individuals with colon cancer whose tumors should be tested for MSI. These guidelines are now used to identify tumors that should be tested for mismatch repair defect, either by MSI and/or IHC. These guidelines are more sensitive than another criteria set, “Revised Amsterdam Minimum Criteria for Clinical Definition of HNPCC” or Amsterdam Criteria II. However, up to 50% of individuals with Lynch Syndrome fail to meet the revised Bethesda guidelines. Hampel and colleagues (2008) found that limiting colon tumor analysis only to those individuals who fulfill Bethesda criteria would fail to identify 28% of cases of Lynch syndrome. Some have advocated IHC and/or MSI screening of all CRCs and endometrial cancers regardless of age at diagnosis or family history. This approach was endorsed for colon cancer by the EGAPP Working Group from the Center for Disease Control (EGAPP Working Group, 2009). A survey of US hospitals reported that routine tumor testing with HHC, MSI or both is currently performed at 71% of NCI cancer centers, 36% of American College of Surgeons accredited community hospital cancer programs, but only 15% of community hospitals. Given the small portion (2%-4%) of colorectal cancers associated with the Lynch Syndrome, there is varied opinion as to which colorectal tumors should be screened with MSI and/ or IHC (Hampel, 2008; NCCN, 2022; Palomaki, 2009).
Prediction Models
Several validated computer models are available to estimate the likelihood that an individual affected with cancer carries a pathogenic variant in an MMR gene associated with Lynch syndrome. These include but are not limited to the MMRpro, MMRpredict, and PREMM1, 2, 5, 6 (Prediction of Mismatch Repair Gene Mutations in MLH1, MSH2, and MSH6) prediction models. While the general purpose of each model is the same, each has been developed differently.
The NCCN (2022) recommends that testing for Lynch syndrome (MLH1, MSH2, MSH6, PMS2, EPCAM sequence analysis) includes individuals who meet the Bethesda guidelines or the Amsterdam II criteria, who have a CRC diagnosis prior to age 50, or have a predicted risk for Lynch syndrome greater than 5% on one of the following prediction models: MMRpredict, MMRpro or PREMM5.
Familial Adenomatous Polyposis (FAP) and Attenuated FAP
Classical FAP and attenuated FAP (AFAP) are autosomal dominant genetic disorders caused by a germline mutation in the APC (adenomatous polyposis coli) gene. Nearly 80% of individuals with FAP have a truncating mutation of the APC gene. FAP accounts for less than 1% of all colorectal cancers, but individuals harboring APC gene mutations are recommended early enhanced screening, with colectomy or proctocolectomy when the polyp burden becomes heavy and cannot be effectively managed by polypectomy. A clinical diagnosis of classical FAP is based on the presence of at least 100 polyps although fewer polyps may be present in younger age groups. The lifetime risk for colon cancer (most are left sided) with classic FAP approaches 100% by the age 50. At older ages, individuals with FAP may exhibit hundreds to thousands of colonic adenomatous polyps. Individuals with FAP are also at a higher risk for developing other cancers, including duodenal cancer, hepatoblastoma and thyroid cancer. Other possible associated findings of individuals with FAP include desmoid tumors, and congenital hypertrophy of retinal pigment epithelium. Currently, family members are often diagnosed at adolescence with genetic testing for their specific familial mutation (NCCN, 2022).
Attenuated FAP is a variant of FAP with a later onset of disease and fewer adenomatous polyps, usually 10 to less than 100. Adenomatous polyps in AFAP are more likely to occur in the right colon and may take the form of diminutive sessile adenomatous polyps. The onset of colon cancer is later with AFAP, but by age 80 the risk of colon cancer is nearly 70%. Both FAP and AFAP have an increased risk of other cancers, including duodenal cancer, hepatoblastoma and thyroid cancer. Individuals with FAP and AFAP are also at increased risk of developing desmoid tumors which are nonmalignant, but may become life threatening due to their locally invasive and aggressive growth. Confirmation of FAP and AFAP requires the identification of a germline mutation in the APC gene (NCCN, 2022).
MYH-associated Polyposis (MAP)
MAP is an autosomal recessive inherited polyposis syndrome that predisposes some individuals to attenuated adenomatous polyposis and colorectal cancer. Mutations in the MutY human homolog (MUTYH or MYH) gene prevent cells from correcting mistakes that are made when DNA is copied (DNA replication) in preparation for cell division. The gene product is a DNA glycosylase which enables oxidative DNA damage repair. The majority of individuals with MAP generally have fewer than 100 polyps although there are some instances where the individuals have greater than 1000 polyps. Traditional serrated adenomas as well as hyperplastic polyps and sessile serrated polyps (SSP) may also be seen in this setting. Some individuals with MAP may also meet the criteria for serrated polyposis syndrome (SPS). The median age of affected individuals at the time of diagnosis is typically between the mid-40s and the late 50s. Individuals with MAP develop fewer adenomas at a later age than individuals with APC mutations, but also carry a high risk of CRC (35-63%). Studies of multiple FAP registries have shown that 7%-19% of individuals with the FAP phenotype but without detectable APC mutation carry biallelic mutations in the MYH gene (NCI, 2017).
Genetic testing for APC and/or MUTYH is important to distinguish between FAP/AFAP, MAP and colonic polyposis of unknown etiology. Grover and colleagues (2012) conducted a cross-sectional study of more than 7000 individuals and found that the prevalence of pathogenic APC mutation was 80% for individuals with at least 1000 adenomas, 56% for individuals with 100-999 adenomas, 10% for individuals with 20-99 adenomas, and 5% for those with 10-19 adenomas. In the same cohort, the prevalence of biallelic MUTYH mutations was 2%, 7%, 5% and 4%, respectively.
Genetic Counseling
According to the National Society of Genetic Counselors (NSGC, 2006), genetic counseling is the process of assisting individuals to understand and adapt to the medical, psychological and familial ramifications of a genetic disease. This process typically includes the guidance of a specially trained professional who:
Definitions |
Desmoid tumor: A type of benign, locally invasive fibrous tumor capable of growing anywhere in the body.
Familial adenomatous polyposis (FAP): An inherited disorder characterized by the presence of adenomatous polyps throughout the colon that commonly progress to develop colon cancer.
First-degree relative: Any relative who is a parent, sibling, or offspring.
The National Human Genome Research Institute of the National Institutes of Health (NIH) defines the following terms in the context of potential transmission of inherited conditions associated with genetic mutations as follows:
Genetic testing: A type of test that is used to determine the presence or absence of a specific gene or set of genes to help diagnose a disease, screen for specific health conditions, and for other purposes.
Hereditary nonpolyposis colorectal cancer (HNPCC [Lynch Syndrome]): An inherited colorectal cancer syndrome that accounts for 5% to 8% of all colorectal cancers.
Hypermethylation: A process that occurs when additional methyl groups are added to the cytosine or adenine DNA nucleotides.
Medullary thyroid cancer: The type of thyroid cancer that develops from the C cells of the thyroid gland.
Multiple endocrine neoplasia Type 2 (MEN2): A hereditary disorder in which individuals develop a type of thyroid cancer accompanied by recurring cancer of the adrenal glands.
Mutation: A change in DNA sequence.
Second-degree relative: Any relative who is a grandparent, grandchild, uncle, aunt, niece, nephew, or half-sibling.
Third-degree relative: Any relative who is a first cousin, great grandparent or great grandchild.
References |
Peer Reviewed Publications:
Government Agency, Medical Society, and Other Authoritative Publications:
Websites for Additional Information |
Index |
EPCAM
Attenuated Familial Adenomatous Polyposis (AFAP)
Familial Adenomatous Polyposis (FAP)
Hereditary Non-Polyposis Colorectal Cancer (HNPCC)
Lynch Syndrome
MMRpredict
MMRpro
MYH-associated polyposis (MAP)
PREMM 1, 2, 6
The use of specific product names is illustrative only. It is not intended to be a recommendation of one product over another, and is not intended to represent a complete listing of all products available.
History |
Status | Date | Action |
09/27/2023 | Updated Coding section with 10/01/2023 ICD-10-CM changes; added D13.91, D48.110-D48.119 replacing D48.1, Z83.710-Z83.719 replacing Z83.71. | |
Reviewed | 11/10/2022 | Medical Policy & Technology Assessment Committee (MPTAC) review. Updated Description, Background/Overview, Definitions and Reference sections. |
Reviewed | 11/11/2021 | MPTAC review. Updated Background/Overview and Reference sections. |
Reviewed | 11/05/2020 | MPTAC review. Updated Background/Overview and Reference sections. Reformatted Coding section. |
New | 11/07/2019 | MPTAC review. Initial document development. Moved content related to gene panel testing from GENE.00028 Genetic Testing for Colorectal Cancer Susceptibility to GENE.00052 Whole Genome Sequencing, Whole Exome Sequencing, Gene panels, and Molecular Profiling. Moved remaining content of GENE.00028 Genetic Testing for Colorectal Cancer Susceptibility to new clinical utilization management guideline document with a new title, Genetic Testing for Lynch Syndrome, Familial Adenomatous Polyposis (FAP), Attenuated FAP and MYH-associated Polyposis. |
Federal and State law, as well as contract language, and Medical Policy take precedence over Clinical UM Guidelines. We reserve the right to review and update Clinical UM Guidelines periodically. Clinical guidelines approved by the Medical Policy & Technology Assessment Committee are available for general adoption by plans or lines of business for consistent review of the medical necessity of services related to the clinical guideline when the plan performs utilization review for the subject. Due to variances in utilization patterns, each plan may choose whether to adopt a particular Clinical UM Guideline. To determine if review is required for this Clinical UM Guideline, please contact the customer service number on the member's card.
Alternatively, commercial or FEP plans or lines of business which determine there is not a need to adopt the guideline to review services generally across all providers delivering services to Plan’s or line of business’s members may instead use the clinical guideline for provider education and/or to review the medical necessity of services for any provider who has been notified that his/her/its claims will be reviewed for medical necessity due to billing practices or claims that are not consistent with other providers, in terms of frequency or in some other manner.
No part of this publication may be reproduced, stored in a retrieval system or transmitted, in any form or by any means, electronic, mechanical, photocopying, or otherwise, without permission from the health plan.
© CPT Only - American Medical Association