Lynch Syndrome Testing - CAM 169

Description
Lynch syndrome (LS) (also known as hereditary non-polyposis colorectal cancer; HNPCC) is the most common form of hereditary colorectal (CRC) and endometrial cancers (EMC), resulting from an autosomal dominant inactivation of any of four mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2) leading to microsatellite instability (MSI) and associated with an increased risk of colorectal, endometrial, stomach, small bowel, and ovarian cancers.

Background 
Lynch syndrome (LS) is recognized by a hereditary predisposition to colorectal, endometrial and other cancers. It accounts for approximately 1% to 3% of all colorectal cancers and 2% to 5% of endometrial cancers (Hampel et al., 2005). In addition to colorectal and endometrial cancers, patients may present with ovarian, urinary tract, stomach, small bowel, hepatobiliary, sebaceous gland and central nervous system neoplasms (Barrow, Khan, Lalloo, Evans & Hill, 2013).

Inactivation by germline mutations or epigenetic silencing in any of four DNA mismatch repair genes (MLH1, MSH2, MSH6 and PMS2) is known to result in Lynch syndrome (Jansen, Menko, Brosens, Giardiello & Offerhaus, 2014). Mutations of the upstream EPCAM gene, which result in silencing of the MSH2 gene, produce a phenotype very similar to LS (Ligtenberg et al., 2009). Mutations in MLH1 and MSH2 are most common (90%) followed by MSH6 (10%) and PMS2 (6% ) (Jansen et al., 2014).

The lifetime risk of CRC is greatly increased in LS patients, but varies significantly from 10-74%, depending on which MMR gene is inactivated (Brosens, Offerhaus & F, 2015). Average age at CRC diagnosis in LS patients is 44 to 61 years, with tumors primarily arising proximal to the splenic flexure (Giardiello et al., 2014b). There is also a high rate of metachronous CRC (16% at 10 years; 41% at 20 years) in LS patients (Win et al., 2013). The histopathology of LS colorectal cancer is often poorly differentiated, with signet cell histology, abundant extracellular mucin, tumor infiltrating lymphocytes and a lymphoid host response to tumor (Peltomäki PT, 2010). LS patients have improved survival rates compared to similar stage spontaneous CRC (Brosens et al., 2015). Lifetime risk of endometrial cancer is significantly increased to 15 – 71% in women with mutation-specific variability (Giardiello et al., 2014b). Increased lifetime risk has also been observed in urinary, ovarian, stomach, hepatobiliary, small bowel, brain, pancreatic and prostate cancers (Brosens et al., 2015).

Several sets of clinical criteria have been developed to identify patients with LS. In 1990, the International Collaborative Group on Hereditary Nonpolyposis Colorectal Cancer (HNPCC) established criteria (Amsterdam I Criteria) for HNPCC (Vasen, Mecklin, Khan & Lynch, 1991), which were updated to be more sensitive in 1999 (Vasen, Watson, Mecklin & Lynch, 1999). The Revised Bethesda Guidelines are a third set of clinicopathologic criteria developed in 2004 to improve identification of individuals who deserve investigation for LS (Umar et al., 2004).

However, as use of clinical criteria and modeling to identify patients with LS has less than optimal sensitivity and efficiency, universal screening for LS (Cohen et al., 2016; Kidambi et al., 2015) has been recommended (Provenzale et al., 2016). Analysis by immunohistochemical testing for the MLH1/MSH2/MSH6/PMS2 proteins and/or MSI testing are commonly used to screen for LS phenotypes (Syngal et al., 2015). Tumors with loss of MLH1 should undergo analysis to exclude BRAF mutation or MLH1 promoter hypermethylation (Giardiello et al., 2014a). Patients with evidence of LS should be referred for genetic evaluation (EGAPP, 2009; Robson et al., 2015; Sepulveda et al., 2017).

Cancer Risks in Individuals With Lynch Syndrome Age ≤ 70 Years Compared to the General Population (Brosens et al., 2015)

Cancer Type General Population Risk Lynch Syndrome (MLH1 and MSH2 heterozygotes)
Risk Mean Age of Onset
Colon 4.8% 52% – 82%

44 – 61 years

Endometrium

2.7%

25% – 60%

48 – 62 years

Stomach

< 1%

6% –13%

56 years

Ovary

1.4%

4% – 12%

42.5 years

Hepatobiliary tract

< 1%

1.4% – 4%

Not reported

Urinary tract

< 1%

1% – 4%

~ 55 years
Small bowel

< 1%

3% – 6%

49 years

Brain/central nervous system

< 1%

1% – 3%

~ 50 years
Sebaceous neoplasms

< 1%

1% – 9%

Not reported

Regulatory Status
On Oct. 27, 2017 the FDA approved VENTANA MMR IHC Panel for patients diagnosed with colorectal cancer (CRC) to detect mismatch repair (MMR) proteins deficiency as an aid in the identification of probable Lynch syndrome and to detect BRAFV600E protein as an aid to differentiate between sporadic CRC and probable Lynch syndrome.

Additionally, many labs have developed specific tests that they must validate and perform in house. These laboratory-developed tests (LDTs) are regulated by the Centers for Medicare & Medicaid Services  (CMS) as high-complexity tests under the Clinical Laboratory Improvement Amendments of 1988 (CLIA ’88). As an LDT, the U.S. Food and Drug Administration has not approved or cleared this test; however, FDA clearance or approval is not currently required for clinical use.

Policy
Application of coverage criteria is dependent upon an individual’s benefit coverage at the time of the request. Specifications pertaining to Medicare and Medicaid can be found in Section VII of this policy document.

Consideration of both maternal and paternal family histories is necessary in the evaluation of individuals for risk of carrying a Lynch syndrome gene mutation; each lineage must be considered separately.  

  1. With a known familial mutation, testing of the familial deleterious Lynch Syndrome gene mutation is considered MEDICALLY NECESSARY in an individual who has received genetic counseling and is at least 18 years of age, with the following conditions:
    1. Testing is limited to the known familial mutation
    2. If the specific familial mutation is unknown, Lynch syndrome panel testing is covered in accordance with Avalon Policy AHS-M2066-Genetic Cancer Susceptibility Using Next Generation Sequencing
  2. With a diagnosis of any Lynch syndrome associated cancer (see Note 2), testing of the familial deleterious Lynch Syndrome gene mutation OR tumor testing with immunohistochemistry (IHC) and/or microsatellite instability (MSI)  is considered MEDICALLY NECESSARY in an individual who has received genetic counseling and who meets any of the following criteria:
    1. Has a personal history of a tumor with MMR deficiency determined by PCR, NGS, or IHC diagnosed at any age
    2. Diagnosed before the age of 50 years
    3. Another synchronous or metachronous LS-related cancer
    4. At least one first-degree or second-degree relative with LS-related cancer diagnosed by the age of 50 years
    5. At least two first-degree or second-degree relatives with LS-related cancers regardless of age.
  3. With a known family history (see Note 1), testing of the familial deleterious Lynch Syndrome gene mutation is considered MEDICALLY NECESSARYin an individual who has received genetic counseling and is at least 18 years of age ONLY if the family members affected by breast, ovarian, pancreatic, metastatic or intraductal prostate cancer, fallopian tube, or primary peritoneal cancers are not available for testing AND:
    1. At least one first-degree relative with colorectal or endometrial cancer diagnosed by the age of 50 years
    2. At least one first-degree relative with colorectal or endometrial cancer AND another synchronous or metachronous LS-related cancer (See Note 2)
    3. At least two first-degree or second-degree relatives with LS-related cancer (See Note 2) AND at least one of the relatives must be diagnosed by the age of 50 years
    4. At least three first-degree or second-degree relatives with LS-related cancers (See Note 2), regardless of age
    5. Has at least a 5% risk of having an MMR gene pathogenic variant based on predictive models (PREMM5, MMRpro, MMRpredict)

The following does not meet coverage criteria due to a lack of available published scientific literature confirming that the test(s) is/are required and beneficial for the diagnosis and treatment of a patient’s illness. 

  1. Genetic testing for susceptibility to colorectal cancer is considered NOT MEDICALLY NECESSARY for all other purposes, including, but not limited to, testing of the general population.

Note 1: Close blood relatives include 1st-degree relatives (e.g., parents, siblings, and children), 2nd-degree relatives (e.g., grandparents, aunts, uncles, nieces, nephews, grandchildren, and half-siblings), and 3rd-degree relatives (great-grandparents, great-aunts, great-uncles, great-grandchildren, and first cousins), all of whom are on the same side of the family.

Note 2: According to the NCCN, “LS-related cancers include colorectal, endometrial, gastric, ovarian, pancreas, urothelial, brain (usually glioblastoma), biliary tract, small intestinal cancers, as well as sebaceous adenomas, sebaceous carcinomas, and keratoacanthomas as seen in Muir-Torre syndrome (NCCN, 2018, 2019, 2021).”

Policy Gudielines 
If the tumor of the affected individual (self or family member) is available, consider initial testing of the tumor with immunohistochemistry (IHC) and/or microsatellite instability (MSI) tests.

* Germline Lynch syndrome genetic testing may include testing of the gene(s) that are indicated (based on plausible eitiologies) by the abnormal tumor test result, or instead, multi-gene testing that includes MLH1, MSH2, MSH6, PMS2, and EPCAM concurrently may be performed.

Table of Terminology 

Term

Definition

ACG

American College of Gastroenterology

AMP

Association for Molecular Pathology

APC

Adenomatous polyposis coli

ASCO

American Society of Clinical Oncology

ASCP

American Society for Clinical Pathology

AUC

Area under curve

CAP

College of American Pathologists

CLIA

Clinical Laboratory Improvement Amendments of 1988

CMS

Centers For Medicare and Medicaid Services

CRC

Colorectal cancer

DFCI

Dana-Farber Cancer Institute (Harvard)

EGAPP

Evaluation of Genomic Applications in Practice and Prevention

EMC

Endometrial cancers

EPCAM

Epithelial cellular adhesion molecule

ESMO

European Society for Medical Oncology

GCU

Genetic counselling unit

GREM1

Gremlin 1

HNPCC

Hereditary non-polyposis colorectal cancer

ICG-HNPCC

The International Collaborative Group on Hereditary Non-Polyposis Colorectal Cancer

IHC

Immunohistochemistry

LDTs

Laboratory developed tests

LS

Lynch syndrome

MLH1

MutL homolog 1

MLH6

MutL homolog 6

MMR

Mismatch repair

MMR-D

Mismach repair protein deficiency

MSH2

MutS homolog 2

MSH6

MutS homolog 6

MSI

Microsatellite instability

MUTYH

MutY DNA glycosylase

NCCN

National Comprehensive Cancer Network

NCI

National Cancer Institute

NGS

Next generation sequencing

NICE

National Institute for Health and Care Excellence

NSGC

National Society of Genetic Counsellors

NTHL1

Nth like deoxyribonucleic acid glycosylase 1

O/E

Observed to expected ratio

PCR

Polymerase chain reaction

PMS2

Post meiotic segregation increased 2 (S. cerevisiae)/PMS1 homolog 2

POLD1

Deoxyribonucleic acid polymerase delta 1

POLE

Deoxyribonucleic acid  polymerase epsilon, catalytic subunit

PREMM5

Prediction model for gene mutations 5

SEOM

Spanish Society of Medical Oncology

TP53

Tumor protein 53

UGI

Upper gastrointestinal

Rationale
Lynch syndrome (LS) is recognized by a hereditary predisposition to colorectal, endometrial, and other cancers due to inactivation by germline mutations or epigenetic silencing in any of four DNA mismatch repair genes: MLH1, MSH2, MSH6, and PMS2. Mutations in MLH1 and MSH2 are most common (90%) followed by MSH6 (10%) and PMS2 (6%) (Jansen et al., 2014). Mutations of the upstream EPCAM gene which result in silencing of the MSH2 gene produce a phenotype very similar to LS (Ligtenberg et al., 2009). LS accounts for approximately 3% to 5% of all colorectal cancers (Yilmaz et al., 2020) and 2% to 5% of endometrial cancers (Hampel et al., 2005). In addition to colorectal and endometrial cancers, patients may present with ovarian, urinary tract, stomach, small bowel, hepatobiliary, sebaceous gland and central nervous system neoplasms (Barrow et al., 2013).

The lifetime risk of colorectal cancer (CRC) is greatly increased in LS patients but varies significantly from 10-74% dependent on which MMR gene is inactivated (Brosens et al., 2015). The average age at CRC diagnosis in LS patients is 44 to 61 years with tumors primarily arising proximal to the splenic flexure (Giardiello et al., 2014). There is also a high rate of metachronous CRC (16% at 10 years; 41% at 20 years) in LS patients (Win et al., 2013). The histopathology of LS colorectal cancer is often poorly differentiated with signet cell histology, abundant extracellular mucin, tumor infiltrating lymphocytes, and a lymphoid host response to tumor (Peltomäki PT, 2010). LS patients have improved survival rates compared to similar stage spontaneous CRC (Brosens et al., 2015). Lifetime risk of endometrial cancer is significantly increased to 15 – 71% of women with mutation specific variability (Giardiello et al., 2014). Increased lifetime risks have also been observed in urinary, ovarian, stomach, hepatobiliary, small bowel, brain, pancreatic and prostate cancers (Brosens et al., 2015).

Cancer Risks in Individuals with Lynch Syndrome Age ≤ 70 Years Compared to the General Population (Brosens et al., 2015) 

 

Cancer Type

 

General Population Risk

Lynch Syndrome (MLH1 and MSH2 heterozygotes)

Risk

Mean Age of Onset

Colon

4.8%

52% – 82%

44 – 61 years

Endometrium

2.7%

25% – 60%

48 – 62 years

Stomach

< 1%

6% – 13%

56 years

Ovary

1.4%

4% – 12%

42.5 years

Hepatobiliary tract

< 1%

1.4% – 4%

Not reported

Urinary tract

< 1%

1% – 4%

~ 55 years

Small bowel

< 1%

3% – 6%

49 years

Brain/central nervous system

< 1%

1% – 3%

~ 50 years

Sebaceous neoplasms

< 1%

1% – 9%

Not reported

Several sets of clinical criteria have been developed to identify patients with LS. In 1990, the International Collaborative Group on Hereditary Nonpolyposis Colorectal Cancer (HNPCC) established criteria (Amsterdam I Criteria) for HNPCC (Vasen et al., 1991), which were updated to be more sensitive in 1999 (Vasen et al., 1999). The Revised Bethesda Guidelines are a third set of clinicopathologic criteria developed in 2004 to improve identification of individuals who deserve investigation for LS; however, they state, “The goal of the Bethesda Guidelines is to identify HNPCC patients, not to identify MSI-H tumors from patients in sporadic populations that may have better prognoses or different therapeutic implications (Umar et al., 2004).”

Analytical Validity
Currently, there exist two main approaches to diagnosing Lynch syndrome. One approach leverages molecular screening of colorectal and endometrial tumor specimens for evidence of defective MMR function (MMR-D) or high-level MSI (MSI-H) to identify patients with cancer who should undergo germline testing for pathogenic MMR gene variants. The other focuses on using direct germline testing performed on patients whose family histories of cancer are suspicious for Lynch syndrome. In recent years, molecular testing has gained traction for identification of individuals with Lynch syndrome due to its robust sensitivity and specificity, testing of which can be generalized into one of four categories: polymerase chain reaction (PCR)-based MSI testing, immunohistochemical staining (or immunohistochemistry [IHC]) for the MMR proteins, MLH1 promoter methylation analysis (or somatic BRAF V600E mutation analysis), and next-generation somatic (and/or germline) sequencing assays (Yurgelun & Hampel, 2018).

The specificity and sensitivity of these methods can be polemical, and thus engender questions of what tests to even employ. Stinton et al. (2021) conducted a systematic review of literature published up to August 2019 to assess the immunohistochemistry and microsatellite instability-based testing (with or without MLH1 promoter methylation testing) for Lynch syndrome in women with endometrial cancer. Thirteen studies consisting of approximately 3500 people were examined, and the researchers determined that, after adjusting for studies with highly selective inclusion criteria, sensitivity ranged from 60.9% – 83.3% for immunohistochemistry, 69.2 – 89.9% for microsatellite instability-based testing, and 72.4-92.3% for studies combining immunohistochemistry, microsatellite instability-based testing, and MLH1 promoter methylation testing. According to the authors, they “found no statistically significant differences in test accuracy estimates (sensitivity, specificity) in head-to-head studies of immunohistochemistry versus microsatellite instability-based testing” and thus concluded that “sensitivity of the index tests were generally high, though most studies had much lower specificity”. However, though the authors “found no evidence that test accuracy differed between IHC and MSI based strategies”, they acknowledged that the evidence base is still quite small and at risk of bias (Stinton et al., 2021).

The complexity of Lynch syndrome likewise evokes the use of complex diagnostic algorithms, oftentimes involving multiple subsequent germline and somatic tests. The utility and efficacy of these algorithms are also points of contention, given the novelty of said algorithms. Through retrospectively reviewing a consecutive series of 702 patients with colorectal cancer and endometrial cancer undergoing paired tumor/germline analysis of the LS genes at a clinical diagnostic laboratory, Salvador et al. (2019) asserted that “Paired testing identified a cause for MMRd tumors in 76% and 61% of patients without and with prior LS germline testing, respectively”, leading the researchers to support inclusion of tumor sequencing as well as comprehensive LS germline testing in the LS testing algorithm.

Statistical models to predict risk of MMR mutations include PREMM5, MMRpredict, and MMRpro.  The PREMM5 clinical prediction algorithm, available at http://premm.dfci.harvard.edu/, “estimates the cumulative probability of an individual carrying a germline mutation in the MLH1, MSH2, MSH6, PMS2, or EPCAM genes” using an individual’s personal and family history of colorectal cancer, endometrial cancer, or other LS-related cancers with the results given as a percentage of overall predicted probability of mutation in one of the four LS-related genes (DFCI, 2016). A study using the clinical and germline data from more than 18,000 individuals published in 2017 validated the use of the PREMM5 model. The report shows that for the four LS-related genes, PREMM5 can distinguish “carriers from noncarriers with an area under the curve (AUC) of 0.81 (95% CI, 0.79 to 0.82), and performance was similar in the validation cohort (AUC, 0.83; 95% CI, 0.75 to 0.92). Prediction was more difficult for PMS2 mutations (AUC, 0.64; 95% CI, 0.60 to 0.68) than for other genes.” The authors conclude, “ PREMM5 provides comprehensive risk estimation of all five LS genes and supports LS genetic testing for individuals with scores ≥ 2.5% (Kastrinos et al., 2017).” Kastrinos et al. (2018) published another article the following year stating that a threshold of ≥ 2.5% is now recommended to improve the identification of PMS2 carriers by enhancing the model’s sensitivity (a threshold of ≥ 5% was previously recommended).

MMRpro, statistical model and software using family history of colorectal and endometrial cancers, is available for free download at http://www4.utsouthwestern.edu/breasthealth/cagene/. “The results give useful information about an individual's colon cancer risk before he or she decides to undergo invasive screenings or expensive genetic testing (Harvard, 2019).” A study released in 2015 concluded that MMRpro was comparable to the PREMM1,2,6 model in discriminating both clinic- and population-based cohorts (Kastrinos et al., 2016). Another study in 2017 investigated the use of MMRpro in predicting MLH1 mutations since, unlike the other LS-related genes, immunohistochemistry is less sensitive as a prescreening test for these mutations. By limiting the scope of the study to MLH1 mutations, MMRpro outperforms the PREMM1,2,6 algorithm (AUC 0.83 versus 0.68, respectively). The authors state, “Considering a threshold of 5%, MMRpro would eliminate unnecessary germline mutation analysis in a significant proportion of cases while keeping very high sensitivity. We conclude that MMRpro is useful to correctly predict who should be screened for a germline MLH1 gene mutation and propose an algorithm to improve the cost-effectiveness of LS diagnosis (Cabreira et al., 2017).”

Likewise, the MMRpredict algorithm, available at http://hnpccpredict.hgu.mrc.ac.uk/, is jointly operated by the Colon Cancer Genetics Group at the University of Edinburgh and MRC Human Genetics Unit of Edinburgh. This algorithm predicts the probability of a mutation carrier of an affected individual using criteria consisting of the age at time of diagnosis, gender, tumor location, synchronicity of tumor, and family history (MRC, 2014). A 2018 study shows that MMRpredict performs better than the PREMM5 model in identifying PMS2 mutation carriers (AUCs 0.72 and 0.51, respectively), and the efficacy of the PREMM5 model is more dependent on the location of the tumor. Both algorithms were comparable in predicting MLH1 and MSH2 mutation carriers (Goverde et al., 2018). These data apparently contradict earlier findings where a previous version of the PREMM model, PREMM1,2,6, performed better than MMRpredict in predicting carriers of MLH1, MSH2, or MSH6 gene mutations. “For clinic- and population-based cohorts, O/E [observed-to-expected ratio] deviated from 1 for MMRPredict (0.38 and 0.31, respectively) and MMRPro (0.62 and 0.36) but were more satisfactory for PREMM1,2,6 (1.0 and 0.70). MMRPro or PREMM1,2,6 predictions were clinically useful at thresholds of 5% or greater and in particular at greater than 15% (Kastrinos et al., 2016).”

Mercado et al. (2012) published a study to assess the sensitivity and specificity of PREMM1,2,6, MMRpredict, and MMRpro in 692 endometrial cancer cases (563 population-based and 129 clinic-based cases). Pathogenic mutations were identified in 3% of the population-based participants and in 62% of the clinic-based participants. “PREMM(1,2,6), MMRpredict, and MMRpro were able to distinguish mutation carriers from noncarriers (AUC of 0.77, 0.76, and 0.77, respectively), among population-based cases. All three models had lower discrimination for the clinic-based cohort, with AUCs of 0.67, 0.64, and 0.54, respectively (Mercado et al., 2012).” For PREMM1,2,6, a sensitivity of 93% and a specificity of 5% was identified in population-based participants and a sensitivity of 99% and specificity of 2% was identified in clinic-based cases. For MMRpredict, a sensitivity of 71% and a specificity of 64% was identified in population-based participants and a sensitivity of 90% and specificity of 0% was identified in clinic-based cases. For MMRpro, a sensitivity of 57% and a specificity of 85% was identified in population-based participants and a sensitivity of 95% and specificity of 10% was identified in clinic-based cases (Mercado et al., 2012). These authors state that the PREMM1,2,6, MMRpredict, and MMRpro seem to have limited utility in the determining which endometrial cancer patients would benefit from Lynch syndrome testing.

Clinical Utility and Validity
As use of clinical criteria and modeling to identify patients with LS has less than optimal sensitivity and can vary in efficacy between different ethnic populations (Lee et al., 2016), universal screening for LS (Cohen et al., 2016; Kidambi et al., 2015) has been recommended (Provenzale et al., 2016). Analysis by immunohistochemical testing for the MLH1/MSH2/MSH6/PMS2 proteins and/or MSI testing are commonly used to screen for LS phenotypes (Syngal et al., 2015). Tumors with loss of MLH1 should undergo analysis to exclude BRAF mutation or MLH1 promoter hypermethylation according to the USPSTF (Giardiello et al., 2014). Moreover, patients with evidence of LS should be referred for genetic evaluation (EGAPP, 2009; Robson et al., 2015; Sepulveda et al., 2017).

Adar et al. (2018) completed a study to determine the value of screening both CRC and endometrial cancer (EMC) tumors in the same population. An immunohistochemistry (IHC) screening program evaluated all patients at two centers newly diagnosed with CRC and/or EMCs. “Genetic testing was recommended for those who had tumors with absent mutS homolog 2 (MSH2), MSH6, or postmeiotoic segregation increased 2 (PMS2) expression and for those who had tumors with absent mutL homolog 1 (MLH1) expression and no v-Raf murine sarcoma viral oncogene homolog B (BRAF) mutation or MLH1 promoter methylation (Adar et al., 2018).” Scores from the PREMM1,2,6 and PREMM5 prediction models were also obtained, along with traditional Amsterdam II criteria and revised Bethesda criteria. Of the 1774 total patients screened for LS (1290 with CRC and 484 with EMC), genetic testing was recommended for 169 patients. LS was diagnosed in 16 patients with CRC and 8 patients with EMC based on traditional detection methods (Amsterdam II criteria, revised Bethesda criteria, PREMM1,2,6 and PREMM5 prediction models). Of the patients genetically tested, the LS diagnosis rate was higher. Specifically, “The Amsterdam II criteria, revised Bethesda criteria, and both PREMM calculators would have missed 62.5%, 50.0%, and 12.5% of the identified patients with LS, respectively (Adar et al., 2018).” The results of this study show that risk assessment tools are likely to miss a percentage of LS diagnoses.

Laish et al. (2021) conducted a retrospective cohort study on young patients with colorectal adenomatous polyps that aimed to “evaluate the yield of germline mutational analysis in diagnosis of LS.” All patients were 45 years or younger, with at least one adenoma removal, and underwent genetic testing by a multigene panel or LS-Jewish founder mutation panel. They found that from the 92 patients that underwent both panels, “18 patients were identified with pathogenic mutations in actionable genes, including LS-associated genes in 6 (6.5%), BRCA2 in 2 (2.5%), GREM1 in 1 (1.2%), and low-penetrance genes — APC I1307K and CHECK2- in 9 (11.4%) patients.” Generally, routine screening for establishing LS in young patients with adenomas is not recommended due to low yield, but the researchers proposed that due to these findings, genetic screening should be offered when they fulfill the clinical guidelines for LS.

Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group
In 2009, the EGAPP Working Group recommended (EGAPP, 2009): 

  1. Offering genetic testing for Lynch Syndrome to individuals with newly diagnosed colorectal cancer to reduce morbidity and mortality in relatives. However, they do not recommend a specific testing protocol.
  2. That individuals with newly diagnosed CRC should be routinely offered counseling and educational materials aimed at informing them and their relatives of the potential benefits and harms associated with genetic testing to identify Lynch Syndrome.  
  3. “Microsatellite instability (MSI) testing or immunohistochemical (IHC) testing (with or without BRAF mutation testing) of the tumor tissue are examples of preliminary testing strategies that could be used to select patients for subsequent diagnostic testing. Diagnostic testing involves MMR gene mutation (and deletion/duplication) testing of the proband, usually using a blood sample. Lynch syndrome is most commonly caused by mutations in the two MMR genes MLH1 and MSH2; less commonly by mutations in MSH6 and PMS2.”

The EGAPP was launched by the CDC Office of Public Health Genomics in 2004. EGAPP’s website, which includes the 2009 Lynch Syndrome guidelines, states that the page is archived and is no longer being updated (EGAPP, 2016).

National Comprehensive Cancer Network (NCCN)
The NCCN lists the following criteria for the evaluation of Lynch Syndrome:  

  • “Known LS pathogenic variant in the family
  • Personal history of a tumor with MMR deficiency determined by PCR, NGS, or IHC diagnosed at any age
  • An individual with colorectal or endometrial cancer and any of the following:
    • Diagnosed < 50 y
    • A synchronous or metachronous LS-related cancer regardless of age
    • 1 first-degree or second-degree relative with LS-related cancer diagnosed < 50 y
    • ≥ 2 first-degree or second-degree relatives with LS-related cancers regardless of age
  • Family history of any of the following:
    • ≥ 1 first-degree relative with colorectal or endometrial cancer diagnosed < 50 y
    • ≥ 1 first-degree relative with colorectal or endometrial cancer and a synchronous or metachronous LS-related cancer regardless of age
    • ≥ 2 first-degree or second-degree relatives with LS-related cancer, including ≥ 1 diagnosed < 50 y
    • ≥ 3 first-degree or second-degree relatives with LS-related cancers regardless of age
  • Increased model-predicted risk for Lynch Syndrome
    • An individual with a ≥ 5% risk of having an MMR gene pathogenic variant based on predictive models (i.e., PREMM5, MMRpro, MMRpredict)
      • Individuals with a personal history of colorectal and/or endometrial cancer with a PREMM5 score of ≥ 2.5% should be considered for multi-gene panel testing.
      • For individuals without a personal history of colorectal cancer and/or endometrial cancer, some data have suggested using a PREMM5 score threshold of ≥2 .5% rather than ≥ 5% to select individuals for MMR genetic testing. Based on these data, it is reasonable for testing to be done based on the ≥ 2.5% score result and clinical judgment. Of note, with the lower threshold, there is an increase in sensitivity, but a decrease in specificity.”

The NCCN considers LS-related cancers to “include colorectal, endometrial, gastric, ovarian, pancreas, urothelial, brain (usually glioblastoma), biliary tract, and small intestinal cancers, as well as sebaceous adenomas, sebaceous carcinomas, and keratoacanthomas as seen in Muir-Torre syndrome.”

The NCCN also states the following: “The panel recommends tumor screening for MMR deficiency for all colorectal and endometrial cancers regardless of age at diagnosis. Consider tumor screening for MMR deficiency for sebaceous neoplasms as well as the following adenocarcinomas: small bowel, gastric, pancreas, biliary tract, brain, bladder, urothelial, and adrenocortical cancers regardless of age at diagnosis. Direct referral for germline testing to rule out LS may be preferred in patients with a strong family history or if diagnosed age < 50y, … MSI-H, or loss of MMR protein expression.”

In the section of the guidelines titled “Strategies for Evaluating for Lynch syndrome in Individuals Meeting Criteria for the Evaluation of Lynch Syndrome,” it is recommended that when a deleterious Lynch syndrome pathogenic variant in a family is known, “the individual should be tested for the familial pathogenic variant.” Moreover, the guidelines recommend that genetic testing should also be offered to at-risk family members.

When no Lynch syndrome pathogenic variant is present in proband or in family, individuals should first refer to the Amsterdam and Bethesda criteria. However, overall, “for individuals without a previously known Lynch syndrome the panel recommends additional evaluation for Lynch syndrome based on clinical criteria, including for individuals with no known Lynch syndrome pathogenic variant who meet the Amsterdam II criteria or Bethesda Guidelines, have a cancer diagnosis prior to age 50 years, or have predicted risk for Lynch syndrome > 5% on one of the following prediction models: MMRpro, PREMM5, or MMRpredict.” However, due to issues of suboptimal sensitivity of clinical criteria when it comes to identifying individuals with Lynch syndrome, “the panel recommends universal screening of all CRCs, in order to maximize sensitivity for identifying individuals with Lynch syndrome (LS) and to simplify care processes.”

In terms of initial tumor testing methodologies, “the panel recommends using only one test [either MSI or IHC testing] initially” and only “If normal results are found and Lynch syndrome is strongly suspected” that the other test be employed. Moreover, “Where genetic testing is recommended, the panel recommends consultation with an individual with expertise in genetics, and germline testing to exclude presence of Lynch-associated mutations.”

The (NCCN, 2021) does not recommend multi-gene testing in the following situations:

1)      When “there is an individual from a family with a known mutation and there is no other reason for multi-gene testing;

2)      the patient’s family history is strongly suggestive of a known hereditary syndrome; and

3)      the patient is diagnosed with CRC with MSI or loss of one or more DNA MMR proteins

In the above three scenarios, syndrome-specific panels may be considered.”

“Multigene testing may be considered (but may not be limited based on clinical judgment) in the following scenarios: 

  • A patient with a personal or family history that meets criteria for more than one hereditary cancer syndrome (eg, Lynch syndrome and BRCA-related breast and/or ovarian cancer)
  • Colonic polyposis with uncertain histology
  • Adenomatous polyposis (specific to APC, MUTYH, GREM1, NTHL1, POLE, and POLD1)
  • Family history does not meet criteria for established testing guidelines but there is suspicion of hereditary cancer, and an appropriate panel is available
  • Family history is limited or unknown, but patient has concerns about hereditary cancer
  • As second-line testing when first-line testing is inconclusive ”(NCCN, 2021).

National Institute for Health and Care Excellence (NICE)
NICE, in 2017, released their guidelines concerning molecular testing for LS in people with CRC. The recommend the following (NICE, 2017): 

  • “Offer testing to all people with colorectal cancer, when first diagnosed, using immunohistochemistry for mismatch repair proteins or microsatellite instability testing to identify tumours with deficient DNA mismatch repair, and to guide further sequential testing for Lynch syndrome .... Do not wait for the results before starting treatment.
  • “If using immunohistochemistry, follow the steps in table 1.”

Table 1: Steps in the immunohistochemistry testing strategy (NICE, 2017)

Step 1

Do an immunohistochemistry 4-panel test for MLH1, MSH2, MSH6 and PMS2.

Step 2

If the MLH1 immunohistochemistry result is abnormal, use sequential BRAF V600E and MLH1 promoter hypermethylation testing to differentiate sporadic and Lynch syndrome-associated colorectal cancers. First do a BRAF V600E test.

If the MSH2, MSH6 or PMS2 immunohistochemistry results are abnormal, confirm Lynch syndrome by genetic testing of germline DNA.

Step 3

If the BRAF V600E test is negative, do an MLH1 promoter hypermethylation test.

tep 4

If the MLH1 promoter hypermethylation test is negative, confirm Lynch syndrome by genetic testing of germline DNA.

  • “If using microsatellite instability testing, follow the steps in table 2.”

Table 2: Steps in the microsatellite instability testing strategy (NICE, 2017)

Step 1

Do a microsatellite instability test.

Step 2

If the microsatellite instability test result is positive, use sequential BRAF V600E and MLH1 promoter hypermethylation testing to differentiate sporadic and Lynch syndrome-associated colorectal cancers. First do a BRAF V600E test.

Step 3

If the BRAF V600E test is negative, do an MLH1 promoter hypermethylation test

Step 4

If the MLH1 promoter hypermethylation test is negative, confirm Lynch syndrome by genetic testing of germline DNA.

  • “Healthcare professionals should ensure that people are informed of the possible implications of test results for both themselves and their relatives, and ensure that relevant support and information is available. Discussion of genetic testing should be done by a healthcare professional with appropriate training (NICE, 2017).”

The NICE published new recommendations dealing with testing strategies for Lynch syndrome in people with endometrial cancer in 2020 (NICE, 2020). Said recommendations are provided below:

“1.1 Offer testing for Lynch syndrome to people who are diagnosed with endometrial cancer. Use immunohistochemistry (IHC) to identify tumours with mismatch repair (MMR) deficiency:  

  • If IHC is abnormal with loss of MLH1, or loss of both MLH1 and PMS2 protein expression, do MLH1 promoter hypermethylation testing of tumour DNA. If MLH1 promoter hypermethylation is not detected, offer germline genetic testing to confirm Lynch syndrome.
  • If IHC is abnormal with loss of MSH2, MSH6 or isolated PMS2 protein expression, offer germline genetic testing to confirm Lynch syndrome.

1.2  Healthcare professionals should inform people about the possible implications of test results for both themselves and their relatives, and give support and information. Discussion of genetic testing and obtaining consent should be done by a healthcare professional with appropriate training.

1.3  Laboratories doing IHC for MMR proteins, MLH1 promoter hypermethylation testing or germline genetic testing should take part in a recognised external quality assurance programme.”

American Society of Clinical Oncology (ASCO)
The American Society of Clinical Oncology (ASCO) recommends that “genetic testing only be conducted in the setting of pre- and post-test counseling” (Robson et al., 2010). In 2015, ASCO stated that “identifying inherited mutations in genes such as BRCA1BRCA2, and the genes associated with Lynch syndrome allows for interventions that can significantly reduce the development of cancer and improve survival. Targeted capture assays employing NGS [next generation sequencing] technology allow for testing many genes simultaneously, including genes that would not necessarily have been tested using the phenotype-directed approach, as well as genes of less clearly established clinical utility” (Robson et al., 2015). According to ASCO, multi-gene panel testing is particularly useful in situations where there are multiple high-penetrance genes associated with a specific cancer, and “one example of such a situation is Lynch syndrome, when the results of immunohistochemical analysis are not available to direct testing” (Robson et al., 2015).

U.S. Multi-Society Task Force on Colorectal Cancer
In 2014, The U.S. Multi-Society Task Force published the following guidelines on Colorectal Cancer (Giardiello et al., 2014):

Testing for MMR deficiency of newly diagnosed CRC should be performed. This can be done for all CRCs, or CRC diagnosed at age 70 years or younger, and in individuals older than 70 years who have a family historyconcerning for LS. Analysis can be done by IHC testing for the MLH1/MSH2/MSH6/PMS2 proteins and/or testing for MSI. Tumors that demonstrate loss of MLH1 should undergo BRAF testing or analysis of MLH1 promoter hypermethylation.” Also, “Individuals who have a personal history of a tumor showing evidence of MMR deficiency (without evidence of MLH1 promoter methylation); uterine cancer diagnosed at younger than age 50 years; a known family MMR gene mutation; fulfill Amsterdam criteria or revised Bethesda guidelines; and/or have a personal risk of ≥5% chance of LS based on prediction models should undergo genetic evaluation for LS.”

Updated 2017 guidelines from the U.S. Multi-Society Task Force give the following guideline for colorectal cancer screening and LS (Rex et al., 2017):  

  • “colonoscopy is recommended at 10-year intervals in average-risk persons and at 1- to 2-year intervals in those with Lynch syndrome.”

However, for specific LS related screening techniques and recommendations, the updated 2017 article states that the Giardiello et al. (2014) guidelines are still the most current.

American Society for Clinical Pathology (ASCP), College of American Pathologists (CAP), Association for Molecular Pathology (AMP), and American Society of Clinical Oncology (ASCO)
The ASCP, CAP, AMP, and ASCO issued guidelines in 2017 stating “BRAF p.V600 mutational analysis should be performed in deficient MMR tumors with loss of MLH1 to evaluate for Lynch Syndrome risk. Presence of a BRAF mutation strongly favors a sporadic pathogenesis. The absence of BRAF mutation does not exclude risk of Lynch syndrome.” In addition, they have added the following recommendation for clinicians: “clinicians should order mismatch repair status testing in patients with colorectal cancers for the identification of patients at high risk for Lynch syndrome and/or prognostic stratification” (Sepulveda et al., 2017).

American College of Gastroenterology (ACG)
In 2015, ACG issued the following practice guidelines for the management of patients with hereditary gastrointestinal cancer syndromes (Syngal et al., 2015):  

  • “All newly diagnosed colorectal cancers should be evaluated for mismatch repair deficiency.
  • Analysis may be done by immunohistochemical (IHC) testing for the MLH1/MSH2/MSH6/PMS2 proteins and/or testing for microsatellite instability; tumors that demonstrate loss of MLH1 should undergo BRAF testing or analysis for MLH1 promoter hypermethylation.
  • Individuals who have a personal history of a tumor showing evidence of mismatch repair deficiency (and no demonstrated BRAF mutation or hypermethylation of MLH1), a known family mutation associated with LS, or a risk of ≥ 5% chance of LS based on risk prediction models should undergo genetic evaluation for LS.
  • Genetic testing of patients with suspected LS should include germline mutation genetic testing for the MLH1, MSH2, MSH6, PMS2, and/or EPCAM genes or the altered gene(s) indicated by IHC testing.”

American Society of Colon and Rectal Surgeons
The American Society of Colon and Rectal Surgeons (Herzig et al., 2017) published guidelines which recommend (based on 2014 U.S. Multi-Society Task Force on Colorectal Cancer): 

“Universal testing (tumor testing): 

  • Testing for MMR deficiency of newly diagnosed CRC should be performed
  • This can be done for all CRCs or CRC diagnosed at age ≤ 70 y and in individuals > 70 y who have a family history concerning for LS
  • Analysis can be done by IHC testing for the MLH1/MSH2/MSH6/PMS2 proteins and/or testing for MSI
  • Tumors that demonstrate loss of MLH1 should undergo BRAF testing or analysis of MLH1 promoter hypermethylation
  • To facilitate surgical planning, tumor testing on suspected CRC should be performed on preoperative biopsy specimens, if possible

Traditional testing (germline testing): 

  • Individuals who have a personal history of a Lynch syndrome–related tumor showing evidence of MMR deficiency (without evidence of MLH1 promoter methylation)
  • Personal history of uterine cancer diagnosed at age <50 y
  • A known family MMR gene mutation
  • Fulfill Amsterdam criteria or revised Bethesda guidelines
  • Have a personal risk of ≥ 5% chance of LS based on prediction models”

Spanish Society of Medical Oncology (SEOM)
The SEOM published guidelines on hereditary colorectal cancer. These guidelines include the following recommendations:  

  • “Different screening strategies for LS of all newly diagnosed CRC and EC [endometrial cancers] can be considered including tumor tests for defective MMR function and/or high-level MSI and/or NGS tumor sequencing including BRAF.
  • In case of lack of expression of MLH1 and PMS2 by immunohistochemistry, BRAFV600E mutation and/or MLH1 promoter hypermethylation should be carried out to rule out sporadic cases.
  • Patients with molecular profiles compatible with LS should be referred to GCU for appropriate counseling and NGS germline genetic testing.
  • In families with fulfillment of rBC or a ≥ 2.5% likelihood of LS on the PREMM5 prediction model, prevalent and/or previous CRC and/or EC should follow the same screening procedure before considering referral to GCU (evidence level B, strength 1).
  • Multigene panel testing for hereditary CRC and polyposis should include the genes:
    • APC, BMPR1A, EPCAM, MLH1, MSH2, MSH6, MUTYH, PMS2, PTEN, SMAD4 and STK11 (evidence level A, strength 1).
    • AXIN2, BLM, GREM1, NTHL1, POLD1, POLE and TP53 (evidence level B, strength 2).
  • Criteria for referral to a GCU and APC/MUTYH or multigene panel testing (evidence level B, strength 1):
    • 1. Patients with > 10 synchronous adenomatous colonic polyps histologically confirmed.
    • 2. Family history of adenomatous colonic polyps (> 10 in > 1 relative), at young age and extracolonic manifestations.
    • 3. Gastric polyps (> 100), in body and fundus, preponderantly fundic glands polyps. Proton pump inhibitor use must be excluded.
    • 4. Consider in: hepatoblastoma, desmoid tumor, cribriform-morular variant of papillary thyroid carcinoma, multifocal or bilateral congenital hypertrophy of retinal pigmented epithelium.
    • 5. Known familial mutation in at-risk relatives (Guillen-Ponce et al., 2020).”

National Society of Genetic Counselors (NSGC) and the Collaborative Group of the Americas on Inherited Colorectal Cancer
The following guidelines were provided by the NSGC and the Collaborative Group of the Americas on Inherited Colorectal Cancer:  

  • “Microsatellite instability (MSI) and immunohistochemistry (IHC) tumor analyses should be performed on CRC or endometrial cancers as the first‐line testing strategy for any patient being evaluated for LS (this includes individuals with CRC or endometrial cancer who meet Amsterdam I or II criteria or Bethesda guidelines).
  • MLH1 promoter methylation and BRAF V600E mutation testing may help to reduce the number of germline genetic tests needed when IHC reveals absence of MLH1 and PMS2. However, NSGC and the CGA‐ICC did not find enough data to recommend one test over the other or both concomitantly.
  • IHC may occasionally yield atypical results. If IHC reveals absent MLH1 or MSH2 only, consider genetic testing of those genes individually. If IHC reveals loss of more than two MMR proteins, consider repeating the IHC analysis. If the results persist or if repeat testing was not performed, consider following the algorithm based on the most likely true results (i.e., if MSH2, MSH6 and MLH1 or PMS2 are all absent, follow the loss of MSH2/MSH6 pathway; if MLH1, PMS2 and MSH6 or MSH2 are all absent, follow the MLH1 and PMS2 pathway). Further, it is worth noting that there is a mononucleotide microsatellite in MSH6 that may cause loss of MSH6 with another MMR germline mutation leading to aberrant IHC staining patterns
  • When MSI testing is stable, but IHC shows absence of one or more MMR proteins, clinical judgment should be used to determine whether tumor studies should be repeated or germline genetic testing should be pursued
  • MSI testing should include, at a minimum, the five markers included in the NCI panel
  • While we recognize that some third party payers may not cover MSI and/or IHC analyses on the tumor of a patient's family member(s) (e.g., the family member is deceased), in our expert opinion, we deem testing the family member(s)’ tumor is justified because: 1) LS is one of a few hereditary cancer syndromes that has a validated screening test to determine if germline genetic testing is warranted; 2) if an affected family member is living, it is likely that MSI and IHC will be covered by that relative's insurance; 3) a negative germline genetic test for all four MMR genes in an unaffected patient is uninformative; 4) the cost of direct germline genetic testing for each MMR gene ranges from $1000 to $1500, whereas the cost of MSI and IHC together is ~$1000; 5) if IHC is abnormal, additional tumor tests (BRAF and MLH1 promoter methylation) may help determine if germline genetic testing is necessary and if it is warranted, testing can be targeted to one or two genes limiting overall costs; and 6) normal MSI and IHC results on an affected individual would significantly lower the likelihood that LS is the explanation for the cancer in the family and germline genetic testing would most likely not be needed.
  • Direct germline genetic testing (refers to both DNA sequencing and a technology that detects large rearrangements, insertions, deletions and duplications) may be considered on an affected or unaffected patient being evaluated for LS when MSI and IHC testing are not feasible.
    • In the event that a tumor block is not available, a family member(s) is not willing or able to participate in testing, there are financial concerns or there is insufficient tissue to do either MSI or IHC testing, when indicated (e.g., high familial risk is present such as Amsterdam criteria), direct germline genetic testing may be considered. It should be noted, however, that negative germline testing in an affected individual who has not had MMR IHC can also be uninformative because there are some individuals with unidentifiable MMR gene mutations that would be followed as having LS based on abnormal IHC (Weissman et al., 2012).”

European Society for Medical Oncology (ESMO) (Stjepanovic et al., 2019; Stoffel et al., 2015)
The ESMO published guidelines in 2015 for familial risk-colorectal cancer. The ASCO has endorsed these guidelines, with minor modifications.

The ASCO endorsement panel has “determined that the recommendations of the ESMO guideline are clear, thorough, and based on the most relevant scientific evidence (ASCO, 2014).” The ASCO endorsed the ESMO guidelines (below) with a few minor qualifying statements (in bold):  

  • “Tumor testing for DNA mismatch repair (MMR) deficiency with immunohistochemistry for MMR proteins and/or MSI should be assessed in all CRC patients. As an alternate strategy, tumor testing should be carried out in individuals with CRC younger than 70 years, or those older than 70 years who fulfill any of the revised Bethesda guidelines
  • If loss of MLH1/PMS2 protein expression is observed in the tumor, analysis of BRAF V600E mutation or analysis of methylation of the MLH1 promoter should be carried out first to rule out a sporadic case. If tumor is MMR deficient and somatic BRAF mutation is not detected or MLH1 promoter methylation is not identified, testing for germline mutations is indicated.
  • If loss of any of the other proteins (MSH2, MSH6, PMS2) is observed, germline genetic testing should be carried out for the genes corresponding to the absent proteins (eg, MSH2, MSH6, EPCAM, PMS2, or MLH1).
  • Full germline genetic testing for Lynch syndrome should include DNA sequencing and large rearrangement analysis
  • Full germline genetic testing of APC should include DNA sequencing and large rearrangement analysis.
  • Germline testing of MUTYH can be initiated by screening for the most common mutations (G396D, Y179C) in the white population followed by analysis of the entire gene in heterozygotes. Founder mutations among ethnic groups should be taken into account. For nonwhite individuals, full sequencing of MUTYH should be considered (Stoffel et al., 2015).”

In 2019, the ESMO updated their clinical practice guidelines for hereditary gastrointestional cancers, including those for Lynch syndrome. In this set of recommendations, the ESMO maintains that tumor testing with IHC for MMR proteins and/or MSI is recommended in individuals with CRC and that if loss of MLH1 is observed in the tumour, analysis of BRAF V600E mutation or analysis of the methylation of the MLH1 promoter should be carried out first to rule out a sporadic case. They also maintained that full germline genetic testing should include DNA sequencing and large rearrangement analysis, as in the previous guidelines, but also proposed that for those with Lynch syndrome,  

  • “Somatic MMR gene testing for patients with unexplained abnormal tumour screening is suggested [III, B]
  • Clinical risk can be assessed using Amsterdam criteria II or the revised Bethesda guidelines
  • MMR IHC and/or MSI screening, with MLH1 promotor hypermethylation analysis in cases of MLH1 expression loss, is recommended for women with endometrial cancer [III, B]
  • Follow-up recommendations in mutation carriers include colonoscopy every 1 – 2 years [III, A], and gynaecological examination (with TV US, CA 125 and endometrial biopsy) on a yearly basis from age 30 to 35 years [IV, C]. In all cases, age of onset in the youngest member of the family is to be considered and surveillance be started 5 years earlier [V, B]. High-quality colonoscopy carried out in dedicated centres is advised [IV, C]. UGI endoscopy surveillance (every 1 – 3 years, from age 30 – 35 years) may be considered in patients at high risk. Prophylactic gynaecological surgery might be an option for female carriers who have completed childbearing or are postmenopausal [IV, C]” (Stjepanovic et al., 2019).

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Coding Section

Code Number

Description

  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 
  81301  Microsatellite instability analysis (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) of markers for mismatch repair deficiency (eg, BAT25, BAT26), includes comparison of neoplastic and normal tissue, if performed 
  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)

(Policy specific gene: EPCAM
  88341 Immunohistochemistry or immunocytochemistry, per specimen; each additional single antibody stain procedure (List separately in addition to code for primary procedure)
  88342 Immunohistochemistry or immunocytochemistry, per specimen; initial single antibody stain procedure  
  88344 Immunohistochemistry or immunocytochemistry, per specimen; each multiplex antibody stain procedure 
  96040  Medical genetics and genetic counseling services, each 30 minutes face-to-face with patient/family 
  S0265 Genetic counseling, under physician supervision, each 15 minutes
ICD-10-CM   C16.0-C16.9  Malignant neoplasm of stomach 
  C17-C17.9 Malignant neoplasm of small intestine
  C18.0-C18.9 Malignant neoplasm, colon
  C240.0-C24.9 Malignant neoplasm of other and unspecified parts of biliary tract
  C25.0-C25.9 Malignant neoplasm of pancreas
  C44.131 - C44.1392  Sebaceous cell carcinoma of skin of eyelid 
  C54.0 - C54.9   Malignant neoplasm of corpus uteri 
  C56.1 - C56.9  Malignant neoplasm of ovary 
  C65.1-C65.9 Malignant neoplasm of renal pelvis
  C66.1-C66.9 Malignant neoplasm of the ureter
  C67.0 - C67.9  Malignant neoplasm of bladder 
  C71.0 - C71.9  Malignant neoplasm of brain 
  D23.0 - D23.9  Other benign neoplasms of skin 
  L85.8 Other specified epidermal thickening
  Z15.04 Genetic susceptibility to malignant neoplasm of endometrium
  Z15.09 Genetic susceptibility to other malignant neoplasm
  Z80.41  Family history of malignant neoplasm of ovary 
  Z80.51 - Z80.59  Family history of malignant neoplasm of urinary tract 
  Z80.8  Family history of malignant neoplasm of other organs or systems 
  Z85.00  Personal history of malignant neoplasm of unspecified digestive organ 
  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 
  Z85.42  Personal history of malignant neoplasm of other parts of uterus 
  Z85.43  Personal history of malignant neoplasm of ovary 
  Z85.53  Personal history of malignant neoplasm of renal pelvis 
  Z85.54  Personal history of malignant neoplasm of ureter 
  Z85.59  Personal history of malignant neoplasm of other urinary tract organ 
  Z85.841  Personal history of malignant neoplasm of brain 

Procedure and diagnosis codes on Medical Policy documents are included only as a general reference tool for each policy. They may not be all-inclusive. 

This medical policy was developed through consideration of peer-reviewed medical literature generally recognized by the relevant medical community, U.S. FDA approval status, nationally accepted standards of medical practice and accepted standards of medical practice in this community, Blue Cross Blue Shield Association technology assessment program (TEC) and other nonaffiliated technology evaluation centers, reference to federal regulations, other plan medical policies, and accredited national guidelines.

"Current Procedural Terminology © American Medical Association. All Rights Reserved" 

History From 2017 Forward     

04/20/2022 

Annual review, policy and notes have been revised extensively for clarity and consistency. Also updating rationale and references. Adding table of terminology. 

04/06/2021 

Annual review, multiple areas of policy reworded related to lynch syndrome variants. Also updating description, rationale and references. 

06/15/2020 

Corrected typo. No other changes made.

04/13/2020 

Annual review, no change to policy intent. Removing criteria related to testing for patients diagnosed by the age of 60. 

04/02/2019 

Annual review, major revision of policy for clarity and specificity of coding and testing criteria. Also adding rationale, regulatory status and updating coding. 

07/26/2018 

Annual review, rewriting medical necessity criteria to address the genes being tested in one medical necessity statement rather than breaking them out individually. Removing age criteria for testing. Updating guidelines to reflect the changes in the policy criteria. 

04/19/2018 

Interim review, month of review changed, no other changes 

08/03/2017 

Interim review clarifying medical necessity statement related to patients with 1 or more first degree relatives. Updating guidelines.

05/01/2017

New Policy

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