Coverage Policies

Effective Date:

a)    This policy will apply to all services performed on or after the above revision date which will become the new effective date.

b)    For all services referred to in this policy that were performed before the revision date, contact customer service for the rules that would apply.

The molecular analysis of solid tumors and hematologic malignancies aims to identify somatic oncogenic mutations in cancer.  These mutations, often called “driver” mutations, are becoming increasingly useful for targeted therapy selection, and may give insight into prognosis and treatment response in a subset of cancers.  In addition, molecular analysis of solid tumors and hematologic malignancies, in particular, can also aid in making a diagnosis of a specific type of malignancy.  For solid tumors, molecular analysis can be performed via direct testing of the tumor (which is addressed in this policy) or via circulating tumor DNA or circulating tumor cells (CTCs) (see Other Related Policies).  For hematologic malignancies, molecular analysis can be performed on blood samples or bone marrow biopsy samples.

For individuals with advanced cancer, somatic comprehensive genomic profiling offers the potential to evaluate a large number of genetic markers in the cancer simultaneously in order to provide potential treatment options beyond the current standard of care.

While the primary goal of the molecular analysis of solid tumors and hematologic malignancies is to identify biomarkers that diagnose or to give prognostic and treatment selection information, this testing also has the potential to uncover clinically relevant germline variations that are associated with a hereditary cancer susceptibility syndrome, and other conditions, if confirmed to be present in the germline. Current tumor testing strategies include tumor-only testing, tumor-normal paired testing with germline variant subtraction, and tumor-normal paired testing with explicit analysis of a group of genes associated with germline cancer predisposition. This is an evolving area and clear guidelines around the optimal approach for identification and reporting of the presumed germline pathogenic variants (PGPVs) are emerging.

Molecular Profiling Panel Testing of Solid Tumors and Hematologic Malignancies

Comprehensive Molecular Profiling Panels for Solid Tumors

1. It is the policy of health plans affiliated with Centene Corporation® that comprehensive molecular profiling panels for solid tumors (0037U, 0048U, 0211U, 81445, 81455) is considered medically necessary when meeting all of the following:
   1. The member/enrollee has recurrent, relapsed, refractory, metastatic, or advanced stages III or IV cancer,
   2. The member/enrollee is seeking further cancer treatment (e.g., therapeutic chemotherapy),
   3. One of the following:
      1. The member/enrollee has not had previous comprehensive solid tumor molecular profiling for the primary cancer diagnosis,
      2. The member/enrollee HAS had previous comprehensive solid tumor molecular profiling for the primary cancer diagnosis, and has a new primary cancer diagnosis for which this testing is being ordered.
2. It is the policy of health plans affiliated with Centene Corporation® that current evidence does not support comprehensive molecular profiling panels for solid tumors (0037U, 0048U, 0211U, 81445, 81455) for all other indications.

Comprehensive Molecular Profiling Panels for Hematologic Malignancies and Myeloid Malignancy Panels

1. It is the policy of health plans affiliated with Centene Corporation® that comprehensive molecular profiling panels for hematologic malignancies and myeloid malignancy panels in bone marrow or peripheral blood (81450, 81455) is considered medically necessary when meeting any of the following:
   1. The member/enrollee has a suspected or confirmed diagnosis of acute myeloid leukemia (AML),
   2. The member/enrollee has persistent cytopenia(s) (at least 4-6 months) and a myelodysplastic syndrome is suspected or has been newly diagnosed,
      1. Other causes of cytopenia(s) have been ruled out, including:

a)    Nutritional anemias (e.g., iron deficiency anemia, folate deficiency anemia, vitamin B12 deficiency anemia),

b)    Thyroid disease,

c)    Drug-induced cytopenia,

d)    Viral infection (e.g., HIV),

1. The member/enrollee was suspected to have a myeloproliferative neoplasm, and both of the following:
   1. JAK2, CALR, MPN, and BCR/ABL analysis were previously performed and the results were negative,
   2. Clinical suspicion for a myeloid neoplasm remains high,
2. The member/enrollee has a diagnosis of chronic myelogenous leukemia, and both of the following:
   1. There has been progression to accelerated phase or blast phase,
   2. BCR-ABL1 kinase domain mutation analysis has been performed and the results were negative.
1. It is the policy of health plans affiliated with Centene Corporation® that current evidence does not support comprehensive molecular profiling panels for hematologic malignancies and myeloid malignancy panels in bone marrow or peripheral blood (81450, 81455) for all other indications.

Note: If a multigene panel is performed, appropriate panel codes should be used. 

Colorectal Cancer Focused Molecular Profiling Panels

1. It is the policy of health plans affiliated with Centene Corporation® that colorectal cancer focused molecular profiling panels (0111U, 81301, 81445) in solid tumors is considered medically necessary when meeting all of the following:
   1. The member/enrollee has suspected or proven metastatic, synchronous or metachronous colorectal cancer,
   2. The member/enrollee is seeking further cancer treatment (e.g., therapeutic chemotherapy,
   3. One of the following:
      1. The member/enrollee has not had previous somatic testing via a multigene cancer panel for the same primary diagnosis of colorectal cancer,
      2. The member/enrollee HAS had previous somatic testing via a multigene cancer panel for a primary colorectal cancer diagnosis, and has a new primary colorectal cancer diagnosis for which this testing is being ordered.
2. It is the policy of health plans affiliated with Centene Corporation® that current evidence does not support colorectal cancer-focused molecular profiling panels (0111U, 81301, 81445) for all other indications.

Note: If a panel is performed, appropriate panel codes should be used.

Lung Cancer Focused Molecular Profiling Panels

1. It is the policy of health plans affiliated with Centene Corporation® that lung cancer focused molecular profiling panels (0022U, 81445) is considered medically necessary when meeting all of the following:
   1. The member/enrollee has a diagnosis of any of the following:
      1. Advanced (stage IIIb or higher) or metastatic lung adenocarcinoma,
      2. Advanced (stage IIIb or higher) or metastatic large cell lung carcinoma,
      3. Advanced (stage IIIb or higher) or metastatic squamous cell lung carcinoma,
      4. Advanced (stage IIIb or higher) or metastatic non-small cell lung cancer (NSCLC) not otherwise specified (NOS),
   2. The member/enrollee is seeking further cancer treatment (e.g., therapeutic chemotherapy),
   3. One of the following:
      1. The member/enrollee has not had previous somatic testing via a multigene cancer panel for the same primary lung cancer diagnosis,
      2. The member/enrollee HAS had previous somatic testing via a multigene cancer panel for a primary lung cancer diagnosis, and has a new primary lung cancer diagnosis for which this testing is being ordered.
2. It is the policy of health plans affiliated with Centene Corporation® that current evidence does not support lung cancer-focused molecular profiling panels (81445, 0022U) for all other indications.

Note: If a panel is performed, appropriate panel codes should be used.

Cutaneous Melanoma Focused Molecular Profiling Panels

1. It is the policy of health plans affiliated with Centene Corporation® that cutaneous melanoma focused molecular profiling panels (81210, 81273, 81311, 81403, 81404, 81445) is considered medically necessary when meeting all of the following:
   1. The member/enrollee has a new diagnosis of stage IV melanoma or has recurrent melanoma,
   2. The member/enrollee is seeking further cancer treatment (e.g. therapeutic chemotherapy),
   3. One of the following:
      1. The member/enrollee has not had previous somatic testing via a multigene cancer panel for the same primary melanoma diagnosis,
      2. The member/enrollee HAS had previous somatic testing via a multigene cancer panel for a primary melanoma diagnosis, and has a new primary melanoma diagnosis for which this testing is being ordered.
2. It is the policy of health plans affiliated with Centene Corporation® that current evidence does not support cutaneous melanoma focused molecular profiling panels (81210, 81273, 81311, 81403, 81404, 81445) for all other indications.

Note: If a panel is performed, appropriate panel codes should be used.

Acute Myeloid Leukemia (AML) Focused Molecular Profiling Panels

1. It is the policy of health plans affiliated with Centene Corporation® that acute myeloid leukemia focused molecular profiling panels (81450) for the diagnosis or evaluation of acute myeloid leukemia (AML) is considered medically necessary when:
   1. The member/enrollee has a suspected or confirmed diagnosis of acute myeloid leukemia (AML).
2. It is the policy of health plans affiliated with Centene Corporation® that current evidence does not support acute myeloid leukemia focused molecular profiling panels (81450) for the diagnosis or evaluation of acute myeloid leukemia (AML) for all other indications.

Note: If a multigene panel is performed, appropriate panel codes should be used.

Myeloproliferative Neoplasms (MPNs) Molecular Profiling Panel

1. It is the policy of health plans affiliated with Centene Corporation® that myeloproliferative neoplasm (MPN) molecular profiling panel (81206, 81207, 81208, 81270, 81219, 81402, 81403) is considered medically necessary when meeting both of the following:
   1. The member/enrollee is suspected to have a myeloproliferative neoplasm (i.e., polycythemia vera, essential thrombocythemia, primary myelofibrosis, and chronic myeloid leukemia),
   2. The panel does not include genes other than JAK2, CALR, MPL, and BCR/ABL1.
2. It is the policy of health plans affiliated with Centene Corporation® that current evidence does not support myeloproliferative neoplasm (MPN) molecular profiling panel (81206, 81207, 81208, 81270, 81219, 81402, 81403) analysis for all other indications.

Single-Gene Testing Of Solid Tumors And Hematologic Malignancies

ABL1 Kinase Domain Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic ABL1 kinase domain analysis (81170) in hematologic malignancies is considered medically necessary when meeting both of the following:
   1. The member/enrollee has a diagnosis of chronic myeloid leukemia (CML) or Ph-like acute lymphoblastic leukemia (ALL),
   2. Any of the following:
      1. Initial response to TKI therapy is inadequate,
      2. Loss of response to TKI therapy,
      3. Disease progression to the accelerated or blast phase,
      4. Relapsed/refractory disease.

BCR/ABL1 Breakpoint Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic BCR/ABL1 breakpoint analysis (0016U, 0040U, 81206, 81207, 81208) in hematologic malignancies is considered medically necessary when meeting either of the following:
   1. The member/enrollee is suspected to have a myeloproliferative neoplasm (i.e., polycythemia vera, essential thrombocythemia, primary myelofibrosis, and chronic myeloid leukemia),
   2. The member/enrollee is undergoing workup for or to monitor disease progression of any of the following:
      1. Acute lymphoblastic leukemia (ALL),
      2. Acute myeloid leukemia (AML),
      3. Chronic myelogenous leukemia (CML),
      4. Lymphoblastic leukemia.

BRAF Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic BRAF variant analysis (81210) in solid tumors and hematologic malignancies is considered medically necessary when meeting either of the following:
   1. The member/enrollee has a diagnosis of any of the following:
      1. Suspected or proven metastatic, synchronous or metachronous colorectal cancer,
      2. Advanced or metastatic non-small-cell lung cancer (NSCLC),
      3. Stage III or stage IV cutaneous melanoma,
      4. Anaplastic thyroid carcinoma or locally recurrent, advanced and/or metastatic papillary, follicular or Hurthle cell thyroid carcinoma,
      5. Low-grade glioma or pilocytic astrocytoma,
   2. The member/enrollee is being evaluated for:
      1. Hairy cell leukemia (for individuals without cHCL immunophenotype).

BRCA1/2 Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic BRCA1/2 variant analysis (81162, 81163, 81164, 81165, 81166, 81167, 81216) in solid tumors is considered medically necessary when:
   1. The member/enrollee has a diagnosis of one of the following:
      1. Ovarian, fallopian tube and/or primary peritoneal cancer,
      2. Metastatic prostate cancer.

CALR Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic CALR variant analysis (81219) in solid tumors or hematologic malignancies is considered medically necessary when:
   1. The member/enrollee is suspected to have a myeloproliferative neoplasm (i.e., polycythemia vera, essential thrombocythemia, primary myelofibrosis, and chronic myeloid leukemia).

CEBPA Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic CEBPA variant analysis (81218) in solid tumors or hematologic malignancies is considered medically necessary when:
   1. The member/enrollee has cytogenetically normal acute myeloid leukemia (AML).

EGFR Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic EGFR variant analysis (81235) in solid tumors is considered medically necessary when:
   1. The member/enrollee has a diagnosis of any of the following:
      1. Advanced or metastatic lung adenocarcinoma,
      2. Advanced or metastatic large cell lung carcinoma,
      3. Advanced or metastatic squamous cell lung carcinoma,
      4. Advanced or metastatic non-small cell lung cancer (NSCLC) not otherwise specified (NOS).

FLT3 Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic FLT3 variant analysis (81245, 81246, 0023U, 0046U) in solid tumors or hematologic malignancies is considered medically necessary when meeting either of the following:
   1. The member/enrollee has suspected or confirmed acute myeloid leukemia (AML),
   2. The member/enrollee has a diagnosis of acute lymphoblastic leukemia (ALL) and previous testing for BCR-ABL1 was negative.

IDH1 and IDH2 Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic IDH1 and IDH2 variant analysis (81120, 81121) in solid tumors is considered medically necessary when:
   1. The member/enrollee has a diagnosis of a glioma.

IGHV Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic IGHV variant analysis (81261, 81262, 81263) in hematologic malignancies is considered medically necessary when:
   1. The member/enrollee has a diagnosis of any of the following:
      1. Chronic lymphocytic leukemia (CLL) or small lymphocytic leukemia (SLL),
      2. Primary cutaneous B-cell lymphoma,
      3. Mantle cell lymphoma,
      4. Post-transplant lymphoproliferative disorder.

JAK2 Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic JAK2 variant analysis (81270, 0017U, 0027U) in solid tumors or hematologic malignancies is considered medically necessary when:
   1. The member/enrollee is suspected to have a myeloproliferative neoplasm (i.e., polycythemia vera, essential thrombocythemia, primary myelofibrosis, and chronic myeloid leukemia).

KIT Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that Somatic KIT variant analysis (81272, 81273) in solid tumors or hematologic malignancies is considered medically necessary when meeting any of the following:
   1. The member/enrollee is suspected to have, or is being worked up for, systemic mastocytosis,
   2. The member/enrollee has a diagnosis of acute leukemia,
   3. The member/enrollee has stage IV cutaneous melanoma,
   4. The member/enrollee has a suspected or confirmed gastrointestinal stromal tumor (GIST).

KRAS Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic KRAS variant analysis (81275, 81276, S3713) in solid tumors is considered medically necessary when meeting either of the following:
   1. The member/enrollee has suspected or proven metastatic, synchronous or metachronous colorectal cancer,
   2. The member/enrollee is undergoing workup for metastasis non-small cell lung cancer.
2. It is the policy of health plans affiliated with Centene Corporation® that current evidence does not support somatic KRAS variant analysis (81275, 81276, S3713) in solid tumors, as a stand alone test, in an individual with non-small cell lung cancer (NSCLC).

MGMT Promoter Methylation Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic MGMT promoter methylation analysis (81287) in solid tumors is considered medically necessary when:
   1. The member/enrollee has a high grade glioma (stage III or IV), including one of the following:
      1. Anaplastic oligodendroglioma,
      2. Anaplastic oligoastrocytoma,
      3. Anaplastic astrocytoma,
      4. Anaplastic glioma,
      5. Glioblastoma.

MLH1 Promoter Methylation Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic MLH1 promoter methylation analysis (81288) in solid tumors is considered medically necessary when meeting both of the following:
   1. The member/enrollee has a diagnosis of colorectal cancer or endometrial (uterine) cancer,
   2. Previous tumor testing showed loss of MLH1 on immunohistochemistry analysis.

MPL Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic MPL variant analysis (81402, 81403) in or hematologic malignancies is considered medically necessary when:
   1. The member/enrollee displays clinical symptoms of a myeloproliferative neoplasm (i.e., polycythemia vera, essential thrombocythemia, primary myelofibrosis, and chronic myeloid leukemia), such as chronically elevated red blood cell counts.

Microsatellite Instability Analysis (MSI)

1. It is the policy of health plans affiliated with Centene Corporation® that somatic microsatellite instability (MSI) analysis (81301) in solid tumors is considered medically necessary when:
   1. The member/enrollee has a diagnosis of any of the following:
      1. Colorectal cancer,
      2. Endometrial cancer,
      3. Locally advanced or metastatic pancreatic adenocarcinoma,
      4. Gastric cancer,
      5. Locally advanced, recurrent or metastatic esophageal and esophagogastric junction cancer,
      6. Recurrent, progressive or metastatic cervical cancer,
      7. Testicular cancer and has had progression after high dose chemotherapy or third-line therapy,
      8. Unresectable or metastatic Ewing’s sarcoma,
      9. Unresectable or metastatic gallbladder cancer,
      10. Unresectable or metastatic intrahepatic or extrahepatic cholangiocarcinoma,
      11. Unresectable or metastatic breast cancer,
      12. Metastatic and/or recurrent small bowel adenocarcinoma,
      13. Metastatic occult primary.

NPM1 Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic NPM1 variant analysis (81310, 0049U) in hematological malignancies is considered medically necessary when:
   1. The member/enrollee has cytogenetically normal acute myeloid leukemia (AML).

NRAS Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic NRAS variant analysis (81311) in solid tumors is considered medically necessary when:
   1. The member/enrollee has suspected or proven metastatic, synchronous or metachronous colorectal cancer.

PIK3CA Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic PIK3CA variant analysis (81309, 0155U, 0177U) in solid tumors is considered medically necessary when meeting either of the following:
   1. The member/enrollee has recurrent or stage IV, HR positive, HER2 negative invasive breast cancer,
   2. The member/enrollee has a diagnosis of uterine carcinosarcoma or uterine rhabdomyosarcoma.

RET Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic RET variant analysis (81404, 81405, 81406) in solid tumors is considered medically necessary when meeting either of the following:
   1. The member/enrollee has a diagnosis of medullary thyroid cancer,
   2. Anaplastic thyroid carcinoma or locally recurrent, advanced and/or metastatic papillary, follicular or Hurthle cell thyroid carcinoma.

TP53 Variant Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that somatic TP53 variant analysis (81405) in bone marrow or peripheral blood is considered medically necessary when meeting either of the following:
   1. The member/enrollee has a diagnosis of chronic lymphocytic leukemia (CLL) or small lymphocytic leukemia (SLL),
   2. The member/enrollee is undergoing diagnostic workup for mantle cell lymphoma (MCL).

Measurable (Minimal) Residual Disease (MRD) Analysis

1. It is the policy of health plans affiliated with Centene Corporation® that measurable (minimal) residual disease analysis (0171U, 81479) in bone marrow or peripheral blood is medically necessary when:
   1. The member/enrollee has a diagnosis of any of the following:
      1. Acute Lymphoblastic Leukemia (ALL),
      2. Multiple Myeloma,
      3. Chronic Lymphoblastic Leukemia

Red Blood Cell Genotyping in Multiple Myeloma

1. It is the policy of health plans affiliated with Centene Corporation® that red blood cell genotyping (81479, 0001U, 0180U, 0221U) in individuals with multiple myeloma is considered medically necessary when meeting all of the following:
   1. The member/enrollee has a diagnosis of multiple myeloma,
   2. The member/enrollee is currently being treated with Daratumumab (DARA),
   3. One of the following:
      1. Auto- or allo-antibodies are detected,
      2. RBC phenotyping cannot be performed due to a transfusion within the prior three months.

Whole Exome and Whole Genome Sequencing in Cancer

1. It is the policy of health plans affiliated with Centene Corporation® that current evidence does not support whole exome sequencing and whole genome sequencing in solid tumors (0013U, 0036U, 81415, 81416) and hematologic malignancies (0014U, 0056U, 81425, 81426).

Genetic Testing to Confirm the Identity of Laboratory Specimens

1. It is the policy of health plans affiliated with Centene Corporation® that current evidence does not support genetic testing to confirm the identity of laboratory specimens (e.g., know error, ToxProtect, ToxLok) (0007U, 0079U, 81265, 81266, 81479), when billed separately, because it is generally considered to be an existing component of the genetic testing process for quality assurance.

Codes Used In This BI:

1. Tumor mutation burden testing is a measurement of mutations carried by tumor cells and is a predictive biomarker that is being studied to evaluate its association with response to immunotherapy.
2. Myeloproliferative Neoplasms are rare overlapping blood diseases in which the bone marrow makes too many red blood cells, white blood cells, or platelets.

There are seven subcategories of myeloproliferative neoplasms:

■     Chronic myeloid leukemia (CML)

■     Polycythemia vera (PV)

■     Primary myelofibrosis (PMF)

■     Essential thrombocytopenia (ET)

■     Chronic neutrophilic leukemia

■     Chronic eosinophilic leukemia

■     Chronic eosinophilic leukemia-not otherwise specified

■     MPN, unclassifiable (MPN-U)

Clinical decision making should not be made based on variants of uncertain significance.

NCCN and ASCO recommend that all individuals diagnosed with ovarian cancer, fallopian tube cancer, or primary peritoneal cancer have germline and somatic tumor testing (if not previously performed) for BRCA1 and BRCA2 mutations.

The genetic testing of tumors and hematologic malignancies (somatic mutation profiling) may reveal incidental germline findings or suspicion of a clinically significant germline mutation. Providers should communicate the potential for these incidental findings with their patients prior to somatic mutation profiling.

ACMG (2020) recognized that tumor testing is an emerging area and that the identification of presumed germline pathogenic variants (PGPVs) have profound health and reproductive implications for the individual with cancer as well as their family members. Thus, individuals undergoing tumor testing should be informed prior to testing that a germline variant may be uncovered. PGPVs should be carefully evaluated, confirmed, and reported when tumor testing is performed. Currently, there is a lack of evidence for best practices to report PGPVs to patients who want them.

National Comprehensive Cancer Network (NCCN):

Colon Cancer

The NCCN guidelines on Genetic/Familial High-Risk Assessment: Colorectal Cancer (v1.2021) state that abnormal MLH1 IHC should be followed by either germline genetic testing or tumor testing for MLH1 methylation for colorectal or endometrial cancers.

The NCCN guidelines on Oncology: Colon Cancer (v2.2021) recommend determination of tumor MMR and MSI in all individuals with colorectal cancer. Additionally, they recommend determination of tumor gene status for RAS and BRAF mutations and HER2 amplification individually or as part of an NGS panel in all individuals with suspected or proven metastatic, synchronous or metachronous colorectal cancer.

Lung Cancer

The NCCN (v3.2021) recommends that at this time when feasible, testing be performed via a broad, panel-based approach for individuals with non-small cell lung cancer. For patients who do not have identifiable driver oncogenes via the broad panel-based approach, RNA-based NGS should be considered in order to detect clinically significant fusion events.

Breast Cancer

The NCCN guidelines on Oncology: Breast Cancer (v8.2021) recommends that recurrent or stage IV HR-positive/HER2-negative breast cancers be assessed for PIK3CA mutations with tumor or liquid biopsy to identify candidates for Alpelisib + fulvestrant. They also recommend that recurrent or stage IV MSH-H/dMMR breast cancers that have progressed following prior treatment be considered for treatment with Pembrolizumab.

Thyroid Carcinoma

The NCCN (v2.2021) guidelines on thyroid carcinoma recommend molecular diagnostic testing for evaluating FNA results that are suspicious for follicular cell neoplasms or AUS/FLUS and somatic RET testing in all individuals with newly diagnosed medullary thyroid carcinoma. Additionally they comment that molecular testing has shown to be beneficial when making targeted therapy decisions. The guideline also comments that individuals with anaplastic thyroid cancer and/or metastatic disease should undergo molecular testing including BRAF, NTRK, ALK, RET and tumor mutational burden if not previously done.

Acute Myeloid Leukemia

The NCCN guidelines on acute myeloid leukemia (v2.2021) state that a variety of gene mutations are associated with specific prognoses and may guide medical decision making while other mutations may have therapeutic implications. Presently this includes c-KIT, FLT-ITD, FLT-TKD, NPM1, CEBPA, IDH1/IDH2, RUNX1, ASXL1, and TP53. Additionally, they recommend that ASXL1, BCR-ABL1 and PML-RAR alpha be tested in all patients and further recommend that multiplex gene panels and NGS analysis be used for a comprehensive prognostic assessment.

Myelodysplastic Syndromes

The NCCN guidelines on myelodysplastic syndromes (v3.2021) state that genetic testing for somatic mutations in genes associated with MDS using gene panels is highly recommended.

Myeloproliferative Neoplasms

The NCCN guidelines on myeloproliferative neoplasms (v2.2021) recommend that FISH or RT-PCR to detect BCR-ABL1 transcripts is recommended to exclude the diagnosis of CML. Additionally, they recommend that molecular testing for JAK2 mutations is recommended in initial work-up for all patients with suspected MPN. They further recommend that if testing for JAK2 mutations is negative, additional testing of MPL and CALR mutations should be performed. Alternatively, molecular testing using a multi-gene NGS panel that includes JAK2, MPL and CALR can be used as part of the initial work-up in all patients. The guidelines also state that NGS may also be useful to establish the clonality in certain circumstances and may identify second, third and fourth mutations that may hold prognostic relevance.

Chronic Myelogenous Leukemia

The NCCN guidelines on chronic myelogenous leukemia (v1.2022) outline recommended methods for diagnosis and treatment management of chronic myelogenous leukemia, including BCR-ABL1 tests for diagnosis, monitoring, and ABL kinase domain single nucleotide variants. Guidelines for discontinuation of tyrosine kinase inhibitor therapy are detailed.

Pediatric Acute Lymphoblastic Leukemia

The NCCN guidelines on pediatric acute lymphoblastic leukemia (v2.2021) recommend that the presence of recurrent genetic abnormalities, specifically BCR-ABL1 and ETV6-RUNX1, should be evaluated using karyotyping, FISH, or RT-PCR. They further recommend that if testing for those recurrent genetic abnormalities is negative, additional testing for recurrent genetic abnormalities is encouraged in some patients and may aid in risk stratification.

Acute Lymphoblastic Leukemia

The NCCN guidelines on acute lymphoblastic leukemia (v2.2021) recommend that the presence of recurrent genetic abnormalities, specifically BCR-ABL1, should be evaluated using karyotyping, FISH, or RT-PCR. They further recommend that if testing for BCR-ABL1 is negative, additional testing for recurrent genetic abnormalities associated with Ph-like ALL is essential.

B-Cell Lymphomas

The NCCN guidelines on B-cell lymphoma (v2.2021) include molecular testing for BCR-ABL as one of the essential steps in diagnostic testing for lymphoblastic leukemia.

The NCCN guidelines on B-cell lymphoma (v2.2021) recommend Tp53 mutation analysis for patients with a diagnosis of mantle cell lymphoma in order to direct treatment selection, as patients with a TP53 mutation have been associated with poor prognosis when treated with conventional therapy.

Hairy Cell Leukemia

The NCCN guideline on Hairy Cell Leukemia (v1.2022) recommends molecular testing for BRAF V600E as a useful part of diagnostic work-up for individuals that do not have cHCL Immunophenotype.

Cutaneous Melanoma

The NCCN guideline on Cutaneous Melanoma (v2.2021) recommends BRAF mutation testing in patients with stage III cutaneous melanoma at high risk for recurrence. Additionally, the panel strongly encourages testing for BRAF and KIT gene mutations in all patients with stage IV melanoma as this could impact treatment options. They further recommend that if feasible, broader genomic profiling with NGS panels be performed in individuals with stage IV or recurrent melanoma especially if the test results could guide future treatment options.

Central Nervous System Cancers

The NCCN guideline on Central Nervous System Cancers (v2.2021) states that BRAF fusion and/or mutation testing is clinically indicated in patients with low-grade glioma or pilocytic astrocytoma and that MGMT promoter methylation analysis is an essential part of work-up for all high grade gliomas (grade III and IV). The panel also recommends IDH mutation testing in patients with glioma.

Epithelial Ovarian Cancer/Fallopian Tube Cancer/Primary Peritoneal Cancer

The NCCN guideline on epithelial ovarian cancer/fallopian tube cancer/primary peritoneal cancer (v1.2021) recommends that all patients with ovarian cancer, fallopian tube cancer or primary peritoneal cancer should have genetic risk evaluation and germline and somatic testing of BRCA1 and BRCA2 if not previously done. In addition to BRCA1/2 testing, other methods for evaluating HR deficiency status (e.g. genomic instability, loss of heterozygosity) can be considered. Additional somatic tumor testing can be considered at the physician’s discretion to identify genetic alterations for which FDA-approved tumor specific or tumor-agnostic targeted therapy options exist.

Prostate Cancer

The NCCN guideline on prostate cancer (v1.2022) recommend evaluating tumor for alterations in homologous recombination DNA repair genes such as BRCA1, BRCA2, ATM, PALB2, FANCA, RAD51D, CHEK2 and CDK12 in patients with metastatic prostate cancer and tumor testing for MSI-H and/or dMMR can be considered.

Pancreatic Cancer

The NCCN guideline on pancreatic cancer (v2.2021) recommends MSI testing and/or MMR testing for all patients with locally advanced or metastatic pancreatic adenocarcinoma.

Gastric Cancer

The NCCN guideline on gastric cancer (v1.2021) recommends MSI and MMR testing should be performed for all newly diagnosed gastric cancers. Additionally, the guideline recommends, PD-L1 and HER2 testing if metastatic disease is documented/suspected.

Esophageal and Esophagogastric Junction Cancer

The NCCN guideline on esophageal and esophagogastric junction cancer (v1.2021) recommends MSI by PCR, MMR by IHC, PD-L1 and HER2 testing if metastatic disease is documented/suspected.

Occult Primary

The NCCN guideline on occult primary (v1.2022) recommends MSI and MMR testing as part of the initial work up for patients with cancer of unknown primary. The guideline further recommends consideration of NGS to identify actionable genomic aberrations in individuals with localized adenocarcinoma or carcinoma not otherwise specified.

Testicular Cancer

The NCCN guideline for testicular cancer (v1.2021) recommends MSI testing in individuals with testicular cancer who have had progression after high-dose chemotherapy or third line therapy.

Chronic Lymphocytic Leukemia/Small lymphocytic Leukemia

Current NCCN guidelines for CLL/SLL (v1.2022) recommend TP53 sequencing analysis and IGHV mutation analysis to inform prognosis and therapeutic options for patients diagnosed with CLL/SLL or upon progression or recurrence. Minimal residual disease testing at the end of treatment for CLL is recommended.

Gastrointestinal Stromal Tumors (GISTs)

Current NCCN guidelines (v1.2021) recommend KIT mutation analysis to aid in diagnosis of and treatment selection for a gastrointestinal stromal tumor.

American Society of Clinical Oncology (ASCO)

Colorectal Cancer

ASCO (2015) endorsed the following guidelines related to MSI, BRAF, and MLH1 testing in the assessment of CRC:

●     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 the tumor is MMR deficient and somatic BRAF mutation is not detected or MLH1 promoter methylation is not identified, testing for germline mutations is indicated.

ASCO, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology (2017) published the following recommendations for the use of molecular biomarkers for the evaluation of colorectal cancer:

●     Patients with CRC considered for anti-EGFR therapy must receive RAS mutational testing. Mutational analysis should include KRAS and NRAS codons 12 and 13 of exon 2, 59 and 61 of exon 3, and 117 and 146 of exon 4

●     BRAF p.V600 (BRAF c.1799 [p.V600]) mutational analysis should be performed in CRC tissue in patients with CRC for prognostic stratification

●     BRAF p.V600 mutational analysis should be performed in dMMR 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                                                                                         

●     Clinicians should order MMR status testing in patients with CRCs for the identification of patients at high risk for Lynch syndrome and/or prognostic stratification                                                                             

●     There is insufficient evidence to recommend BRAF c.1799 p.V600 mutational status as a predictive molecular biomarker for response to anti-EGFR inhibitors

Lung Cancer

The American Society of Clinical Oncology (2018) endorsed the College of American Pathologists/International Association for the Study of Lung cancer/Association of Molecular Pathology Clinical Practice Guideline Update for Molecular Testing for the Selection of Patients with Lung Cancer for Treatment with Targeted Tyrosine Kinase Inhibitors which recommends that physicians should use molecular testing for the appropriate genetic targets on either primary or metastatic lung lesions to guide initial therapy selection. They further recommend that multiplexed genetic sequencing panels are preferred where available over multiple single gene tests to identify other treatment options beyond EGFR, ALK, BRAF,  and ROS1.

The panel recommends that EGFR, ALK, ROS1 and BRAF testing should be performed on all patients with advanced lung adenocarcinoma. They went on to state that RET, HER2, KRAS, and MET molecular testing are not indicated as stand alone tests but are appropriate to include as part of a larger testing panel

Acute Leukemia

ASCO (2018) endorsed the College of American Pathologists and American Society of Hematology Guideline with the following relevant guidelines for the initial workup for acute leukemia:

●     Recommendation 5. In addition to performing morphologic assessment (blood and BM), the pathologist or treating clinician should obtain sufficient samples and perform conventional cytogenetic analysis (ie, karyotype), appropriate molecular genetic and/or FISH testing, and FCI. The flow cytometry panel should be sufficient to distinguish AML (including APL), including early T-ALL, B-ALL, and AL of ambiguous lineage in all patients diagnosed with AL. Molecular genetic and/or FISH testing does not, however, replace conventional cytogenetic analysis (Strong recommendation).

●     Recommendation 12. For patients with suspected or confirmed AL, the pathologist or treating clinician should ensure that flow cytometry analysis or molecular characterization is comprehensive enough to allow subsequent detection of MRD (Strong recommendation).

●     Recommendation 13. For pediatric patients with suspected or confirmed B-ALL, the pathologist or treating clinician should ensure that testing for t(12;21)(p13.2;q22.1); ETV6-RUNX1, t(9;22)(q34.1;q11.2); BCR-ABL1, KMT2A (MLL) translocation, iAMP21, and trisomy 4 and 10 is performed (Strong recommendation).

●     Recommendation 14. For adult patients with suspected or confirmed B-ALL, the pathologist or treating clinician should ensure that testing for t(9;22)(q34.1;q11.2); BCR-ABL1 is performed. In addition, testing for KMT2A (MLL) translocations may be performed. (Strong recommendation for testing for t(9;22)(q34.1;q11.2) and BCR-ABL1; Recommendation for testing for KMT2A (MLL) translocations).

●     Recommendation 15. For patients with suspected or confirmed ALL, the pathologist or treating clinician may order appropriate mutational analysis for selected genes that influence diagnosis, prognosis, and/or therapeutic management, which include, but are not limited to, PAX5, JAK1, JAK2, and/or IKZF1 for B-ALL and NOTCH1 and/or FBXW7 for T-ALL. Testing for overexpression of CRLF2 may also be performed for B-ALL (Recommendation).

●     Recommendation 16. For pediatric and adult patients with suspected or confirmed AML of any type, the pathologist or treating clinician should ensure that testing for FLT3-ITD is performed. The pathologist or treating clinician may order mutational analysis that includes, but is not limited to, IDH1, IDH2, TET2, WT1, DNMT3A, and/or TP53 for prognostic and/or therapeutic purposes. (Strong recommendation for testing for FLT3-ITD; Recommendation for testing for other mutational analysis).

●     Recommendation 17. For adult patients with confirmed core binding factor (CBF) AML (AML with t(8;21)(q22; q22.1); RUNX1-RUNX1T1 or inv(16)(p13.1q22)/t(16;16)(p13.1;q22); CBFB-MYH11), the pathologist or treating clinician should ensure that appropriate mutational analysis for KIT is performed. For pediatric patients with confirmed CBF AML; RUNX1-RUNX1T1 or inv(16)(p13.1q22)/t(16;16)(p13.1;q22); CBFB-MYH11, the pathologist or treating clinician may ensure that appropriate mutational analysis for KIT is performed. (Strong recommendation for testing for KIT mutation in adult patients with CBF AML; Expert consensus opinion for testing for KIT mutation in pediatric patients with CBF AML).

●     Recommendation 18. For patients with suspected APL, the pathologist or treating physician should also ensure that rapid detection of PML-RARA is performed. The treating physician should also order appropriate coagulation studies to evaluate for disseminated intravascular coagulation (Strong recommendation).

Germline Testing and Somatic Mutation Profiling

ASCO (2020) published the following recommendations for somatic and germline genetic testing for women diagnosed with ovarian cancer:

●     All women diagnosed with epithelial ovarian cancer should have germline genetic testing for BRCA1/2 and other ovarian cancer susceptibility genes. In women who do not carry a germline pathogenic or likely pathogenic BRCA1/2 variant, somatic tumor testing for BRCA1/2 pathogenic or likely pathogenic variants should be performed. Women with identified germline or somatic pathogenic or likely pathogenic variants in BRCA1/2 genes should be offered treatments that are US Food and Drug Administration (FDA) approved in the upfront and the recurrent setting.

●     Women diagnosed with clear cell, endometrioid, or mucinous ovarian cancer should be offered somatic tumor testing for mismatch repair deficiency (dMMR). Women with identified dMMR should be offered FDA-approved treatment based on these results.

●     Genetic evaluations should be conducted in conjunction with health care providers familiar with the diagnosis and management of hereditary cancer.

●     First- or second-degree blood relatives of a patient with ovarian cancer with a known germline pathogenic cancer susceptibility gene variant should be offered individualized genetic risk evaluation, counseling, and genetic testing.

●     Clinical decision making should not be made based on a variant of uncertain significance.

●     Women with epithelial ovarian cancer should have testing at the time of diagnosis.

American College of Medical Genetics and Genomics:

Germline Implications of Somatic Mutation Profiling

ACMG (2020) published the following points to consider for clinical professionals in regard to the reporting of germline variation in patients undergoing tumor testing:

●     Individuals undergoing tumor testing should undergo informed consent of the possibility that a PGPV might be discovered. However, if there is a clinical indicator for germline cancer predisposition, then dedicated germline testing should be ordered.

●     Patient choice and autonomy (opt-out of PGPV result return) should be respected.

●     When automated methods are used for pre- and posttesting education and counseling, clinicians with experience in cancer genetics should be available to answer specific questions.

●     Patients should be informed that discovery of a PGPV would prompt referral for genetic consultation and the possibility of confirmatory germline testing.

●     Confirmatory germline testing should be performed in a clinical laboratory that has adequate resources and expertise in conducting germline testing and interpreting and reporting the test results.

●     Positive germline test results should be returned by qualified and experienced clinicians (e.g., oncologists with genetics expertise, geneticists, and genetic counselors).

ACMG (2020) published the following points to consider for laboratory professionals in regard to the reporting of germline variation in patients undergoing tumor testing:

●     There are three tumor testing strategies: tumor-only testing, tumor-normal paired testing with germline variant subtraction, or tumor-normal paired testing with full analysis of the germline data from a subset of genes associated with cancer predisposition.

●     Tumor-normal paired testing is not a substitute for dedicated germline testing unless the germline application was designed, validated, and implemented as part of the tumor-normal paired testing protocol.

●     A known founder variant in a cancer predisposition gene detected on tumor-only testing is almost always germline, but still merits orthogonal confirmation.

●     Copy-number variation and variant characteristics such as large indels or homopolymers may affect variant allele frequencies and may require specialized testing methods to report.

●     Clinical data such as tumor type, age at cancer onset, bilateral or multiple tumors, and family history of cancer can help inform the evaluation of PGPVs.

●     Using “normal” adjacent tissue in tumor-normal paired testing should be discouraged to avoid the risk of false positives/negatives due to field “cancerization” effects.

●     Clonal hematopoiesis of indeterminate potential (CHIP) and aberrant clonal expansion (ACE) should be factored into genomic analyses, to minimize false-positive germline results or false-negative somatic results.

U.S. Food and Drug Administration (FDA):

Comprehensive Tumor Molecular Profiling Panels

On November 30, 2017, FoundationOne CDx (Foundation Medicine, Inc.) was approved by the U.S. Food and Drug Administration (FDA) through the premarket approval process as a companion diagnostic to identify patients who may benefit from treatment with a defined set of targeted therapies in accordance with the approved therapeutic product labeling. Additionally, F1CDx is intended to provide tumor mutation profiling to be used by qualified health care professionals in accordance with professional guidelines in oncology for cancer patients with solid malignant neoplasms.

On November 15, 2017, MSK-IMPACT (Memorial Sloan Kettering) was approved by the U.S Food and Drug Administration (FDA) through the premarket approval process. The MSK-IMPACT assay is a qualitative in vitro diagnostic test that uses targeted next generation sequencing of formalin-fixed paraffin-embedded tumor tissue matched with normal specimens from patients with solid malignant neoplasms to detect tumor gene alterations in a broad multi gene panel. The test is intended to provide information on somatic mutations (point mutations and small insertions and deletions) and microsatellite instability for use by qualified health care professionals in accordance with professional guidelines, and is not conclusive or prescriptive for labeled use of any specific therapeutic product. MSK-IMPACT is a single-site assay performed at Memorial Sloan Kettering Cancer Center.