Medicare NCD 90.2: What Labs Need to Know About NGS Coverage for Somatic and Germline Cancer Testing
Short answer: Medicare's National Coverage Determination 90.2 nationally covers FDA-approved or cleared next-generation sequencing for patients with recurrent, relapsed, refractory, metastatic, or stage III or IV cancer who have not had the same test. Since January 27, 2020 it also covers germline testing for breast or ovarian cancer patients meeting stated criteria.
What is NCD 90.2 and why does it still matter?
NCD 90.2 is the Medicare national policy for next-generation sequencing, or NGS, in cancer. According to the CMS Medicare Coverage Database, it applies to NGS diagnostic laboratory tests for somatic (acquired) and germline (inherited) cancer. Testing must be performed in a CLIA-certified laboratory and ordered by a treating physician. The policy leaves coverage of RNA sequencing and protein analysis to the Medicare Administrative Contractors, or MACs.
The NCD matters beyond its own text because other policies point back to it. Local MolDX coverage policies for NGS tests state that an NGS test must also abide by all conditions in NCD 90.2. Our review of the MolDX inherited cancer syndromes LCD shows that cross-reference in practice. A lab that understands the national rule can see which claim denials are about the patient, which are about the test, and which are about the report.
The Coverage Database shows version 1 effective March 16, 2018 and version 2 effective January 27, 2020, and says the NCD was last reviewed in January 2020. Its revision log through 2026 lists quarterly ICD-10 coding maintenance and transmittal replacements. Apart from a September 2025 entry that updated the Policy section without describing the change, none of those entries describes a change to the coverage criteria. The database also displays a notice that the page for version 2 is an older version, so billing teams should confirm the current text before relying on any summary, including this one.
How did NCD 90.2 start as a somatic-only policy?
The 2018 version addressed tumor testing. Under that original NCD, as described by the health policy publication Discoveries in Health Policy, coverage was tied to patients with advanced cancer and to companion diagnostic tumor tests. Stakeholders argued that this focus inadvertently blocked coverage of germline testing.
That dispute reached CMS in 2019. A 360Dx report from May 2019 stated that CMS reopened the NCD to seek public comment on germline testing, with a comment period from April 29 to May 29 of that year. It said CMS was reconsidering only the evidence for germline tests used to identify hereditary cancer patients who may benefit from targeted treatments, and that sixty organizations had written to CMS asking it to protect coverage of NGS-based hereditary cancer risk testing for early-stage patients. According to Discoveries in Health Policy, CMS posted a draft in October 2019 and the final revision on January 20, 2020. The germline provisions took effect for services on or after January 27, 2020.
What must be true for somatic NGS to be nationally covered?
Section B.1 of the NCD sets patient criteria and test criteria, and all of them apply. On the patient side, the person has recurrent, relapsed, refractory, metastatic, or advanced stage III or IV cancer. The patient has not been previously tested with the same test using NGS for the same cancer genetic content. The patient has also decided to seek further cancer treatment, for example therapeutic chemotherapy.
On the test side, the NGS test must have FDA approval or clearance as a companion in vitro diagnostic, or have an FDA-approved or cleared indication for the patient's cancer. The results must also be given to the treating physician for management of the patient using a report template that specifies treatment options.
Somatic testing that does not meet these criteria is nationally non-covered under section C.1. That is a firm statement in the policy text, not a gap left to the contractor. A lab offering a laboratory-developed tumor panel without an FDA-approved or cleared status should therefore expect that a claim under this NCD will not be supported by the national rule, and should check how the relevant MAC treats the test locally.
What does NCD 90.2 say about germline testing?
Section B.2 covers germline testing nationally for a narrower group. The patient has ovarian or breast cancer, has a clinical indication for germline testing for hereditary breast or ovarian cancer, has a risk factor for germline breast or ovarian cancer, and has not had a previous germline test using NGS for the same germline genetic content. The test must have FDA approval or clearance, and the results must go to the treating physician in a report template that specifies treatment options.
Section D gives MACs discretion to cover germline testing for any cancer diagnosis when the patient has a clinical indication for hereditary cancer testing, a risk factor for germline cancer, and no prior identical germline NGS test. The text of the page does not define "risk factor" or "clinical indication," so the national policy alone does not tell a lab which documentation will satisfy a reviewer. The MAC provision also does not restate the FDA approval requirement found in B.2, which is one reason local policies such as MolDX use technical assessments for laboratory-developed tests. For the clinical side of who is usually considered for this testing, see our overview of NCCN hereditary cancer testing guidelines.
How should lab and revenue cycle teams use this?
Start by sorting your NGS menu into three groups: tests with FDA approval or clearance that fit B.1 or B.2, laboratory-developed tests that rely on MAC discretion or a local technical assessment, and tests outside cancer entirely, which the NCD does not address. Each group has a different coverage source, and mixing them is a common cause of avoidable denials.
Next, build the repeat-testing rule into order review. Both the somatic and germline sections exclude a patient who has already had the same NGS test for the same genetic content. A reflex order or a repeat request should be checked against prior results before the claim is built. Then confirm that the report format matches what the policy describes, since the NCD names a report template specifying treatment options as a condition for both somatic and germline coverage.
Finally, align diagnosis coding with the clinical story. A somatic claim needs a diagnosis that shows advanced disease. A germline claim needs documentation of the indication and the risk factor. Our ICD-10 hereditary cancer code guide and the overview of genetic testing denials cover how missing documentation turns into rejected claims. Teams that want policy checks built into the order-to-claim workflow can learn more at ScreenMyGene.
Frequently asked questions
Does NCD 90.2 cover all NGS cancer tests?
No. It covers somatic NGS only when the patient has recurrent, relapsed, refractory, metastatic, or advanced stage III or IV cancer and the test is FDA-approved or cleared as described. Somatic testing outside those criteria is nationally non-covered, and RNA sequencing and protein analysis are left to the MACs.
When did germline testing become part of the NCD?
Germline coverage took effect for services on or after January 27, 2020. CMS posted a draft in October 2019 and the final revision on January 20, 2020, according to Discoveries in Health Policy. The 2018 version covered only somatic testing.
Which patients qualify for national germline coverage?
Patients with ovarian or breast cancer who have a clinical indication and a risk factor for hereditary breast or ovarian cancer and no prior germline NGS test for the same content. Other cancer diagnoses fall under MAC discretion with similar criteria.
Does the NCD cover repeat testing?
Not for the same content. The somatic section requires that the patient has not been tested with the same NGS test for the same cancer genetic content, and the germline section requires no prior germline NGS test for the same germline content.
Is the policy text current?
The database shows version 2, effective January 27, 2020, with quarterly coding maintenance since. It also shows an older-version notice on that page, so labs should confirm the latest text in the Medicare Coverage Database before billing.
This article is educational and intended for laboratory, clinical, and revenue cycle professionals. It is not legal, coding, clinical, or reimbursement advice and does not replace CMS or payer documents. Verify all policy text against the current National Coverage Determination and your Medicare Administrative Contractor's policies before billing.
Sources: CMS Medicare Coverage Database, NCD 90.2 Next Generation Sequencing (NGS), versions 1 and 2 and revision history (accessed October 12, 2026); Discoveries in Health Policy, "CMS posts revised NCD for NGS," January 2020; GenomeWeb 360Dx, "CMS Reopens National Coverage Determination for NGS Testing in Advanced Cancer," May 2019.