NCD 90.2 is Medicare's National Coverage Determination for next-generation sequencing (NGS), originally finalized in March 2018 and amended in 2020. It sets the national framework for when Medicare covers NGS as a diagnostic laboratory test for patients with cancer, and it applies to both somatic and germline testing.

When does Medicare cover NGS for cancer under NCD 90.2?

Coverage requires that the test is performed in a CLIA-certified laboratory and ordered by the treating physician, and that the patient has either recurrent, relapsed, refractory, or metastatic cancer or advanced stage III or IV cancer, has not already been tested with the same NGS test for the same primary cancer diagnosis, and has decided to seek further cancer treatment. Tests that are FDA-approved or cleared as companion diagnostics for the patient's cancer have a defined national coverage pathway; other NGS tests may be covered at the Medicare Administrative Contractor's discretion when the same clinical criteria are met.

Why does a test that NCD 90.2 covers still get denied?

Because coverage in principle is not the same as a payable claim. The most common reasons an otherwise-covered NGS test is denied are that the required cancer stage or status is not clearly documented, the test duplicates a prior NGS test for the same diagnosis, or the ordering and documentation do not establish that the criteria were met. Medicare NGS denial rates actually rose as coverage expanded, which underscores that meeting the criteria on paper is what gets claims paid.

NCD 90.2 Decoded: When Medicare Covers Next-Generation Sequencing for Cancer

Q: Does Medicare cover germline (inherited) cancer testing under NCD 90.2?

Yes, within limits. The criteria apply to both somatic and germline mutations, and a 2020 amendment expanded coverage to include germline testing for certain patients with ovarian or breast cancer who have clinical and family-history features suggestive of hereditary cancer. Specific coverage still depends on the criteria and on the applicable contractor's policy.

Every oncology practice and molecular lab eventually asks the same question about a cancer NGS test: will Medicare pay for it? The honest answer lives in a single National Coverage Determination, NCD 90.2, and while it is often summarized as "Medicare covers NGS for advanced cancer," that summary hides the specific conditions that actually decide whether a given claim is paid or denied. This article walks through what the rule requires, in plain language, and where claims tend to fall apart even when the test was appropriate.

Disclaimer: This is educational, not medical, legal, or billing advice, and it is not a coverage determination for any specific patient or claim. Coverage rules change, Medicare Administrative Contractors apply local policies, and the only authoritative source is the current NCD and applicable LCD language. Always verify against CMS's current policy and consult qualified clinical, billing, and compliance professionals before making coverage or treatment decisions. Use this information at your own risk.

What NCD 90.2 is, and why it exists

NCD 90.2 is Medicare's national rule for covering next-generation sequencing as a diagnostic laboratory test in patients with cancer. It was finalized in March 2018 and amended in 2020. Before it existed, coverage for cancer NGS was a patchwork of local decisions; the NCD was meant to create a consistent national floor for when these tests are reasonable and necessary.

The thing to understand about the rule's design is that it does two different jobs at once. It establishes a national coverage pathway for certain tests, and it leaves room for local contractor discretion for others. Knowing which door a given test comes through is the first step to predicting whether it will be paid.

The two doors to coverage

The cleaner path is for tests with FDA standing. When an NGS test is FDA-approved or cleared as a companion in vitro diagnostic and is used for an indication that matches the patient's cancer, NCD 90.2 provides a defined national coverage pathway, provided the patient also meets the clinical criteria below and the results are furnished to the treating physician to guide management. This is why FDA companion-diagnostic status matters so much commercially: it is the most predictable route to Medicare coverage for an NGS assay.

The second path covers everything else. For NGS tests that are not FDA-approved companion diagnostics, the NCD allows Medicare Administrative Contractors (MACs) to determine coverage when the same clinical criteria are met. This is where the MolDX program and its Local Coverage Determinations do much of the real work, and it is why coverage for the same test can look different depending on the contractor and jurisdiction. "Medicare covers it" is rarely a national yes-or-no; for many tests it is a contractor-level decision operating inside the national framework.

The criteria that actually decide it

Both doors share the same core clinical gate. Under NCD 90.2, NGS is covered as a diagnostic laboratory test for a patient with cancer when all of the following hold:

The test is performed in a CLIA-certified laboratory.
The test is ordered by the treating physician.
The patient has either recurrent, relapsed, refractory, or metastatic cancer, or advanced stage III or IV cancer.
The patient has not already been tested with the same NGS test for the same primary cancer diagnosis (the rule does not cover repeating the identical test for the same cancer).
The patient has decided to seek further cancer treatment (for example, therapeutic chemotherapy).

Read that list as a checklist, because that is how it functions on a claim. Miss any one of the elements, or fail to document it, and a test that is "covered" in the abstract becomes a denial in practice. The criteria are also explicit that they apply to both somatic and germline mutations, which leads to the next point.

Somatic, germline, and the 2020 expansion

The 2018 NCD was primarily understood as a somatic-testing rule, tumor testing to guide treatment. The 2020 amendment widened it. It extended coverage to include germline (inherited) testing for certain patients with ovarian or breast cancer who have clinical features and a family or personal history suggestive of a hereditary cancer syndrome.

This distinction is not academic, because somatic and germline testing answer different questions and carry different documentation expectations. Somatic testing asks what is driving this tumor and how to treat it; germline testing asks whether the patient carries an inherited risk that affects them and their family. A claim that blurs the two, or that applies the wrong framework to the test performed, invites a denial even when some coverage pathway existed. Matching the test, the indication, and the documentation to the right framework is part of getting paid.

The three things that most often get a covered test denied

Here is the practical layer the NCD itself does not spell out. When an NGS test that should qualify under NCD 90.2 is denied anyway, it usually traces to one of three failures.

The first is stage or status not clearly documented. The criteria turn on the patient having recurrent, relapsed, refractory, metastatic, or advanced stage III/IV disease. If that status is not unambiguously captured in the record and reflected on the claim, the reviewer cannot confirm the gate was met, and the safe default for a payer is denial.

The second is duplicate testing. The NCD does not cover repeating the same NGS test for the same primary cancer diagnosis. A second run that looks like a repeat, even for a defensible clinical reason, can be denied unless the distinction is made clear.

The third is ordering and documentation gaps, the test ordered by someone other than the treating physician, or a record that does not establish the patient had decided to pursue further treatment. These are not clinical disagreements; they are evidentiary gaps that prevent the payer from confirming the criteria were satisfied.

Why "covered" keeps producing denials

If NCD 90.2 establishes coverage, you would expect denials to fall over time. The data shows the opposite, and it is worth confronting. A 2025 JAMA Network Open study of Medicare cancer-NGS claims found the denial rate rose from 16.8% before the NCD to 20.3% after its 2018 implementation to 27.4% after the 2020 amendment. Coverage broadened; denials climbed.

The explanation is the throughline of this whole topic: coverage and payability are different things. Each expansion of the rule added criteria, and every added criterion is one more condition a claim must document and satisfy. Broader coverage expressed as more detailed rules generates more denials, not fewer, unless the ordering, documentation, and claim keep precise pace with the policy. Coverage tells you a test can be paid. Meeting every criterion, on the record and on the claim, is what gets it paid.

The strategic takeaway

NCD 90.2 is a good teacher because it makes the central lesson of molecular reimbursement concrete: the gap between "this test is covered" and "this claim will be paid" is filled entirely by specific, current, well-documented criteria. The rule is national, but its application is local, contractor-dependent, and constantly refined through LCDs and program guidance.

For practices and labs, the durable response is to treat coverage criteria as living rules rather than static knowledge, mapped to each test and indication, kept current as the NCD, the LCDs, and the contractor policies evolve, and applied at the point of ordering and billing so the documentation matches what today's policy actually requires. Keeping that rule layer accurate and current across payers and tests is exactly what Converus is built to do. The criteria in NCD 90.2 will keep changing; what should not change is your ability to meet them on every claim.

Sources

National Coverage Determination (NCD 90.2): Next Generation Sequencing — Centers for Medicare & Medicaid Services (finalized March 2018; amended 2020)
Decision Memo, Next Generation Sequencing for Medicare Beneficiaries with Advanced Cancer (CAG-00450R) — Centers for Medicare & Medicaid Services
Medicare Expands Access to Genetic Diagnostic Tests for Certain Ovarian and Breast Cancers — analysis of the 2020 NCD 90.2 germline expansion
Claim Denials for Cancer-Related Next-Generation Sequencing in Medicare — JAMA Network Open, April 18, 2025 (doi:10.1001/jamanetworkopen.2025.5785; PubMed 40249617)