Key facts for NCD 90.2
- Benefit category
- Diagnostic Laboratory Tests, Diagnostic Services in Outpatient Hospital, Diagnostic Tests (other)
- Effective date
- 01/27/2020
- Implemented 11/13/2020
- Transmittal
- Transmittal 10346
- Versions published
- 2
- Manual chapter
- 90
- NCD Manual (Pub. 100-03)
TL;DR
NCD 90.2 sets Medicare's national policy for next generation sequencing (ngs) under the benefit category "Diagnostic Laboratory Tests, Diagnostic Services in Outpatient Hospital, Diagnostic Tests (other)", effective 01/27/2020 and implemented 11/13/2020. Effective for services performed on or after March 16, 2018, the Centers for Medicare & Medicaid Services (CMS) has determined that Next Generation Sequencing (NGS) as a diagnostic laboratory test is reasonable and necessary and covered nationally, when… It has been revised 1 time since publication and binds every Medicare Administrative Contractor nationally.
Item or service described
A. General
Clinical laboratory diagnostic tests can include tests that, for example, predict the risk associated with one or more genetic variations. In addition, in vitro companion diagnostic laboratory tests provide a report of test results of genetic variations and are essential for the safe and effective use of a corresponding therapeutic product. Next Generation Sequencing (NGS) is one technique that can measure one or more genetic variations as a laboratory diagnostic test, such as when used as a companion in vitro diagnostic test.
This National Coverage Determination (NCD) is only applicable to diagnostic lab tests using NGS for somatic (acquired) and germline (inherited) cancer. Medicare Administrative Contractors (MACs) may determine coverage of diagnostic lab tests using NGS for RNA sequencing and protein analysis.
Indications and limitations of coverage
B. Nationally Covered Indications
1. Somatic (Acquired) Cancer
Effective for services performed on or after March 16, 2018, the Centers for Medicare & Medicaid Services (CMS) has determined that Next Generation Sequencing (NGS) as a diagnostic laboratory test is reasonable and necessary and covered nationally, when performed in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory, when ordered by a treating physician, and when all of the following requirements are met:
a. Patient has:
• either recurrent, relapsed, refractory, metastatic, or advanced stage III or IV cancer; and
• not been previously tested with the same test using NGS for the same cancer genetic content, and
• decided to seek further cancer treatment (e.g., therapeutic chemotherapy).
b. The diagnostic laboratory test using NGS must have:
• Food & Drug Administration (FDA) approval or clearance as a companion in vitro diagnostic; and,
• an FDA-approved or -cleared indication for use in that patient’s cancer; and,
• results provided to the treating physician for management of the patient using a report template to specify treatment options.
2. Germline (Inherited) Cancer
Effective for services performed on or after January 27, 2020, CMS has determined that NGS as a diagnostic laboratory test is reasonable and necessary and covered nationally for patients with germline (inherited) cancer, when performed in a CLIA-certified laboratory, when ordered by a treating physician and when all of the following requirements are met:
a. Patient has:
• ovarian or breast cancer; and,
• a clinical indication for germline (inherited) testing for hereditary breast or ovarian cancer; and,
• a risk factor for germline (inherited) breast or ovarian cancer; and
• not been previously tested with the same germline test using NGS for the same germline genetic content.
b. The diagnostic laboratory test using NGS must have all of the following:
• FDA-approval or clearance; and,
• results provided to the treating physician for management of the patient using a report template to specify treatment options.
C. Nationally Non-Covered Indications
1. Somatic (Acquired) Cancer
Effective for services performed on or after March 16, 2018, NGS as a diagnostic laboratory test for patients with acquired (somatic) cancer are non-covered if the cancer patient does not meet the criteria noted in section B.1., above.
D. Other
1. Somatic (Acquired) Cancer
Effective for services performed on or after March 16, 2018, Medicare Administrative Contractors (MACs) may determine coverage of NGS as a diagnostic laboratory test for patients with advanced cancer only when the test is performed in a CLIA-certified laboratory, when ordered by a treating physician, and when the patient has:
• either recurrent, relapsed, refractory, metastatic, or advanced stages III or IV cancer; and,
• not been previously tested with the same test using NGS for the same cancer genetic content, and
• decided to seek further cancer treatment (e.g., therapeutic chemotherapy).
2. Germline (Inherited) Cancer
Effective for services performed on or after January 27, 2020, MACs may determine coverage of NGS as a diagnostic laboratory test for patients with germline (inherited) cancer only when the test is performed in a CLIA-certified laboratory, when ordered by a treating physician, when results are provided to the treating physician for management of the patient and when the patient has:
• any cancer diagnosis; and,
• a clinical indication for germline (inherited) testing of hereditary cancers; and,
• a risk factor for germline (inherited) cancer; and,
• not been previously tested with the same germline test using NGS for the same germline genetic content.
(This NCD last reviewed January 2020)
Text reproduced from the CMS Medicare Coverage Database record for NCD 90.2 version 2. View the original on cms.gov.
Revision history
08/2026 - Transmittal 13752 issued May 26, 2026, is being rescinded and replaced by Transmittal 13910, dated August 14, 2026, to remove business requirement 14464.5, NCD 250.4 Treatment of Actinic Keratosis from the change request. All other information remains the same.( TN 13910 ) (CR14464)
08/2026 - The purpose of this Change Request (CR) is to provide a quarterly maintenance update of ICD-10 coding conversions and other coding updates specific to National Coverage Determinations (NCDs). No policy is being changed as a result of these updates. ( TN 13906 ) (CR14537)
05/2026 - The purpose of this Change Request (CR) is to provide a quarterly maintenance update of ICD-10 coding conversions and other coding updates specific to NCDs. No policy is being changed as a result of these updates. ( TN 13752 ) (CR14464)
04/2026 - Transmittal 13623 issued February 05, 2026, is being rescinded and replaced by Transmittal 13760, dated April 30, 2026, to remove business requirement 14356.4 and the corresponding spreadsheet for NCD 250.4 Treatment of Actinic Keratosis as this NCD was moved to the October 2026 CR. All other information remains the same. ( TN 13760 ) (CR14356)
02/2026 - The purpose of this Change Request (CR) is to provide a quarterly maintenance update of ICD-10 coding conversions and other coding updates specific to National Coverage Determinations (NCDs). No policy is being changed as a result of these updates. ( TN 13623 ) (CR14356)
09/2025 - Transmittal 13400 issued September 05, 2025, is being rescinded and replaced by Transmittal 13438, dated September 30, 2025, to add a new attachment to ensure the functionality of the NCD zip URL is working properly and to update the Policy section. All other information remains the same.
The purpose of this Change Request (CR) is to provide a maintenance update of ICD-10 coding changes specific to NCDs. ( TN 13438 ) (CR14197)
08/2025 - The purpose of this Change Request (CR) is to provide a maintenance update of ICD-10 coding changes specific to NCDs. ( TN 13375 ) (CR14197)
03/2025 - The purpose of this Change Request (CR) is to provide a quarterly maintenance update of ICD-10 coding conversions and other coding updates specific to National Coverage Determinations (NCDs). No policy is being changed as a result of these updates. ( TN 13097 ) (CR13939)
05/2024 - The purpose of this Change Request (CR) is to provide a quarterly maintenance update of ICD-10 coding conversions and other coding updates specific to National Coverage Determinations (NCDs). No policy is being changed as a result of these updates. ( TN 12626 ) (CR13596)
01/2024 - Transmittal 12355 issued November 09, 2023, is being rescinded and replaced by Transmittal 12444, January 4, 2024 to add clarifying verbiage to NCD 90.2, business requirement 13278.2, and related edits to NCD 90.2, Next Generation Sequencing, attached spreadsheet. All other information remains the same. ( TN 12444 ) (CR13278)
01/2024 - Transmittal 12350 issued November 03, 2023, is being rescinded and replaced by Transmittal 12440 dated January 3, 2024, to make changes to NCD 90.2, Next Generation Sequencing, spreadsheet to align with revisions being made to CR 13278. All other information remains the same. ( TN 12440 ) (CR13391)
11/2023 - The purpose of this Change Request (CR) is to provide a maintenance update of ICD-10 conversions and other coding updates specific to NCDs. These NCD coding changes are the result of newly available codes, coding revisions to NCDs released separately, or coding feedback received. ( TN 12355 ) (CR13278)
11/2023 - The purpose of this Change Request (CR) is to provide a quarterly maintenance update of ICD-10 coding conversions and other coding updates specific to National Coverage Determinations (NCDs). No policy is being changed as a result of these updates.( TN 12350 ) (CR13391)
10/2023 - The purpose of this Change Request (CR) is to provide a quarterly maintenance update of ICD-10 coding conversions and other coding updates specific to National Coverage Determinations (NCDs). No policy is being changed as a result of these updates. ( TN 12319 ) (CR13391)
08/2023 - The purpose of this Change Request (CR) is to provide a maintenance update of ICD-10 conversions and other coding updates specific to NCDs. ( TN 12184 ) (CR13278)
05/2023 - The purpose of this Change Request (CR) is to provide a quarterly maintenance update of ICD-10 coding conversions and other coding updates specific to National Coverage Determination (NCDs). No policy is being changed as a result of these updates. ( TN 12017 ) (CR13166)
06/2022 - Transmittal 11055, dated October 21, 2021, is being rescinded and replaced by Transmittal 11461, dated, June 21, 2022 to revise BR 12483.1 and corresponding spreadsheet to align with changes made in previous CR 12124 and later CR 12705. All other information remains the same. ( TN 11461 ) (CR12483)
06/2022 - Transmittal 11400, dated May 4, 2022, is being rescinded and replaced by Transmittal 11460, dated, June 17, 2022, to update NCD 90.2, NGS, spreadsheet to conform with changes in CR 12124, and change the implementation date for all business requirements except 12705.6 to 30 days from issuance of this correction. All other information remains the same.( TN 11460 ) (CR12705)
06/2022 - Transmittal 10832, dated June 2, 2021, is being rescinded and replaced by Transmittal 11453, dated, June 10, 2022, to revise NCD 90.2, NGS, revises business requirement 12124.2 and 12124.2.1 and its associated spreadsheet of coding by retainining all ICD-10 NOC diagnosis codes proposed for deletion effective July 1, 2022. ( TN 11453 ) (CR12124)
How this NCD shows up on remittances
A service denied under a National Coverage Determination returns CARC 50 (not deemed medically necessary) with remark N386 (decision based on an NCD); a denial citing a local policy instead carries N115. Because NCDs bind nationally, the appeal path is documentation that the patient meets the indications above, not a contractor-policy argument.
How QuickIntell applies NCD 90.2
QuickAuth checks the ordered service and diagnosis against NCD and LCD criteria before the encounter, QuickCode validates the diagnosis pairing on the claim, and QuickRCM routes CARC 50 denials with the policy text and the covered-code list attached so the appeal starts with evidence.
Frequently asked questions — NCD 90.2
What does NCD 90.2 cover?
Effective for services performed on or after March 16, 2018, the Centers for Medicare & Medicaid Services (CMS) has determined that Next Generation Sequencing (NGS) as a diagnostic laboratory test is reasonable and necessary and covered nationally, when performed in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory, when ordered by a treating physician, and when all of the following… The full indications and limitations are reproduced on this page from the CMS Medicare Coverage Database.
When did NCD 90.2 take effect?
The current version (2) is effective 01/27/2020, implemented 11/13/2020, published in transmittal 10346. CMS lists 2 versions of this NCD.
Does a Local Coverage Determination override NCD 90.2?
No. A National Coverage Determination binds all Medicare Administrative Contractors; an LCD can only address services or circumstances the NCD leaves open. Claims denied under this NCD typically return CARC 50 with remark N386 (NCD) rather than N115 (LCD).
Sources
Every figure on this page is taken from the CMS publications below, as released by the Centers for Medicare & Medicaid Services. Projection built 2026-10-02. Verify against the primary file before billing or contracting decisions.
- Medicare Coverage Database NCDs via the CMS Coverage APIVersion API snapshot 2026-09-27 · effective 2026-09-20 · file national-coverage-ncd.jsonSHA-256 a90fadfd264b9ef4…
Disclaimer
This page reproduces the CMS National Coverage Determination text and, for laboratory NCDs, the CMS ICD-10 edit lists, as an operational reference. Coverage decisions depend on the full policy, the claim and the contractor; nothing here is legal, clinical or billing advice. CPT codes are shown as numbers only; CPT descriptors are copyright AMA.