Foundation Medicine

Machine learning is a feature layer on a sequencing business whose value stands without it. What oncologists order is genomic profiling: FoundationOne CDx and its liquid, hematologic, residual disease and germline siblings, read in Foundation Medicine's laboratories. The learned component in the clinical report is HRDsig, a homologous recombination deficiency signature the company says it developed with machine learning from more than 100 copy number features. A fragment based variant origin algorithm is investigational.

For drug developers, FoundationInsights adds natural language search from its partner Manifold, which is Manifold's model, and Foundation Medicine says it uses AI and machine learning in its real world data solutions without describing them.

Ask which results on a report come from a trained model, and which data products rely on model extraction.

The signature reaches an oncologist inside a laboratory report, labeled for what it is, and the controls around it are not described. Foundation Medicine separates HRDsig from the FDA approved results on the report and calls it a professional service, and the treating oncologist decides what it means for therapy.

What is not published is the mechanism: who reviews the signature before release, when it is withheld for low tumor content or poor sample quality, and how a corrected result is communicated.

Ask which sample conditions suppress an HRDsig result and how corrected reports are issued.

The approach is named without version and update discipline. Foundation Medicine describes HRDsig as a scar based genomic signature built with machine learning from more than 100 copy number features, and its variant origin algorithm as a fragmentomics method that separates clonal hematopoiesis, germline and tumor variants. FoundationInsights' natural language search is named as Manifold's.

No version history for HRDsig or notice to ordering clinicians when the signature changes is published.

Ask which HRDsig version your reports carry and how version changes are communicated.

The clinical model chain is in house, and the outside model for the data platform is named. HRDsig is developed and run by Foundation Medicine in its own laboratory, with no outside model provider. FoundationInsights' natural language search comes from Manifold, named in the October 2025 release.

What Manifold receives, and on what retention and training terms, is not published, and no subprocessor list covers the clinical or data platforms.

Ask whether Manifold processes de identified data only, under what terms, and for the processors that handle identifiable patient data.

Regulatory grade evidence for the assay, and company research for the model. FoundationOne CDx carries FDA approval with more than 40 companion diagnostic indications, which rests on analytical and clinical validation reviewed by FDA, and Foundation Medicine reports a median eight day turnaround. HRDsig is described in the company's research recap as developed with machine learning across copy number features and presented in its research program; its clinical validation is not set out on the pages describing it, and it sits outside the FDA reviewed assay.

Foundation Medicine reports results from more than 800,000 patients in its de identified dataset, which is scale rather than evidence for the signature.

Ask for the HRDsig validation against treatment response, by tumor type, with patient numbers and the publication.

The data use position is stated broadly. Foundation Medicine's notice says it may use protected health information to create de identified information, which then falls outside the notice, that researchers may access information for research, and that a sale of protected health information requires authorization. The de identified results of more than 800,000 patients underpin FoundationInsights and the database built with Flatiron Health, and a patient opt out page is published. No retention period, de identification method or statement on training models is set out in the notice.

Safety engineering for HRDsig, meaning how a faulty signature result would be detected and handled, is not published.

Ask what the patient opt out covers, how long samples and sequence data are kept, and whether patient data trains HRDsig or other models.

Covered entity obligations are stated and a substantive privacy document reaches the patient. Foundation Medicine's HIPAA Notice of Privacy Practices, effective since 25 May 2018 and last modified 1 June 2026, covers Foundation Medicine, Inc. and Saga Diagnostics US, Inc., describes uses and disclosures of protected health information, and says business associates such as billing services are bound by contract to safeguard it. Separate website, California, and EEA and UK notices and a patient opt out page are published.

As the testing laboratory, Foundation Medicine contracts with providers as a covered entity, so no customer business associate agreement applies to ordered tests; the agreements behind FoundationInsights are not published.

Ask which outside parties, including Roche affiliates, receive identifiable patient data, and on what terms.

Nothing independent covering information security is published. Foundation Medicine's legal and privacy pages list its privacy notices and opt out, and its laboratory credentials and FDA approval address testing quality, but no SOC 2 report, HITRUST certification, ISO/IEC 27001 certificate, penetration testing statement or trust center is published for the clinical systems or for FoundationInsights.

Ask for a security attestation covering clinical reporting systems and FoundationInsights, with scope and date.

The lead product holds an FDA approval and the AI's position beside it is stated. FoundationOne CDx is an FDA approved next generation sequencing in vitro diagnostic covering 324 genes, microsatellite instability and tumor mutational burden, with more than 40 approved companion diagnostic indications. The approval is PMA P170019, granted 30 November 2017, and its latest supplement, P170019/S060, was approved on 27 May 2026 and adds a companion diagnostic indication for homologous recombination repair gene alterations. Foundation Medicine states plainly that HRDsig is a professional service and not part of the FDA approved assay, so a buyer can see which results the approval covers and which it does not.

The approval does not cover the learned signature, and the variant origin algorithm is labeled investigational.

Ask for the current approval and indication list for the assay version you would order, and how HRDsig results are validated under the laboratory's own procedures.

The model is developed inside a regulated laboratory and no evaluation by group is published. HRDsig was developed with machine learning from copy number features and is reported under the laboratory's professional services, but no results by tumor type, ancestry or sample type, and no change control for the signature, are set out on the pages describing it. Copy number based signatures can behave differently across tumor types and tumor content, which is where a buyer would look first.

Ask for HRDsig performance by tumor type and ancestry and how changes to the signature are approved and communicated.

Foundation Medicine is the covered entity laboratory, HRDsig is part of the result it reports, and its Notice of Privacy Practices gives the patient a right to ask for incomplete or incorrect information to be amended, a route against the laboratory directly that reaches the report.

No error rate for HRDsig at its reporting threshold, and no warranty or remediation commitment attached to a signature result, is published.

Ask for HRDsig's false positive and false negative rates against a reference method, and what Foundation Medicine does when a reported signature is revised.

Integration is offered with no system named. Foundation Medicine lists record system integration among its ordering options for FoundationOne CDx, alongside online and fax ordering, without naming a record system, standard, marketplace listing or live site on the test page. Its database built with Flatiron Health is a research data partnership rather than an integration reference.

Ask which record systems receive Foundation Medicine results today, at which sites, and whether genomic findings, including HRDsig, arrive as discrete data.

A single laboratory service with location implied. Foundation Medicine sequences and reports from its own US laboratories, and FoundationInsights is described as a cloud based analytics platform without a named host or region. Separate EEA and UK notices exist for its website, and nothing published says where clinical data rests or whether any crosses a border to Roche affiliates.

Ask where sequence data, reports and FoundationInsights data are hosted and whether any processing occurs outside the United States.

No price is published and how the testing is paid for can be established. FoundationOne CDx has national Medicare and Medicare Advantage coverage for qualifying patients, and financial assistance may be available for patients with out of pocket costs; the coverage determines what Medicare pays the laboratory rather than a price. FoundationInsights and data access for drug developers are sold under agreements with no published rate.

Ask for the list price and typical patient responsibility for FoundationOne CDx, and how FoundationInsights access is priced.

Coverage is named with validation behind part of it. FoundationOne CDx is approved for advanced solid tumors with more than 40 companion diagnostic indications naming specific cancers and therapies, which sets out where the assay is validated. HRDsig is reported across solid tumors as a professional service, without a published statement of the tumor types in which it has been validated.

Ask which tumor types HRDsig is validated in and how a result is labeled for a tumor type outside that set.