MatchMiner Genomics – MatchMiner

Clinical trials with genomic eligibility criteria are increasingly common, and those criteria can be very complex. At the same time, the number of patients whose tumors have been sequenced continues to grow. Together, these trends make it difficult for clinicians to manually match patients to the right trials.

MatchMiner Genomics matches patients to trials with a custom matching process, the MatchEngine, which integrates clinical trial eligibility structured into Clinical Trial Markup Language (CTML) with genomic sequencing of patients’ tumors.

It supports both sides of the patient-trial matching process: identify candidate trials for a specific patient, or identify candidate patients for a specific trial.

protocol-24-117.ctml.yaml CTML

protocol_no: 24-117
treatment_list:
  step:
    - arm:
        - arm_code: A
          match:
            - and:
                - genomic:
                    hugo_symbol: EGFR
                    protein_change: p.L858R
                    variant_category: Mutation
                - clinical:
                    oncotree_primary_diagnosis: Non-Small Cell Lung Cancer
                    age_numerical: ">=18"

Example patient (synthetic)

Variants: EGFR p.L858R TP53 p.R273H
Diagnosis: Lung adenocarcinoma
Age: 64

Matches protocol 24-117, arm A

Lung adenocarcinoma matches "Non-Small Cell Lung Cancer" because OncoTree, a standard classification of cancer types, files it under non-small cell lung cancer.

How it works

MatchMiner Genomics has three open-source parts: the MatchEngine, an API, and a web interface. You supply patient data and trial criteria written in CTML. Matches are candidates for the patient’s care team to review, not a guarantee of eligibility. The care team and trial staff confirm eligibility against the full protocol.

Load patient data

Structured genomic results (mutations, copy number changes, structural variants, signatures) and clinical data, fed from your institution’s pipelines.

Patient data format

Curate trials in CTML

Curators write each trial’s genomic, clinical, and demographic eligibility in CTML, a human-readable YAML or JSON format.

CTML reference

Run the MatchEngine

The MatchEngine checks every patient against every open trial arm and stores the matches. It can run nightly or whenever new data lands.

Source on GitHub

Review matches

Clinicians and trial staff browse, filter, and act on matches in the web interface, inside your institution’s firewall.

Try the demo setup

Three ways to find a match

Start from a patient

A patient’s clinical care team opens MatchMiner Genomics and sees a list of trials matching the genomic profile of that patient’s tumor.

Start from a trial

Trial staff save a filter for their trial’s eligibility and get a running list of patients who fit, updated as new patients are sequenced.

Search trials directly

Staff search open trials by gene, variant, or diagnosis to review options for an individual alteration by hand.

MatchMiner Genomics patient view. A sidebar shows patient details with placeholder values and filters for gene, tissue, age, drug, phase, and disease center. The main panel reports 7 trial matches based on OncoPanel results and lists them by rank. Each lists the matching alteration (IDH1 p.R132H, variant-level match), the disease center, an open-to-accrual status, and colored tags for genes, cancer types, drugs, and phase. — Patient view. One patient’s trial matches, ranked by how closely the genomic alteration matches. Identifiers are placeholders.

MatchMiner Genomics patient matches list for a saved filter. Status tabs across the top: new, pending, flagged, contacted, eligible, deferred, not eligible, enrolled. Each row shows a placeholder MRN, the filter name, a cancer diagnosis such as anaplastic oligodendroglioma, the IDH1 p.R132H mutation, tier 1 actionability, variant allele frequency around 40 percent, and buttons to email or open the match. — Trial view. Patients who match a saved filter, with their diagnosis, alteration, and allele frequency. Staff track each patient from new to enrolled. Identifiers are placeholders.

At Dana-Farber

MatchMiner Genomics has been in clinical use at Dana-Farber since 2016. It reads results from OncoPanel, Dana-Farber’s in-house tumor sequencing test, and now also from the commercial Exact Sciences OncoExTra test.

At Dana-Farber, January 2022

~170: open precision medicine trials curated in CTML
84%: of patients had at least one trial match
220+: patients enrolled on a trial as a result of MatchMiner

The design and these results are described in Klein H. et al., MatchMiner: an open-source platform for cancer precision medicine, npj Precision Oncology 2022;6:69.

Run it at your institution

MatchMiner Genomics is free to deploy. A small instance runs on a laptop. Get started covers the data, infrastructure, and people you’ll need.