CoMMpass Interim Analysis¶

The CoMMpass study was designed to collect and release genomic and clinical data in an iterative fashion over the course of the project. This structure ensured that researchers, pharmaceutical partners, and internal MMRF teams had access to high quality data in a timely and reproducible manner. Each Interim Analysis (IA) served as a defined “data cut”, incorporating new patients, new follow-up visits, or refinements to analytical pipelines and quality control standards.

Across the lifespan of CoMMpass, 24 interim analyses were planned, culminating in IA24, the final comprehensive release of harmonized clinical and genomic data for all study participants.

Data Release Framework¶

Each Interim Analysis release contained multiple data layers:

Data Layer	Description	Example Outputs
Clinical Data	Updated patient-level variables (diagnosis, treatments, outcomes)	Clinical.tsv, therapy tables
Genomic Data	WGS/WES VCFs, RNA-seq expression, CNV, SV, and annotation files	.vcf.gz, .maf, .counts.txt
Metadata	Sample identifiers, assay QC metrics, version tracking	Sample manifests, readme logs
Documentation	README, change logs, pipeline versions	IA11_README.txt, JetStream logs

Accessing CoMMpass IA Releases¶

All CoMMpass Interim Analysis releases are available through the Projects Page in Virtual Lab.

Step 1: Navigate to Projects¶

From the Virtual Lab homepage, click Projects under Core Tools
This opens the full list of available datasets

Projects Page

Step 2: Select an IA Release¶

Locate the desired project (e.g., MMRF-IA11, MMRF-IA22, MMRF-IA24)
Click the Project ID link to open the project details page

Select IA24

Step 3: Open the Repository¶

On the project page, click View Files (top right)
This opens the Repository, where all files for that IA release are stored

View Files

Step 4: Download Files¶

Files can be downloaded in two ways:

Option A: Individual Download

Click a file name to download directly

Option B: Cart-Based Download (Recommended)

Add files to your cart using the cart icon
Or select Add All Files to Cart
Proceed to download via the cart interface

Accessing IA24 (Final Release)¶

IA24 differs from historic releases in that it includes the full set of clinical and molecular data generated across the study. As a result, the Repository contains tens of thousands of files, including raw and processed genomic data.

Step 1: Open IA24 Repository¶

Navigate to Projects → MMRF-COMMPASS-IA24
Click View Files

Step 2: Apply Filters to Identify Key Files¶

To locate commonly used datasets such as summary outputs and clinical tables:

In the left-hand filter panel:
Expand Data Category
Select:
- Summary Data Files
- Clinical Data Tables

Applying these filters will reduce the file list substantially (e.g., from ~60,000 files to a focused set of relevant datasets).

View Files

Step 3: Review Filtered Results¶

Filtered results may include:

Summary-level datasets (e.g., mutation summaries, expression summaries)
Harmonized clinical data tables (e.g., labs, treatments, outcomes)

Step 4: Download Files¶

Files can be downloaded in two ways:

Option A: Individual Download

Click a file name to download directly

Option B: Cart-Based Download (Recommended)

Add files to your cart using the cart icon
Or select Add All Files to Cart
Proceed to download via the cart interface

For additional details, see the Repository & Data Download documentation.