PDMR Database

Patient-Derived Models Repository (PDMR) Database User Help Guide

PDMR Model Naming Structure, Types of Data Available

The NCI PDMR naming structure was developed to track each enrolled patient with a unique 6-digit randomized identifier and each collected specimen with a 3-digit collection code and letter indicating the type of tissue collected for model generation (e.g., 18-guage tissue biopsy = “T,” resected material = “R”, blood-origin/circulating tumor cells = “B”, malignant effusions = “M”). This combination (123456-000-R) gives a unique identifier to every specimen collected from enrolled patients and is used to create the unique distribution lot identifier.

PDXs (samples) are generally serial passaged subcutaneously, and the lineage can be tracked using the host-mouse identifier (an alphanumeric 3-digit identifier). The PDMR defines passage 0 (P0) as the first mouse passage implanted with the original human specimen. So, a P2 PDX would have a total of 9 digits if it was serially passaged (A12BC3D4E).

• If a PDX was generated through an alternate implant site, not subcutaneous, the letters “AL” will appear in the PDX name, and a note will be listed in the Specimen Notes defining the alternate implant location.
• If a PDX was generated by regrowth from a viably cryo-preserved fragment, the letters “RG” will appear in the PDX name. For instance, A12BC3_RG-D4E would indicate that the P2 tumor was generated from a regrowth of a cryopreserved fragment from the P1 tumor A12BC3.
• A sample labeled “Originator” represents the provided patient material and will at the minimum include pathological assessment. If there was sufficient tissue, sequence data will also be available.
• Tumors with a tendency for early necrosis resulting in a hollow, liquid-filled mass are sometimes pooled to try to rescue the line and implanted in an alternate site such as mammary fat pad. If the model was successfully developed, the passage number and the word “POOL” will be listed instead of a mouse ID. For example, P1POOL_AL-UT7 indicates a model where multiple P0 samples were pooled for a P1 implant at an alternative implant site in the tumor UT7.
• There are some exceptions to these rules as early in the PDMR development we did not truly appreciate the complexity that would result. In those cases, alternate implant sites such as mammary fat pad or thigh muscle are noted in the Specimen Notes section, but may not be represented in the PDX name.

PDC and CAF cultures (samples) are defined simply by addition of the model type as the Sample Name (e.g., 123456-000-R-PDC). The first in vitro passage is P1, whether the model is derived from patient or PDX material; details on origin are provided in the database. If a 2D culture is derived from an organoid culture, the passage is iterative to the organoid passage number (see image above).

PDMR Model Naming Structure, Types of Data Available

Patient	Diagnosis by CTEP SDC Code (sub-set of MEDdra disease codes) Diagnosis sub-type Gender Date of Diagnosis (MM/YYYY only) Age at Diagnosis Known Metastatic Sites Limited Medical Information Current and Prior Therapies Known Genetic Mutations and Tumor Markers of Patient Additional Medical History, if Provided Social History Race/Ethnicity Occupation Smoking History Specimens Collected for PDMR
Patient Specimen Information	Collection Procedure (e.g., biopsy, resection) Biopsy/Resection Site Date and Age at Collection Summary of Results for Human Pathogens Specimen Notes: may include PDX IHC/Pathology findings of interest for model or alternate implant methodologies (if not subcutaneous) Distribution Lot Availability Representative PDX Growth Curve by Passage (Median Tumor Volume)
Sample	Samples include representative individual PDXs from a model and when available, originating patient material for the provided specimen Passage number (P0 represented first implant) PDM Type (e.g., PDX, Originator) Pathology Data including 4x and 20x images, percent observed tumor content, percent necrosis, percent stromal component, and brief pathology write-up List of available Sequence files including Whole Exome and RNASeq. Affymetrix data are currently not available Detailed List of Variant Calls Using NCI’s Cancer Gene Panel (currently 62 genes based on NCI MPACT Clinical Protocol)
In Development	Patient-derived organoid models (PDOrg) Consensus Genomic Variants: list of variants that are 100% represented in PDX whole exome sequencing data Germline Whole Exome Sequence Whole Mouse Imaging (e.g., MRI, US) Designation of Metastatic PDX Models Preclinical Drug Study Results