Metadata Dictionary

Sex of the patient.

Patient Ethnic group. Can be derived from self-assessment or genetic analysis.

Diagnosis of the patient when first diagnosed at age_at_initial_diagnosis - this can be different than the diagnosis at the time of collection which is collected in the sample section.

Age category at time of sampling.

Alcohol intake of the patient, self-reported

If a first-degree relative of the patient has been diagnosed with a cancer of the same or different type.

Unique ID of the patient tumour sample used to generate cancer models.

Collection event corresponding to each time a patient was sampled to generate a cancer model, subsequent collection events are incremented by 1.

Patient age at collection.

Collected tumour type.

Site of collection of the tissue sample (can be different than the primary site if tumour type is metastatic).

Stage of the patient at the time of collection.

The implanted tumour grade value.

Positive virology status at the time of collection. Any relevant virology information which can influence cancer like EBV, HIV, HPV status.

Is patient treatement information avalaible and sharable? If yes fill out following treatment columns: treatment_naive_at_collection, treated_at_collection, treated_prior_to_collection.

Was the patient being treated for cancer at the time of tumour sample collection. This includes any of the following: radiotherapy, chemotherapy, targeted therapy, homorno-therapy.

Patient’s response to treatment.

Define any limitation of access of the model per type of users like academia, industry, academia and industry, or national limitation if needed (e.g. no specific consent for sequencing).

Contact email for any requests from users about models. If multiple, include as comma separated list.

If the center has a contact form rather than a contact email include the link here.

Host mouse strain name (e.g. NOD-SCID, NSG, etc).

Organ or anatomical site used for the PDX tumour engraftment (e.g. mammary fat pad, Right flank).

Description of the type of material grafted into the mouse. (e.g. tissue fragments, cell suspension).

Passage number: When different host strains, or PDX Engraftment Site or PDX Engraftment Type or PDX Engraftment Material were used during the PDX line generation, please add passage - add rows per model as needed. We assume that passage 0 corresponds to first engraftment - if not the case please indicate what passage 0 correspond to. passage number- add rows if columns D,E,F, G changes - if no change and always same D,E,F,G add 'all' as passage value to specify the conditions are the same in all passages.

Please provide the supplier brief acronym or name followed by a colon and thel number or name use to reference the model.

Catalogue number of model, if commercial.

Depmap accession, Cellusaurus accession or another id. Please place in comma separated list.

Any technique used to validate PDX against their original patient tumour, including fingerprinting, histology, immunohistochemistry.

Provide a list of all passages where validation was performed. Passage 0 correspond to first engraftment (if this is not the case please define how passages are numbered).

If model type is 3D: Organoid or cell lines, Morphological features of the model.

Was STR analysis done on the model?

Presence of tumour vs stroma or normal cells.

Most common name associated with the model. Please use the CCLE name if available.

Type of organoid or cell model.

Unique ID of the patient tumour sample used to generate the model.

Unique identifier for each media formulation (Catalogue number).

Coating on plate model was grown in.

Passage number at time of sequencing/screening.

What are the details of the contamination.

Additional drug/compounds the model was grown with.

If the model has been part of a published study include PubMed IDs separated by commas.

Model supplier type - commercial, academic, other.

Link to purchasable cell model, if commercial.

Depmap accession, Cellusaurus accession or another id. Please place in comma separated list.