SUBMIT MODELS / HELPDESK

We are recruiting PDX models data !!

For all questions, comments, website feedback: helpdesk

SUBMIT YOUR PDX DATA TO THE PDX FINDER TO INCREASE THEIR VISIBILITY

We are recruiting PDX models data !! For all PDX data submission requests: submissions

WHY SUBMITTING YOUR DATA TO PDX FINDER:

PDX Finder is the first free global PDX models catalogue to facilitate PDX models discovery, we display PDX models metadata and data from academia, large consortia and CROs. We have nearly 2000 models for 7 different resources and growing fast !

We can collect and display your data, making you more discoverable and visible for end users. We are supported by Public funding and our service is completely free to providers and users.

DATA FORMAT:
The PDX Finder team is accepting metadata in a variety of formats and would recommend you are using the PDX Finder data template – checklist from this template is shown below:

The spreadsheet contains several sub-sheets separated by level of information – with relevant example values to guide users, we will be happy to guide you through the full template via teleconference.

If imputing PDX data in the template is not possible, we recommend using it as a checklist for the data PDX producers will provide and submit the data via direct upload of files collection or database dumps – PDX team will do the rest.

In addition to these metadata, we encourage producers to send data (OMIC or drug dosing studies for example). PDX Finder can upload and store any OMIC data and drug dosing making models even more discoverable – see here for examples:

Other data types can also be sent, immunohistochemitry, expression data, images and many more.
Don’t hesitate to suggest additional metadata/data , PDX Finder team is flexible and we are happy to accommodate your data/needs.

CATEGORY CATEGORY ESSENTIAL/DESIRABLE ATTRIBUTE NAME FIELD
EXAMPLE
FIELD
ESSENTIAL/DESIRABLE
patient essential patient anonymous ID A0088 essential
patient sex Female essential
cancer relevant history lynch syndrome desirable
Ethnicity (we should use race term to be in sync with the american datasets) EASTERN EUROPEAN desirable
First Diagnosis colorectal carcinoma desirable
Age at first diagnosis 43 desirable
patient/tumour at collection time for PDX essential patient anonymous ID A0088 essential
patient sampleID CRC0228PRH0000000000D01000 essential
date of tumour collection Oct 2015 if several collections this is essential otherwise desirable
collection event collection event 1 if several collections this is essential otherwise desirable
elapsed time between collections 0 if several collections this is essential otherwise desirable
age at collection 70 essential
Diagnosis at time of collection colorectal carcinoma essential
Collected tumour type primary essential
Primary site colon essential
Site of collection colon essential
Stage T2,N1,M0 desirable
Stage classification TNM staging system desirable
Grade Grade 1 desirable
Grade classification Not Specified desirable
Virology status HIV, EBV, HPV desirable
Is patient treatement information avalaible and sharable yes essential
Treatment Naive at time of collection not treatment naive desirable
Is the patient treated for cancer AT the time of collection yes desirable
Was the patient treated for cancer PRIOR to the time of collection yes desirable
Model ID CRC0228PR essential
patient treatment information detail desirable patient anonymous ID A0088 essential
Treatment name fluorouracil + leucovorin + oxaliplatin essential
Treatment dose 12 mg/kg+ 20 mg/m2+85 mg/m2 desirable
treatment starting date treatment starting date essential
duration of the treatment in month 3 desirable
response of the current treatment progressive disease desirable
classification used to define response to treatment RECIST 1.1 desirable
PDX model detail essential Model ID CRC0014LM essential
engraftment host strain name NOD SCID essential
engraftment host strain nomenclature NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ essential
PDX Engraftment Site colon essential
PDX Engraftment Type orthotopic essential
PDX Engraftment Material tissue fragment essential
PDX engraftment material status fresh desirable
Passage all essential
pubmed ID PMID: 27771609 desirable
PDX model validation essential Model ID CRC0228PR essential
validation technique Fingerprinting essential
validation description high concordance between xenograft and patient tumour essential
Passages in which validation was performed 1, 2 essential
validation host strain nomenclature NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ essential
dataset derived from patient and xenograft samples desirable sample ID CRC0014LMX0A01201TUMD01000 essential
Sample origin xenograft essential
Passage 1 essential
Model ID CRC0014LM essential
host strain nomenclature NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ essential
Molecular Characterization type copy number alteration essential
platform name IRCC PCR essential
platform technology digitalPCR essential
platform description platform.txt essential
analysis protocol analysisprotocol.txt essential
Omic results file name 456CNA.txt essential
Omic Raw data sharing Yes essential
OMIC Raw data file https://www.ebi.ac.uk/ena/data/view/PRJNA451206 essential if yes in Omic Raw data sharing column
sharing and contact essential Model ID CRC0228PR essential
data provider type academia essential
Model accessibility academia only essential
EurOPDX access modalities transnational access essential
Contact email 123@mail.com essential
Contact name John Doe essential
Contact form link http://tumor.informatics.jax.org/mtbwi/pdxDetails.do?modelID=J000106527 essential if you want the contact the provider to be a form
Model Link to center database http://tumor.informatics.jax.org/mtbwi/pdxDetails.do?modelID=TM01220 essential if you want the model to be linked from Finder to your open database
Data provider name The Jackson laboratory essential
Data provider abbreviation/acronym JAX essential
Project name projectABC essential
breast and/or colorectal diagnostic markers essential for breast and colorectal cancers sample ID BC0014LMH0A02201TUMD03000 essential
Sample origin xenograft essential
Passage 1 essential if xenograft sample
host strain nomenclature NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ essential if xenograft sample
Model ID BC0014 essential
Reporting HER-2, Progesterone Receptor and Estrogen Receptor status is mandatory for breast cancers – reporting KRAS, NRAS, BRAF and microsatellite status is mandatory for colorectal cancers Marker name HER-2 essential
Marker status postive/negative essential
essential/additional marker essential MARKERS FOR BREAST essential
technique name (no acronym) FISH essential
Protocol file name analysisprotocol.txt desirable
results file name image.png desirable