Cell Model Passports Changelog

improvementMutation data added for 23 models.

improvementThe CMP gene set updated to align with HGNC release 24-07-02.

improvementThe following datasets have been re-imported using the updated gene set; Mutations, RNA-Seq and Fusions. Downloads and website pages for other datasets are restricted to genes within the updated gene set with the exception of CRISPR datasets that currently link to Project Score.

improvementRNA-Seq dataset has been updated to include Broad Depmap 24Q2 release. Sanger TPM values are now calculated using RSEM to align with the Broad Depmap data.

improvementCancer predisposition variant (CPV) annotation has been added to the download of annotated of genes.

improvementOrganoid mutation data now includes CPVs.

improvementMultiomics Data: Multiomics data downloads added to download page.

improvementModel Page: Adjusted panel layout and improved model relationship panel formatting

improvementBrowse Models Page: New filter for models that have cancer predisposition variants.

improvementTutorials: Added a new page for video tutorials.

improvementCNV Data: Data for an extra 21 organoid models.

improvementModel Page: Updated colours for the word cloud.

improvementModel Page: Added sorting and improved driver alteration selection to the Mutations & Copy Number Alterations panel

improvementMutation Data: Updated organoid cancer driver and cancer predisposition variant flagging (https://depmap.sanger.ac.uk/documentation/datasets/mutation/).

improvementModels: New Mesothelioma cell lines added with mutation data

improvementMutation Data: Updated cell line cancer driver and cancer predisposition variant flagging (https://depmap.sanger.ac.uk/documentation/datasets/mutation/)

improvementDownloads Page: Updated cancer driver and cancer predisposition download files (https://depmap.sanger.ac.uk/documentation/datasets/gene-annotation-mapping/)

improvementModels: GDSC growth estimate added

improvementSynonyms: Synonyms updated for organoid models

featureBrowse Models Page: New filter for models that are commercially available.

improvementProteomics data: Protein intensity values acquired using data-independent acquisition mass spectrometry (DIA-MS). Publication: Gonçalves, E., Poulos, R.C., Cai, Z., et al., Pan-cancer proteomic map of 949 human cell lines, Cancer Cell, (2022) https://www.cell.com/cancer-cell/fulltext/S1535-6108(22)00274-4.

featureModel Page: New proteomics data panel

featureDownloads Page: Proteomics data downloads now available

featureBrowse Models Page: Proteomics added to Dataset Availability filter.

improvementModels: New clinical data fields added for 130 organoid models

improvementModels: New MSI data for cell lines

featureModel Page: Clinical Profile tab on Model Information panel

featureBrowse Models Page: Addition of filtering based on clinical data

featureDownloads Page: Separation of model and gene information

improvementModel Page: Download files for individual models

improvementModels: 43 new organoid models added with mutation, CNV and RNASeq data

improvementModels: 28 new organoid models added with mutation, CNV and RNASeq data

improvementCNV Data: New organoid data added with total copy number and categorical CNA calls derived from WGS data processed through PURPLE.

improvementRNASeq Data: Data added for organoids.

featureModel Page: Mutation panel now also displays copy number alterations of driver gene

featureModel Page: Wordcloud updated to display copy number alterations where there is an amplification in a gain of function driver gene or a deletion in a loss of function driver gene.

bug-fixModel Page: Fixed display/hide columns functionality on the fusions panel.

improvementCNV Data: New data added with total copy number and categorical CNA calls derived from WES data processed through PureCN.

featureModel Page: Mutation panel now only shows coding and driver variants and new fields including VAF, Cancer Pre-disposition Variant and Effect.

featureModel Page: New RNASeq panel added.

featureModel Page: Wordcloud updated to use new driver gene and effect annotation to colour genes.

improvementModel Page: Dataset availability panel navigation improvements.

improvementDownload Page: Improved download page navigation.

improvementDocumentation: Updated and redirected to depmap.sanger.ac.uk/documentation/.

improvementCancer Drivers: Cancer Driver Gene list replaced with a new version built using intOGen & COSMIC Tier 1 lists.

improvementCancer Drivers: Cancer Driver Mutation list added.

improvementWES & WGS Mutation: Dataset remapped to GRCh38 and annotated with new Cancer Driver list.

improvementRNA-Seq: TPM values added.