Glossary of Terms
Descriptions of all the cell model annotations found within the Cancer Dependency Map at Sanger.
The core identifiers used by the passport represent each point in the Patient, Sample, Model hierarchy. See model relationships for additional information.
|External Resource Identifiers||
Additional commonly used identifiers and database links to support cross referencing and integration of data sets. Currently these comprise of:
|Supplier & Catalogue Identifiers||
Repositories and cell banks where the cell model can be obtained with their associated catalogue ID's.
Model: Descriptors & Derivation Information
The name of the model as used by the Sanger Dependency Map. Synonyms are also been provided where applicable.
Describes the site of the tumour from which the sample was taken. Where a model was derived from a metastatic tissue lists the site of the primary tumour.
A broad disease classification describing the sample tumour. Cancer type also highlights samples obtained from non-cancerous tissue. All cancer types are NCIT terms.
|Cancer Type Detail & NCIT ID||
The most detailed description of the tumour available on the passport using NCI Thesaurus terms. Definitions of these terms are available via the NCIT ID links.
Defines the sample as originating from:
The location in the body or tissue from which the sample was taken.
Models have been grouped into three categories, Adherent, Semi-Adherent and Suspension.For detailed information on the cell type and morphology refer to the repository documentation. Only applies to cell line models.
A description of the relationship between models linked to the same patient and the source of the data to support this relationship.
Model treatments occur during or following model derivation. Drug resistant subclones are the most frequent example.
The date that the model was generated, sourced from repositories or publications.
The original (or earliest available) publication outlining how the cell model was established.
|Species, Gender & Ethnicity||
Basic patient information. Ethnicity has been divided into six broad classifications based on the data available, for more specific data refer to the cell model supplier.
The age of the patient at the time sample tissue was obtained for model derivation. All ages are presented in years.
Describes the patient’s smoking history:
|Sample Treatment (Prior Treatment) & Treatment Details||
Treatment data has been annotated both at the sample and model level.Sample treatment refers to any therapy the patient received prior to sampling and has been broadly classified into groups such as chemotherapy and radiotherapy. Treatment Details provides specific information on the drugs or treatment undertaken.
A set of clinical descriptions used within to describe tumours.
Details descriptions of the subclassification can be found here.
Describes the size of the tumour and and it’s spread from the location in which it originated. Stage descriptions within the passports associated with organoids use established NHS standards found here.
Provides information on the cell types and aggressiveness of a tumour. Grade descriptions within the passports associated with organoids use established NHS standards here.
Displays the microsatellite instability status of a cell model. Models have been characterised using the following markers; BAT25, BAT26, D5S346, D2S123 and D17S250. See here for further details
Refers to the ploidy status of the cell model determined by using mean copy-number obtained from PICNIC using the Affymetrix SNP6 data. See here for further details
|Mutations per Mb||
Shows the mutation rate per Mb estimated from Whole Exome Sequencing. See here for further details
Project Score & CRISPR KO
|Core Fitness Gene||
Genes which are required for the fitness of the majority of cell lines from a given cancer type or across multiple cancer types.
Quantitative measure of the reduction of cell viability elicited by a gene inactivation, via CRISPR-Cas9 targeting. This is based on Bayes Factor value computed using BAGEL starting from CRISPRcleanR corrected gene depletion fold changes, and scaled to a 5% false discovery rate threshold (from classifying reference essential/non-essential genes based on BF rankings)
|Corrected Fold Change||
CRISPRcleanR corrected gene depletion fold change, computed between average representation of targeting sgRNAs at the end of screening versus the plasmid library.
A supervised learning method for analysing gene knockout screens and inferring gene fitness effects, starting from the observation of those elicited by two reference sets of essential/non-essential genes. Further details can be found in the corresponding article.
An unsupervised method for identifying and correcting gene-independent responses to CRISPR-Cas9 targeting; based on segmentation of sgRNA fold change values across the genomes. Further details can be found in the corresponding article.