Glossary of Terms

Descriptions of all the cell model annotations found within the Cancer Dependency Map at Sanger.

Model Terms


Model: Identifiers

Passport Identifiers

The core identifiers used by the passport represent each point in the Patient, Sample, Model hierarchy. See model relationships for additional information.

  • Sanger IDentifier Patient (SIDP)
  • Sanger IDentifier Sample (SIDS)
  • Sanger IDentifier Model (SIDM)
External Resource Identifiers

Additional commonly used identifiers and database links to support cross referencing and integration of data sets. Currently these comprise of:

  • COSMIC
  • Cellosaurus (RRID)
  • Broad (CCLE)
Supplier & Catalogue Identifiers

Repositories and cell banks where the cell model can be obtained with their associated catalogue ID's.

Model: Descriptors & Derivation Information

Model Name

The name of the model as used by the Sanger Dependency Map. Synonyms are also been provided where applicable.

Tissue

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.

Cancer Type

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.

Tissue Status

Defines the sample as originating from:

  • Tumour
  • Metastasis
  • Normal
  • Transformed (e.g. lymphoblastoid cells transformed using Epstein Barr virus)
  • Precancerous (e.g. Adenoma or Barrett's Esophagus)
Sample Site

The location in the body or tissue from which the sample was taken.

Growth Properties

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.

Relationship Details

A description of the relationship between models linked to the same patient and the source of the data to support this relationship.

Model Treatment

Model treatments occur during or following model derivation. Drug resistant subclones are the most frequent example.

Date Generated

The date that the model was generated, sourced from repositories or publications.

Publication

The original (or earliest available) publication outlining how the cell model was established.

Clinical Information

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.

Age

The age of the patient at the time sample tissue was obtained for model derivation. All ages are presented in years.

Smoking Status

Describes the patient’s smoking history:

  • Current Smoker
  • Ex-Smoker
  • Non-Smoker
  • Never Smoked
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.

TNM Status

A set of clinical descriptions used within to describe tumours.

  • Tumour (T) describes the size of the tumour.
  • Node (N) details if the cancer has spread to the lymph nodes.
  • Metastasis (M) describes if the cancer has spread to other areas on the body.

Details descriptions of the subclassification can be found here.

Tumour Stage

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.

Tumour Grade

Provides information on the cell types and aggressiveness of a tumour. Grade descriptions within the passports associated with organoids use established NHS standards here.

Model Genomics

MSI Status

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

  • MSI: Microsatellite Instable
  • MSS: Microsatellite Stable
Ploidy

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.

Fitness Score

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.

BAGEL

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.

CRISPRcleanR

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.