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gCSI

Acronym

The Genentech Cell Line Screening Initiative (gCSI)

Description

The Genentech Cell Line Screening Initiative (gCSI) was undertaken independently of CCLE and GDSC to to address the concerns of inconsistencies across large-scale pharmacogenomic studies. In gCSI, Genentech independently characterized the response of 410 cancer cell lines to a subset ​agents tested by GDSC and CCLE. Genentech also evaluated three specific aspects of the screening protocols that are relevant to measured drug response: readout of cell viability (metabolic versus DNA content), seeding density strategy, and cell culture media conditions.

Resource

compareDrugScreens package

RNA-seq data

RNA-seq and SNP array data

Publication

A comprehensive transcriptional portrait of human cancer cell lines, Nature Biotechnology 2015

Reproducible pharmacogenomic profiling of cancer cell line panels, Nature 2016

Data types

Data Type Assay/Platform Raw Processed
Pharmacological CellTiter Glo Yes AUC, IC50
mRNA Expression Illumina RNA-seq Yes VSN/DESeq counts, RPKM
DNA Copy Number Illumina 2.5M SNP Yes PICNIC
DNA Mutation Sanger No CSV

PharmacoGx

PharmacoSet object for: gCSI

Number of cell lines tested across datasets01002003004005006007008009001k1.1k# cell lines FIMMGRAYUHNBreastgCSICTRPv2CCLEGDSC100050848475488810611109
Number of tissues tested across datasets05101520253035# tissues GRAYUHNBreastFIMMCCLEgCSICTRPv2GDSC100011422232536
Number of compounds tested acrossdatasets050100150200250300350400450500# compounds UHNBreastgCSICCLEFIMMGRAYGDSC1000CTRPv2416245290250544
Number of experiments held acrossdatasets050k100k150k200k250k300k350k# experiments UHNBreastFIMMgCSIGRAYCCLEGDSC1000CTRPv25225616455941311670225480395263