The related 2012 nature publication is titled the cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity. The ccle cancer cell line encyclopedia project is a collaboration between the broad institute, and the novartis institutes for biomedical research and its genomics institute of the novartis research foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational. The 1914 tumors from the cancer genome atlas tcga and 260 cell lines from the cell line encyclopedia ccle used here represent 6 cancer typessubtypes. Garraway, a senior associate member of the broad institute, an associate professor at harvard medical school and danafarber cancer institute, and a cocorresponding author of the paper. Gene expression, mutation, methylation, rnaseq and metabolomics data are downloadable.
The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity. But researchers now have access to large sets of genome data from clinical samples investigated by the cancer genome atlas tcga a nationwide project that eventually will catalogue genetic changes in more than 20 cancer types and close to a thousand cancer cell lines that are being characterized in the cancer cell line encyclopedia. From the available 19,000 gene expressions we use relieff to screen top 250 features. Compound pages have been updated to include a new data availability tile, as well as a new compound response vs. Cancer program scientific tools and resources broad. The cancer cell line encyclopedia ccle, authored by scientists at the broad institute, danafarber cancer institute, the genomics institute of the novartis foundation, and the novartis.
Please see below for a partial list of resources or refer to the list of cancer related data, software and tools. On this page, weve detailed ccle metadata that are available for viewing and filtering cancer cell line encyclopedia ccle data in the data browser, and the datasets api. Cancer cell lines are important model systems to study normal and aberrant cellular processes. The other study, the cancer cell line encyclopedia, tested 24 drugs against 1,036 cell lines. Studies expand and update an encyclopedia of cancer cell lines. I have downloaded some ccle cancer cell line encyclopedia rnaseq data from the cghub website. The ccle cancer cell line encyclopedia project is a collaboration between the broad institute, and the novartis institutes for biomedical research and its genomics institute of the novartis research foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer. Xena displays gene expression data from the metastatic cancer study published in robinson et al 2017 integrative clinical genomics of metastatic cancer. Using drug response data to identify molecular effectors. Mar 28, 2012 the cancer cell line encyclopedia ccle, authored by scientists at the broad institute of harvard and mit, harvardaffiliated danafarber cancer institute, the genomics institute of the novartis foundation, and the novartis institutes for biomedical research, is described in the march 29 issue of the journal nature. The ccle represents roughly 1,000 cell lines from 36 cancer types. The cancer cell line encyclopedia ccle, authored by scientists at the broad institute, danafarber cancer institute, the genomics institute of the novartis foundation, and the novartis institutes for biomedical research, is described in.
Human cell line derived from metastasis of cancer occurred in oral cavity, the same patient as t3m1 clone2 and t3m1 cl10. Cancer cell line encyclopedia five key discoveries seven. Mar 28, 2012 the cancer cell line encyclopedia presents the first results from a largescale screen of some 947 cancer cell lines with 24 anticancer drugs, with the aim of identifying specific genomic. That one appeared at about the same time, and its authors said.
Genomics cloud pilots expand data access national cancer. Sep 30, 20 using the cancer cell line encyclopedia ccle as a reference guide, the researchers narrowed in on a potential therapeutic target in pediatric acute lymphoblastic leukemia all, a white blood. This page is a placeholder for the cancer cell line encylopedia ccle proteomics data. Introduction to ccle land content array suite wiki. Cancer cell line encyclopedia ccle the cgc knowledge center. In an effort to help researchers design clinical trials and advance cancer research, novartis and the broad institute have produced the cancer cell line encyclopedia ccle that catalogs the genetic and molecular profiles of nearly 1,000 human cancer cell lines. The ccle project is a collaboration between the broad institute of mit and harvard, and the novartis institutes for biomedical research and its genomics institute of the novartis research foundation. Tumor suppressors status in cancer cell line encyclopedia. The cancer cell line encyclopedia ccle project started in 2008 as a collaboration between the broad institute, and the novartis institutes for biomedical research and its genomics institute of the novartis research foundation. Thankfully, due to efforts made by others, such as the cancer cell line encyclopedia ccle and klijn et al. We plan to make the following available here upon publication. To further understand the metabolic diversity of cancer, we profiled 225 metabolites in 928 cell lines from more than 20 cancer types in the cancer cell line encyclopedia ccle using liquid. The original cancer cell line encyclopedia ccle is expanded with deeper characterization of over 1,000 cell lines, including genomic, transcriptomic, and proteomic data, and.
All cell lines with tp53 inactivated by any mechanism are insensitive to nutlin3. New cell line selector supports adding features and filtering by cell line data. The cancer cell line encyclopedia ccle is a collection of more than 900 diverse cancer lines representing different tissues and sites of origin, and encompasses a wide variety of cancer driver mutations. Evaluating cell lines as tumour models by comparison of. The cancer cell line encyclopedia ccle is a collaborative effort of the broad institute and the novartis institutes for biomedical research 5. Cancer cell lines are useful model systems for medical research. One such initiative is the cancer cell line encyclopedia ccle. The cancer dependency map project at broad institute.
Viewing mutations requires login and acceptance of the terms of access. Several largescale genomic studies have been generated through work funded by the national cancer institute nci such as the cancer genome atlas tcga, therapeutically applicable research to generate effective therapies target, the cancer genome characterization initiative cgci, and the cancer cell line encyclopedia ccle. Cell line pages now have cellosaurus links, cosmic links, str profiles, and cell line aliases where applicable. Writing the book of cancer knowledge danafarber cancer. In order to test our theory on real dataset, we obtain gene expression and normalized area under the curve auc values for the cell lines tested on the drug 17aag from the cancer cell line encyclopedia ccle.
Normalized data in spreadsheet form links to mass spectrometer raw files tables and sql script to populate a postgresql database to allow custom computational analysis. Nov 20, 2015 furthermore, most annotations have not used ontologies or controlled vocabularies. We look forward to continuing to collaborate with the gdc in the months ahead to ensure the timely availability through the cgc of new data releases for this dataset. Distribution of cancer types in the ccle by lineage. The ccle is a collaborative effort between novartis and the broad institute that has released mutation data for 1,651 genes representing nearly 1,000 cell lines. Each cell line was genetically characterized through a series of highthroughput analyses at the broad institute.
Large panels of comprehensively characterized human cancer models, including the cancer cell line encyclopedia ccle, have provided a rigorous framework with which to study genetic variants, candidate targets, and smallmolecule and biological therapeutics and to identify new markerdriven cancer dependencies. In order to generate such resource we constructed a novel comprehensive computational framework for the assessment of tumor suppressor functional status. Robustness of our model was validated by crossvalidation and an independent dataset, the cancer genome project cgp. The diagonal of the heatmap shows the pearson correlation between corresponding sample types. The cancer cell line encyclopedia project is a collaboration between the broad institute, and the novartis institutes for biomedical research and its genomics institute of the novartis research foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct. When coupled with pharmacological profiles for 24 anticancer drugs across 479 of the cell lines, this collection allowed identification of genetic, lineage. Cancer cell line encyclopedia ccle by novartis and broad. Mar 30, 2012 the cancer cell line encyclopedia ccle, authored by scientists at the broad institute, danafarber cancer institute, the genomics institute of the novartis foundation, and the novartis institutes for biomedical research, is described in the march 29 issue of the journal nature.
Its original release included gene expression, dna copy numbers, and hybrid capture sequencing. The experiment was performed in multiplex format with 9 biological samples per plex and one common sample to normalize between plexes. Quantitative proteomics of the cancer cell line encyclopedia. Putting cancers vulnerabilities on the map cancer cell lines evolve in ways that affect how they respond to drugs loss of a dna repair system creates a unique vulnerability in many cancer types. Mar 28, 2012 here we describe the cancer cell line encyclopedia ccle. The cancer cell line encyclopedia project is a collaboration between the broad institute, and the novartis institutes for biomedical research and its genomics institute of the novartis research foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic.
Because cell lines and tumors are separate datasets, the. Mar 29, 2012 novartis has launched the cancer cell line encyclopedia ccle to enlist the cancer cell lines in the world this work of the novartis has been published online in the march 28 issue of the journal nature. Each dot represents cell line with tp53 inactivation status marked by color. The cancer cell line encyclopedia is a database of gene expression, genotype, and drug sensitivity data for human cancer cell lines. The cancer cell line encyclopedia ccle database was conceived to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models approximately 110 models.
In addition to describing the dataset in depth, the authors give a nice proof of principle in identifying specific transcriptional profiles in nras mutant cancers that correlate with sensitivity to. Experiment cancer cell lines from the cancer cell line encyclopedia rnaseq mrna baseline. Writing the book of cancer knowledge we hope that the cancer cell line encyclopedia will be a preclinical resource that could guide clinical trials, said levi a. Studies expand and update an encyclopedia of cancer cell. Access the ccle public project by selecting cancer cell line encyclopedia ccle from public projects in the top navigation bar. The cancer cell line encyclopedia ccle, authored by scientists at the broad institute, danafarber cancer institute, the genomics institute of the novartis foundation, and the novartis institutes for biomedical research, is described in the march 29 issue of the journal nature. Ccle cancer cell line encyclopedia cclf cancer cell line factory drug repurposing hub. The ccle contains open access sequencing data in the form of reads aligned to the hg19 reference genome for nearly cancer cell line samples, as available from cghub on. Writing the book of cancer knowledge broad institute. You may have been redirected here from the broad cancer program resource gateway, which is no longer active. These efforts enable a systematic comparison of tumours and cell lines at the level of dna copynumber, mutation and mrna expression data across a diversity of tumour types. Quantitative proteomes of 375 cancer cell lines for the cancer cell line encyclopedia ccle reveal correlated protein expression between multiple pathways and complexes as well as associations between protein complexes and genetic features including microsatellite instability, individual gene mutations, and sensitivity to gene knockdowns. We hope that the cancer cell line encyclopedia will be a preclinical resource that could guide clinical trials, said levi a. Garraway, a senior associate member of the broad institute, an associate professor at harvard medical school and danafarber cancer institute, and a cocorresponding author of.
It includes 1,046 cell lines and has molecular data for the i mrna expression, ii dna copy number, iii single nucleotide polymorphisms from snp array and iv mutational status of 1,600 genes. A new chapter in acute lymphoblastic leukemia research. The goal is to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational. The ccle provides public access analysis and visualization of dna copy number, mrna expression, mutation data and more, for cancer cell lines. In this publication we expand the cancer cell line encyclopedia to include quantitative proteome profiling by mass spectrometry of 375 cell lines from diverse lineages. Comprehensive characterization of circular rnas in. The ccle cancer cell line encyclopedia project is a collaboration between the broad institute, and the novartis institutes for biomedical research and its genomics institute of the novartis research foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link. Writing the book of cancer knowledge harvard gazette. The broadnovartis cancer cell line encyclopedia ccle contains genomic profiles of around 1,000 cell lines that are used as models for various tumour types6. We report systematically derived status of 69 known or putative tumor suppressors, across 799 samples of the cancer cell line encyclopedia. Global expression landscape of circrnas across cancer cell lines. The cancer cell line encyclopedia ccle is one of several genomic datasets 20. Anticancer drug sensitivity prediction in cell lines from. The landscape of cancer cell line metabolism nature medicine.
Tumorsvarymoreintheextentofalterationsby cancer typethandocelllines we compared mutations and copy number alterations cnas in cell lines. Comparison of dna copynumber profiles gistic gscores between cell lines and primary tumors. The goal is to conduct a detailed genetic and pharmacologic characterization. This page is about the meanings of the acronymabbreviationshorthand ccle in the medical field in general and in the cancer terminology in particular. The cancer cell line encyclopedia enables predictive. A immortal human cell line cell that has the characteristics. Here we describe the cancer cell line encyclopedia ccle. In the bottomright part of the project information box, click copy project. The cancer cell line encyclopedia ccle project is a collaboration between the broad institute, the novartis institutes for biomedical research and the genomics novartis foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models. The number of cases for each cancer type denoted by 24letter codes present in ccle, viewed using the cancer genomics cloud. The cancer cell line encyclopedia ccle is an effort to generate largescale profiling datasets across nearly 1,000 cell lines from diverse tissue lineages.
The list of acronyms and abbreviations related to ccle cancer cell line encyclopedia. Writing the book of cancer knowledge here there be dependencies. To this aim, we here used gene expression features and drug sensitivity data in cancer cell line encyclopedia ccle to build a predictor based on support vector machine svm and a recursive feature selection tool. Comparing cancer cell lines and tumor samples by genomic profiles. Nutlin3 sensitivity across 491 ccle cell lines in relation to tp53 status. Nextgeneration characterization of the cancer cell line. Cancer cell line encyclopedia ccle the cgc knowledge. Large panels of comprehensively characterized human cancer models, including the cancer cell line encyclopedia ccle, have provided a rigorous framework with which to.
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