The number of analyzed cancer genes with likely oncogenic mutations ranged from five in the microsatellitestable colorectal cancer line ht29 apc, braf, smad4, pik3ca, and tp53 to one. Software has been designed to analyse all this information in the database. Growth ratecorrected gr doseresponse metrics across a panel of 71 breast cancer cell lines treated with a library of small molecule and antibody perturbagens. Comparative proteogenomics profiling of nonsmall and small. Is there a database linking cell lines and mutations. Rnaseq data from 1,083 human cancer cell lines is downloaded from ccle and genentech a and mutation information for the cell lines is. But at the turn of the 21st century, some expression irregularities were observed, raising doubts about how closely. We detected point mutations leading to nonconservative amino acid substitutions and nonsense mutations in 50% 612 of the cell lines sequenced, and all the mutations.
Mhci genotype restricts the oncogenic mutational landscape. A threebase deletion codon 45 was identified in the cell line hct 116, whereas cell lines sw 48, hca 46, caco 2, and. Open pipelines for integrated tumor genome profiles reveal. We did not find mutations in exon 2 of the klf6 gene in any of the 32 tumour samples that we examined nor in the human prostate tumour cell lines pc3, du145 and lncap. Apr 21, 2009 database for mutations in cancer cell lines. The database is now maintained at the international agency for research on cancer iarc and is updated twice a year.
As of october 1997, the database contained records of mutations either germline, somatic, or from cell lines. As of october 1997, the database contained records of mutationseither germline, somatic, or from cell lines. The core of cosmic, an expertcurated database of somatic mutations cell lines project mutation profiles of over 1,000 cell lines used in cancer research cosmic3d an interactive view of cancer. Such molecular profiling includes point mutations, gene fusions, copy number.
Furthermore, 5 cell lines are associated with del1p and fam46c mutations doublehit events table s1. Im looking to create a database of cell lines i use and their characterisitcs i. Ampullary carcinoma baylor college of medicine, cell reports 2016. Notably, 10 cell lines are characterized by tp53 mutation and del17p underlining hmcls with tp53 biallelic event, known to be associated with a dramatic impact on survival in mm table s1. Start using cosmic by searching for a gene, cancer type, mutation, etc. You must accept the terms of access before registering. Cancerresourceupdated database of cancerrelevant proteins. Most of the mutations described in this database originate either. Atcc has created a list of atcc tumor cell lines based on the gene mutation information maintained in the sanger institute cosmic database.
Is there any consolidated database on cancer cell line. The mutation, gene expression, and copy number variation cnv data were collected from three representative databases on cell lines ccle cancer cell line encyclopedia, cosmic. The p53 mutations in cell lines compendium is a novel and original application that provides an id card for each cell line included in the umd tp53 database. Evaluating cell lines as tumour models by comparison of.
A exome sequencing data from mm cell lines and control samples ebvimmortalized bcells were processed in. Relative cell counts and normalized growth rate inhibition values across technical replicates. Users can navigate the database via tissue, cancertype, genetic feature. Database of germline and somatic mutations in human. However, proper choice of cell lines for experimental purposes is often difficult because genotype andor expression data are missing or scattered in diverse resources. A software have been designed in order to analyse all these informations in the database.
Many cancer cell lines are available and efforts are ongoing to derive new models. In two cell lines, there was apparent instability of the bcatenin mrna. Tumor cell lines become more powerful research models and drug discovery tools when the genetic abnormalities that drive their phenotype are known. In its place, the project and website was replaced with data from the full exome sequencing of 1015 cancer cell lines. Hi all, im wondering is there any databasedatasets that have pure immune cell lines rnaseq da. If the same mutation was reported in more than one article, only the first report is taken into account. A data base is described in which over 2,500 mutations in the p53 gene of human tumors and tumor cell lines are compiled from a systematic search of reports published before 1 january. Gda, a webbased tool for genomics and drugs integrated analysis. Multiple signatures of somatic mutations have been identified in cancer genomes. Jci isocitrate dehydrogenase mutations suppress stat1 and. Cosmic a great collection of info on cell lines and mutations found within them. The p53 mutation database consists of a list of point mutations in thep53 gene of human tumors and cell lines, compiled from the published literature and made available through electronic media. Cancer cell line encyclopedia novartisbroad, nature 2012.
The current version includes 2,000 and 500 cell lines with mutant tp53 and wildtype tp53 respectively. Is there a karyotype database for human cell lines. Dysfunctional keap1nrf2 interaction in nonsmallcell lung. Introduction familial adenomatouspolyposis fap is an autosomaldominant precancerous condition characterized by the. Target mutations were selected based on their frequency reported in database, and clinical significance and on the applicability of crisprcas9 by considering distance from pam site, and offtargets. The cell lines project in cosmic is an effort to fully. Growing in both content and scope, cosmic holds details on millions of mutations across thousands of cancer types. Description, genelevel mutation profiles for cancer cell lines. Gemiccl gene expression and mutations in cancer cell lines is an online database of human cancer cell lines that provides genotype and expression information. Comprehensive characterization of the mutational landscape.
Cancerresource enables the capability of uploading external expression and mutation data and comparing them to the databases cell lines. Database of p53 gene somatic mutations in human tumors and. Tp53 mutations appeared in two cell lines and three tumors, and rare and deleterious mutations in pde4dip were most prevalent, appearing in all tumors and mia paca2 and panc. Comprehensive characterization of the mutational landscape in. Is there any software to create a database of cell lines. It includes both molecular informations about the mutations and also clinical data about the patients. While numerous expression deficiencies have been described in jurkat, genetic explanations have only been provided for a handful of defects. Jci isocitrate dehydrogenase mutations suppress stat1. A database is described in which over 700 mutations in the human apc gene of tumors colon cancer predominantly are compiled from the literature. Indeed, analyzing a database of native peptides found in complex with an hlaa. Exome sequences of 1,001 human cancer cell lines and 577 xenografts revealed most common mutational signatures, indicating past activity of the underlying processes, usually in appropriate cancer types. Molecular characterization of breast cancer cell lines.
Major study uses horizons hap1 cell lines to screen thousands of brca1 mutations sep 20, 2018 1. Analysis workflow and human myeloma cell lines hmcls mutational landscape. We have successfully generated 88 hetero and homozygous mutant cell lines at the targeted sites of 36 genes representing a total of 125 mutations. Is there any consolidated database on cancer cell line mutations. Measurement, gene mutation by hybrid capture sequencing.
Quantitative proteomic analysis of two nsclc cells a549, h1975 and two sclc cell lines h69, h1975. Characterizing mutational signatures in human cancer cell. Acceptance of the terms of access is a prerequisite for using this. We have collected mutation, gene expression and copy number variation cnv data from three representative databases on cell linescancer. Cellminercdb for integrative crossdatabase genomics and. Mutation analysis of 24 known cancer genes in the nci60. Gdsc genelevel mutation and methylation data numbers in red. Our objective was to characterize a large, commonly. Jan 01, 1996 a database is described in which over 700 mutations in the human apc gene of tumors colon cancer predominantly are compiled from the literature. Five different mutations 26% were found in the remaining 21cell lines from 19 patients. The number of analyzed cancer genes with likely oncogenic mutations ranged from five in the microsatellitestable colorectal cancer line ht29 apc, braf, smad4, pik3ca, and tp53 to one tp53 in several other lines. All cell lines were maintained in a humidified incubator in 5% co 2 at 37c. In figure 1b, 9 cell lines were identified as nrf2.
These tools are ed by the university of texas md anderson cancer center and by the individual employees of the cancer center who helped develop them. Within the current database, truncating and missense mutations are equally represented 11 vs. Ideally i would need a database which will tell me. In release 67 there was a major update to the cosmic cell lines project. Hcc1806 cell line hms lincs database hms lincs project. Furthermore, this database also provides potential shared neoantigens generated from all possible combinations of recurrent mutations and highly frequent hla alleles. Nonexonic snps detected in these 9 cell lines are summarized in the. The information provided by the database could facilitate the subsequent experimental design and validation and the discovery of potential targets for cancer immunotherapy. Cancer is a disease of genome alterations that arise through the acquisition of multiple somatic dna sequence mutations. Daer all dose anyone knows a link for a database for mutations in cultured human colon and beast cancer cell.
The capillary sequencing data of 800 cell lines across 64 genes was archived available to download. It leverages overlaps of cell lines and drugs across databases to examine. Only nonsynonymous mutations are listed, as this study focuses solely on changes in the amino acid sequence. Some of these mutations can be critical for the development of a. Catenin mutations in cell lines established from human. Breast cancer cell lines are frequently used as model systems to study the cellular properties and biology of breast cancer. Raw gene expression data of ccle and nci60 cell lines were downloaded from gene. Database of germline and somatic mutations in human tumors and cell lines p53 and apc gene mutations.
Experiment data base cell line data base cldb, the first database set up within the interlab project, contains detailed information on human and animal cell lines that are available in many italian. Human plasma cell leukemia cell line, established from the peripheral blood of a 33yearold woman with igg plasma cell leukemia. Database of germline and somatic mutations in human tumors and cell lines. Its purpose is to help us track usage for reports to our funding agencies and for insights into improving the portal. The core of cosmic, an expertcurated database of somatic mutations.
Cosmic, the catalogue of somatic mutations in cancer is an expertcurated database encompassing the wide variety of somatic mutation mechanisms causing human cancer. Analysis of human prostate cancers and cell lines for. Preparation of the standard cell lines for reference. A genomewide survey of mutations in the jurkat cell line. You just add the track for mutations and edit the cell lines you want included, then ho to the location of interest and see all of the mutated cell lines at that location window. Good if you want to look forunderstand particular genetic aspects of a line. A data base is described in which over 2,500 mutations in the p53 gene of human tumors and tumor cell lines are compiled from a systematic search of reports published before 1 january 1994. The genetic study of the nci cell lines reported numerous mutations present in these 9 cell lines. Introduction familial adenomatouspolyposis fap is an autosomaldominant precancerous condition characterized by the appearance of hundreds to thousands of adenomatous polyps throughout the entire colorectum. Mutation analysis of 24 known cancer genes in the nci60 cell. I particularly like the info cellosaurus hosts on different names and common misspellings of names for cell lines. The jurkat cell line has an extensive history as a model of t cell signaling. Our objective was to characterize a large, commonly employed panel of breast cancer cell lines obtained from the american type culture collection atcc 304500 k to enable researchers to make more informed decisions in selecting cell lines for specific studies.
Cancer drug resistance database scientific reports. Cosmic, the catalogue of somatic mutations in cancer, is the worlds largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer. Cell lines project mutation profiles of over 1,000 cell lines used in cancer research. Major study uses horizons hap1 cell lines to screen. Cell model passportsa hub for clinical, genetic and functional. Cell lines database the tp53 website the tp53 web site. Another two cell lines, h446 and h446 own tp53 and rb1 gene mutations and represent semi suspension and suspension sclc cell lines, respectively. As part of our continuing efforts to characterize and authenticate the cell lines in the cell biology collection, atcc has developed a comprehensive database of short tandem repeat. Acceptance of the terms of access is a prerequisite for using this site. Table 1 lists all these various mutations reported from the study in column 2 for each of the cell line. Daer all dose anyone knows a link for a database for mutations in cultured human colon and beast cancer cell lines. But at the turn of the 21st century, some expression irregularities were observed, raising doubts about how closely the cell line paralleled normal human t cells. This still represents relatively more truncating mutations associated with rcc than in the overall database, but the current trend seems to indicate that the initial imbalance was an artefact of the limited. Data from 1994 are being added intermittently, with a systematic search and update scheduled for december, 1994.
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