Cell lines were primarily snp genotype matched to the sanger. This software is designed to support multiapplication functionality, including analysis of amplified fragment length polymorphism afl. Broad cancer cell line encyclopedia ccle cell image library. Data and scientific tools from many of our cancer research projects can now be accessed via broad data, software and tools. Simple, fast and accurate human cell line authentication by. The user may compare their samples str profile against a database of reference genotypes using a percentmatch calculation.
The database of genotypes and phenotypes dbgap and. Node colors show the support for each clade, based on 100 resamplings light blue lower support, dark blue higher support. Mouse cell lines have contamination and widespread aneuploidy. Mdamb361 cell line hms lincs database hms lincs project. Here, we report conbase for the identification of somatic mutations in single cell dna sequencing data. Human cell line identity verification danafarber cancer. The genotypetissue expression gtex project nature genetics. Throughput lung cancer cell line screening for genotype. Accurate variant calling and genotyping represent major limiting factors for downstream applications of single cell genomics.
Cell line authentication can verify whether the genotype of the cell line in question is identical to the genotype of the presumed parental cells. Cell lines are invaluable biomedical research tools, and recent literature has emphasized the importance of genotype authentication and characterization. The fragment analysis service offers the ampflstr identifiler plus assay for cell line identification sold by applied biosystems. Pdf a bioinformatics analysis of the cell line nomenclature. This site still includes former features, such as tp53 history, tp53 information or the tp53 mutation database. Calling genotypes from public rnasequencing data enables. The new tp53 website has been launched with a novel design, updated information and improved readability. Description, the cancer cell line encyclopedia is a database of gene expression, genotype, and drug sensitivity data for human cancer cell lines. 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.
Bayesian genotype calling can mitigate these issues, but previously has only been implemented in software that. Mar 30, 2020 we used transfac software to predict that ct. Cell line 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 laboratories and in some of the most important european cell banks and cell culture collections. Gtex portal, cancer cell lines encyclopedia, cbioportal. Conbase leverages phased read data from multiple samples in a dataset to achieve increased confidence in somatic variant calls and genotype. A data portal for the cells, cell biology, data and tools made freely and publicly available by the allen institute for cell science. Mutation frequency also depends on the visibility of that mutation to the immune system across patients. Data analysis was executed using the filemaker pro software package filemaker inc, santa clara, ca and dedicated software programming. Genemarkerhids builtin cell line authentication application allows the user to search for matches between their sample files and a database of preloaded cell line genotypes.
The sensitivity of cancer cells to anticancer drugs is a crucial factor for. High coverage sequencing of the human genome diversity project hgdp cell line panel samples on the illumina x10. Pgrn tools pgrn hub pharmacogenomics research network. Dec 26, 2011 the gangliosideinduced differentiationassociated protein 1 gene gdap1, which is involved in the charcotmarietooth disease cmt, the most commonly inherited peripheral neuropathy, encodes a protein anchored to the mitochondrial outer membrane. A locusspecific database for mutations in gdap1 allows. Cell line authentication, cell line identification company. We have developed computational methods cell line authentication by snp profiling, clasp for cell line authentication and copy number analysis based on a costefficient snp array, and we provide a reference database of commonly used mouse strains and cell lines.
Former name this is the name of the cell line before it was entered into the database. To date, no genomic reference for this cell line has been released, and experiments have relied on the human reference genome. The software allows use of both realtime and endpoint data files for data. Aug 31, 2018 when characterizing novel cell lines, we used snp genotyping alignment to compare the tumor to the resulting cell line. Is there any software to create a database of cell lines. Is there any software to create a database of cell lines and their. A wholecell computational model predicts phenotype from.
Conbase leverages phased read data from multiple samples in a dataset to achieve increased confidence in somatic variant calls and genotype predictions. Karyotyping is performed to identify the species as well as variation within the cell line. 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 str dna profiles for all of our human cell. It offers a database for exploring details of individual genes and proteins of interest, as well as systematically analyzing transcriptomes and proteomes in broader contexts, in order to increase our understanding of human cells. Thus, patientlevel mhci genotypebased restriction of the landscape. Query the database after genotyping, proceed directly to the cell line authentication application. The international mouse phenotyping consortium impc is a global effort to identify the function of every proteincoding gene in the mouse genome. Nov 20, 2015 human cancer cell lines are an important resource for research and drug development. In this paper we report a minimal and extensible data infrastructure for the management and exchange of genotype tophenotype experiments, including an object model for genotype and phenotype data xgapom, a simple file format to exchange data using this model xgaptab and easytocustomize database software.
Methods are now in place to genotype human cell lines using well characterized procedures used in the forensic community based on short tandem repeat str markers. Both drug combinations bendamustine with akt inhibitors, and disulfiram with mek inhibitors were also effective in a second colon cancer cell line dld. Phenotypes in human cell lines and their relationships with specific genotypes and drugs can be found in the genomics of drug sensitivity in. Mar 01, 2019 low or uneven read depth is a common limitation of genotypingbysequencing gbs and restriction siteassociated dna sequencing radseq, resulting in high missing data rates, heterozygotes miscalled as homozygotes, and uncertainty of allele copy number in heterozygous polyploids. Date this is easily entered using a popup calendar. Overall, these results demonstrate that such chemicalgenetic resources can be used to derive specific predictions of synergism for drug combinations. Neighborjoining tree of 117 cell line samples based on genotypes from 3,552 snp markers. May 29, 20 here we describe the genotypetissue expression gtex project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between.
Jul 20, 2012 the whole cell model therefore presents a hypothesis of an emergent control of cell cycle duration that is independent of genetic regulation. Softgenetics software powertools for genetic analysis. Expression levels were obtained for each of the lines. Start using cosmic by searching for a gene, cancer type, mutation, etc. Home about data contact login ccle logo broad logo. Global distribution of energy the model also provided an opportunity to develop a quantitative assessment of cellular energetics, which represents one of the most connected aspects of our model. Here, we report gene expression and mutations in cancer cell lines gemiccl, an online database of human cancer cell lines that provides genotype and expression information. Im looking to create a database of cell lines i use and their characterisitcs i. Data can be analyzed from a number of applied biosystems platforms. Snp array profiling of mouse cell lines identifies their.
Figure 2a shows results for the prostate adenocarcinoma cell line pc3. However, proper choice of cell lines for experimental purposes is often difficult because genotype andor expression data are missing or scattered in diverse resources. The core of cosmic, an expertcurated database of somatic mutations. A tool for discovering drug sensitivity and gene expression. Data are gene expression profile of 917 human cancer cell lines.
However, the available annotations of cell lines are sparse, incomplete, and. Key features gexp genetic analysis system provides simple, fast and accurate cell line authentication by str profiling detects cell line cross contamination down to 2. Human cancer cell lines are an important resource for research and drug development. One database for cell lines, one for plasmids, one for primers and one for reagents.
Cancer program scientific tools and resources broad institute. The database of genotypes and phenotypes dbgap is a national institutes of health nih sponsored repository charged to archive, curate and distribute information. The allen institute for cell science presents the allen cell explorer. Epigenetic and genetic features of 24 colon cancer cell. Sample genotypes obtained from your current project will be. Aug 01, 20 hela is the most widely used model cell line for studying human cellular and molecular biology. Cell line name the american tissue culture collection name can be entered here. Cell line authentication softgenetics software powertools for. The geo series and sample numbers used for each sample grouping is as follows.
These data were either tumor dna or cancer cell line dna. The cancer cell line encyclopedia project is a collaboration between the broad institute, and the novartis institutes for biomedical research. Collaborative research in computational neuroscience crcns complete genomics public data. Chinese hamster ovary cho cell line authentication nist. Mhci genotype restricts the oncogenic mutational landscape. When characterizing novel cell lines, we used snp genotyping alignment to compare the tumor to the resulting cell line. The cell atlas currently covers 12390 genes 63% for which there are available antibodies. Each cell line was assigned a unique identifier number to facilitate recovery from liquid nitrogen storage facilities, and also to track how often cell lines were defrostedfrozen. However, the available annotations of cell lines are sparse, incomplete, and distributed in multiple repositories. Edges represent the association relation of dsnps, chromatin features with or without treatment, cell lines, and. Karyotyping is performed on all htert immortalized cell lines and on many atcc classic cell lines.
Our growing catalogue of mammalian gene function is freely available for researchers. Hid genemarker software from softgenetics is available for clients to check out and analyze data. Here, the users sample is most closely matched to hct116, although the sample differs from the reference at the tpox locus. Genemapper software is a flexible fragment analysis software package that provides quality dna sizing and allele calls for all applied biosystems genetic analyzers. Although this is theoretically sufficient to separate different cell lines, it is not necessarily sufficient if the cell lines are related. The following software packages and utilities can be downloaded freely. The complete genotype information is compared to the database allowing to identify the correct cell line identity. These samples were not part of a matched pair and so genotype. Hla class i and ii genotype of the nci60 cell lines. Both a simple genotype aa, bb homozygous or ab heterozygous and a complex interpretation of the genotype are given for example, in a triploid region of the genome the genotype. Effective design and interpretation of molecular genetic studies performed using hela cells require accurate genomic information. In the end, this approach might be simpler, if you have access to tissues from individuals with the specific. The phenotypic presentations of patients carrying gdap1 mutations are heterogeneous, making it difficult to determine genotype phenotype. All trademarks are the property of thermo fisher scientific and its subsidiaries unless otherwise specified.
Gemiccl gene expression and mutations in cancer cell lines is an online database of human cancer cell lines that provides genotype and expression information. Genemapper idx software thermo fisher scientific us. We then searched the database of msderived peptides from each cell line to determine whether the mutation was observed in complex with the mhci on the cell surface. It has been estimated that 1836% of cell lines utilized in biomedical research are contaminated andor are completely misidentified 1. Network of msspecific dsnps generated by using a graph database and showing the dsnp rs62420820 in the k562 cell line, a genomewide significant signal in the imsgc ms gwas, but subthreshold in the cohortspecific kknms gwas. Genotype my biosoftware bioinformatics softwares blog. Snp rs17079281 decreases lung cancer risk through creating an. Genonets server is a tool that provides the following features. To assist with the analysis, genemarker hid software is equipped with an embedded cell line authentication application. Genomic biomarkers discovered in a 141 cell line training set were validated in. Not for use in diagnostic and therapeutic applications. If the parental cells genotypes have been determined by a recognized repository atcc, dsmz, or jcrb, the genotype of the submitted cells can be compared to genotypes in the database. Reanalyzing publicly available raw rnaseq data, we.
This assay does identify human genomic dna for 15 tetranucleotide repeat loci and the amelogenin gender determination marker. We have collected mutation, gene expression and copy number variation cnv data from three representative databases on cell linescancer cell line encyclopedia. A bioinformatics analysis of the cell line nomenclature. The cansar database 7 maintains cell line information with mutation. Cancer program scientific tools and resources broad. What software do you use for your cell line database. Yfiler kits and globalfiler kits are for forensic or paternity use only. Otherwise, the parental cells will need to be genotyped as well as the cells of interest. Cell lines project mutation profiles of over 1,000 cell lines used in cancer research. Karyotyping is a basic and indispensable test performed routinely to determine if the line has maintained a stable genotype.
Please see below for a partial list of resources or refer to the list of cancerrelated data, software and tools. The databases of cancer cell line encyclopedia ccle 3 and. Browse cell lines 5 ways to validate and extend your research using knockout cell models read more about how knockout cell lines, either together with gene rescue and replication of disease mutations, or as an independent cell. The human protein atlas hpa consortium is committed to aid in the fight against the health consequences of the covid19 pandemic. Phenotype databases for genetic screens in human cells. Systematic identification of combinatorial drivers and targets in. Here we describe the genotype tissue expression gtex project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between. We use an old access database to keep track of our cell lines, however, our uni does not support the access program anymore. I tried genevestigator on the recommendation of this thread but found no data on either cell line. Affymetrix snp array data for cell line and tumor genotype. Therefore we have introduced a cell line authentication service.
Hepatitis c virus hcv is one of the most common viruses that infects the lives of more than 170 million people worldwide and is one of the leading causes of chronic liver disease, cirrhosis, and hepatocellular carcinoma. Consequently, verification of human and stem cell line identity is of critical significance since the validity of data obtained depends on authenticity of the cell line. You may have been redirected here from the broad cancer program resource gateway, which is no longer active. Since several databases did not provide raw sequencing data, we. To select samples for eqtl and ase analyses we decided to exclude all tumorderived cell line samples where genotype calling is inherently difficult due to the presence of somatic copy number aberrations, by excluding all nonlymphoblastoid cell line.
Taqman genotyper software allows the use of controls and reference panels for accurate genotype calling. In order to do this pairwise comparison as each cell model was developed, we added additional data from the geo database during the normalization step. Contribute to opengeneawesomebiodatasets development by creating an account on github. Here we describe the genotype tissue expression gtex project, which will establish a resource database and associated tissue bank for the scientific community to. We offer testing at 24 loci to determine the genotype of your cell line with certainty. The misidentification of cell lines has been a problem in the scientific community for the past 50 years.
Or you could try to immortalize a primary cell type of known genotype using htert. Cosmic, the catalogue of somatic mutations in cancer, is the worlds largest and most comprehensive resource for exploring the impact of. Msderived peptides from each cell line to determine whether the mutation was observed in complex with the mhci on the cell surface. Source the person who created the cell line or the source can be entered here. If the parental cells have been genotyped by atcc, the genotype of submitted cells can be compared to genotypes in the atcc database. It is updated daily, and the entries contain copious links to other genetics resources. The hhmi web site for early career investigators has some good resources and advice. A wholecell computational model predicts phenotype from genotype. Please see below for a partial list of resources or refer to. You may have been redirected here from the broad cancer program. In this study, the presumed breast adenocarcinoma cell line, nciadrres 2, and human ovarian carcinoma cell line, ovcar8, were determined to share 99% of genotype calls out of 10 000 snps.
Filemaker pro lets you view in various formats and is highly customizable and pretty, but if you want simple, just use an excel spreadsheet. You can search the cellular phenotype database for a gene and retrieve the lossoffunction phenotypes observed, in human cells, by suppressing the expression of the selected gene. Omim focuses on the relationship between phenotype and genotype. In a brief, cancer is the decision of the cell to choose the innovativeadaptive phenotype and understanding the genotype does not mean understanding cancer. A laboratory inventory system for oligonucleotides. Genemapper software is used to analyze the data and. The genomic and transcriptomic landscape of a hela cell line. A whole cell computational model predicts phenotype from genotype previous article muopioid receptors and dietary protein stimulate a gutbrain neural circuitry limiting food intake next article genomewide single cell. Files listing the snp calls for each cell line identified by picnic analysis of affymetrix snp6. These samples were not part of a matched pair and so genotype alignment was not reported for these samples. The sanger institute also reported that two glioblastoma cell lines, snb19 and u251, exhibited a nearidentical genotype. An extensive database has been accumulated that could be used to select individual cells lines for specific experimental designs based on their global genetic and. Since the database only contains peptides mapping to the consensus human proteome reference, we searched for the native versions of the peptides tables s1as1e.
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