The iarc tp53 database compiles various types of data and information on human tp53 gene variations related to cancer. Over 50% of melanomas carry a braf mutation, and of these over 80% carry a hyperactivating mutation braf v600e, leading to aberrant activation of the mapksignaling pathway. Please see below for a partial list of resources or refer to the list of cancer related data, software and tools. Cell lines project catalogue of somatic mutations in cancer.
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. Search mutationssnps search celllines tp53 reference sequences. The table below gives an overview of databases for that serve specifically for oncogenomic research. The overview tab shows a plot that enables the user to view all variants for each gene within the cell line of a selected cancer type. 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. 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. Determining differentially required genes between p53 wt or mutant cell lines from sirna data and making a heatmap. Transformed cancer cell lines rnaseq database hi, i am trying to find a database which has rnaseq data for cancer cell lines transformed from. The estimated incidence rates of colorectal cancer are highest in australianew zealand and western europe. Please note that cell line data are also included in the dataset od somatic mutations.
The cancer genomics hub cghub is a central repository for the genomic information generated through three different programs at the national cancer institute nci of the united states, namely, the cancer genome atlas tcga, the cancer cell line encyclopedia ccle, and the therapeutically applicable research to generate effective treatments target projects. This cell line panel is designed to help investigators unravel the relationship between tp53 p53 gene mutations and oncogenesis. Hi, i am trying to find a database which has rnaseq data for cancer cell lines transformed from. Cultures may be homogeneous or heterogeneous for these cell types. The monoclonal model of cancer and the cancer stem cell model are not mutually exclusive. Cell lines gain cancerrelated mutations the scientist. Note that this is not a comprehensive list and does not contain databases that have a generic focus. Cancer program scientific tools and resources broad. The cell lines project in cosmic is an effort to fully profile over cell lines regularly used in cancer research. Online lung cancer mutation database to help oncologists in.
If not, which databases could i try to bash together to get what i need. Ideally i would need a database which will tell me. Brca1 mutation analysis of 41 human breast cancer cell. As with primary ovarian tumors, mutation status of cancer genes like arid1a and tp53 and a general immunoprofile serve well for establishing histotype of ovarian cancer cell we describe specific biomarkers and molecular features to reclassify generic ovarian carcinoma cell lines into type specific categories. All cancers have to overcome the same spectrum of regulatory functions in order to grow and progress, but the genes involved may.
Deleterious brca1 mutations were identified in four breast cancer cell lines tables 1 and 2. Is there any public database to look for the mutational status of a cell line. A549 lung, adenocarcinoma, carcinoma mutations cell. Mutations in 10,000 patients with metastatic cancer. If you are not an expert in cell biology, the book takes care to explain concepts in the context of cancer. These authors reported the same brca1 mutation and an identical pattern of allelic. Molecular characterization of breast cancer cell lines. Online lung cancer mutation database to help oncologists in decision making. Frequent mutations of chromatin remodeling gene arid1a in. Somatic evolution is the accumulation of mutations and epimutations in somatic cells the cells of a body, as opposed to germ plasm and stem cells during a lifetime, and the effects of those mutations and epimutations on the fitness of those cells. National engineering laboratory for cereal fermentation technology, jiangnan university, wuxi, china. Cell line mutation descriptions for 304500k can be found on the atcc. Actionable mutation profiles of nonsmall cell lung cancer.
Colon atlas colorectal cancer databasebowel cancer. The cancer cell line encyclopedia enables predictive. Atcc has created a list of atcc tumor cell lines based on the gene mutation information maintained in the sanger institute cosmic database. Experiments using cell culture are used for developing new diagnostic tests and new treatments for diseases. In many cases it originates from the cell line name. You may have been redirected here from the broad cancer program resource gateway, which is no longer active. Apr 27, 2017 istock, selvanegra among 140 human embryonic stem cell lines used for basic research or clinical development, five have gathered mutations in the tumor suppressor gene tp53, according to the results of a screen published yesterday april 26 in nature. Be aware that many cell lines may have different tp53 status according to different studies. As a special feature each search is supported by an autosuggestion functionality allowing, e. Neuroblastoma cell lines center for cancer research. A immortal human stomachderived cell line cell that has the characteristics. Using a database that catalogs clinically actionable mutations, they found that 37% of patients had at least one clinically actionable mutation. Download files catalogue of somatic mutations in cancer. Is there any consolidated database on cancer cell line.
For decades, human tumorderived cell lines have been a cornerstone of cancer research and have shaped our understanding of the genetic and. Data and scientific tools from many of our cancer research projects can now be accessed via broad data, software and tools. 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. Is there a database linking cell lines and mutations. In contrast, three other nsclc cell lines h1781, h1666, and h441 cells expressing wildtype egfr are resistant. One way of dealing with that heterogeneity is to test large numbers of patientderived cell lines for common vulnerabilities.
Mar 29, 2012 image caption cells from a cancer line known as hela. For all cell lines, dna copy number, mrna, mirna and protein expression profiles were generated. Reports of the adaptation of neuroblastoma cell lines to serumfree. A devoted mother of five who was escorted briskly to the jim crow section of johns hopkins for her cancer treatments. May 17, 2011 for cell line queries we offer searches by cell line name or frequently used synonyms. Syngeneic cell line reference database taconic biosciences. Researchers identify novel mutation in melanoma cancer cells. Cell lines by genetic mutation tumor cell lines become more powerful research models and drug discovery tools when the genetic abnormalities that drive their phenotype are known. Atcc tumor cell panels combine authenticated, wellcharacterized cell lines with mutation data from the sanger institute catalogue of somatic mutations in cancer cosmic to create powerful tools for cancer research and drug discovery. Ingelheim, germany, 16 march, 2020 boehringer ingelheim today announced the launch of a patient outcomes database which will provide clinicians with important information when considering optimal treatment for nonsmall cell lung cancer nsclc patients harboring specific uncommon epidermal growth factor receptor egfr mutations.
The umd tp53 mutation database includes the tp53 status of more than 80,400 tumors, individuals with germline mutations and cell lines. However, proper choice of cell lines for experimental purposes is often difficult because genotype andor expression data are missing or scattered in diverse resources. I want to know if the cell lines that i am using are mutatedor wild type for several genes that we are interested in. Typespecific cell line models for typespecific ovarian. Initially, the breast cancer and skin cancer cell lines from the sclp dataset were selected and their gene expression profiles were illustrated in a pca plot. The immortal life of henrietta lacks 2010 is a nonfiction book by american author rebecca. Cancer development requires genetic changes in several different oncogenes and tumor suppressors. Cancer cell lines with mutant kras genes the heterogeneity of human cancers is a major obstacle to developing therapies. Sep 03, 2015 in this recent study, a group of researchers from boston university school of medicine busm identified a new genetic mutation in melanoma cancer cells using bioinformatics to understand gene mutations at the level of the protein complex apcc that regulates cell replication cycles. They can be a primary source of cancer data, offer a certain level of analysis processed data or even offer online data mining. The cancer and disease mutation databases comprise a total of 872 125 and 27 148 peptide entries from 25 642 and 29 proteins, respectively.
Please see the appendix for a full listing of atcc breast cancer cell line, as well as for lists of cell lines that have been organized according to gene mutation or that are part of a paired tumornormal set. Databases and web tools for cancer genomics study sciencedirect. In 2002, the cancer genome project identified braf as the most frequently mutated gene in melanoma davies et al. This information is maintained in a separate, but parallel system alongside cosmic and regularly updated to highlight the most valuable information across the cell line panel. Lung cancer is the most common malignancy and the leading cause of cancer related deaths worldwide 18. Where can i find mutation databases specialized in cancer. General biologygeneticsmutation wikibooks, open books for. Cell lines database the tp53 website the tp53 web site. 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.
Cancer stem cell hypothesis might explain such phenomena as metastasis and remission. You just add the track for mutations and edit the cell. The current version includes 2,000 and 500 cell lines with mutant tp53 and wildtype tp53 respectively. Our data supports the use of prototype clear cell lines, such as tov21g and jhoc5, and questions the use of skov3 and a2780 as models of highgrade serous carcinoma. 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. Data include mutations identified in benign proliferations, primary and metastatic tumors, recurrences, and cancer cell lines. Breast cancer cell line classification and its relevance with. Comparing cancer cell lines and tumor samples by genomic profiles. We retrieved the cell line annotation, including name, disease, tissue, and mutation information timestamp 2012. See detailed information on database contents in the users guide. It is the third most common cancer and has the fourth highest mortality rate reported worldwide.
The experiment was performed in multiplex format with 9 biological samples per plex and one common sample to. Id like to find gene expression data for a few different primary cell lines. The ubc40 urothelial bladder cancer cell line index. Understanding the functions of mutant p53 will help in the development of new therapeutic. A description line for each entry provides the parent protein id and name, the cdna and proteinlevel mutation site and type, the originating database, and the disease or cancer tissue type and. Tumorsvarymoreintheextentofalterationsby cancer typethandocelllines we compared mutations and copy number alterations cnas in cell lines. Mutations for cell line a549 lung, adenocarcinoma, carcinoma. This may be due to cell line misidentification, crosscontamination or sequencing techniques see pmid28127703, pmid24700732 or atcc for discussions on these issues.
Colorectal or bowel cancer originates from either the colon or the rectum. Is there any consolidated database on cancer cell line mutations. Hela is an immortal cell line used in scientific research. The web site includes the database requires registration, laboratory methods, forum and resources. This is an international collaboration hosted by the nih national human genome research institute. Database of somatic mutations associated with cancer and their accompanying publications. List of databases for oncogenomic research wikipedia. There is growing evidence that these mutant p53s have both lost wildtype p53 tumor suppressor activity and gained functions that help to contribute to malignant progression.
These data were obtained from the european collection of cell cultures. Taconic biosciences syngeneic cell line reference database. Cancer genome project an overview sciencedirect topics. Only mutations in germ line cells can be passed on to children, while mutations elsewhere can cause cell death or cancer. Mutations can have a variety of different effects depending on the type of mutation, the significance of the piece of genetic material affected and whether the cells affected are germ line cells. Is there a database to find out which genes are expressed. The immortal life of henrietta lacks and millions of other books are available for instant. Start using cosmic by searching for a gene, cancer type, mutation, etc. The realworld database includes all available data from. Gemiccl gene expression and mutations in cancer cell lines is an online database of human cancer cell lines that provides genotype and expression information. Cancer stem cell arises by clonal evolution as a result of selection for the cell with the highest fitness in the neoplasm. Jun 23, 2009 each cell line is described, insofar as the information is available, by standard name, cancer type, information on the patient anonymized, origin of the cells, chromosomal ploidy, doubling time in culture, and mutation status with respect to cancer genes of interest e. No mutations of arid1a are listed in the cancer gene census of the cosmic database, but chromosomal translocations that involve this gene have been identified in a human breast cancer and a human lung cancer cell line. A total of 7 oncogenic mutations were found in the 14 genes table 3.
The resulting page presents a card with general information on the sample name, synonyms, tissue, histology, etc. Gsu a immortal human stomachderived cell line cell that has the characteristics. The importance of cancer cell lines as in vitro models in cancer. The heterogeneity of human cancers is a major obstacle to developing therapies. 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. 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.
The cancer cell line encyclopedia is a database of gene expression, genotype, and drug sensitivity data for human cancer cell lines. This database allows users to browse drugs, drug targets and cell lines. Targeted dna sequencing was performed for 27 cancer cell lines in addition to sanger sequencing of selected genes in 31 cell lines. The cellosaurus, a cellline knowledge resource ncbi nih. Many different types of cancer show a high incidence of tp53 mutations, leading to the expression of mutant p53 proteins.
In h3255 cells, a lung adenocarcinoma cell line with the egfr l858r mutation, high sensitivity to growth inhibition induced by gefitinib is seen. A number of samples can be taken from a single tumour and a number of tumours can be obtained from one individual. Cancerdr coveres 116 drug targets correspond to these anticancer drugs and provide the comprehensive information about these targets such as their function, structure, and their gene sequences in respective cancer cell lines. The sample name can be derived from a number of sources. The first volume of a book of cancer knowledge has been published, which scientists say will speed up the search for new cancer drugs. Epigenetic and genetic features of 24 colon cancer cell lines. Breast cancer cell lines are frequently used as model systems to study the cellular properties and biology of breast cancer. Atcc breast cancer research resource book is coming soon. Broad does not represent that the database is free of errors or bugs or suitable for any particular tasks. Catalogue of somatic mutations in cancer cosmic, and a number of. This evolutionary process has first been shown by the studies of bert vogelstein in colon cancer. Scientists study the behaviour of isolated cells grown in the laboratory for insights into how cells function in the body in health and disease. Also the characterization of cancer cell lines is essential for the development of new. Databases for oncogenomic research are biological databases dedicated to cancer data and oncogenomic research.
The database is a research database and is provided as is. May 22, 2015 urothelial bladder cancer is a highly heterogeneous disease. This is a list of major breast cancer cell lines that are primarily used in breast cancer research. An alteration may be a cancer driver, but it may not be actionable if there is no existing therapy that targets it. The ccle provides public access analysis and visualization of dna copy number, mrna expression, mutation data and more, for cancer cell lines. Human plasma cell leukemia cell line, established from the peripheral blood of a 33yearold woman with igg plasma cell leukemia. 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. Many specialized cellline databases have been established over the. Included was the previously reported large homozygous deletion in hl. Xiaofeng dai 1, 2, hongye cheng 1, 2, zhonghu bai 1, 2, jia li 1, 2. My favorite tool for this is the ucsc genome browser since you can bisualize the mutations per cell line per chromosomal locatikn. This is a list of major breast cancer cell lines that are primarily used in breast cancer.
Intogen collects and analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes. The online database brings together data on all the. 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 catalogue of somatic mutations in cancer, and nci60. The book is about henrietta lacks and the immortal cell line, known as hela, that came from lackss cervical cancer cells in 1951.
Breast cancer information core an on line breast cancer mutation database. Mutation analysis of 24 known cancer genes in the nci60. 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. Other sources include names assigned by the annotators, or an incremented number assigned during an anonymisation process. Knockdown of arid1a in a leukemia cell line confers resistance to fasmediated apoptosis. The umd tp53 variant database includes a full description of the 6,870 tp53 variants found in the database with 70 novel features associated with each tp53 variant.
It seems the transition from a normal, healthy cell to a cancer cell is a stepwise progression. Mutation analysis of 24 known cancer genes in the nci60 cell. On the righthand side, different sections display all known cancer genome information for the sample. Is there an online tool or database that can show which genes have been found to be expressed in different cell types. Human gastric cancer cell line derived from metastasis at liver. It is the oldest and most commonly used human cell line. This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma ubc cell lines including information on origin, mutation status of genes implicated in bladder cancer fgfr3, pik3ca, tp53, and ras, copy number alterations assessed using high density snp arrays. Intriguingly, the mdamb435 cell line, which was originally classified as a breast cancer cell line, was closer to the group of skin cancer cell lines.
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