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A provincial biobank resource to support translational cancer research at the BC Cancer Agency, across Canada and internationally. This biobank collects biospecimens (tissues and blood), and clinical information and processes these to create anonymous cases that can be studied by cancer researchers to understand how cancer develops, how it grows, how it spreads, and how it responds to treatment. These tissues and data are obtained from patients who undergo surgery to treat a tumor and who have generously provided their consent for the TTR to collect tissues that are unused after diagnosis has been completed. The TTR is a provincial program that currently comprises a core biobank at the Vancouver Island Center, Victoria, that offers participation in the program to patients in Victoria and Nanaimo. The TTR works with other banks and expert translational research groups in BC, to create expanded capacity for collection and opportunities for research access to tissue resources. The TTR operates under the management and oversight of the director, a scientific advisory board, and the UBC BCCA Research Ethics Board. The TTR operates within organizational policies and a commitment to protection of donor privacy that is embodied in all standard operating procedures and aspects of the repository. The TTR is also a founding member and contributor to the development of provincial (BC BioLibrary) and national (CTRNet) initiatives to promote biobanking.
Proper citation: British Columbia Tumour Tissue Repository (RRID:SCR_004597) Copy
Biospecimen repository of normal and diseased human material from a variety of tissues and conditions along with clinical annotation. Both frozen aliquots and paraffin embedded tissue are available. Biospecimens are available to qualified researchers with IRB approval. * Preliminary inquires please contact Cheryl Spencer at cheryl.spencer (at) bmc.org
Proper citation: Boston University Biospecimen Archive Research Core (RRID:SCR_005363) Copy
http://www.einstein.yu.edu/centers/ictr/
Patient-derived specimens are essential to research in genomics, proteomics, and biomarkers. We provide banking for biological fluid and tissue specimens as well as human DNA and RNA. We provide secure archival sample storage as well as clinically-annotated specimen biobanks for defined research projects. The core serves the human research blood and tissue banking needs of clinical and translational researchers. Samples can be banked by an individual PI or by a consortium of investigators. All samples are tracked and archived using a secure tracking database, the Einstein-Montefiore Bio-Repository Databank (EM-BRED), http://informatics30.aecom.yu.edu/em-bred/default.aspx. EM-BRED provides qualified investigators with a solution to securely link patient specimens to clinical and pathological data. It consists of a user-friendly query engine that allows for comprehensive specimen search, and ultimately to build clinical annotations of relevance. The facility works under the best practices set out by NCI and ISBER (2006) for collection, storage, and retrieval of human biological materials for research.
Proper citation: Einstein-Montefiore Institute for Clinical and Translational Research Biorepository (RRID:SCR_005297) Copy
A publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis.
Proper citation: pSTIING (RRID:SCR_002045) Copy
http://molonc.bccrc.ca/platforms/btb/
The Molecular Oncology department hosts the breast cancer tumour tissue repository (BREAST-TTR), a project within the agency-wide tumour tissue repository. The BREAST-TTR comprises several important banks of breast tissues, contemporaneous as well as archival. The main banks are: * 3000 frozen breast cancers, linked to 15 year outcomes data from the BCCA Breast Cancer Outcomes Unit. This archival bank consists of frozen tissue, DNA and RNA, and a tissue microarray of the cases. * Live-cryopreserved cancers. At present around 50 individual cases of metastatic breast cancer, with tumour material cryopreserved for subsequent cell culture/xenograft work. * Comptemporary bank. Between the TTR in Victoria and the accrual site in Vancouver, approximately 1300 contemporaneous (within last 4 years) breast cancers with matched normal DNA and outcomes linkages.
Proper citation: British Columbia Breast Cancer Tumour Bank (RRID:SCR_006671) Copy
http://www.braintumourbank.ca/pages/about.html
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. The mission of the Canadian Virtual Brain Tumour Bank (CVBTB) is to facilitate clinical, molecular and translational research through the provision of well-characterized tissue linked to clinical data and to become a standardized national tissue resource whereby scientific needs are met, addressed and accelerated through a common public accessible core the CVBTB. Recognizing the need to encourage systemic banking of brain tumor tissues throughout the country and to link banks of brain tumor tissue samples with academic and scientific institutions that require these samples, the CVBTB was established. Under the sponsorship of Schering Plough Canada Inc. and in association with the Canadian Brain Tumour Consortium (CBTC), the CVBTB looks to act as a resource for all researchers to provide them with information on the types of brain tumor tissue samples available and to direct them to the tumor tissue banking sites holding these samples. The CVBTB also looks to provide information on standard operating procedures regarding aspects of tumor tissue banking such as tissue accrual, storage and shipment and the processing of blood samples such as serum and lymphocytes. The CVBTB currently consists of four brain tumour tissue banking sites (Toronto Western Hospital - Toronto, Ontario; London Health Sciences Centre - London, Ontario; McGill University - Montreal, Quebec; University of Calgary - Calgary, Alberta) and is continuously looking for more institutions to be a part of the CVBTB. If your institution would like to become a part of the CVBTB, please contact the CVBTB coordinator.
Proper citation: Canadian Virtual Brain Tumour Bank (RRID:SCR_004221) Copy
http://sourceforge.net/projects/mutascope/
Software suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.
Proper citation: Mutascope (RRID:SCR_001265) Copy
http://www.nitrc.org/projects/ibsr
Data set of manually-guided expert segmentation results along with magnetic resonance brain image data. Its purpose is to encourage the development and evaluation of segmentation methods by providing raw test and image data, human expert segmentation results, and methods for comparing segmentation results. Please see the MediaWiki for more information. This repository is meant to contain standard test image data sets which will permit a standardized mechanism for evaluation of the sensitivity of a given analysis method to signal to noise ratio, contrast to noise ratio, shape complexity, degree of partial volume effect, etc. This capability is felt to be essential to further development in the field since many published algorithms tend to only operate successfully under a narrow range of conditions which may not extend to those experienced under the typical clinical imaging setting. This repository is also meant to describe and discuss methods for the comparison of results.
Proper citation: Internet Brain Segmentation Repository (RRID:SCR_001994) Copy
http://bioinformatics.oxfordjournals.org/content/early/2012/05/10/bioinformatics.bts271.full.pdf
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. The method employs a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, whilst leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. The method has superior accuracy and sensitivity on impure samples compared to approaches based on either diploid genotype likelihoods or general allele-frequency tests.
Proper citation: Strelka (RRID:SCR_005109) Copy
http://ranchobiosciences.com/gse4922/
Curated data set of a study that investigated the expression profiles of 347 primary invasive breast tumors on Affymetrix microarrays. Three separate breast cancer cohorts were analyzed: 1) Uppsala (n=249), 2) Stockholm (n=58), 3) Singapore (n=40). The Uppsala and Singapore data can be accessed in GSE4922. The Stockholm cohort data can be accessed at GEO Series GSE1456.
Proper citation: GSE4922 (RRID:SCR_003557) Copy
http://www.cnio.es/ES/grupos/plantillas/presentacion.asp?grupo=50004308
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The need to use human neoplastic tissue under ideal conditions is currently of particular importance due to the development molecular pathology techniques that allow large-scale studies of genetic expression that are also of clinical significance. The Tumour Bank Network (TBN), instigated and coordinated by the Molecular Pathology Programme (MMP) aims to respond to this need by the promoting of Tumour Banks in Spanish hospitals. This will be achieved through the application of homogeneous procedures for the collection, processing and storage of neoplastic and normal tissue samples in such a way as to make molecular studies possible, avoiding that avoid the intrinsic bias of multi-centre studies possible. These Hospital Tumour Banks are based within the Pathology Departments of the collaborating Hospitals, that are interconnected through a computer-based network. In this way, each Centre''s tissue remains in the Hospital itself, thereby playing a key role in the development of the welfare, teaching and research activities within the Hospital. At the same time, it represents a tool to encourage of multi-hospital cancer research and of cooperation between basic and clinical researchers, constituting important collaboration between biomedical disciplines. The design does not correspond to a Central Tumour Bank, but that of a cooperative and coordinated Network of Hospital Banks, based on simple, homogeneous and optimal tissue treatment protocols. This Network is promoted by the Centro Nacional de Investigaciones Oncologicas (CNIO), which thereby undertakes the work of coordinating the network, using and maintaining the database, adhering to quality control. The aim of the CNIO's TBN is to acquire neoplastic and control non-neoplastic material of all types of malignant neoplasias, in the form of tissue fixed in formalin and paraffin embedded, of samples that are unfixed or frozen according to conventional methods as set out in Annexe 1 and even, exceptionally as fresh tissue. When other types of samples are required to carry out a specific project, the central office of the TBN will draw up a protocol with the group leading the project for the collection and maintenance of the tissue and clinicopathological data required for the proposed research. These protocols will be disseminated among the Associated Hospitals in order to gather the previously agreed number cases. Basic data surrounding the processing and preservation conditions for each case will be sent to the central office of the Bank, which under no circumstances will reveal the identity of the patient. Any Spanish cancer research team will be able to request tissue from the Tissue Bank Network. Absolute priority will be afforded to projects whose principal researcher belongs to one of the Associated Centres of the TNB, to other institutions with special agreements concerning the exchange of samples, and to the CNIO's researchers.
Proper citation: Spanish National Tumour Bank Network (RRID:SCR_008707) Copy
http://www.capitalbiosciences.com/
Biological products including Cell Immortalization Products, Clinically Defined Human Tissue, cDNA ORF Clones, Premade Adenoviruses, Purified Proteins, Viral Expression Systems and others as well as services like Custom Recombinant Adenovirus Production, Custom Recombinant Lentivirus Production, Protein Detection and Quantification and Stable Cell Line Production for academic and governmental research institutes, pharmaceutical and biotechnology industry. Capital Biosciences offers most types of human tissues, normal and diseased, with extensive clinical history and follow up information. Standard specimen format: Snap-frozen(flash-frozen), Formalin fixed and paraffin embedded (FFPE) tissues, Blood and blood products, Bone marrow, Total RNA, Genomic DNA, Total Proteins, Primary cell cultures, Viable frozen tissue. Tumor tissue samples include: Bladder cancer, Glioblastoma, Medulloblastoma, Breast Carcinoma, Cervical Cancer, Colorectal Cancer, Endometrial Cancer, Esophageal Cancer, Head and Neck (H&N) Carcinoma, Hepatocellular Carcinoma (HCC), Hodgkin's lymphoma, Kidney, Renal Cell Carcinoma, Lung Cancer, Non-Small Cell (NCSLC), Lung Cancer, Small Cell (SCLC), Melanoma, Mesothelioma, non-Hodgkin's Lymphoma, Ovarian Adenocarcinoma, Pancreatic Cancer, Prostate Cancer, Stomach Cancer.
Proper citation: Capital Biosciences (RRID:SCR_004879) Copy
https://github.com/ding-lab/msisensor
A C++ software program for automatically detecting somatic and germline variants at microsatellite regions. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples.
Proper citation: MSIsensor (RRID:SCR_006418) Copy
http://bioinf.wehi.edu.au/socrates/
Software for detecting genomic rearrangements in tumors that utilizes only split-read data. It features single nucleotide resolution, high sensitivity, and high specificity in simulated data. It takes advantage of parallelism for efficient use of resources.
Proper citation: Socrates (RRID:SCR_006411) Copy
Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.
Proper citation: AbsCN-seq (RRID:SCR_006409) Copy
A contract research organization (CRO) specializing in preclinical oncology services. As a pioneer in the field of patient derived tumor xenografts (PDX), they provide tailored solutions to the problems faced by preclinical oncology researchers. They assist with the identification of the best drug candidates and the validation of their targets and deliver in-depth bioinformatics analyses, laying the groundwork for the successful planning of clinical trials. Their diverse tumor model collection enables them to recommend the right assays and models to answer their customers' questions. Their AAALAC accredited facilities with IVC system, separate model development unit, large cage capacity of over 14,500 mice and proprietary electronic measurement system with an integrated database and by continuously maintaining important PDX models in mice, they are able to provide the highest standard of testing within a reasonable timeframe.
Proper citation: Oncotest (RRID:SCR_000489) Copy
http://sourceforge.net/projects/variantmaster/
Software program that extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation in a family, as well as the probability of it being de novo or somatic. In familial cases, various modes of inheritance are considered: X-linked, autosomal dominant, and recessive (homozygosity or compound heterozygosity). Moreover, it integrates phenotypes and genotypes, and employs Annovar to produce additional information as allelic frequencies in general population and damaging scores.
Proper citation: VariantMaster (RRID:SCR_000569) Copy
http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/somaticcall-manual
Software program that finds single-base differences (substitutions) between sequence data from tumor and matched normal samples. It is designed to be highly stringent, so as to achieve a low false positive rate. It takes as input a BAM file for each sample, and produces as output a list of differences (somatic mutations). Note: This software package is no longer supported and information on this page is provided for archival purposes only.
Proper citation: SomaticCall (RRID:SCR_001196) Copy
http://cran.r-project.org/web/packages/expands/
Software that characterizes coexisting subpopulations (SPs) in a tumor using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model amplifies the statistical power to detect coexisting genotypes, by fully exploiting run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting SPs in the tumor bulk, the mutations specific to each SP and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting SPs from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as an input to obtain stable results.
Proper citation: ExPANdS (RRID:SCR_005199) Copy
http://gmt.genome.wustl.edu/somatic-sniper/current/
Software program to identify single nucleotide positions that are different between tumor and normal (or, in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the differences. It outputs a file in a format very similar to Samtools consensus format. It uses the genotype likelihood model of MAQ (as implemented in Samtools) and then calculates the probability that the tumor and normal genotypes are different. This probability is reported as a somatic score. The somatic score is the Phred-scaled probability (between 0 to 255) that the Tumor and Normal genotypes are not different where 0 means there is no probability that the genotypes are different and 255 means there is a probability of 1 ? 10(255/-10) that the genotypes are different between tumor and normal. This is consistent with how the SAM format reports such probabilities. It is currently available as source code via github or as a Debian APT package.
Proper citation: SomaticSniper (RRID:SCR_005108) Copy
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