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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   

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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   

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http://bioinformatics.oxfordjournals.org/content/early/2014/01/02/bioinformatics.btt759.abstract?sid=e62f3c2b-26dc-428b-ba24-99e92a277d77

Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.

Proper citation: AbsCN-seq (RRID:SCR_006409) Copy   

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http://www.proteinatlas.org/

Open access resource for human proteins. Used to search for specific genes or proteins or explore different resources, each focusing on particular aspect of the genome-wide analysis of the human proteins: Tissue, Brain, Single Cell, Subcellular, Cancer, Blood, Cell line, Structure and Interaction. Swedish-based program to map all human proteins in cells, tissues, and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.

Proper citation: The Human Protein Atlas (RRID:SCR_006710) Copy   

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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   

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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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http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_indels_SomaticIndelDetector.html

Tool for calling indels in Tumor-Normal paired sample mode.

Proper citation: SomaticIndelDetector (RRID:SCR_005107) Copy   

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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   

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https://www.urmc.rochester.edu/neurosurgery/specialties/neurooncology.aspx

Collaborative neuro-oncology research program with a tissue repository (tumor bank) containing a wide range of clinical specimens, which they make available to researchers in order to study the effects of new drugs on a large number and wide range of tumor specimens. They provide highly coordinated, complex care in neurosurgery, radiation oncology, medical oncology, and neurology to patients afflicted with tumors of the brain and spine by combining the newest technologies and treatments available anywhere in the world. The program is formed from a multidisciplinary group with a goal of helping patients navigate the complex issues surrounding brain and spinal cancer care. The researchers are working to increase the number of targets that could be considered for anti-angiogenesis therapy. Many of their studies focus on the blood vessel cells (endothelial cells) themselves, which, unlike tumor cells, rarely mutate and so might be less likely to become resistant to therapy and are also more easily reached through the bloodstream. Their researchers are also attempting to better understand the changes in the blood-brain barrier (BBB) that are associated with fluid accumulation and brain swelling (edema) in neuro-oncology patients. Normal brain tissue is shielded from the rest of the body by the BBB. This barrier is composed of very tight blood vessels that prevent most substances from entering the brain. Brain tumors have a leaky BBB ����?? this feature can be used to identify tumors on MRI scans. They have identified specific molecules that appear to be associated with the leaky, abnormal vessels while the normal blood vessels with intact BBB produce these molecules at very low levels or not at all. Inhibiting the function of these molecules may help control or prevent disruption of the BBB and limit cerebral edema in brain tumor patients, as well as patients suffering from stroke or traumatic brain injury.

Proper citation: University of Rochester Program for Brain Tumors and Spinal Tumors (RRID:SCR_005343) Copy   

•   Source: SciCrunch Registry
  

http://ucneuroscience.com/

Leading treatment, research and teaching center for complex neurological conditions based at the University Hospital and the UC College of Medicine. Its physicians and researchers have created national models for evidence-based treatment and research of complex conditions, including ischemic and hemorrhagic stroke, brain aneurysms, brain and spinal cord trauma, brain tumors, Parkinson's disease, epilepsy and seizure disorders, multiple sclerosis, trigeminal neuralgia, Alzheimer's disease and memory disorders, mood disorders, and neuromuscular disorders. UCNI includes a team of more than 100 experts from 15 specialties who collaborate across disciplines to provide the most comprehensive diagnoses and treatments possible.

Proper citation: University of Cincinnati Neuroscience Institute (RRID:SCR_005345) Copy   

•   Source: SciCrunch Registry
  

http://bioinfo-out.curie.fr/projects/snp_gap/

Software for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured by single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes.

Proper citation: Genome Alteration Print (RRID:SCR_012016) Copy   

•   Source: SciCrunch Registry
  

http://www.oncotest.com/

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   

•   Source: SciCrunch Registry
  

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   

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http://patchwork.r-forge.r-project.org/

Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data.

Proper citation: Patchwork (RRID:SCR_000072) Copy   

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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   

•   Source: SciCrunch Registry
  

http://hcc.musc.edu/research/resources/biorepository/

The Hollings Cancer Center Tissue Biorepository & Research Pathology Services Shared Resource provides investigators with a centralized infrastructure that promotes biomedical research involving the use and study of human biospecimens. The shared resource is comprised of four integrated components: Biospecimens and data bank, Laser Capture Microdissection, Tissue Microarray, and Research Pathology Services. These components, along with extensive staff expertise, offer a comprehensive means by which researchers can utilize valuable human biospecimens and cutting edge technology to support basic, translational and clinical research. Services: * Biospecimen and Data Bank ** Collecting, processing, and banking of tissue, saliva, urine, blood, plasma, serum, and other tissue derivatives; including those for protocol driven studies ** Retrieval of banked specimens linked to clinicopathologic data, while maintaining patient confidentiality, for research use ** Quality control of collected tissue by the Tissue Biorepository Director, a trained pathologist: verification of diseased state and assessment of tumor purity, etc ** Quality control of DNA/RNA/protein isolated from collected tissue using the Agilent Bioanalyzer * Laser Capture Microdissection ** Identification, localization, and microdissection of targeted cell populations (from human and animal tissue sources) ** Extraction of DNA/RNA/protein from microdissected samples. ** Quality analysis and quality control of isolated nucleic acid using Agilent Bioanalyzer * Tissue Microarray ** Create custom and standard TMAs ** Consultation and technical support in the construction and analyses of TMA * Research Pathology Services ** Macrodissection of tissue prior to isolation of DNA/RNA/protein to increase tumor purity ** Immunohistochemistry and In-situ hybridization ** Quantitative image analysis on conventional and TMA sections, including tissue scoring, Ki-67 labeling index, microvascular density counting, and tissue microarray scoring, etc. * Bio-molecular Assessment ** Cellular DNA, RNA and protein prepared by the Tissue Repository from banked specimens or any other biomolecules submitted by investigators can be qualitatively assessed by Agilent Bioanalyzer, prior to use for downstream applications such as microarray and/or qRT-PCR analysis

Proper citation: Hollings Cancer Center Tissue Biorepository and Research Pathology Services Shared Resource (RRID:SCR_004626) Copy   

•   Source: SciCrunch Registry
  

http://neurosurgery.ucsf.edu/index.php/research_tissue_bank.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Brain Tumor Research Center Tissue Bank began collecting tissue in 1978 and has established an organized repository of characterized tissues--frozen, paraffin-embedded, blood and cultures--that are maintained in a manner useful for a wide range of studies. Samples are collected only from patients who have agreed to have their tissues banked and used for future research. Consent documents are maintained in a secure area and associated clinical data are held in a double-password protected computer database. Each sample received into the Tissue Bank is non-identifying number. No protected health information (PHI) is released. To obtain samples, investigators submit a request form to the Manager. The request form requires an explanation of the tissue requested (type, number of samples, justification), description of the study, CHR approval (see new policy regarding human vs. non-human research) and Project Leader authorization. The Manager reviews each request for feasibility before presentation to the Scientific Core Committee. The UCSF Neurosurgery Tissue Bank makes its inventory of stock cell lines available to all investigators. Requested cells are grown in T-25 flasks and shipped FedEx Priority Overnight at the receipient's expense. However, if you prefer, we can ship the frozen cells, packed in dry ice. (Note: some countries restrict dry ice shipments.)

Proper citation: UCSF Brain Tumor Tissue Bank (RRID:SCR_000647) Copy   

•   Source: SciCrunch Registry
  

http://www.som.soton.ac.uk/research/sites/cruk/translation/tumour.asp

Collects and distributes human tissue for ethically approved studies to aid the study of cancer biology and other associated research. All tissue is collected with patient consent and tissue is distributed only to ethically approved studies. The purpose of the Tissue Bank is to source, organize, collect, prepare, store and distribute a diverse collection of human tissues and biological products. This valuable core resource is available to all local academics and researchers. The on-site bank allows for rapid access to a plethora of biological materials supported by an informatics system of databases acting as an inventory management system. In addition, the Tissue Bank provides a licensed facility to store surplus tissue when studies close. Tissues currently available include normal and malignant snap frozen blocks, freshly prepared spleen and lymph nodes, fresh biopsy tissues, blood products and biological fluids. Collections can be organized by bank staff or ran in parallel with current research activities and include a wide variety of cancer classifications. We currently hold over 38,000 vials. Tissue Availability: Lymphoma - solid tissue and cells - 843; Breast - solid tissue and cells - 540; Colon - solid tissue and cells - 238; Lung - solid tissue and cells - 43; Upper Gi - BIOPSY tissue - 114; Pleural fluid and cells - 14

Proper citation: Southampton Tumour Bank (RRID:SCR_000673) Copy   

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http://www.mycancergenome.org/

A freely available online personalized cancer medicine knowledge resource for physicians, patients, caregivers and researchers that gives up-to-date information on what mutations make cancers grow and related therapeutic implications, including available clinical trials. It is a one-stop tool that matches tumor mutations to therapies, making information accessible and convenient for busy clinicians.

Proper citation: My Cancer Genome (RRID:SCR_004140) Copy   

•   Source: SciCrunch Registry
  

http://www.startthecure.com/clinical_tumor_bank.php

Biospecimen repository for tumor specimens, available to all researchers actively engaged in cancer research whether they are in University, Academic, or Pharmaceutical industry, with a goal to accelerate the discovery and development of new agents for the treatment and cure of cancer. The START tumor bank was created to make tumor tissue gifted by patients receiving care or treatment at The START Center available to all researchers involved in developing a better understanding of the biology of cancer or those engaged in the discovery of new therapies. The START Tumor Bank is a department within the PK Department and handles skin and tumor biopsies required by clinical trial protocols. A member of the PK Department is present during biopsy procedures for immediate processing of the sample for the trial. Additionally, the Tumor Bank collects and banks the tumor tissues of patients who consent. This tissue is then stored for future use by researchers developing new therapies.

Proper citation: START Tumor Bank (RRID:SCR_004258) Copy   

•   Source: SciCrunch Registry