The Experts below are selected from a list of 63915 Experts worldwide ranked by ideXlab platform

Xiaohu Gao - One of the best experts on this subject based on the ideXlab platform.

  • Multicolor multicycle Molecular Profiling with quantum dots for single-cell analysis
    Nature Protocols, 2013
    Co-Authors: Pavel Zrazhevskiy, Lawrence D True, Xiaohu Gao
    Abstract:

    Here we present a detailed protocol for Molecular Profiling of individual cultured mammalian cells using multicolor multicycle immunofluorescence with quantum dot probes. It includes instructions for cell culture growth and processing (2 h + 48–72 h for cell growth), preparation and characterization of universal quantum dot probes (4.5 h + overnight incubation), cyclic cell staining (∼4.5 h per cycle) and image analysis (varies by application). The use of quantum dot fluorescent probes enables highly multiplexed, robust quantitative Molecular imaging with a conventional fluorescence microscopy setup, whereas the probe preparation methodology, using a self-assembly between protein A–decorated universal quantum dots and intact primary antibodies, offers a fast, simple and purification-free route for an on-demand preparation of antibody-functionalized quantum dot libraries. As a result, this protocol can be used by biomedical researchers for a variety of cell staining applications, and, with further optimization, for staining of other biological specimens (e.g., clinical tissue sections).

  • Quantum dot imaging platform for single-cell Molecular Profiling
    Nature communications, 2013
    Co-Authors: Pavel Zrazhevskiy, Xiaohu Gao
    Abstract:

    Study of normal cell physiology and disease pathogenesis heavily relies on untangling the complexity of intracellular Molecular mechanisms and pathways. To achieve this goal, comprehensive Molecular Profiling of individual cells within the context of microenvironment is required. Here we report the development of a multicolour multicycle in situ imaging technology capable of creating detailed quantitative Molecular profiles for individual cells at the resolution of optical imaging. A library of stoichiometric fluorescent probes is prepared by linking target-specific antibodies to a universal quantum dot-based platform via protein A in a quick and simple procedure. Surprisingly, despite the potential for multivalent binding between protein A and antibody and the intermediate affinity of this non-covalent bond, fully assembled probes do not aggregate or exchange antibodies, facilitating highly multiplexed parallel staining. This single-cell Molecular Profiling technology is expected to open new opportunities in systems biology, gene expression studies, signalling pathway analysis and Molecular diagnostics.

Pavel Zrazhevskiy - One of the best experts on this subject based on the ideXlab platform.

  • Multicolor multicycle Molecular Profiling with quantum dots for single-cell analysis
    Nature Protocols, 2013
    Co-Authors: Pavel Zrazhevskiy, Lawrence D True, Xiaohu Gao
    Abstract:

    Here we present a detailed protocol for Molecular Profiling of individual cultured mammalian cells using multicolor multicycle immunofluorescence with quantum dot probes. It includes instructions for cell culture growth and processing (2 h + 48–72 h for cell growth), preparation and characterization of universal quantum dot probes (4.5 h + overnight incubation), cyclic cell staining (∼4.5 h per cycle) and image analysis (varies by application). The use of quantum dot fluorescent probes enables highly multiplexed, robust quantitative Molecular imaging with a conventional fluorescence microscopy setup, whereas the probe preparation methodology, using a self-assembly between protein A–decorated universal quantum dots and intact primary antibodies, offers a fast, simple and purification-free route for an on-demand preparation of antibody-functionalized quantum dot libraries. As a result, this protocol can be used by biomedical researchers for a variety of cell staining applications, and, with further optimization, for staining of other biological specimens (e.g., clinical tissue sections).

  • Quantum dot imaging platform for single-cell Molecular Profiling
    Nature communications, 2013
    Co-Authors: Pavel Zrazhevskiy, Xiaohu Gao
    Abstract:

    Study of normal cell physiology and disease pathogenesis heavily relies on untangling the complexity of intracellular Molecular mechanisms and pathways. To achieve this goal, comprehensive Molecular Profiling of individual cells within the context of microenvironment is required. Here we report the development of a multicolour multicycle in situ imaging technology capable of creating detailed quantitative Molecular profiles for individual cells at the resolution of optical imaging. A library of stoichiometric fluorescent probes is prepared by linking target-specific antibodies to a universal quantum dot-based platform via protein A in a quick and simple procedure. Surprisingly, despite the potential for multivalent binding between protein A and antibody and the intermediate affinity of this non-covalent bond, fully assembled probes do not aggregate or exchange antibodies, facilitating highly multiplexed parallel staining. This single-cell Molecular Profiling technology is expected to open new opportunities in systems biology, gene expression studies, signalling pathway analysis and Molecular diagnostics.

Tracy L. Stockley - One of the best experts on this subject based on the ideXlab platform.

  • Molecular Profiling of advanced solid tumors and patient outcomes with genotype matched clinical trials the princess margaret impact compact trial
    Genome Medicine, 2016
    Co-Authors: Tracy L. Stockley, Amit M Oza, Hal K Berman, Natasha B Leighl, Jennifer J Knox
    Abstract:

    Background The clinical utility of Molecular Profiling of tumor tissue to guide treatment of patients with advanced solid tumors is unknown. Our objectives were to evaluate the frequency of genomic alterations, clinical “actionability” of somatic variants, enrollment in mutation-targeted or other clinical trials, and outcome of Molecular Profiling for advanced solid tumor patients at the Princess Margaret Cancer Centre (PM).

  • MG-131 Incidental germline findings in tumour Molecular Profiling by next generation sequencing
    Journal of Medical Genetics, 2015
    Co-Authors: Tracy L. Stockley, Mariam Thomasa, Djamel Harbia, Mahadeo A. Sukhai, Tong Zhang, Trevor Pugha, Lillian L. Siu, Phil Bedard, Suzanne Kamel Reid
    Abstract:

    Objectives Molecular Profiling of solid tumours using Next Generation Sequencing (NGS) aims to detect tumour-specific somatic mutations for targeted drug treatments. Parallel testing of tumour and blood samples can enable identification and verification of of tumour-specific somatic mutations. However testing blood may also reveal incidental germline variants in cancer predisposition genes. The objective of this study was to determine type and frequency of clinically relevant incidental germline variants from Molecular Profiling of paired tumour/blood samples. Design/methods NGS Molecular Profiling data of tumour/blood pairs from 467 patients (934 samples) with metastatic solid tumours enrolled in the Princess Margaret IMPACT clinical trial were reviewed. NGS testing used Illumina TruSeq Cancer Amplicon Panel (TSCAP) on the MiSeq. The TSCAP targets regions of 48 genes including 8 genes on the ACMG germline incidental list (APC, PTEN, MLH1, RET, RB1, STK11, TP53, VHL). Results Data review revealed 2 previously reported pathogenic cancer predisposition mutations: TP53 c.817C >T in a breast cancer patient, and RET c.1900T >A in a thyroid cancer patient. Three other patients had acquired mutations of JAK2 or TP53 in blood, confirmed by serial testing that likely represented secondary changes related to previous cancer treatments. In addition 93 germline variants of uncertain significance were identified; 9/93 were recurrent and may represent benign germline changes. Conclusions Solid tumour NGS Molecular Profiling using paired tumour/blood samples can incidentally identify pathogenic germline mutations in cancer predisposition genes. Appropriate consent and genetic counselling support is crucial for NGS tumour Molecular Profiling using blood/tumour pairs.

John W. Gillespie - One of the best experts on this subject based on the ideXlab platform.

  • Molecular Profiling of cancer.
    Toxicologic pathology, 2004
    Co-Authors: John W. Gillespie, Michael R. Emmert-buck, Gallya Gannot, Michael A Tangrea, Mamoun Ahram, Carolyn J M Best, Verena E Bichsel, Emmanuel F Petricoin, Rodrigo F Chuaqui
    Abstract:

    The objective of Molecular Profiling of cancer is to determine the differential expression of genes and proteins from human tissue in the progression from normal precursor tissue to preneoplastic tissue to cancer in order to discover diagnostic, prognostic, and therapeutic markers. With the development of high-throughput analytical techniques such as microarrays and 2-D PAGE as well as the development of tools for cell procurement from histological sections such as laser capture microdissection (LCM), it is now possible to perform Molecular analyses on specific cell populations from tissue. Since recognition of specific cell populations is critical, there is a need to optimize fixation and embedding not only to improve preservation of biomolecules, but also to maintain excellent histology. We have shown that 70% ethanol fixation of prostate tissue improves the recovery of DNA, RNA, and proteins over routine formalin fixation and maintains histological quality comparable to formalin. There is also a need to develop new technologies in order to expand the range of tissue types that can be analyzed. The development and applications of Layered Expression Scanning (LES) for the Molecular analysis of whole tissue sections are discussed.

  • Handling of clinical tissue specimens for Molecular Profiling studies.
    Current issues in molecular biology, 2003
    Co-Authors: Isabel M. Leiva, Michael R. Emmert-buck, John W. Gillespie
    Abstract:

    The relationship between gene expression profiles and cellular phenotypes is an important aspect of functional genomics. Clinical tissue specimens will play a vital role in this effort. The usefulness of tissue for Molecular Profiling is significantly influenced by the manner of specimen handling. Crucial components of this process include the optimization of the methods of tissue fixation and embedding, not only to obtain excellent histological detail, but also to promote the elucidation of the gene and protein expression profiles. In this article, we describe handling of clinical specimens using whole-mount prostate as an example, the use of new high-throughput techniques that allow Molecular Profiling analysis and the use of a webbased 3-dimensional model to combine these data to make it available to clinicians and the research community. Complete protocols and additional discussion are available on the website, http://cgapmf.nih.gov.

Alexander J. Lazar - One of the best experts on this subject based on the ideXlab platform.

  • Molecular Profiling of sarcomas: new vistas for precision medicine
    Virchows Archiv, 2017
    Co-Authors: Tariq Al-zaid, Wei-lien Wang, Neeta Somaiah, Alexander J. Lazar
    Abstract:

    Sarcoma is a large and heterogeneous group of malignant mesenchymal neoplasms with significant histological overlap. Accurate diagnosis can be challenging yet important for selecting the appropriate treatment approach and prognosis. The currently torrid pace of new genomic discoveries aids our classification and diagnosis of sarcomas, understanding of pathogenesis, development of new medications, and identification of alterations that predict prognosis and response to therapy. Unfortunately, demonstrating effective targets for precision oncology has been elusive in most sarcoma types. The list of potential targets greatly outnumbers the list of available inhibitors at the present time. This review will discuss the role of Molecular Profiling in sarcomas in general with emphasis on selected entities with particular clinical relevance.