The Experts below are selected from a list of 21468 Experts worldwide ranked by ideXlab platform
Jan M Orenstein - One of the best experts on this subject based on the ideXlab platform.
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an informatics model for tissue banks lessons learned from the cooperative prostate cancer tissue resource
BMC Cancer, 2006Co-Authors: Ashokkumar A Patel, Andre Kajdacsyballa, Jules J Berman, Milton W Datta, Rajiv Dhir, John R Gilbertson, Jonathan Melamed, Anil V Parwani, Rajnish Gupta, Jan M OrensteinAbstract:Background Advances in molecular biology and growing requirements from Biomarker Validation studies have generated a need for tissue banks to provide quality-controlled tissue samples with standardized clinical annotation. The NCI Cooperative Prostate Cancer Tissue Resource (CPCTR) is a distributed tissue bank that comprises four academic centers and provides thousands of clinically annotated prostate cancer specimens to researchers. Here we describe the CPCTR information management system architecture, common data element (CDE) development, query interfaces, data curation, and quality control.
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an informatics model for tissue banks lessons learned from the cooperative prostate cancer tissue resource
BMC Cancer, 2006Co-Authors: Ashokkumar A Patel, Andre Kajdacsyballa, Jules J Berman, Milton W Datta, Rajiv Dhir, John R Gilbertson, Jonathan Melamed, Anil V Parwani, Rajnish Gupta, Jan M OrensteinAbstract:Advances in molecular biology and growing requirements from Biomarker Validation studies have generated a need for tissue banks to provide quality-controlled tissue samples with standardized clinical annotation. The NCI Cooperative Prostate Cancer Tissue Resource (CPCTR) is a distributed tissue bank that comprises four academic centers and provides thousands of clinically annotated prostate cancer specimens to researchers. Here we describe the CPCTR information management system architecture, common data element (CDE) development, query interfaces, data curation, and quality control. Data managers review the medical records to collect and continuously update information for the 145 clinical, pathological and inventorial CDEs that the Resource maintains for each case. An Access-based data entry tool provides de-identification and a standard communication mechanism between each group and a central CPCTR database. Standardized automated quality control audits have been implemented. Centrally, an Oracle database has web interfaces allowing multiple user-types, including the general public, to mine de-identified information from all of the sites with three levels of specificity and granularity as well as to request tissues through a formal letter of intent. Since July 2003, CPCTR has offered over 6,000 cases (38,000 blocks) of highly characterized prostate cancer biospecimens, including several tissue microarrays (TMA). The Resource developed a website with interfaces for the general public as well as researchers and internal members. These user groups have utilized the web-tools for public query of summary data on the cases that were available, to prepare requests, and to receive tissues. As of December 2005, the Resource received over 130 tissue requests, of which 45 have been reviewed, approved and filled. Additionally, the Resource implemented the TMA Data Exchange Specification in its TMA program and created a computer program for calculating PSA recurrence. Building a biorepository infrastructure that meets today's research needs involves time and input of many individuals from diverse disciplines. The CPCTR can provide large volumes of carefully annotated prostate tissue for research initiatives such as Specialized Programs of Research Excellence (SPOREs) and for Biomarker Validation studies and its experience can help development of collaborative, large scale, virtual tissue banks in other organ systems.
Ruedi Aebersold - One of the best experts on this subject based on the ideXlab platform.
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using data independent high resolution mass spectrometry in protein Biomarker research perspectives and clinical applications
Proteomics Clinical Applications, 2015Co-Authors: Tatjana Sajic, Ruedi Aebersold, Yansheng LiuAbstract:In medicine, there is an urgent need for protein Biomarkers in a range of applications that includes diagnostics, disease stratification, and therapeutic decisions. One of the main technologies to address this need is MS, used for protein Biomarker discovery and, increasingly, also for protein Biomarker Validation. Currently, data-dependent analysis (also referred to as shotgun proteomics) and targeted MS, exemplified by SRM, are the most frequently used mass spectrometric methods. Recently developed data-independent acquisition techniques combine the strength of shotgun and targeted proteomics, while avoiding some of the limitations of the respective methods. They provide high-throughput, accurate quantification, and reproducible measurements within a single experimental setup. Here, we describe and review data-independent acquisition strategies and their recent use in clinically oriented studies. In addition, we also provide a detailed guide for the implementation of SWATH-MS (where SWATH is sequential window acquisition of all theoretical mass spectra)-one of the data-independent strategies that have gained wide application of late.
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Biomarker Validation in blood specimens by selected reaction monitoring mass spectrometry of N-glycosites.
Methods in molecular biology (Clifton N.J.), 2011Co-Authors: Reto Ossola, Oliver Rinner, Paola Picotti, Ralph Schiess, Lukas Reiter, Ruedi AebersoldAbstract:Targeted mass spectrometry using selected reaction monitoring (SRM) has emerged as the method of choice for the Validation in blood serum, plasma, or other clinically relevant specimens of Biomarker candidates arising from comparative proteomics or other discovery strategies. Here, we describe a method in which N-glycosites are selectively enriched from biological specimens by solid phase capture and PNGase F release, and then analyzed by SRM. Focusing the highly sensitive targeted mass spectrometry method on a subproteome enriched for secreted and shed proteins reproducibly identifies and quantifies such proteins in serum and plasma at the low nanogram per milliliter (ng/mL) concentration range. This protocol is intended to give an introduction to SRM-based targeted mass spectrometry with a special focus on the Validation of Biomarker candidates.
Ashokkumar A Patel - One of the best experts on this subject based on the ideXlab platform.
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an informatics model for tissue banks lessons learned from the cooperative prostate cancer tissue resource
BMC Cancer, 2006Co-Authors: Ashokkumar A Patel, Andre Kajdacsyballa, Jules J Berman, Milton W Datta, Rajiv Dhir, John R Gilbertson, Jonathan Melamed, Anil V Parwani, Rajnish Gupta, Jan M OrensteinAbstract:Background Advances in molecular biology and growing requirements from Biomarker Validation studies have generated a need for tissue banks to provide quality-controlled tissue samples with standardized clinical annotation. The NCI Cooperative Prostate Cancer Tissue Resource (CPCTR) is a distributed tissue bank that comprises four academic centers and provides thousands of clinically annotated prostate cancer specimens to researchers. Here we describe the CPCTR information management system architecture, common data element (CDE) development, query interfaces, data curation, and quality control.
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an informatics model for tissue banks lessons learned from the cooperative prostate cancer tissue resource
BMC Cancer, 2006Co-Authors: Ashokkumar A Patel, Andre Kajdacsyballa, Jules J Berman, Milton W Datta, Rajiv Dhir, John R Gilbertson, Jonathan Melamed, Anil V Parwani, Rajnish Gupta, Jan M OrensteinAbstract:Advances in molecular biology and growing requirements from Biomarker Validation studies have generated a need for tissue banks to provide quality-controlled tissue samples with standardized clinical annotation. The NCI Cooperative Prostate Cancer Tissue Resource (CPCTR) is a distributed tissue bank that comprises four academic centers and provides thousands of clinically annotated prostate cancer specimens to researchers. Here we describe the CPCTR information management system architecture, common data element (CDE) development, query interfaces, data curation, and quality control. Data managers review the medical records to collect and continuously update information for the 145 clinical, pathological and inventorial CDEs that the Resource maintains for each case. An Access-based data entry tool provides de-identification and a standard communication mechanism between each group and a central CPCTR database. Standardized automated quality control audits have been implemented. Centrally, an Oracle database has web interfaces allowing multiple user-types, including the general public, to mine de-identified information from all of the sites with three levels of specificity and granularity as well as to request tissues through a formal letter of intent. Since July 2003, CPCTR has offered over 6,000 cases (38,000 blocks) of highly characterized prostate cancer biospecimens, including several tissue microarrays (TMA). The Resource developed a website with interfaces for the general public as well as researchers and internal members. These user groups have utilized the web-tools for public query of summary data on the cases that were available, to prepare requests, and to receive tissues. As of December 2005, the Resource received over 130 tissue requests, of which 45 have been reviewed, approved and filled. Additionally, the Resource implemented the TMA Data Exchange Specification in its TMA program and created a computer program for calculating PSA recurrence. Building a biorepository infrastructure that meets today's research needs involves time and input of many individuals from diverse disciplines. The CPCTR can provide large volumes of carefully annotated prostate tissue for research initiatives such as Specialized Programs of Research Excellence (SPOREs) and for Biomarker Validation studies and its experience can help development of collaborative, large scale, virtual tissue banks in other organ systems.
Anil V Parwani - One of the best experts on this subject based on the ideXlab platform.
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the development and deployment of common data elements for tissue banks for translational research in cancer an emerging standard based approach for the mesothelioma virtual tissue bank
BMC Cancer, 2008Co-Authors: Sambit K Mohanty, Anil V Parwani, Amita T Mistry, Waqas Amin, Andrew K Pople, Linda Schmandt, Sharon Winters, Erin Milliken, Nancy B Whelan, Ghada N FarhatAbstract:Background Recent advances in genomics, proteomics, and the increasing demands for Biomarker Validation studies have catalyzed changes in the landscape of cancer research, fueling the development of tissue banks for translational research. A result of this transformation is the need for sufficient quantities of clinically annotated and well-characterized biospecimens to support the growing needs of the cancer research community. Clinical annotation allows samples to be better matched to the research question at hand and ensures that experimental results are better understood and can be verified. To facilitate and standardize such annotation in bio-repositories, we have combined three accepted and complementary sets of data standards: the College of American Pathologists (CAP) Cancer Checklists, the protocols recommended by the Association of Directors of Anatomic and Surgical Pathology (ADASP) for pathology data, and the North American Association of Central Cancer Registry (NAACCR) elements for epidemiology, therapy and follow-up data. Combining these approaches creates a set of International Standards Organization (ISO) – compliant Common Data Elements (CDEs) for the mesothelioma tissue banking initiative supported by the National Institute for Occupational Safety and Health (NIOSH) of the Center for Disease Control and Prevention (CDC).
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an informatics model for tissue banks lessons learned from the cooperative prostate cancer tissue resource
BMC Cancer, 2006Co-Authors: Ashokkumar A Patel, Andre Kajdacsyballa, Jules J Berman, Milton W Datta, Rajiv Dhir, John R Gilbertson, Jonathan Melamed, Anil V Parwani, Rajnish Gupta, Jan M OrensteinAbstract:Background Advances in molecular biology and growing requirements from Biomarker Validation studies have generated a need for tissue banks to provide quality-controlled tissue samples with standardized clinical annotation. The NCI Cooperative Prostate Cancer Tissue Resource (CPCTR) is a distributed tissue bank that comprises four academic centers and provides thousands of clinically annotated prostate cancer specimens to researchers. Here we describe the CPCTR information management system architecture, common data element (CDE) development, query interfaces, data curation, and quality control.
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an informatics model for tissue banks lessons learned from the cooperative prostate cancer tissue resource
BMC Cancer, 2006Co-Authors: Ashokkumar A Patel, Andre Kajdacsyballa, Jules J Berman, Milton W Datta, Rajiv Dhir, John R Gilbertson, Jonathan Melamed, Anil V Parwani, Rajnish Gupta, Jan M OrensteinAbstract:Advances in molecular biology and growing requirements from Biomarker Validation studies have generated a need for tissue banks to provide quality-controlled tissue samples with standardized clinical annotation. The NCI Cooperative Prostate Cancer Tissue Resource (CPCTR) is a distributed tissue bank that comprises four academic centers and provides thousands of clinically annotated prostate cancer specimens to researchers. Here we describe the CPCTR information management system architecture, common data element (CDE) development, query interfaces, data curation, and quality control. Data managers review the medical records to collect and continuously update information for the 145 clinical, pathological and inventorial CDEs that the Resource maintains for each case. An Access-based data entry tool provides de-identification and a standard communication mechanism between each group and a central CPCTR database. Standardized automated quality control audits have been implemented. Centrally, an Oracle database has web interfaces allowing multiple user-types, including the general public, to mine de-identified information from all of the sites with three levels of specificity and granularity as well as to request tissues through a formal letter of intent. Since July 2003, CPCTR has offered over 6,000 cases (38,000 blocks) of highly characterized prostate cancer biospecimens, including several tissue microarrays (TMA). The Resource developed a website with interfaces for the general public as well as researchers and internal members. These user groups have utilized the web-tools for public query of summary data on the cases that were available, to prepare requests, and to receive tissues. As of December 2005, the Resource received over 130 tissue requests, of which 45 have been reviewed, approved and filled. Additionally, the Resource implemented the TMA Data Exchange Specification in its TMA program and created a computer program for calculating PSA recurrence. Building a biorepository infrastructure that meets today's research needs involves time and input of many individuals from diverse disciplines. The CPCTR can provide large volumes of carefully annotated prostate tissue for research initiatives such as Specialized Programs of Research Excellence (SPOREs) and for Biomarker Validation studies and its experience can help development of collaborative, large scale, virtual tissue banks in other organ systems.
Jennifer E Van Eyk - One of the best experts on this subject based on the ideXlab platform.
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an empirical approach to signature peptide choice for selected reaction monitoring quantification of uromodulin in urine
Clinical Chemistry, 2016Co-Authors: Eric Grote, Jennifer E Van Eyk, Jie Zhu, Christine Jelinek, Anna Kottgen, Josef CoreshAbstract:BACKGROUND: Many avenues have been proposed for a seamless transition between Biomarker discovery data and selected reaction monitoring (SRM) assays for Biomarker Validation. Unfortunately, studies with the abundant urinary protein uromodulin have shown that these methods do not converge on a consistent set of surrogate peptides for targeted mass spectrometry. As an alternative, we present an empirical peptide selection work flow for robust protein quantification. METHODS: We compared the relative SRM signal intensity of 12 uromodulin-derived peptides between tryptic digests of 9 urine samples. Pairwise CVs between the 12 peptides were 0.19–0.99. We used a correlation matrix to identify peptides that reproducibly tracked the amount of uromodulin protein and selected 4 peptides with robust and highly correlated SRM signals. Absolute quantification was performed with stable isotope–labeled versions of these peptides as internal standards and a standard curve prepared from a tryptic digest of purified uromodulin. RESULTS: Absolute quantification of uromodulin in 40 clinical urine samples yielded interpeptide correlations of ≥0.984 and correlations of ≥0.912 with ELISA data. The SRM assays were linear over >3 orders of magnitude and had typical interdigest CVs of <10%, interinjection CVs of <7%, and intertransition CVs of <7%. CONCLUSIONS: Comparing the apparent abundance of a plurality of peptides derived from the same target protein makes it possible to select signature peptides that are unaffected by the unpredictable confounding factors inevitably present in biological samples.
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multiplex assays for Biomarker research and clinical application translational science coming of age
Proteomics Clinical Applications, 2010Co-Authors: Florian S Schoenhoff, William J Savage, Pingbo Zhang, Jennifer E Van EykAbstract:Over the last decade, translational science has come into the focus of academic medicine, and significant intellectual and financial efforts have been made to initiate a multitude of bench-to-bedside projects. The quest for suitable Biomarkers that will significantly change clinical practice has become one of the biggest challenges in translational medicine. Quantitative measurement of proteins is a critical step in Biomarker discovery. Assessing a large number of potential protein Biomarkers in a statistically significant number of samples and controls still constitutes a major technical hurdle. Multiplexed analysis offers significant advantages regarding time, reagent cost, sample requirements and the amount of data that can be generated. The two contemporary approaches in multiplexed and quantitative Biomarker Validation, antibody-based immunoassays and MS-based multiple (or selected) reaction monitoring, are based on different assay principles and instrument requirements. Both approaches have their own advantages and disadvantages and therefore have complementary roles in the multi-staged Biomarker verification and Validation process. In this review, we discuss quantitative immunoassay and multiple reaction monitoring/selected reaction monitoring assay principles and development. We also discuss choosing an appropriate platform, judging the performance of assays, obtaining reliable, quantitative results for translational research and clinical applications in the Biomarker field.