Institutes, Departments, and Laboratories :: Research

University of Texas MD Anderson Cancer Center

Comparison of Pinnacle and SameSpots for Spot Quantification and Differential Expression in 2-Dimensional Gel Electrophoresis Studies
Jeffrey S. Morris Sun, 15 Feb 2009 04:27:12 -0800
2-DE is an important method for proteomics. Accurate spot detection and quantification on the resulting images is a challenging task, but must be done effectively for the technology to fulfill its potential. Traditional analytical methods have significant weaknesses, including spot mismatching and missing data. These problems require time-consuming manual editing to correct, which dramatically decreases throughput and compromises the objectivity and reproducibility of the analysis. To address this issue, we developed Pinnacle, a new method that markedly improves spot detection and quantification precision. Another new method implemented in Progenesis SameSpots, a commercial 2-DE analysis product, has also been touted as an improvement upon traditional approaches. In this study, we compared Pinnacle and SameSpots in spot detection and precision of quantification using two different dilution series, and evaluated the detection of differentially expressed proteins in two differential expression experiments. We found that SameSpots at times had problems with spot delineation, while Pinnacle did not. While both Pinnacle and SameSpots showed marked improvement in precision of spot quantifications over conventional methods, Pinnacle yielded spot quantifications with greater validity and reliability than SameSpots. Pinnacle detected more differentially expressed proteins than SameSpots, which may be a result of its increased precision and improved spot delineation.
Statistical Issues in Proteomic Research
Jeffrey S. Morris Thu, 31 Jul 2008 11:03:24 -0700

Microproteomics: Analysis of protein diversity in small samples
Howard B. Gutstein Fri, 13 Jun 2008 14:38:53 -0700
Proteomics, the large-scale study of protein expression in organisms, offers the potential to evaluate global changes in protein expression and their post-translational modifications that take place in response to normal or pathological stimuli. One challenge has been the requirement for substantial amounts of tissue in order to perform comprehensive proteomic characterization. In heterogeneous tissues, such as brain, this has limited the application of proteomic methodologies. Efforts to adapt standard methods of tissue sampling, protein extraction, arraying, and identification are reviewed, with an emphasis on those appropriate to smaller samples ranging in size from several microliters down to single cells. The effects of miniaturization on these analyses are highlighted using neuroscience-related examples, as are statistical issues unique to the high-dimensional datasets generated by proteomic experiments.
Pinnacle: A Fast, Automatic Method for Detecting and Quantifying Protein Spots in 2-Dimensional Gel Electrophoresis Data
Jeffrey S. Morris Tue, 04 Dec 2007 09:44:53 -0800
Motivation: One of the key limitations for proteomic studies using 2-dimensional gel electrophoresis (2DE) is the lack of rapid, robust, and reproducible methods for detecting, matching, and quantifying protein spots. The most commonly used approaches involve first detecting spots and drawing spot boundaries on individual gels, then matching spots across gels, and finally quantifying each spot by calculating normalized spot volumes. This approach is time con-suming, error-prone, and frequently requires extensive manual edit-ing, which can unintentionally introduce bias into the results.Results: We introduce a new method for spot detection and quanti-fication called Pinnacle that is automatic, quick, sensitive and spe-cific, and yields spot quantifications that are reliable and precise. This method incorporates a spot definition that is based on simple, straightforward criteria rather than complex arbitrary definitions, and results in no missing data. Using dilution series for validation, we demonstrate Pinnacle outperformed two well-established 2DE analysis packages, proving to be more accurate and yielding smaller CVs. More accurate quantifications may lead to increased power for detecting differentially expressed spots, an idea supported by the results of our group comparison experiment. Our fast, automatic analysis method makes it feasible to conduct very large 2DE-based proteomic studies that are adequately powered to find important protein expression differences.Availability: Matlab code to implement Pinnacle is available from the authors upon request for non-commercial use.
Laser capture sampling and analytical issues in proteomics
Howard Gutstein Tue, 04 Dec 2007 09:35:54 -0800
Proteomics holds the promise of evaluating global changes in protein expression and post-translational modificaiton in response to environmental stimuli. However, difficulties in achieving cellular anatomic resolution and extracting specific types of proteins from cells have limited the efficacy of these techniques. Laser capture microdissection has provided a solution to the problem of anatomical resolution in tissues. New extraction methodologies have expanded the range of proteins identified in subsequent analyses. This review will examine the application of laser capture microdissection to proteomic tissue sampling, and subsequent extraction of these samples for differential expression analysis. Statistical and other quantitative issues important for the analysis of the highly complex datasets generated are also reviewed.
Statistical contributions to proteomic research
Jeffrey S. Morris Wed, 04 Apr 2007 12:55:09 -0700
Proteomic profiling has the potential to impact the diagnosis, prognosis, and treatment of various diseases. A number of different proteomic technologies are available that allow us to look at many proteins at once, and all of them yield complex data that raise significant quantitative challenges. Inadequate attention to these quantitative issues can prevent these studies from achieving their desired goals, and can even lead to invalid results. In this chapter, we describe various ways the involvement of statisticians or other quantitative scientists in the study team can contribute to the success of proteomic research, and we outline some of the key statistical principles that should guide the experimental design and analysis of such studies.

 

Subscribe to Cancer RSS feed

Addenbrookes Hospital: Oncology - Academic and research resource center serving the East Anglia region of England.

AMC Cancer Research Center - Non-profit institute dedicated to prevention located in Denver, Colorado. Includes current research, health information and other related resources.
Meta Description: [ AMC Cancer Research Center is a not-for-profit research institute dedicated to the prevention of cancer and other chronic diseases. ]

BC Cancer Agency - Provides a list of locations, patient information, services, information for health professionals, research and donations. Multiple sites in British Columbia, Canada.

Bergen Oral Cancer Group - Research center at the University of Bergen in Norway that focuses on the biology and causes of this condition.
Meta Description: [ UIB-The Centre for International Health-Education and research ]

British Columbia Cancer Research Center - Includes research information, publications, training opportunities and researcher profiles. Located in Vancouver, Canada.
Meta Description: [ BC Cancer Research Centre website has cancer research information, publications, training opportunities, and researcher profiles for scientists, postdoctoral fellows, and graduate students. ]

Cancer Institute of Iran - Located in Imam Khomeini hospital, Iran.

Cancer Research and Biostatistics - Non-profit organization utilizes the application of biostatistical principles and methods. Located in Seattle, Washington.

Cancer Research Center of Hawaii - University affiliate unites researchers, modern equipment and technology to improve prevention and treatment. Located in Honolulu, Hawaii.
Meta Description: [ Cancer Research Center of Hawaii: Unites top researchers, modern equipment and technology in improving cancer prevention and treatment. ]

Cancer Research UK Clinical Centre at Leeds - Areas include clinical trials, psychosocial oncology, biological and immunotherapy work, genetics and screening.

Cancer Stress and Immunity Research - Survivor and quality of life issues examined at Ohio State University. Offers a Meaning in Life survey.
Meta Description: [ Cancer stress research and cancer immunity research projects. Behavioral, biological and psychological cancer research. Stress and Immunity Cancer Projects. ]

City of Hope - Overview of the physicians, researchers and scientists working toward a cure for cancer and life threatening diseases. [California]
Meta Description: [ A leading Southern California biomedical research and treatment center, and hospital for cancer and other life-threatening diseases. ]

Cold Spring Harbor Laboratory: Cancer Research - Basic research facility devoted to the understanding of the fundamental biology of human cancer. [New York]

Fox Chase Cancer Center - Devoted to improving treatment through basic research, prevention research, cancer control and clinical medicine. Located in Philadelphia, Pennsylvania.
Meta Description: [ The mission of Fox Chase Cancer Center is to reduce the burden of human cancer through the pursuit of new knowledge in basic biological research; to conduct research specifically related to cancer causes, prevention, and treatment; to apply this knowledge to the prevention of cancer; and to rende... ]

Fred Hutchinson Cancer Research Center - Information for scientific researchers, patients and educators. Located in Seattle, Washington.
Meta Description: [ The mission of Fred Hutchinson Cancer Research Center is the elimination of cancer as a cause of human suffering and death. The center conducts research of the highest standards to improve prevention and treatment of cancer and related diseases. ]

In Silico Oncology Group - Development of computer models to optimize tumor therapy planning. Consortium includes the National Technical University of Athens in Zografos, Greece.

Irish Clinical Oncology Research Group - Information for physicians and patients about clinical research, with links to patient support groups. Located in Dublin, Ireland.
Meta Description: [ Ireland's cancer clinical trial organisation, dedicated to helping Irish patients gain early access to the latest cancer treatments through research. ICORG is a professional organisation which offers international agencies a fast track to the set-up and successful completion of high quality res... ]

Laboratory of Immunology and Biology of Metastasis - Research, resources, publications, links and personnel from this division of the Department of Experimental Pathology at the University of Bologna, Italy.
Meta Description: [ Laboratory of Immunology and Biology of Metastasis, Cancer Research Section, Department of Experimental Pathology, University of Bologna, Bologna, Italy ]

Meharry Medical College/Vanderbilt-Ingram Cancer Center Partnership - Encourages research aimed at prevention and improved care in minority and underserved populations.

NCI: Center for Cancer Research - Provides current research information for patients, physicians, and scientists. Conducts clinical trials at the National Institutes of Health in Bethesda, Maryland.

Rational Therapeutics Cancer Laboratories - Analysis of programmed cell death using the patient's own tumor cells to try to establish a treatment of choice. [California]
Meta Description: [ Rational Therapeutics provides laboratory analysis of cancer cells to determine the best chemotherapy drug combination for a patient, using the EVA chemosensitivity test based on apoptosis (programmed cell death). ]

404 Salk Institute for Biological Studies: Cancer Center - Research programs have included tumor virology, molecular, cell, and developmental biology. [California]

San Antonio Cancer Institute - University affiliate and associate of the Cancer Therapy and Research Center in Texas. Includes genetics, drug development, prevention and control.
Meta Description: [ The San Antonio Cancer Institute (SACI) represents the combined cancer research programs of the Cancer Therapy and Research Center (CTRC) and The University of Texas Health Science Center at San Antoino (UTHSCSA). Major research activities are underway in breast, prostrate and GI cancers, pediatr... ]

Southern Alberta Cancer Research Institute - Canadian organization that oversees scientists and physicians involved in laboratory-based studies, clinical trials, epidemiology and health services research.
Meta Description: [ The Southern Alberta Cancer Research Institute brings together researchers and physicians involved in laboratory based research, clinical trials, epidemiological research, health services research and others in an ongoing effort to further prevent, aid early detection of and improve treatments fo... ]

Stehlin Foundation for Cancer Research - Information about innovative approaches to cancer treatment; including Pancreatic cancer trials, desmoplastic small round cell tumor and nude mice research, and the camptothecin project.
Meta Description: [ Pancreatic cancer trials. Cancer clinic, oncology clinic. Breast cancer, breast cancer treatment. Innovative approaches to cancer treatment. ]

The Wistar Institute - Provides information about this NCI-designated Cancer Center and its orientation to research in basic science. Located in Philadelphia, Pennsylvania.

404 Van Andel Reseach Institute - Biomedical research facility with a mission to improve human health, beginning with a focus on cancer. [Michigan]
Meta Description: [ The Van Andel Research Institutute VARI ]

Walther Cancer Institute - Indianapolis, Indiana based organization which supports oncology projects in affiliation with several midwestern Universities.