3,194 research outputs found
Tests for finding complex patterns of differential expression in cancers: towards individualized medicine
BACKGROUND: Microarray studies in cancer compare expression levels between two or more sample groups on thousands of genes. Data analysis follows a population-level approach (e.g., comparison of sample means) to identify differentially expressed genes. This leads to the discovery of 'population-level' markers, i.e., genes with the expression patterns A > B and B > A. We introduce the PPST test that identifies genes where a significantly large subset of cases exhibit expression values beyond upper and lower thresholds observed in the control samples. RESULTS: Interestingly, the test identifies A > B and B < A pattern genes that are missed by population-level approaches, such as the t-test, and many genes that exhibit both significant overexpression and significant underexpression in statistically significantly large subsets of cancer patients (ABA pattern genes). These patterns tend to show distributions that are unique to individual genes, and are aptly visualized in a 'gene expression pattern grid'. The low degree of among-gene correlations in these genes suggests unique underlying genomic pathologies and high degree of unique tumor-specific differential expression. We compare the PPST and the ABA test to the parametric and non-parametric t-test by analyzing two independently published data sets from studies of progression in astrocytoma. CONCLUSIONS: The PPST test resulted findings similar to the nonparametric t-test with higher self-consistency. These tests and the gene expression pattern grid may be useful for the identification of therapeutic targets and diagnostic or prognostic markers that are present only in subsets of cancer patients, and provide a more complete portrait of differential expression in cancer
BioSunMS: a plug-in-based software for the management of patients information and the analysis of peptide profiles from mass spectrometry
<p>Abstract</p> <p>Background</p> <p>With wide applications of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), statistical comparison of serum peptide profiles and management of patients information play an important role in clinical studies, such as early diagnosis, personalized medicine and biomarker discovery. However, current available software tools mainly focused on data analysis rather than providing a flexible platform for both the management of patients information and mass spectrometry (MS) data analysis.</p> <p>Results</p> <p>Here we presented a plug-in-based software, BioSunMS, for both the management of patients information and serum peptide profiles-based statistical analysis. By integrating all functions into a user-friendly desktop application, BioSunMS provided a comprehensive solution for clinical researchers without any knowledge in programming, as well as a plug-in architecture platform with the possibility for developers to add or modify functions without need to recompile the entire application.</p> <p>Conclusion</p> <p>BioSunMS provides a plug-in-based solution for managing, analyzing, and sharing high volumes of MALDI-TOF or SELDI-TOF MS data. The software is freely distributed under GNU General Public License (GPL) and can be downloaded from <url>http://sourceforge.net/projects/biosunms/</url>.</p
Clinical decision modeling system
<p>Abstract</p> <p>Background</p> <p>Decision analysis techniques can be applied in complex situations involving uncertainty and the consideration of multiple objectives. Classical decision modeling techniques require elicitation of too many parameter estimates and their conditional (joint) probabilities, and have not therefore been applied to the problem of identifying high-performance, cost-effective combinations of clinical options for diagnosis or treatments where many of the objectives are unknown or even unspecified.</p> <p>Methods</p> <p>We designed a Java-based software resource, the Clinical Decision Modeling System (CDMS), to implement Naïve Decision Modeling, and provide a use case based on published performance evaluation measures of various strategies for breast and lung cancer detection. Because cost estimates for many of the newer methods are not yet available, we assume equal cost. Our use case reveals numerous potentially high-performance combinations of clinical options for the detection of breast and lung cancer.</p> <p>Results</p> <p>Naïve Decision Modeling is a highly practical applied strategy which guides investigators through the process of establishing evidence-based integrative translational clinical research priorities. CDMS is not designed for clinical decision support. Inputs include performance evaluation measures and costs of various clinical options. The software finds trees with expected emergent performance characteristics and average cost per patient that meet stated filtering criteria. Key to the utility of the software is sophisticated graphical elements, including a tree browser, a receiver-operator characteristic surface plot, and a histogram of expected average cost per patient. The analysis pinpoints the potentially most relevant pairs of clinical options ('critical pairs') for which empirical estimates of conditional dependence may be critical. The assumption of independence can be tested with retrospective studies prior to the initiation of clinical trials designed to estimate clinical impact. High-performance combinations of clinical options may exist for breast and lung cancer detection.</p> <p>Conclusion</p> <p>The software could be found useful in simplifying the objective-driven planning of complex integrative clinical studies without requiring a multi-attribute utility function, and it could lead to efficient integrative translational clinical study designs that move beyond simple pair wise competitive studies. Collaborators, who traditionally might compete to prioritize their own individual clinical options, can use the software as a common framework and guide to work together to produce increased understanding on the benefits of using alternative clinical combinations to affect strategic and cost-effective clinical workflows.</p
The Degree of Segmental Aneuploidy Measured by Total Copy Number Abnormalities Predicts Survival and Recurrence in Superficial Gastroesophageal Adenocarcinoma
Abstract Background: Prognostic biomarkers are needed for superficial gastroesophageal adenocarcinoma (EAC) to predict clinical outcomes and select therapy. Although recurrent mutations have been characterized in EAC, little is known about their clinical and prognostic significance. Aneuploidy is predictive of clinical outcome in many malignancies but has not been evaluated in superficial EAC
Proceedings from the Inaugural American Initiative in Mast Cell Diseases (AIM) Investigator Conference
The American Initiative in Mast Cell Diseases (AIM) held its inaugural investigator conference at Stanford University School of Medicine in May 2019. The overarching goal of this meeting was to establish a Pan-American organization of physicians and scientists with multidisciplinary expertise in mast cell disease. To serve this unmet need, AIM envisions a network where basic, translational, and clinical researchers could establish collaborations with both academia and biopharma to support the development of new diagnostic methods, enhanced understanding of the biology of mast cells in human health and disease, and the testing of novel therapies. In these AIM proceedings, we highlight selected topics relevant to mast cell biology and provide updates regarding the recently described hereditary alpha-tryptasemia. In addition, we discuss the evaluation and treatment of mast cell activation (syndromes), allergy and anaphylaxis in mast cell disorders, and the clinical and biologic heterogeneity of the more indolent forms of mastocytosis. Because mast cell disorders are relatively rare, AIM hopes to achieve a coordination of scientific efforts not only in the Americas but also in Europe by collaborating with the well-established European Competence Network on Mastocytosis.The research reported in this publication was supported by the National Center for Advancing Translational Sciences of the National Institutes of Health (NIH) (award no. R13TR002722 to J.G.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. We thank The Mast Cell Disease Society, Inc (TMS), a national 501c3 nonprofit, for their partnership and support of AIM, for patient-centered research, and for sponsoring international physicians at this inaugural meeting. J.G. expresses gratitude for the support of the Charles and Ann Johnson Foundation, the staff of the Stanford Mastocytosis Center, and the Stanford Cancer Institute Innovation Fund. M.C., J.J.L., and D.D.M. are supported in part by the Division of Intramural Research of the National Institute of Allergy and Infectious Diseases, NIH. D.F.D. is supported by the Asthma and Allergic Diseases Cooperative Research Centers Opportunity Fund (award no. U19AI07053 from the NIH). P.V. has been supported by the Austrian Science Fund (FWF) (grant nos. F4701-B20, F4704-B20, and P32470-B)
Non-Parametric Change-Point Method for Differential Gene Expression Detection
We proposed a non-parametric method, named Non-Parametric Change Point
Statistic (NPCPS for short), by using a single equation for detecting
differential gene expression (DGE) in microarray data. NPCPS is based on the
change point theory to provide effective DGE detecting ability.NPCPS used the data distribution of the normal samples as input, and detects
DGE in the cancer samples by locating the change point of gene expression
profile. An estimate of the change point position generated by NPCPS enables
the identification of the samples containing DGE. Monte Carlo simulation and
ROC study were applied to examine the detecting accuracy of NPCPS, and the
experiment on real microarray data of breast cancer was carried out to
compare NPCPS with other methods.Simulation study indicated that NPCPS was more effective for detecting DGE in
cancer subset compared with five parametric methods and one non-parametric
method. When there were more than 8 cancer samples containing DGE, the type
I error of NPCPS was below 0.01. Experiment results showed both good
accuracy and reliability of NPCPS. Out of the 30 top genes ranked by using
NPCPS, 16 genes were reported as relevant to cancer. Correlations between
the detecting result of NPCPS and the compared methods were less than 0.05,
while between the other methods the values were from 0.20 to 0.84. This
indicates that NPCPS is working on different features and thus provides DGE
identification from a distinct perspective comparing with the other mean or
median based methods
Search for the standard model Higgs boson in the H to ZZ to 2l 2nu channel in pp collisions at sqrt(s) = 7 TeV
A search for the standard model Higgs boson in the H to ZZ to 2l 2nu decay
channel, where l = e or mu, in pp collisions at a center-of-mass energy of 7
TeV is presented. The data were collected at the LHC, with the CMS detector,
and correspond to an integrated luminosity of 4.6 inverse femtobarns. No
significant excess is observed above the background expectation, and upper
limits are set on the Higgs boson production cross section. The presence of the
standard model Higgs boson with a mass in the 270-440 GeV range is excluded at
95% confidence level.Comment: Submitted to JHE
Measurement of the t t-bar production cross section in the dilepton channel in pp collisions at sqrt(s) = 7 TeV
The t t-bar production cross section (sigma[t t-bar]) is measured in
proton-proton collisions at sqrt(s) = 7 TeV in data collected by the CMS
experiment, corresponding to an integrated luminosity of 2.3 inverse
femtobarns. The measurement is performed in events with two leptons (electrons
or muons) in the final state, at least two jets identified as jets originating
from b quarks, and the presence of an imbalance in transverse momentum. The
measured value of sigma[t t-bar] for a top-quark mass of 172.5 GeV is 161.9 +/-
2.5 (stat.) +5.1/-5.0 (syst.) +/- 3.6(lumi.) pb, consistent with the prediction
of the standard model.Comment: Replaced with published version. Included journal reference and DO
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