10 Best Healthcare Data Sets With Examples Healthcare data sets include a vast amount of medical data, various measurements, financial data, statistical data, demographics of specific populations, and insurance data, to name just a few, gathered from various healthcare data sources. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. To learn more, visit the MITRE Open-Source Project Page for a list of the projects that you can contribute to, and check the contact section below for other opportunities at MITRE. Colorectal adenoma can develop into colorectal cancer. Genome-wide germline correlates of the epigenetic landscape of prostate cancer. Abida, W. et al. Similar concerns apply to molecular subtyping. Gentles, A. J. et al. Opin. The purpose of this study is to design and create a System Information On Inpatient Clinic Prima Husada Pacitan used to assist officers in managing patient data, data doctors who treat patients, keep the existing schedule data on Inpatient Clinical Prima Husada. and TCGA, as Barwick et al. Egevad, L., Delahunt, B., Srigley, J. R. & Samaratunga, H. International Society of Urological Pathology (ISUP) grading of prostate cancer - An ISUP consensus on contemporary grading. Eur. Anytime you go to a medical professional your data will be recorded by the doctors and nurses for their internal databases. Gene expression patterns are correlated across datasets. Syntheas Generic Module Framework (GMF) enables the modeling of various diseases and conditions that contribute to the medical history of synthetic patients. Prognostic risk scores are calculated from a select set of genes; thus, missing genes and assay platform differences can impact the reliability of the computed scores67. PubMed We evaluated the overall copy number landscape and found that independent datasets showed highly similar patterns of copy number gain and loss in primary tumors (Taylor et al.4,39, TCGA2, Baca et al.58) (Fig. and Barwick et al.42,43 While datasets with gene expression from metastatic tumors are few, the pattern of correlation between Chandran et al.54,55, Abida et al.56, and Taylor et al.4,39 were lower, likely due to the intrinsic heterogeneity of measuring gene expression from samples in the metastatic setting. I don't need to have access to any code, but I would be willing to purchase one if it . The processed MAE objects exported from the package are the main focus of the package; however, from a developer point of view, they also offer natural potential for future extensions such as: a) adding new studies and exporting them as new MAE objects using the pipelines developed in curatedPCaData; b) supplementing the existing MAE slots with newly derived variables or even adding other primary omics data;or c) extending the existing clinical metadata fields to include new fields. was measured using a custom Agilent microarray. The images or other third party material in this article are included in the articles Creative Commons license, unless indicated otherwise in a credit line to the material. All the code used to generate the processed datasets, as well as the resulting R package are available openly on GitHub (https://github.com/Syksy/curatedPCaData). Integrative genomic profiling of human prostate cancer. The immunedeconv-package26 has proven to be a popular choice as a wrapper R package providing harmonized access to multiple popular cell type deconvolution methods such as EPIC27, ESTIMATE28, MCP-counter29, quanTIseq30, and xCell31. Proc. In the meantime, to ensure continued support, we are displaying the site without styles Improve patient outcomes and team performance with fast, easy access to secure health data. Barwick, B. G. et al. There were three methods that calculated endothelial cell abundance scores (EPIC27, MCP-counter29, and xCell31). This was performed by identifying the study in curatedPCaData that contained the most genes belonging to the scoring method. Frontiers | Molecular characterization of colorectal adenoma and The population size is 3+ million patients. The resulting data is free from cost, privacy, and security restrictions, enabling research with Health IT data that is otherwise legally or practically unavailable. Database Examples Introduction | MongoDB USA 103, 1099110996 (2006). Baca, S. C. et al. They are headquartered in United Shaip offers a human-in-the-loop data platform and services to support all aspects of managing training data for AI/ML development. Commun. Cell 161, 12151228 (2015). (b) Oncoprints (left side) for select prostate cancer-associated genes are displayed across datasets. Mutual exclusivity (right side) was calculated using Fishers exact test (*p<0.05). Wallace, T. A. et al. Sci. JCO Precis Oncol 2017 (2017). Cancer 41, 858887 (2005). 12, 245255 (2011). The Agency for Healthcare Research and Quality (AHRQ) presents the dashboards of patient safety data received for analysis and publication in the Network of Patient Safety Databases (NPSD). Unraveling the Role of Angiogenesis in Cancer Ecosystems. Genomic and transcriptomic data have been generated across a wide range of prostate cancer (PCa) study cohorts. Overall, these benchmarking analyses show that the molecular features in primary prostate cancer are generally reliably and consistently measured across datasets. NICE Advice - Prolaris gene expression assay for assessing long-term risk of prostate cancer progression: NICE (2016). Sample Patient Database. A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Zenodo https://doi.org/10.5281/zenodo.7995819 (2023). Free sample DICOM files | .DCM archive from CT/MRI Scans - Medimodel We also tested for patterns of co-occurrence and mutual exclusivity between these genes. The International Genomics Consortium. For example, the use of high-dimensional molecular data is dependent on a thorough validation of the statistical models in diverse datasets. Uncover data-driven insights that improve your clinical decision-making and care experiences while transforming healthcare operations and outcomes. & Abramovitz, M. GEO, https://identifiers.org/geo:GSE18655 (2009). Multiple studies reported Gleason as the sum of major+minor Gleason grades or a grade group (6, 7, 8), thus groupings were offered as an endpoint with an equal level of granularity, while a finer level of detail was offered in alternate clinical metadata columns when available. From data collection, lic At Diaceutics we believe that every patient should have access to the right treatment at the right time In addition to downloading raw data from GEO, GEOquery was used for downloading the latest array-specific annotations and all three R packages were further utilized to download clinical metadata accompanying the raw data. We used TCGA gene expression for benchmarking inferred risk scores from Decipher. The highlighted genes are the top five up- and down-regulated genes identified across the four datasets using Fishers method to combine p-values. J. Stat. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in The Molecular Taxonomy of Primary Prostate Cancer. In addition to the primary omic data types themselves, such as gene expression measurements by RNA sequencing or microarrays, there are now an array of innovative approaches to develop molecular signatures and deconvolution methods to estimate cell types present in bulk tissue. Tables 2 and 3 show the mean and mean percent scores of the predictors and outcomes of patient safety culture as measured on the 12 HSOPSC dimensions. Cancer Res. 41, D991995 (2013). 3b). Herlemann, A. et al. For example, Weiner et al.40,41 studied ethnicity-related PCa-trends, thus the patients had accurate demographics-related metadata commonly available, while samples were just described as being primary tumors. contributed R vignettes; T.D.L., V.S., A.C.S., J.H.C., F.C.F.C., K.S., T.G., B.L.F., S.T., J.C.C. Thank you for visiting nature.com. Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy. The MITRE Corporation is a not-for-profit company working in the public interest, operating multiple Federally Funded Research and Development Centers (FFRDCs). Nat. The Spearman correlation was calculated for the correlation patterns between datasets and displayed for AR (left side) and ERG (right side) in both primary and metastatic tumors. Article 1c were calculated using Spearmans rank correlation. A 17-gene assay to predict prostate cancer aggressiveness in the context of Gleason grade heterogeneity, tumor multifocality, and biopsy undersampling. PubMed CAS CAS There is growing interest in using data captured in electronic health records (EHRs) for patient registries. PubMed 35, 19911998 (2017). The cross-study analyses presented herein demonstrate the strength of leveraging multiple studies in PCa; however, it is important to understand and incorporate relative differences between studies, their aims, design, and the underlying composition in such data analysis. For reproducibility and to provide users with example code, analyses and results presented in the following sections are made available as vignettes through the curatedPCaData package. For data with raw copy number alteration available, these were processed using rCGH (R package version v1.26.0) with functions readAgilent, adjustSignal, segmentCGH, and EMnormalize. The mutational landscape of lethal castration-resistant prostate cancer. The omic data types were preprocessed and annotated, and clinical variables were mapped to a common data dictionary to ensure consistent annotation of the samples. Correspondence to Br. Copyright 2017 The MITRE Corporation | Approved for Public Release; Distribution Unlimited. Article Sherman, B. T. et al. To determine the impact that gene missingness on the precomputed scores would have on those studies without all genes, we benchmarked the Oncotype DX66, Decipher11, and Prolaris10 risk scores and the AR score. & Butte, A. J. xCell: digitally portraying the tissue cellular heterogeneity landscape. SyntheaTM is driven by a global community of developers, academics and healthcare experts. visualized data and analyses; T.G., B.L.F., S.T., J.C.C. Nucleic Acids Res. ADS 70, 64486455 (2010). PLoS One 8, e66855 (2013). Background: Osteoarthritis is a leading cause of pain and disability. The response variable is remiss, which has the value 1 if the patient experienced cancer remission, and 0 otherwise. Zenodo https://doi.org/10.5281/zenodo.7996377 (2023). Cox proportional hazard models and Kaplan-Meier (KM) curves were fitted with survival (R package version v3.3-1) and plotted using survminer (R package version v0.4.9), and the corresponding p-values were calculated using log-rank tests. Hieronymus, H., Schultz, N., Taylor, B. S. & Sawyers, C. L. GEO https://identifiers.org/geo:GSE54691 (2014). A harmonized resource of integrated prostate cancer clinical, -omic, and signature features, https://doi.org/10.1038/s41597-023-02335-4. We followed uniform naming conventions for all the metadata fields and leveraged data in the original publications to obtain maximum information in case information wasnt readily available in these public repositories38. While deconvolution methods vary in the types of cells that they estimate, the overall methodology has been shown to produce robust predictions and comparison between methods have been shown to be mostly consistent and robust, which is covered in depth by Sturm et al.32 and was a major motivation to develop the immunedeconv R package. GEO, https://identifiers.org/geo:GSE21032 (2010). Research projects also provide patient data as well as historical records and family medical information. Gene expression patterns across datasets. Houlahan, K. E. et al. Most neurologists already interact with databases frequently. This retrospective cohort study was conducted using data from an integrated SuValue database, which includes 221 hospitals across China covering more than 200,000 of population with longitudinal follow-up to 10 . Spearmans rank correlation was used to assess the non-linear association between endothelial cell scores in Fig. Create an issue on our github page, or send us an email. 75, 10211034 (2015). Healthcare | Microsoft Power BI PubMed Bernau, C. et al. Downloads | Synthea - MITRE Due to the different platforms (sequencing, different brands, and versions of microarrays) used to assess gene expression, not all datasets have the same set of genes. Mermel, C. H. et al. Signal. ADS A harmonized resource of integrated prostate cancer clinical, -omic The resulting datasets were thus standardized to be as comparable as possible, while retaining details essential to the studies. It basically calls every touchpoint that a given patient has with the healthcare system. Personal health records and patient portals are powerful tools for managing your health. J. Cancer Res. Prolaris, a 34-gene signature, also proved to be highly robust whereby removing 10 random genes from the Prolaris gene list in the Kunderfranco et al. Cross-study validation for the assessment of prediction algorithms. Gene expression, as measured by microarrays or RNA sequencing, is the most common molecular measurement in the curatedPCaData package (Table1). PubMed On the other hand, Friedrich et al.46,47, Hieronymus et al.6,74, ICGC-CA75, and TCGA2 also reported overall survival, but they present a more indolent form of the disease with a lower count of deaths, making survival modeling more challenging. Furthermore, biochemical recurrence is often used as a surrogate for progression-free survival and is reported in Barwick et al.42,43, Sun et al.51,52, Taylor et al.4,39 and TCGA2; of these four datasets, we focused our Cox models for recurrence on Taylor et al. The TCGA Prostate Cancer (PRAD) dataset was downloaded from Xena Browser85, due to better data quality and providing tumor samples and normal samples separately, instead of providing relative tumor to normal gene expression found in cBioPortal processed data. Google Scholar. There are 20 genes that are used to calculate the AR score and we found that by removing 10 at random still provides an average AR score with a correlation of 0.930 (median=0.935; FigureS2d). Cancer Genome Atlas Research Network. NPSD Dashboards. Hieronymus, H. et al. Patient data is used by both medical professionals and businesses: Despite the differences in reported variables, a considerable amount of clinical information is made available across independent datasets to draw associations with molecular features. 1b). Leveraging the MAE class, we supply the data in the curatedPCaData R package (https://github.com/Syksy/curatedPCaData). Hospital Data | NIH Library Patient samples with a high endothelial score show significantly shorter times to biochemical relapse (Fig. 2120, 223232 (2020). Google Scholar. 77, e39e42 (2017). Benefits of this research is to provide convenience to the officers for patient . Namely, we conveniently provide Decipher35, Oncotype DX36, and Prolaris37 risk scores as well as Androgen Receptor (AR) scores2. Biomarkers Prev. Google Scholar. Barrett, T. et al. Cancer Res. Cell Biol. Urol. HCUP-US NIS Overview The explanatory variables are the results from blood tests and physiological measurements on each patient. Thus,. For these genes, we found the copy number alteration and mutation patterns to be consistent across datasets (Fig. The consistent data processing and harmonization of gene names across datasets provide a ready to use resource for meta-analysis. as the benchmarking study for Prolaris (Table2). Oncogene 32, 23152324, 2324.e14 (2013). The package provides open and accessible data and analysis pipelines with maximum flexibility for data analysts and prostate cancer researchers. You can download the MS Access database (and others) at box.com. 71, 24762487 (2011). The HCAHPS survey The sample DICOM files have been anonymised of all patient information so can be used freely. For each dataset, we calculated the Pearson correlation of all genes within the dataset to Androgen Receptor (AR) and the ETS transcription factor, ERG. Additional consideration should be given to how studies reported the common end-point of Gleason grade. Sample Database for Patient Tracking Created Date: 4/19/2017 2:40:06 PM . Patient records help diagnose individuals with medical issues. used a very targeted custom DASL gene panel (<1,000 genes) making cell composition estimation unreliable for most methods. With a virtually limitless supply of synthetic patients, Synthea provides the foundational health data that researchers, clinicians, policy makers and software developers need to architect the next generation of Health IT solutions. Laajala, T. D. et al. Patient Data: Best Datasets & Databases 2023 | Datarade Sturm, G., Finotello, F. & List, M. Immunedeconv: An R Package for Unified Access to Computational Methods for Estimating Immune Cell Fractions from Bulk RNA-Sequencing Data. Rev. SQL Hospital Database - Exercises, Practice, Solution - w3resource Normally, that would be a tough job for a database. Sample Database: hospital With the help of a Hospital Database, this exercises will help you undestand simple SQL select queries to advanced multi table JOIN queries.
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