CEBPA mutations are of prognostic relevance in acute myeloid leukemia (AML) and are currently detected using a combination of denaturing high-performance liquid chromatography (DHPLC), gene scan/fragment length analysis, and direct Sanger sequencing. Next-generation deep pyrosequencing, principally, allows for the highly sensitive detection of molecular mutations. However, standard 454 chemistry laboratory procedures lack efficient amplification of guanine-cytosine (GC)-rich amplicons during the emulsion PCR (emPCR) steps allowing direct massively parallel clonal amplification of PCR products.
View Article and Find Full Text PDFUnlabelled: The R453Plus1Toolbox is an R/Bioconductor package for the analysis of 454 Sequencing data. Projects generated with Roche's data analysis software can be imported into R allowing advanced and customized analyses within the R/Bioconductor environment for sequencing data. Several methods were implemented extending the current functionality of Roche's software.
View Article and Find Full Text PDFBackground: Survival or outcome information is important for clinical routine as well as for clinical research and should be collected completely, timely and precisely. This information is relevant for multiple usages including quality control, clinical trials, observational studies and epidemiological registries. However, the local hospital information system (HIS) does not support this documentation and therefore this data has to generated by paper based or spreadsheet methods which can result in redundantly documented data.
View Article and Find Full Text PDFThe most frequent translocation t(8;21) in acute myeloid leukemia (AML) generates the chimeric AML1/ETO protein, which blocks differentiation and induces self-renewal in hematopoietic progenitor cells. The underlying mechanisms mediating AML1/ETO-induced self-renewal are largely unknown. Using expression microarray analysis, we identified the Groucho-related amino-terminal enhancer of split (AES) as a consistently up-regulated AML1/ETO target.
View Article and Find Full Text PDFEpigenetic changes play a crucial role in leukemogenesis. HDACs are frequently recruited to target gene promoters by balanced translocation derived oncogenic fusion proteins. As important epigenetic effector mechanisms, histone deacetylases (HDAC) have emerged as potential therapeutic targets.
View Article and Find Full Text PDFBackground: Visualization of DNA microarray data in two or three dimensional spaces is an important exploratory analysis step in order to detect quality issues or to generate new hypotheses. Principal Component Analysis (PCA) is a widely used linear method to define the mapping between the high-dimensional data and its low-dimensional representation. During the last decade, many new nonlinear methods for dimension reduction have been proposed, but it is still unclear how well these methods capture the underlying structure of microarray gene expression data.
View Article and Find Full Text PDFBackground: The pathology report of radical prostatectomy specimens plays an important role in clinical decisions and the prognostic evaluation in Prostate Cancer (PCa). The anatomical schema is a helpful tool to document PCa extension for clinical and research purposes. To achieve electronic documentation and analysis, an appropriate documentation model for anatomical schemas is needed.
View Article and Find Full Text PDFStud Health Technol Inform
December 2010
Design and implementation of healthcare information systems affect both computer scientists and health care professionals. In this paper we present our approach to integrate the management of information systems in the education of healthcare professionals and computer scientists alike. We designed a multidisciplinary course for medical and informatics students to provide them with practical experience concerning the design and implementation of medical information systems.
View Article and Find Full Text PDFStud Health Technol Inform
December 2010
Information about the quality of life from patients being treated in routine medical care is important for the attending physician. This data is also needed in research for example to evaluate the therapy and the course of the disease respectively. Especially skin diseases often negatively affect the quality of life.
View Article and Find Full Text PDFPurpose: Chronic myelomonocytic leukemia (CMML) is a clonal hematopoietic malignancy that is characterized by features of both a myeloproliferative neoplasm and a myelodysplastic syndrome. Thus far, data on a comprehensive cytogenetic or molecular genetic characterization are limited.
Patients And Methods: Here, we analyzed 81 thoroughly characterized patients with CMML (CMML type 1, n = 45; CMML type 2, n = 36) by applying next-generation sequencing (NGS) technology to investigate CBL, JAK2, MPL, NRAS, and KRAS at known mutational hotspot regions.
The World Health Organization classification of acute myeloid leukemia (AML) is hierarchically structured and integrates genetics, data on patients' history, and multilineage dysplasia (MLD). The category "AML with myelodysplastic syndrome (MDS)-related changes" (AML-MRC) is separated from "AML not otherwise specified" (AML-NOS) by presence of MLD, MDS-related cytogenetics, or history of MDS or MDS/myeloproliferative neoplasm (MPN). We analyzed 408 adult patients categorized as AML-MRC or AML-NOS.
View Article and Find Full Text PDFAge is a strong adverse prognostic factor in acute myeloid leukemia. Little is known about the biology of acute myeloid leukemia in elderly patients. The aim of this study was to identify genes with age-dependent changes of expression in leukemic blasts and their relevance for the patient prognosis.
View Article and Find Full Text PDFAcute myeloid leukemia (AML) is commonly associated with alterations in transcription factors because of altered expression or gene mutations. These changes might induce leukemia-specific patterns of histone modifications. We used chromatin-immunoprecipitation on microarray to analyze histone 3 lysine 9 trimethylation (H3K9me3) patterns in primary AML (n = 108), acute lymphoid leukemia (n = 28), CD34(+) cells (n = 21) and white blood cells (n = 15) specimens.
View Article and Find Full Text PDFBackground: Differences in survival have been reported between pediatric and adult acute lymphoblastic leukemia. The inferior prognosis in adult acute lymphoblastic leukemia is not fully understood but could be attributed, in part, to differences in genomic alterations found in adult as compared to in pediatric acute lymphoblastic leukemia.
Design And Methods: We compared two different sets of high-density single nucleotide polymorphism array genotyping data from 75 new diagnostic adult and 399 previously published diagnostic pediatric acute lymphoblastic leukemia samples.
Background: Delayed patient recruitment is a common problem in clinical studies. Hospital information systems (HIS) contain data items relevant for inclusion or exclusion criteria of these studies.
Purpose: We developed and assessed a system to support patient recruitment using HIS data.
Background: Multiple gene expression signatures derived from microarray experiments have been published in the field of leukemia research. A comparison of these signatures with results from new experiments is useful for verification as well as for interpretation of the results obtained. Currently, the percentage of overlapping genes is frequently used to compare published gene signatures against a signature derived from a new experiment.
View Article and Find Full Text PDFMotivation: The analysis of a number of different genetic features like copy number (CN) variation, gene expression (GE) or loss of heterocygosity has considerably increased in recent years, as well as the number of available datasets. This is particularly due to the success of microarray technology. Thus, to understand mechanisms of disease pathogenesis on a molecular basis, e.
View Article and Find Full Text PDFStud Health Technol Inform
December 2009
Cancer is the second leading cause of death worldwide and in focus of epidemiological research. In Germany the cancer registration law stipulates an electronic report to the population-based cancer registry (PBCR). In this context the Comprehensive Cancer Centre Münster (CCCM) required a new concept to support the obligation to register cancer diseases.
View Article and Find Full Text PDFStud Health Technol Inform
December 2009
Currently documentation processes for routine patient care and clinical research are kept separate (dual source). Due to overlaps between routine and research documentation, a single source approach provides opportunities to improve efficiency of medical documentation given the large workload of physicians related to documentation. Organisational, technical and regulatory conditions need to be considered for the design of single source systems.
View Article and Find Full Text PDFTranslocation of chromosomes 8 and 21, t(8;21), resulting in the AML1-ETO fusion gene, is associated with acute myeloid leukemia. We searched for additional genomic abnormalities in this acute myeloid leukemia subtype by performing single nucleotide polymorphism genomic arrays (SNP-chip) analysis on 48 newly diagnosed cases. Thirty-two patients (67%) had a normal genome by SNP-chip analysis (Group A), and 16 patients (33%) had one or more genomic abnormalities including copy number changes or copy number neutral loss of heterozygosity (Group B).
View Article and Find Full Text PDFGlioblastoma multiforme (GBM) is an extremely malignant brain tumor. To identify new genomic alterations in GBM, genomic DNA of tumor tissue/explants from 55 individuals and 6 GBM cell lines were examined using single nucleotide polymorphism DNA microarray (SNP-Chip). Further gene expression analysis relied on an additional 56 GBM samples.
View Article and Find Full Text PDFBackground: Delayed patient recruitment is a common problem in clinical trials. According to the literature, only about a third of medical research studies recruit their planned number of patients within the time originally specified.
Objectives: To provide a method to estimate patient accrual rates in clinical trials based on routine data from hospital information systems (HIS).
J Am Med Inform Assoc
August 2009
Hospital Information Systems (HIS) handle a large number of different types of documents. Exchange and analysis of data from different HIS is facilitated by the use of standardized codes to identify document types. HL7's Clinical Document Architecture (CDA) uses LOINC (logical observation identifiers names and Codes) codes for clinical documents.
View Article and Find Full Text PDFBackground: Timely and accurate information is important to guide the medical treatment process. We developed, implemented and assessed an order-entry system to support documentation of prostate histologies involving urologists, pathologists and physicians in private practice.
Methods: We designed electronic forms for histological prostate biopsy reports in our hospital information system (HIS).