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1004 Publications visible to you, out of a total of 1004
fcGENE: a versatile tool for processing and transforming SNP datasets
Genetical Statistics and Systems Biology

Abstract (Expand)

BACKGROUND Modern analysis of high-dimensional SNP data requires a number of biometrical and statistical methods such as pre-processing, analysis of population structure, association analysis and …d genotype imputation. Software used for these purposes often rely on specific and incompatible input and output data formats. Therefore extensive data management including multiple format conversions is necessary during analyses. METHODS In order to support fast and efficient management and bio-statistical quality control of high-dimensional SNP data, we developed the publically available software fcGENE using C++ object-oriented programming language. This software simplifies and automates the use of different existing analysis packages, especially during the workflow of genotype imputations and corresponding analyses. RESULTS fcGENE transforms SNP data and imputation results into different formats required for a large variety of analysis packages such as PLINK, SNPTEST, HAPLOVIEW, EIGENSOFT, GenABEL and tools used for genotype imputation such as MaCH, IMPUTE, BEAGLE and others. Data Management tasks like merging, splitting, extracting SNP and pedigree information can be performed. fcGENE also supports a number of bio-statistical quality control processes and quality based filtering processes at SNP- and sample-wise level. The tool also generates templates of commands required to run specific software packages, especially those required for genotype imputation. We demonstrate the functionality of fcGENE by example workflows of SNP data analyses and provide a comprehensive manual of commands, options and applications. CONCLUSIONS We have developed a user-friendly open-source software fcGENE, which comprehensively supports SNP data management, quality control and analysis workflows. Download statistics and corresponding feedbacks indicate that software is highly recognised and extensively applied by the scientific community.

Authors: Nab Raj Roshyara, Markus Scholz

Date Published: 22nd Jul 2014

Publication Type: Journal article

Genomic and epigenomic co-evolution in follicular lymphomas.
LIFE Adult

Abstract (Expand)

Follicular lymphoma (FL) with a t(14;18) is a B-cell neoplasm clinically characterized by multiple recurrencies. In order to investigate the clonal evolution of this lymphoma, we studied paired primary … and relapse tumor samples from 33 patients with recurrent non-transformed t(14;18)-positive FL. We reconstructed phylogenetic trees of the evolution by taking advantage of the activation-induced cytidine deaminase (AID)-mediated somatic hypermutation (SHM) active in the germinal center reaction using sequences of the clonal VHDHJH rearrangements of the immunoglobulin heavy chain (IGH) locus. Mutational analysis of the IGH locus showed evidence for ongoing somatic mutation and for counter-selection of mutations affecting the BCR conformation during tumor evolution. We further followed evolutionary divergence by targeted sequencing of gene loci affected by aberrant SHM as well as of known driver genes of lymphomagenesis, and by array-based genome-wide chromosomal imbalance and DNA methylation analysis. We observed a wide spectrum of evolutionary patterns ranging from almost no evolution to divergent evolution within recurrent non-transformed t(14;18) FL. Remarkably, we observed a correlation of the magnitude of evolutionary divergence across all genetic and epigenetic levels suggesting co-evolution. The distribution of coding mutations in driver genes and the correlation with SHM suggest CREBBP and AID to be potential modifiers of genetic and epigenetic co-evolution in FL.

Authors: M. Loeffler, M. Kreuz, A. Haake, D. Hasenclever, H. Trautmann, C. Arnold, K. Winter, K. Koch, W. Klapper, R. Scholtysik, M. Rosolowski, S. Hoffmann, O. Ammerpohl, M. Szczepanowski, D. Herrmann, R. Kuppers, C. Pott, R. Siebert

Date Published: 17th Jul 2014

Publication Type: Not specified

Human Diseases: follicular lymphoma

Excellent outcome of young adults with aggressive non-Hodgkin lymphomas treated with CHOP-like regimens.
GLA - German Lymphoma Alliance

Abstract

Not specified

Authors: K. Hohloch, S. Zeynalova, G. Held, M. Ziepert, M. Loeffler, G. Wulf, N. Schmitz, M. Pfreundschuh, L. Trumper

Date Published: 10th Jul 2014

Publication Type: Not specified

Human Diseases: non-Hodgkin lymphoma

Elevated serum free light chains do not predict outcome of elderly patients with aggressive CD20(+) B-cell lymphomas.
GLA - German Lymphoma Alliance

Abstract

Not specified

Authors: M. Achenbach, J. T. Bittenbring, M. Ziepert, E. Regitz, G. Ott, A. Rosenwald, M. Pfreundschuh, B. Altmann, G. Held

Date Published: 1st Jul 2014

Publication Type: Not specified

Human Diseases: B-cell lymphoma

Evaluating the performance of clinical criteria for predicting mismatch repair gene mutations in Lynch syndrome: a comprehensive analysis of 3,671 families.
GC-HNPCC - German Consortium for Hereditary Non-Polyposis Colorectal Cancer

Abstract (Expand)

Carriers of mismatch repair (MMR) gene mutations have a high lifetime risk for colorectal and endometrial cancers, as well as other malignancies. As mutation analysis to detect these patients is expensive … and time-consuming, clinical criteria and tumor-tissue analysis are widely used as pre-screening methods. The aim of our study was to evaluate the performance of commonly applied clinical criteria (the Amsterdam I and II Criteria, and the original and revised Bethesda Guidelines) and the results of tumor-tissue analysis in predicting MMR gene mutations. We analyzed 3,671 families from the German HNPCC Registry and divided them into nine mutually exclusive groups with different clinical criteria. A total of 680 families (18.5%) were found to have a pathogenic MMR gene mutation. Among all 1,284 families with microsatellite instability-high (MSI-H) colorectal cancer, the overall mutation detection rate was 53.0%. Mutation frequencies and their distribution between the four MMR genes differed significantly between clinical groups (p < 0.001). The highest frequencies were found in families fulfilling the Amsterdam Criteria (46.4%). Families with loss of MSH2 expression had higher mutation detection rates (69.5%) than families with loss of MLH1 expression (43.1%). MMR mutations were found significantly more often in families with at least one MSI-H small-bowel cancer (p < 0.001). No MMR mutations were found among patients under 40-years-old with only colorectal adenoma. Familial clustering of Lynch syndrome-related tumors, early age of onset, and familial occurrence of small-bowel cancer were clinically relevant predictors for Lynch syndrome.

Authors: V. Steinke, S. Holzapfel, M. Loeffler, E. Holinski-Feder, M. Morak, H. K. Schackert, H. Gorgens, C. Pox, B. Royer-Pokora, M. von Knebel-Doeberitz, R. Buttner, P. Propping, C. Engel

Date Published: 1st Jul 2014

Publication Type: Not specified

Human Diseases: colon cancer

Past and next 10 years of medical informatics
Management of health information systems

Abstract (Expand)

More than 10 years ago Haux et al. tried to answer the question how health care provision will look like in the year 2013. A follow-up workshop was held in Braunschweig, Germany, for 2 days in May, … 2013, with 20 invited international experts in biomedical and health informatics. Among other things it had the objectives to discuss the suggested goals and measures of 2002 and how priorities on MI research in this context should be set from the viewpoint of today. The goals from 2002 are now as up-to-date as they were then. The experts stated that the three goals: \textquotedblpatient-centred recording and use of medical data for cooperative care\textquotedbl; \textquotedblprocess-integrated decision support through current medical knowledge\textquotedbl and \textquotedblcomprehensive use of patient data for research and health care reporting\textquotedbl have not been reached yet and are still relevant. A new goal for ICT in health care should be the support of patient centred personalized (individual) medicine. MI as an academic discipline carries out research concerning tools that support health care professionals in their work. This research should be carried out without the pressure that it should lead to systems that are immediately and directly accepted in practice.

Authors: F. Uckert, Elske Ammenwerth, C. Dujat, A. Grant, Reinhold Haux, A. Hein, A. Hochlehnert, Petra Knaup-Gregori, C. Kulikowski, J. Mantas, V. Maojo, M. Marschollek, L. Moura, M. Plischke, R. Rohrig, Jürgen Stausberg, K. Takabayashi, Alfred Winter, Klaus-Hendrik Wolf, A. Hasman

Date Published: 1st Jul 2014

Publication Type: Journal article

Assessing the prognoses on health care in the information society 2013 - thirteen years after
Management of health information systems

Abstract (Expand)

Health care and information technology in health care is advancing at tremendous speed. We analysed whether the prognoses by Haux et al. - first presented in 2000 and published in 2002 [1] - have been … fulfilled in 2013 and which might be the reasons for match or mismatch. Twenty international experts in biomedical and health informatics met in May 2013 in a workshop to discuss match or mismatch of each of the 71 prognoses. After this meeting a web-based survey among workshop participants took place. Thirty-three prognoses were assessed matching; they reflect e.g. that there is good progress in storing patient data electronically in health care institutions. Twenty-three prognoses were assessed mismatching; they reflect e.g. that telemedicine and home monitoring as well as electronic exchange of patient data between institutions is not established as widespread as expected. Fifteen prognoses were assessed neither matching nor mismatching. ICT tools have considerably influenced health care in the last decade, but in many cases not as far as it was expected by Haux et al. in 2002. In most cases this is not a matter of the availability of technical solutions but of organizational and ethical issues. We need innovative and modern information system architectures which support multiple use of data for patient care as well as for research and reporting and which are able to integrate data from home monitoring into a patient centered health record. Since innovative technology is available the efficient and wide-spread use in health care has to be enabled by systematic information management.

Authors: Petra Knaup-Gregori, Elske Ammenwerth, C. Dujat, A. Grant, A. Hasman, A. Hein, A. Hochlehnert, C. Kulikowski, J. Mantas, V. Maojo, M. Marschollek, L. Moura, M. Plischke, R. Rohrig, Jürgen Stausberg, K. Takabayashi, F. Uckert, Alfred Winter, Klaus-Hendrik Wolf, Reinhold Haux

Date Published: 1st Jul 2014

Publication Type: Journal article

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