Genetical Statistics and Systems Biology
OverviewThe group is interested in omic-level studies including the genome, methylome, transcriptome, and metabolome of the general population as well as of various diseases including cardiovascular diseases, pneumonia, sepsis, obesity, and brain cancers. Additionally, we aim at transfering results of biomathematical model simulations into clinical practice e.g. by haematopoietic growth-factor opimization during cytotoxic chemotherapy and optimization of EPO applications in chronic kidney disease.
The group is interested in omic-level studies including the genome, methylome, transcriptome, and metabolome of the general population as well as of various diseases including cardiovascular diseases, pneumonia, sepsis, obesity, and brain cancers. Additionally, we aim at transfering results of biomathematical model simulations into clinical practice e.g. by haematopoietic growth-factor opimization during cytotoxic chemotherapy and optimization of EPO applications in chronic kidney disease.
The group aims to develop and apply statistical and bioinformatic methods in genetics. This comprises e.g. the planning and conduction of studies, the management and analysis of high-dimensional molecular genetic data (germ line mutations, tumour cell line mutations, expression data, metabolomics), population genetics and integrative genome analyses. The work is accompanied by statistical or continuous modelling of diseases or physiological processes. For this purpose, we cooperate with different national and international study groups of different disease entities or phenotypes.
Programme: This Project is not associated with a Programme
LHA-ID: 7Q0CTG2ND8-7
Funding codes:- BMBF
- ESF
- Freistaat Sachsen
Public web page: http://www.imise.uni-leipzig.de/en/Groups/GenStat/
Organisms: Homo sapiens
Human Diseases: No Human Disease specified
Leipzig Health Atlas PALs: Markus Scholz
Project start date: 1st Jan 2013
Related items
Projects: Leipzig Health Atlas, German Consortium for Hereditary Breast and Ovarian Cancer, LIFE- Leipzig Research Center for Civilization Diseases, LIFE Adult, German Lymphoma Alliance (GLA), LIFE Head and Neck Cancer Group, Footprints of Sepsis Framed Within Community Acquired Pneumonia in the Blood Transcriptome, Genetical Statistics and Systems Biology, Genomic and transcriptomic heterogeneity of colorectal tumours arising in Lynch syndrome, German Consortium for Hereditary Non-Polyposis Colorectal Cancer, German Glioma Network, German Competence Network Sepsis (SepNet), Natural Language Processing for Clinical Research, LIFE Heart, Molecular mechanisms in malignant lymphoma, Molecular Mechanisms in Malignant Lymphomas - Demonstrators of Personalized Medicine, Individualized model-based managing of the next-cycle thrombopenia of CHOEP/CHOP treated patients based on platelets dynamics during the previous cycles, LIFE Child, MMML-MYC-SYS, ProstataCA, COVID-19 Leipzig
Institutions: Institute for Medical Informatics, Statistics and Epidemiology
https://orcid.org/0000-0001-8344-0658
Markus Scholz
Scientific Speaker Institution
Institut für Medizinische Informatik, Statistik und Epidemiologie
Universität Leipzig
Härtelstraße 16-18
04107 Leipzig
Resutls of different OMICS-level using LIFE Adult and LIFE Heart data are presented (Publications, Supplemental Data, & Summary Statistics).
Snapshots: No snapshots
We analysed if measuring PWV in different segments of the body leads to association with different genetic variants, as well as different heritability and different genetic correlation with other biological traits. Furthermore we searched for shared genetic architecture concerning PWV, blood pressure (BP) and coronary artery disease (CAD) and examined the causal relationship between PWV and BP.
We defined six operationalizations of CPB considering plaques in common carotid arteries, carotid bulb, and internal carotid arteries (maximal plaque area, mean plaque area, sum of plaque areas at all six regions, maximal degree of stenosis, mean degree of stenosis, and sum of stenosis at all six regions).
Link to publication (PMID, DOI), Supplemental Figures and Tables, and Summary Statistics of GWAS will be made available upon acceptance of our manuscript.
Supplement Data for Publication including Supplement Material & Results (eQTL annotation, Mendelian Randomization (MR), further significant loci), Figures (correlation plot of steroid hormones, scatter plot of genetic effect sizes, regional association plots, scatter plots of MR) and Tables (Correlations, GWAS summary statistics, interaction tests, MR results)
Summary statistics from GWAS of baPWV, bfPWV, cfPWV
All samples (adjusted for age, sex and log_sys)
These data is intended for research purposes only.
Citation: tbc
When using this data acknowledge the source as follows: 'Data on PWV has been contributed by LIFE-Adult investigators and has been downloaded from https://www.health-atlas.de/assays/34'
For any enquiries about the datasets, please contact Michael Rode (michael.rode@imise.uni-leipzig.de) or Markus Scholz (markus.scholz@imise.uni-leipzig.de)
...
Submitter: Michael Rode
Assay type: Genome Wide Association
Technology type: SNP Array
Snapshots: No snapshots
We are releasing the summary data from our GWAS of carotid plaque burden traits, pending on acceptance of our publication, to empower other researchers to examine variants or loci in which they are interested for associations. These data are intended for research purposes only.
Citation:
When using this data acknowledge the source as follows: 'Data on carotid plaque burden has been contributed by LIFE-Adult investigators and has been downloaded from https://www.health-atlas.de/assays/31 '
For any
...
Submitter: Janne Pott
Assay type: Genome Wide Association
Technology type: SNP Array
Snapshots: No snapshots
We are releasing the summary data from our meta-analyses of steroid hormones, to empower other researchers to examine variants or loci in which they are interested for association with these hormonal traits. These data are intended for research purposes only.
Citation:
Pott et al. (2019) Genetic Association Study of Eight Steroid Hormones and Implications for Sexual Dimorphism of Coronary Artery Disease. J Clin Endocrinol Metab 104: 5008–5023. PubMed ID: 31169883
When using this data acknowledge
...
Submitter: Janne Pott
Assay type: Genome Wide Association
Technology type: SNP Array
Snapshots: No snapshots
The primary goal of this study was to identify genetic loci associated with steroid hormone levels (cortisol, DHEA-S, testosterone, estradiol, progesterone, 17-hydroxyprogesterone, androstenedione, and aldosterone). In a secondary analysis, we searched for causal effects of steroid hormones on coronary artery disease.
Submitter: René Hänsel
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Data for visualisation of associations and causal relationsships of SNPs, gene expression, and metabolites based on 1,856 individuals of the LIFE Heart study
Creator: Markus Scholz
Submitter: Christoph Beger
Data file type: OMICs Data
Human Diseases: kidney disease
DownloadSummary statistics from GWAS of CPS_mean for
- all samples (adjusted for age and sex)
- men only (adjusted for age)
- women only (adjusted for age)
These data are intended for research purposes only.
Citation:
Pott et al. (2020) Genome-wide analysis of carotid plaque burden suggests a role of IL5 in men. PLOS ONE. PubMed ID: 32469969
When using this data acknowledge the source as follows: 'Data on mean degree of stenosis has been contributed by LIFE-Adult investigators and has been downloaded
...
Summary statistics from GWAS of CPS_sum for
- all samples (adjusted for age and sex)
- men only (adjusted for age)
- women only (adjusted for age)
These data are intended for research purposes only.
Citation:
Pott et al. (2020) Genome-wide analysis of carotid plaque burden suggests a role of IL5 in men. PLOS ONE. PubMed ID: 32469969
When using this data acknowledge the source as follows: 'Data on sum of stenosis has been contributed by LIFE-Adult investigators and has been downloaded from
...
Summary statistics from GWAS of CPS_max for
- all samples (adjusted for age and sex)
- men only (adjusted for age)
- women only (adjusted for age)
These data are intended for research purposes only.
Citation:
Pott et al. (2020) Genome-wide analysis of carotid plaque burden suggests a role of IL5 in men. PLOS ONE. PubMed ID: 32469969
When using this data acknowledge the source as follows: 'Data on maximal degree of stenosis has been contributed by LIFE-Adult investigators and has been downloaded
...
This shiny app facilitates the download and searching of the summary statistics from "Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci" (https://doi.org/10.1093/hmg/ddv194).
Creators: Markus Scholz, Carl Beuchel, Holger Kirsten
Submitter: Carl Beuchel
Model type: Not specified
Model format: R package
Environment: Shiny
External LinkThis Shiny-App implements the calculation of several CAP (Community-Aquired-Pneumonia) severity scores for one or multiple patients based on user-updated data.
Creators: Markus Scholz, Maciej Rosolowski, Carl Beuchel
Submitter: Carl Beuchel
Model type: Algebraic equations
Model format: R package
Environment: Shiny
View contentPreprocessing Illumina HT12v4 gene expression data including quality filtering, data transformation and normalisation and batch-effect removal as well as visualisation
Creators: Markus Scholz, Holger Kirsten
Submitter: Christoph Beger
Model type: Not specified
Model format: R package
Environment: Not specified
Creators: Markus Scholz, Carl Beuchel, Yuri Kheifetz, Sibylle Schirm
Submitter: Carl Beuchel
Model type: Ordinary differential equations (ODE)
Model format: R package
Environment: Shiny
This is an interactive version of figure 4 of the publication „Integration of Genome-Wide SNP Data and Gene-Expression Profiles Reveals Six Novel Loci and Regulatory Mechanisms for Amino Acids and Acylcarnitines in Whole Blood“.
Creator: Markus Scholz
Submitter: René Hänsel
Model type: Not specified
Model format: R package
Environment: Not specified
Abstract (Expand)
Authors: J. Pott, F. Beutner, K. Horn, H. Kirsten, K. Olischer, K. Wirkner, M. Loeffler, M. Scholz
Date Published: 30th May 2020
Publication Type: Journal
Human Diseases: cardiovascular system disease, atherosclerosis
Abstract (Expand)
Authors: Carl Beuchel, Susen Becker, Julia Dittrich, Holger Kirsten, Anke Toenjes, Michael Stumvoll, Markus Loeffler, Holger Thiele, Frank Beutner, Joachim Thiery, Uta Ceglarek, Markus Scholz
Date Published: 17th Aug 2019
Publication Type: Not specified
Abstract (Expand)
Authors: J. Pott, YJ. Bae, K. Horn, A. Teren, Andreas Kühnapfel, H. Kirsten, U. Ceglarek, Markus Löffler, J. Thiery, J. Kratzsch, Markus Scholz
Date Published: 6th Jun 2019
Publication Type: Not specified
Human Diseases: coronary artery disease
Abstract (Expand)
Authors: P. Ahnert, P. Creutz, K. Horn, F. Schwarzenberger, M. Kiehntopf, H. Hossain, M. Bauer, F. M. Brunkhorst, K. Reinhart, U. Volker, T. Chakraborty, M. Witzenrath, M. Loffler, N. Suttorp, M. Scholz
Abstract (Expand)
Authors: J. Pott, R. Burkhardt, F. Beutner, K. Horn, A. Teren, H. Kirsten, L. M. Holdt, G. Schuler, D. Teupser, M. Loeffler, J. Thiery, M. Scholz
Introduction
The platform can be found at the following address:
https://apps.health-atlas.de/hemato-models/
This platform enables data fitting, results presentation and next cycle prediction/management using hematopoietic models, developed by our modeling group in IMISE:
a) Erythropoiesis model
b) Individualised thrombopoiesis model [1] integrated with a model of bone-remodelling [2] as well as with PK models of few cytotoxic drugs [3,4]
c) Integral hemathopoiesis model (above thrombopoiesis
...
Creators: Markus Scholz, Carl Beuchel, Sibylle Schirm, Yuri Kheifetz
Submitter: Carl Beuchel
Supplement Data for Publication including Supplement Material & Results (eQTL annotation, Mendelian Randomization (MR), further significant loci), Figures (correlation plot of steroid hormones, scatter plot of genetic effect sizes, regional association plots, scatter plots of MR) and Tables (Correlations, GWAS summary statistics, interaction tests, MR results)
Creator: Janne Pott
Submitter: René Hänsel
