A5003404072- Genetic Associations and Epidemiology
- Acute Myeloid Leukemia Research
- Epigenetics and DNA Methylation
- Gene expression and cancer classification
- Genetic Mapping and Diversity in Plants and Animals
- Bioinformatics and Genomic Networks
- Genomics and Chromatin Dynamics
- Nutrition, Genetics, and Disease
- RNA modifications and cancer
- Cognitive Abilities and Testing
- Health, Environment, Cognitive Aging
- Folate and B Vitamins Research
- Amyotrophic Lateral Sclerosis Research
- Myeloproliferative Neoplasms: Diagnosis and Treatment
- Chronic Myeloid Leukemia Treatments
- Birth, Development, and Health
- Melanoma and MAPK Pathways
- Cancer-related gene regulation
- Autophagy in Disease and Therapy
- Molecular Biology Techniques and Applications
- Cell death mechanisms and regulation
- Genomic variations and chromosomal abnormalities
- Genomics and Phylogenetic Studies
- TGF-β signaling in diseases
- Protein Degradation and Inhibitors
Amsterdam Neuroscience
2017-2019
Vrije Universiteit Amsterdam
2017-2019
Delft University of Technology
2010-2018
Amsterdam UMC Location Vrije Universiteit Amsterdam
2016-2017
Netherlands Bioinformatics Centre
2015
Erasmus MC
2009-2013
Abstract A main challenge in genome-wide association studies (GWAS) is to pinpoint possible causal variants. Results from GWAS typically do not directly translate into variants because the majority of hits are non-coding or intergenic regions, and presence linkage disequilibrium leads effects being statistically spread out across multiple Post-GWAS annotation facilitates selection most likely variant(s). Multiple resources available for post-GWAS annotation, yet these can be time consuming...
Abstract Humans vary substantially in their willingness to take risks. In a combined sample of over one million individuals, we conducted genome-wide association studies (GWAS) general risk tolerance, adventurousness, and risky behaviors the driving, drinking, smoking, sexual domains. We identified 611 approximately independent genetic loci associated with at least our phenotypes, including 124 tolerance. report evidence substantial shared influences across tolerance behaviors: 72 contain...
Canonical Wnt signaling regulates the self-renewal of most if not all stem cell systems. In blood system, role has been subject much debate but there is consensus that high signals lead to loss reconstituting capacity. To better understand this phenomenon, we have taken advantage a series hypomorphic mutant Apc alleles resulting in broad range dosages hematopoietic cells (HSCs) and performed whole-genome gene expression analyses. Gene profiling functional studies show HSCs with APC mutations...
ABSTRACT A main challenge in genome-wide association studies (GWAS) is to prioritize genetic variants and identify potential causal mechanisms of human diseases. Although multiple bioinformatics resources are available for functional annotation prioritization, a standard, integrative approach lacking. We developed FUMA: web-based platform facilitate GWAS results, prioritization genes interactive visualization annotated results by incorporating information from state-of-the-art biological databases.
Abstract Frontotemporal dementia (FTD) is a neurodegenerative disorder predominantly affecting the frontal and temporal lobes. Genome-wide association studies (GWAS) on FTD identified only few risk loci. One of possible explanations that clinically, pathologically, genetically heterogeneous. An important open question to what extent epigenetic factors contribute whether these vary between clinical subgroup. We compared DNA-methylation levels cases (n = 128), with Amyotrophic Lateral...
The GTEx Consortium reported that hierarchical clustering of RNA profiles from 25 unique tissue types among 1641 individuals accurately distinguished the types, but a multidimensional scaling failed to generate 2D projection data separates tissue-subtypes. In this study we show by t-Distributed Stochastic Neighbor Embedding is in line with cluster analysis which allows more detailed examination and visualization human relationships.
Acute Myeloid Leukemia (AML) is characterized by various cytogenetic and molecular abnormalities. Detection of these abnormalities important in the risk-classification patients but requires laborious experimentation. Various studies showed that gene expression profiles (GEP), signatures derived from GEP, can be used for prediction subtypes AML. Similarly, successful was also achieved exploiting DNA-methylation (DMP). There are, however, no compared classification accuracy performance between...
The wingless-Int (WNT) pathway has an essential role in cell regulation of hematopoietic stem cells (HSC). For Acute Myeloid Leukemia (AML), the malignant counterpart HSC, currently only a selective number genes WNT are analyzed by using either gene expression or DNA-methylation profiles for identification prognostic markers and potential candidate targets drug therapy. It is known that mRNA controlled specific patterns can infer ability to differentiate biological differences, thus combined...
Abstract The use of genome-wide data in cancer research, for the identification groups patients with similar molecular characteristics, has become a standard approach applications therapy-response, prognosis-prediction, and drug-development. To progress these applications, trend is to move from single measurements cancer-type towards measuring several different characteristics across multiple cancer-types. Although current approaches shed light on various cancer-types, detailed relationships...
Acute myeloid leukemia (AML) results from multiple genetic and epigenetic aberrations, many of which remain unidentified. Frequent loss large chromosomal regions marks haplo-insufficiency as one the major mechanisms contributing to leukemogenesis. However, haplo-insufficient genes (HIGs) are involved in leukemogenesis is largely unknown powerful experimental strategies aimed at their identification currently lacking. Here, we present a new approach discover HIGs, using retroviral integration...