Human and Clinical Genetics, LUMC

LGTC - Next-generation Sequencing Analysis

The group primarily works on analysis of next-generation sequencing (NGS) data, as well as providing advice to NGS users. This includes knowledge of how to handle different platforms and applications, as well as keeping up to date with current NGS analysis tools. We also develop our own in-house analysis pipelines and tools. An additional project of this group includes support of CORE_TF, a web site for identification of conserved and over-represented transcription factor binding sites in ChIP and expression data.

Michiel van Galen: data analysis support and tool developer

Jaap van der Heijden: genome variation data analysis and tool developer

Yuching Lai: genome variation data analysis and tool developer

Henk Buermans: micro-RNA data analysis and tool developer

Matthew Hestand: coordinator, data analysis support, and tool developer

Microarray Analysis

The group works on different aspects of microarray data analysis, including platform comparison, sample size determination, and study design. In addition to expression profiling, we work on the analysis of different types of microarray data, e.g. array-CGH, SNP arrays, and methylation arrays. We develop new statistical tools for optimizing study design and for the analysis and integration of microarray experiments and apply them to genomics projects carried out within our institute.

Peter-Bram 't Hoen: developer and superuser of microarray analysis tools

Maarten van Iterson: statistical methods and tools for design, analysis, and integration of genomic experiments

Judith Boer: coordinator, developer, and superuser of microarray analysis tools

Databases and Annotation

The group works on the development and maintenance of the web-based locus-specific database LOVD (Leiden Open source sequence Variation Database) and on proper nomenclature of sequence variations. This latter aspect, in the Mutalyzer package, also aims to determine the functional effects of sequence variations (under development).

Ivo Fokkema: LOVD and HCG database developer

Jacopo Celli: LOVD database set-up and curator support

Gerard Schaafsma: LOVD tool developer

Jeroen Laros: Development of algorithms and tools for sequence (variant) analysis and annotation

Peter Taschner: coordinator

BioSemantics

The BioSemantics group investigates and develops new ways to analyse biological data and information through computational means. A prime focus is methodology for discovering hidden biological relations from text, biological databases, and knowledge held by experts; resources that go beyond a single researcher or a single group. In Leiden we focus on applying this research ('meta-analysis') to help build better hypotheses for a number of cases within the Human Genetics department. Thereby we establish a feedback loop between computer scientists, software developers and biologists. The group is a collaboration between the Center for Human and Clinical Genetics at theLeiden University Medical Center and the Medical Informatics department of the ErasmusMC University Medical Center of Rotterdam.

LUMC members:

Herman van Haagen: research and tool developer

Bharat Singh: software developement

Peter-Bram 't Hoen: 'user expert' of BioSemantic methods

Marco Roos: project coordination and bioinformatics research, e-science liaison

Barend Mons: founder and senior advisor, founder of the Concept Web Alliance

BioInformatics Courses and Tutorials

DNA chip and array technology: "Analysis of microarray gene expression data" -Lectures & Practicals

Next-gen sequencing technology: "Next generation sequencing (NGS) data analysis "

Getting started in R: information for first time R users including several practicals for microarray data analysis

Tools originating from the department

Anni 2.1: a multipurpose text-mining tool for the life sciences

CORE_TF: Conserved and Over-REpresented Transcription Factor binding sites

LOVD: Leiden Open source sequence Variation Database

MaRe: Microarray Retriever

Mutalyzer: Sequence variant nomenclature check

SIM: Integrated Analysis on two human genomic datasets

SSPA: Sample Size and Power Analysis for Microarray Data

WWW-links originating from the department

Leiden Muscular Dystrophy data pages (incl. muscular dystrophy mutation databases)
Duchenne and Becker muscular dystrophy (DMD / BMD), Limb-Girdle muscular dystrophy (SCARMD, LGMD), diagnostic techniques

Classifying unclassified BRCA1/BRCA2 variants found in the Dutch population

ArrayNL platform: DNA chip & micro-array technology in Nederland

Center for Human and Clinical Genetics - LUMC

BioInformatics Groups and Aims