Innovation through gene discovery
In 2010 the Great Ormond Street Hospital (GOSH) Biomedical Research Centre (BRC) of the National Institute for Health Research (NIHR) funded the development of the Centre for Translational
Research-GOSgene to facilitate rapid gene identification in uncharacterised
GOSgene brings UCL/ICH research expertise to PIs and clinicians working with congenital disorders to enable the discovery of new genes. Our initiative ultimately supports genetic counselling, helps improving diagnostic testing and will guide further functional analysis aimed at understanding the pathogenesis of disease and improving patients’ management or developing novel therapies.
GOSgene provides an infrastructure and a step-by-step guidance for selected projects involving linkage analysis and/or next generation sequencing (NGS). We offer a comprehensive and flexible service from clinical samples to target gene identification.
GOSgene analytical expertise
GOSgene routinely quantify and QC all samples before normalising and sending them to the chosen sequence provider. The group are able to extract high quality DNA and RNA from a range of biological specimens and prepare them for a range of downstream applications.
Following data analysis and interpretation, all potential candidate variants are validated using Sanger sequencing and, where applicable, segregation analyses are performed in additional family members.
The GOSgene team also possess the molecular biology skills required to perform a number of cell culture techniques such as, growing and harvesting standard cell lines through to the production of iPSC cells and their differentiation in to specific cellular lineages.
A major strength within GOSgene is its expertise in the use of cutting-edge computational architecture. We have access to large servers, virtual machines, High Performance Computing machines and we are actively working with eMedlab to develop robust analytical pipelines for whole genome and transcriptomic analysis.
For Sample tracking and the consolidation of all identified genomic variants GOSgene have built a bespoke LIMs system and developed ‘in house’ databases that contain information on all called SNVs, CNVs (combined CNV data from 3 algorithms), electronic phenotype data (using Human Phenotype Ontology) and a QC database detailing quality statistics for all samples.
GOSgene use a range of commercial and open source software programs for the interpretation of NGS data. For exome and WGS data the Qiagen Variant AnalysisTM software is used to filter and annotate the variants in coordination with a number of publicly available databases that are used to further characterise potentially causative variants.
For transcrptomic analysis, GOSgene is using a range of open source software programs such as WGCNA and others to identify deferentially expressed genes, gene fusions and alternative splicing events.
Furthermore, GOSgene are exploring the use of network analysis tools to perform higher-order exploratory analyses of their datasets and are actively researching a number of approaches in this developing field.
The identification of a causative variant is just the first step in the process of improving patient benefit. GOSgene has the belief that through gene identification a better understanding of disease pathology will be possible which will in turn, eventually lead to improved therapeutics or even, through genetic therapies, the prevention of the disease developing in the first place. To this end we work closely with our colleagues from Experimental and Personalised Medicine.