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Ultra High Throughput sequencing platform for functional genome analysis

Applicant Antonarakis Stylianos
Number 121418
Funding scheme R'EQUIP
Research institution Dépt de Médecine Génétique & Développement Faculté de Médecine
Institution of higher education University of Geneva - GE
Main discipline Genetics
Start/End 01.08.2008 - 31.07.2009
Approved amount 391'795.00
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All Disciplines (4)

Discipline
Genetics
Molecular Biology
Infectious Diseases
Immunology, Immunopathology

Keywords (9)

Genomic and phenotypic variability; Genetic disorders (Monogenic and complex); Target genes of transcription factors; MHC class II gene expression; Digital gene expression; Identification of new transcripts; Antimicrobial resistance development; Genetic variation and selection process; High throughput DNA sequencer

Lay Summary (English)

Lead
Lay summary
A high throughput DNA sequencer was acquired. This laboratory equipment will be able to sequence genomes of humans in order to discover the causes of hereditary disorders, identify functional elements in the genomes, sequence the genomes of other species and pathogens, identify RNAs that could explain cancerogenesis. The machine will be utilized by many scientists not only in the University of Geneva but also in other Swiss Institutions.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Associated projects

Number Title Start Funding scheme
105895 Regulation and deregulation of MHC class II genes 01.01.2005 Project funding (Div. I-III)
116075 Large-scale evaluation of bacterial genome content for the identification of epidemiological and virulence basis in MRSA 01.05.2007 Project funding (Div. I-III)
108401 Détection et mécanismes moléculaires de la résistance aux glycopeptides chez les staphylocoques dorés 01.05.2005 Project funding (Div. I-III)
144085 Regulation of antigen presentation and antigen presenting cell function 01.01.2013 Project funding (Div. I-III)
127375 Chromosome 21: functional genomics and molecular pathophysiology of its disorders 01.10.2009 Project funding (Div. I-III)
163180 Chromosome 21: functional genomics and molecular pathophysiology of trisomy 21 01.10.2015 Project funding (Div. I-III)
127255 Regulation of MHC class II expression and antigen presenting cell function 01.01.2010 Project funding (Div. I-III)
105602 Chromosome 21: functional genomics and molecular pathophysiology of its disorders 01.10.2004 Project funding (Div. I-III)
108708 EURODYNA 2004-32: Environmental stress-induced dynamic modulation of chromatin structure, gene expression 01.12.2004 Project funding (special)
113565 The mammalian circadian timing system: Oscillators, inputs, and outputs 01.01.2007 Project funding (Div. I-III)
116716 Molecular mechanisms of telomere capping and lengh regulation 01.04.2007 Project funding (Div. I-III)
112370 Kinetic analysis of S.aureus biofilm regulation by using combined imaging and genome-wide approaches 01.05.2006 Project funding (Div. I-III)

Abstract

The novel ultra high throughput sequencing (UHTS) platforms will revolutionize the study of genomic information in medical research and health care, and enable important discoveries that may transform the practice of medicine. The SOLiD platform, based on sequencing by oligonucleotide ligation and detection, is Applied Biosystems'next-generation system for ultra high-throughput DNA analysis, which generates high quality data for both current and future DNA analysis projects such as whole genome sequencing, medical sequencing, genotyping, gene expression, new transcript and small RNA discovery. The SOLiD System interrogates each base twice for errors during sequencing, resulting in high accuracy sequence data allowing detection of sequence variation including single nucleotide polymorphisms (SNPs), gene copy number variation, single base duplication, inversion, insertion and deletion. The SOLiD platform can generate approximately one gigabase of useable data (equivalent of one-third of the human genome) per run of 72 hours, which makes it one of the highest throughput new-generation sequencing platforms. As presented in this grant application, participants describe research projects exploring various aspects of genetic and genomics research. 1) A comprehensive definition of the contribution of the extensive sequence variation present in the human genome to diseases. Determination of the diploid sequences of small, targeted fractions of the human genome in the context of rare monogenic and common, complex disorders. 2) Unbiased identification of genes regulated by transcription factors involved in various biological processes by direct UTH sequencing of chromatin- immunoprecipitated samples (ChIP-seq experiments)3) Role of long range chromatin interactions in the regulation of MHC gene expression. Circular chromosome conformation capture (4C)-sequencing approach will be used to map long-range interactions engaged by specific bait sequences, including well studied MHC-II promoters4) Pathogenesis and gene regulation of Staphylococcus Aureus. Unbiased digital gene expression studies, including detection and regulation of small non-coding RNAs, time-series analyses of genomic changes during antimicrobial resistance development or during in vivo infections, and analyses of the genetic variations and selection process identified during lab evolution studies will be performed.All of these projects necessitate access to ultra high throughput sequencing capabilities. The acquisition of this equipment is absolutely necessary for the advancement of these various projects, to enhance the competitiveness of the Genetics and Genomics research in the Geneva region and facilitate interactions between different investigators and the industry. Furthermore, many researchers from the University of Geneva (UNIGE) and the “Hôpitaux Universitaires de Genève (HUG), in addition to those directly involved in the grant proposal, have expressed great interest in having such equipment available for their research projects. (see a list of people in the “Necessity of the Equipment” section of the research plan).
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