Personal genomics

Personal genomics or consumer genetics is the branch of genomics concerned with the sequencing, analysis and interpretation of the genome of an individual. The genotyping stage employs different techniques, including single-nucleotide polymorphism (SNP) analysis chips (typically 0.02% of the genome), or partial or full genome sequencing. Once the genotypes are known, the individual's variations can be compared with the published literature to determine likelihood of trait expression, ancestry inference and disease risk. Automated high-throughput sequencers have increased the speed and reduced the cost of sequencing, making it possible to offer whole genome sequencing including interpretation to consumers since 2015 for less than $1,000. The emerging market of direct-to-consumer genome sequencing services has brought new questions about both the medical efficacy and the ethical dilemmas associated with widespread knowledge of individual genetic information. In personalized medici

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Next-generation DNA sequencing techniques

Wilhelm Ansorge

Next-generation high-throughput DNA sequencing techniques are opening fascinating opportunities in the life sciences. Novel fields and applications in biology and medicine are becoming a reality, beyond the genomic sequencing which was original development goal and application. Serving as examples are: personal genomics with detailed analysis of individual genome stretches; precise analysis of RNA transcripts for gene expression, surpassing and replacing in several respects analysis by various microarray platforms, for instance in reliable and precise quantification of transcripts and as a tool for identification and analysis of DNA regions interacting with regulatory proteins in functional regulation of gene expression. The next-generation sequencing technologies offer novel and rapid ways for genome-wide characterisation and profiling of mRNAs, small RNAs, transcription factor regions, structure of chromatin and DNA methylation patterns, microbiology and metagenomics. In this article, development of commercial sequencing devices is reviewed and some European contributions to the field are mentioned. Presently commercially available very high-throughput DNA sequencing platforms, as well as techniques under development, are described and their applications in bio-medical fields discussed.

2009

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Practical Solutions for Protecting Individual Genomic Privacy

Erman Ayday, Jacques Fellay, Zhicong Huang, Jean-Pierre Hubaux, Mathias Jacques Jean-Marc Humbert, Paul Jack Mc Laren, Jean Louis Raisaro, Amalio Telenti

The increasing availability of genomic data has major implications for personal privacy. The issues raised by genomic privacy reside at the crossroads of medicine, computer science, legislation and public policy. We here describe the design and development of new privacy enhancing technologies that aim to find the optimal balance between usability and privacy of genomic data in clinical care and in biomedical research.

2014

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Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

Matthieu Foll, Jeffrey David Jensen, Valeria Montano

Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g., transcription elongation factor NusA and tumor necrosis factor alpha-inducing protein Tip alpha) and hitherto unknown functional genes.

Genetics Society America2015

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Médecine personnalisée

La médecine personnalisée est une médecine cherchant à améliorer la stratification et la prise en charge des patients en utilisant des informations biologiques et des biomarqueurs au niveau des voies

Exome sequencing

Exome sequencing, also known as whole exome sequencing (WES), is a genomic technique for sequencing all of the protein-coding regions of genes in a genome (known as the exome).

Whole genome sequencing

Whole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of

BIO-491: New tools & research strategies in personalized health

We will define the concept of personalized health, describe the underlying technologies, the technological, legal and ethical challenges that the field faces today, and how they are being met.

BIO-463: Genomics and bioinformatics

This course covers various data analysis approaches associated with applications of DNA sequencing technologies, from genome sequencing to quantifying gene expression, transcription factor binding and chromosome conformation.

BIO-373: Genetics and genomics

The theoretical part of this course covers classical genetics and contemporary genomics. Because bioinformatics has become important for genomic research, the course also includes practical applications to genomic analyses using Python, including group projects.