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An introduction to human genomics PowerPoint Presentation

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Description : Check out this medical titled "An introduction to human genomics” by Jacques Fellay.

This medical is about human genomics, the study of the genetic information encoded in the DNA of humans. It encompasses a wide range of topics, including the identification and characterization of genetic variations, the exploration of the relationship between genetic variations and disease, and the development of diagnostic and therapeutic approaches based on genomic information.

One of the primary goals of human genomics is to understand the function of each gene in the human genome, as well as the interactions between genes and other factors that influence human health and disease. This involves studying the genetic variation that exists within human populations, as well as the ways in which that variation contributes to the development of diseases like cancer, heart disease, and neurological disorders.

Human genomics also includes the development of new technologies and tools for analyzing genomic data, such as next-generation sequencing technologies, bioinformatics software, and data visualization tools. These tools are critical for researchers and clinicians who are working to identify and understand the genetic basis of disease, and to develop new treatments and cures.

Overall, human genomics is a rapidly evolving field that has the potential to revolutionize our understanding of human health and disease, and to lead to new and more effective approaches to diagnosis, treatment, and prevention.

Tags : human genomics, DNA, genetic variations, human genome, Medical Genetics, Medical Genetics

Published on : Jun 01, 2023 | Views : 1000 | Downloads : 2

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Are you ready for the genomic age? An introduction to human genomics Jacques Fellay EPFL School of Life Sciences Swiss Institute of Bioinformatics Lausanne, Switzerland
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What is the genome? “It's a shop manual, with an incredibly detailed blueprint for building every human cell. It's a history book - a narrative of the journey of our species through time. It's a transformative textbook of medicine, with insights that will give health care providers new powers to treat, prevent and cure disease.” Francis Collins
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Glossary Genome: the complete genetic constitution of an organism, encoded in nucleic acids Gene: discrete DNA sequence encoding a protein
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3 billions base pairs (ATGC) 20’000 protein-coding genes 99.6% inter-individual identity (yet 4 millions differences) 99% identical to chimpanzee genome (yet 6% different genes) The human genome
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2001: A Species Odyssey
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Exploring the human genome 2002 2008
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International HapMap Project  Identification of common genetic variation in 270 individuals from 4 populations CEU: CEPH (Utah residents with ancestry from northern and western Europe) (30 trios) CHB: Han Chinese in Beijing, China (45 individuals) JPT: Japanese in Tokyo, Japan (45 individuals) YRI: Yoruba in Ibadan, Nigeria (30 trios)
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1000 Genomes Project Whole genome sequencing and complete description of human genetic diversity in >1000 individuals from multiple world populations www.1000genomes.org
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Short video – Sequencing the genome http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel
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We are all different… 4 million DNA variants / individual Single nucleotide variants Multi-nucleotide variants Small insertions/deletions (indels) Large copy number variants (CNVs) Inversions Translocations Aneuploidy
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Glossary SNV = single nucleotide variant: DNA sequence variation in which a single nucleotide — A, T, C or G — differs between members of the same species SNP = single nucleotide polymorphism: SNV occurring commonly within a population (> 1%)
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SNV/SNP
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Glossary Allele: One of a number of alternative forms of the same genetic locus (for example a SNP)
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Glossary Linkage Disequilibrium (LD): Non-random association of alleles that descend from single, ancestral chromosomes (i.e. usually close to each other) Haplotype: Combination of alleles at adjacent locations on a chromosome that are inherited together
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How to read the genome? Genotyping Sequencing
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Glossary Genotyping: Process of determining genetic differences between individuals by using a set of markers Sequencing: Process of determining the full nucleotide order of a DNA sequence
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Genotyping Genome-wide chips: 500K to >1 mio single nucleotide polymorphisms (SNPs)
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SNP output
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High-throughput Sequencing (NGS) Huge amount of data (terabytes) Analysis computationally intensive Dedicated IT infrastructure
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Pipeline Library construction and sequencing Sequencing quality control FASTQ files
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FastQ format – single read A complete, high-coverage genome will have over 1 billion reads
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Pipeline Library construction and sequencing Sequencing quality control FASTQ files Read mapping Sort, index, remove duplicates Mapping quality control BAM files
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Pipeline
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Pipeline Library construction and sequencing Sequencing quality control FASTQ files Read mapping Sort, index, remove duplicates Mapping quality control BAM files Variant Calling Variant calling quality control VCF files
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Pipeline http://www.ncbi.nlm.nih.gov/core/assets/variation/images/popfreq_example.jpg
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Identification of potentially causal variants Individualized care and counseling Pipeline Library construction and sequencing Sequencing quality control FASTQ files Read mapping Sort, index, remove duplicates Mapping quality control BAM files Variant Calling Variant calling quality control VCF files
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Summary of a single human genome
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Whole genome vs. exome sequencing Exome -Coding regions -Cheaper/Faster -Uneven capture of both alleles -Incomplete capture of target region -Bias towards known biology Genome -Complete sequence -Expensive/Throughput -IT issues
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Clinical sequencing? “Sequencing of the genome or exome for clinical applications has now entered medical practice. Several thousand tests have already been ordered for patients, with the goal of establishing diagnoses for rare, clinically unrecognizable, or puzzling disorders that are suspected to be genetic in origin.” Leslie G. Biesecker and Robert C. Green, NEJM, 19 June 2014
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Clinical sequencing? TODAY Rare functional variants (Mendelian diseases) Pharmacogenetic variants (150 gene-drug pairs in the FDA “Table of Pharmacogenomic Biomarkers in Drug Labels”, but only 40 genes involved) Oncogenomics
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IL28B genotype and response to anti-hepatitis C treatment Ge, Fellay et al. Nature 2009
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Clinical sequencing? TOMORROW Neonatal sequencing Maternal blood sequencing DTC genomics brought to doctors
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Clinical sequencing? LATER Complex trait genomics (genome data in every health record) – will depend on in-depth understanding of functional genomic variation
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Eric Green et al., Charting a course for genomic medicine from base pairs to bedside, Nature 2011 A revolution in the making
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Perspective Genomic-based medicine is around the corner Considerable space for new (personal) genomic market in health, nutrition, well-being… Genomic-based medicine is only the beginning of “big-data-based” personalized healthcare
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Perspective None of this can happen without trust