Human Genome Project PDF

Human Genome Project Outline I. Human Genome Project II. Cloning Experiment III. Sequencing Methods Outline I. Human Genome Project II. Cloning Experiment III. Sequencing Methods I. Human Genome Project What is Human Genome Project (HGP) ? An international scientific research...

Human Genome Project Outline I. Human Genome Project II. Cloning Experiment III. Sequencing Methods Outline I. Human Genome Project II. Cloning Experiment III. Sequencing Methods I. Human Genome Project What is Human Genome Project (HGP) ? An international scientific research project that aims to identify the base pairs that make up the human DNA, to describe all genes of the human genome physically and functionally, and to map the gene. o Beginning: 1990 o Finish: 2003 I. Human Genome Project Who took part in the HG Project? US Department of Energy (DOE) Celera, IBM, American National Institute of Health (NIH) Compaq, Dupond Australia, Israel, Brazil, Italy, Canada, Japan, Chinese, Holland, Denmark, Korea, France, Mexican, Germany, Russia, Britain, Sweden I. Human Genome Project Health and Human Services (HHS) established the National Human Genome Research Center (NCHGR) to run the American National Institutes of Health 1989 (NIH) component of the United States Human Genome Project. The first director of the center was James D. Watson, who discovered the double helix structure of DNA together. The NIH and DOE have released a plan for the first five years of an anticipated 15-year project. 1990 Among the objectives of the project are the following. ⇥ Mapping the human genome, ⇥ Determining the order of all 3.2 billion letters, ⇥ mapping and sequencing the genomes of other organisms important to the study of biology, ⇥ Developing technologies to analyze DNA. I. Human Genome Project Terminology I. Human Genome Project I. Human Genome Project I. Human Genome Project I. Human Genome Project I. Human Genome Project Further Reading ⇥ Hood, L. & Galas, D. The digital code of DNA. Nature 421, 444–448 (2003) (link to article) ⇥ International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001) (link to article) ⇥ International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931–945 (2004) (link to article) ⇥ Venter, J. C., et al. The sequence of the human genome. Science 291, 1304–1351 (2001) (link to article) I. Human Genome Project The sequencing journey for different organisms Human Genome Project Timeline of Events https://www.genome.gov/human-genome-project/Timeline-of-Events I. Human Genome Project PEOPLE ARE DIFFERENT I. Human Genome Project Genomics Transcriptomics Proteomics Epigenomics Metabolomics I. Human Genome Project Single-Nucleotide Polymorphism Outline I. Human Genome Project II. Cloning Experiment III. Sequencing Methods II. Cloning Experiment II. Cloning Experiment Cloning Genes Gene cloning: amplifying a specific piece of DNA via a bacteria cell Cloning vector: a replicating DNA molecule attached with a foreign DNA fragment to be introduced into a cell – Has features that make it easier to insert DNA and select for presence of vector in cell. Origin of replication Antibiotic resistance gene Cloning site II. Cloning Experiment II. Cloning Experiment Cloning Genes Plasmid vectors Linkers: synthetic DNA fragments containing restriction sites Transformation of host cells with plasmids Selectable markers are used to confirm whether the cells have been transformed or not. II. Cloning Experiment II. Cloning Experiment II. Cloning Experiment II. Cloning Experiment II. Cloning Experiment Outline I. Human Genome Project II. Cloning Experiment III. Sequencing Methods III. DNA Sequencing Methods Discovery Of DNA Structure and Function ⇥ Deoxyribonucleic acid (DNA) was first discovered and isolated by Friedrich Miescher in 1869. ⇥ In 1953, James Watson and Francis Crick introduced double- Rosalind Franklin Frederick Sanger stranded DNA models based on crystallized X-ray structures pioneer of sequencing studied by Rosalind Franklin. ⇥ The basis for sequencing proteins was first laid in 1955 by the work of Frederick Sanger, who completed the sequence of all the amino acids in insulin, a small protein secreted by the pancreas. James Watson, Francis Crick III. DNA Sequencing Methods Early DNA sequencing methods Chain-termination Methods Maxam-Gilbert Sequencing 1977 1977 Frederick Sanger et al. Allan Maxam and Walter Gilbert Also known as Sanger sequencing. Also known as chemical sequencing. III. DNA Sequencing Methods III. DNA Sequencing Methods What is required for Sanger sequencing? 1) Single-stranded DNA template 2) Primer for DNA synthesis 3) DNA polymerase 4) Deoxynucleotide triphosphates and dideoxynucleotide triphosphates III. DNA Sequencing Methods III. DNA Sequencing Methods Large-Scale Sequencing 1. DNA fragments are broken down into shorter DNA fragments. 2. The fragmented DNAs are cloned into the DNA vector. 3. Amplified in a bacterial host such as Escherichia coli. 4. Short pieces of DNA are sequenced separately. 5. Electronically combined into a long, contiguous string Shotgun method: Analysis of DNA sequences longer than 1000 base pairs III. DNA Sequencing Methods Next Generation Sequencing (NGS) Next-generation sequencing has not only brought high-speed genome sequencing and personalized medicine technology, but also changed the way we look at genome research. NGS - high sequencing capacity With the next generation sequencing technology, hundreds of millions of short sequences (35bp-120bp) are sequenced in a very short time with low cost in a single run. III. DNA Sequencing Methods Next Generation Sequencing (NGS) Application Areas ▪ Transcriptome ▪ Ancestral DNA ▪ Metagenomics ▪ Agricultural Biotechnology ▪ Small RNAs ▪ Methylation Analysis ▪ Chromatin Immunoprecipitation ▪ Sequencing (ChIP-Seq) NGS Systems NGS Methods ▪ Roche 454 Genom Analiz Cihazı ▪ Illumina Genom Analiz Cihazı ▪ Pyrolysis ▪ İyon Torrent ▪ Sanger sequencing ▪ Sequencing by ligation ▪ Ion semiconductor sequencing ▪ Nano sequencing III. DNA Sequencing Methods Bioinformatics Challenges in Analyzing NGS Data → Presence of very large text files It is impossible to store these files in memory These files are very difficult to manage, analyze, store and transfer. → The need for powerful computers and experts Creation of new algorithms and software and their publicly available Linux-based Cooperation of biologists, bioinformaticians and information technology department III. DNA Sequencing Methods Thank You