human-genome-project

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The Human Genome Project:

The Human Genome Project http://www.ornl.gov/sci/techresources/Human_Genome/education/images.shtml

Introduction:

Introduction Until the early 1970’s, DNA was the most difficult cellular molecule for biochemists to analyze. DNA is now the easiest molecule to analyze – we can now isolate a specific region of the genome, produce a virtually unlimited number of copies of it, and determine its nucleotide sequence overnight. Molecular Biology Of The Cell. Alberts et al. 491-495

Introduction:

Introduction At the height of the Human Genome Project, sequencing factories were generating DNA sequences at a rate of 1000 nucleotides per second 24/7. Technical breakthroughs that allowed the Human Genome Project to be completed have had an enormous impact on all of biology….. Molecular Biology Of The Cell. Alberts et al. 491-495

Human Genome Project:

Human Genome Project Goals: ■ identify all the approximate 30,000 genes in human DNA, ■ determine the sequences of the 3 billion chemical base pairs that make up human DNA, ■ store this information in databases, ■ improve tools for data analysis, ■ transfer related technologies to the private sector, and ■ address the ethical, legal, and social issues (ELSI) that may arise from the project. Milestones: ■ 1990: Project initiated as joint effort of U.S. Department of Energy and the National Institutes of Health ■ June 2000: Completion of a working draft of the entire human genome (covers >90% of the genome to a depth of 3-4x redundant sequence) ■ February 2001: Analyses of the working draft are published ■ April 2003: HGP sequencing is completed and Project is declared finished two years ahead of schedule U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org http://www.sanger.ac.uk/HGP/overview.shtml

PowerPoint Presentation:

What does the draft human genome sequence tell us? By the Numbers • The human genome contains 3 billion chemical nucleotide bases (A, C, T, and G). • The average gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases. • The total number of genes is estimated at around 30,000--much lower than previous estimates of 80,000 to 140,000. • Almost all (99.9%) nucleotide bases are exactly the same in all people. • The functions are unknown for over 50% of discovered genes. U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org

PowerPoint Presentation:

What does the draft human genome sequence tell us? How It's Arranged • The human genome's gene-dense "urban centers" are predominantly composed of the DNA building blocks G and C. • In contrast, the gene-poor "deserts" are rich in the DNA building blocks A and T. GC- and AT-rich regions usually can be seen through a microscope as light and dark bands on chromosomes. • Genes appear to be concentrated in random areas along the genome, with vast expanses of noncoding DNA between. • Stretches of up to 30,000 C and G bases repeating over and over often occur adjacent to gene-rich areas, forming a barrier between the genes and the "junk DNA." These CpG islands are believed to help regulate gene activity. • Chromosome 1 has the most genes (2968), and the Y chromosome has the fewest (231). U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org

PowerPoint Presentation:

What does the draft human genome sequence tell us? The Wheat from the Chaff • Less than 2% of the genome codes for proteins. • Repeated sequences that do not code for proteins ("junk DNA") make up at least 50% of the human genome. • Repetitive sequences are thought to have no direct functions, but they shed light on chromosome structure and dynamics. Over time, these repeats reshape the genome by rearranging it, creating entirely new genes, and modifying and reshuffling existing genes. • The human genome has a much greater portion (50%) of repeat sequences than the mustard weed (11%), the worm (7%), and the fly (3%). U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org

PowerPoint Presentation:

What does the draft human genome sequence tell us? How the Human Compares with Other Organisms • Unlike the human's seemingly random distribution of gene-rich areas, many other organisms' genomes are more uniform, with genes evenly spaced throughout. • Humans have on average three times as many kinds of proteins as the fly or worm because of mRNA transcript "alternative splicing" and chemical modifications to the proteins. This process can yield different protein products from the same gene. • Humans share most of the same protein families with worms, flies, and plants; but the number of gene family members has expanded in humans, especially in proteins involved in development and immunity. • Although humans appear to have stopped accumulating repeated DNA over 50 million years ago, there seems to be no such decline in rodents. This may account for some of the fundamental differences between hominids and rodents, although gene estimates are similar in these species. Scientists have proposed many theories to explain evolutionary contrasts between humans and other organisms, including those of life span, litter sizes, inbreeding, and genetic drift. U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org

PowerPoint Presentation:

What does the draft human genome sequence tell us? Variations and Mutations • Scientists have identified about 3 million locations where single-base DNA differences (SNPs) occur in humans. This information promises to revolutionize the processes of finding chromosomal locations for disease-associated sequences and tracing human history. • The ratio of germline (sperm or egg cell) mutations is 2:1 in males vs females. Researchers point to several reasons for the higher mutation rate in the male germline, including the greater number of cell divisions required for sperm formation than for eggs. U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org

What does the draft human genome sequence tell us?:

What does the draft human genome sequence tell us? Led to the discovery of whole new classes of proteins and genes, while revealing that many proteins have been much more highly conserved in evolution than had been suspected. Provided new tools for determining the functions of proteins and of individual domains within proteins, revealing a host of unexpected relationships between them. Molecular Biology Of The Cell. Alberts et al. 491-495

What does the draft human genome sequence tell us?:

What does the draft human genome sequence tell us? By making large amounts of protein available, it has yielded an efficient way to mass produce protein hormones and vaccines Dissection of regulatory genes has provided an important tool for unraveling the complex regulatory networks by which eukaryotic gene expression is controlled. Molecular Biology Of The Cell. Alberts et al. 491-495

How does the human genome stack up?:

How does the human genome stack up? Organism Genome Size (Bases) Estimated Genes Human ( Homo sapiens ) 3 billion 30,000 Laboratory mouse ( M. musculus ) 2.6 billion 30,000 Mustard weed ( A. thaliana ) 100 million 25,000 Roundworm ( C. elegans ) 97 million 19,000 Fruit fly ( D. melanogaster ) 137 million 13,000 Yeast ( S. cerevisiae ) 12.1 million 6,000 Bacterium ( E. coli ) 4.6 million 3,200 Human immunodeficiency virus (HIV) 9700 9 http://doegenomes.org

What Goals Were Established for the Human Genome Project When it Began in 1990?:

What Goals Were Established for the Human Genome Project When it Began in 1990? Identify all of the genes in human DNA. Determine the sequence of the 3 billion chemical nucleotide bases that make up human DNA. Store this information in data bases. Develop faster, more efficient sequencing technologies. Develop tools for data analysis. Address the ethical, legal, and social issues (ELSI) that are arise form the project.

Two Different Groups Worked to Obtain the DNA Sequence of the Human Genome:

Two Different Groups Worked to Obtain the DNA Sequence of the Human Genome The HGP is a multinational consortium established by government research agencies and funded publicly Celera Genomics is a private company whose former CEO, J. Craig Venter, ran an independent sequencing project Differences arose regarding who should receive the credit for this scientific milestone June 6, 2000, the HGP and Celera Genomics held a joint press conference to announce that TOGETHER they had completed ~97% of the human genome

PowerPoint Presentation:

• Gene number, exact locations, and functions • Gene regulation • DNA sequence organization • Chromosomal structure and organization • Noncoding DNA types, amount, distribution, information content, and functions • Coordination of gene expression, protein synthesis, and post-translational events • Interaction of proteins in complex molecular machines • Predicted vs experimentally determined gene function • Evolutionary conservation among organisms • Protein conservation (structure and function) • Proteomes (total protein content and function) in organisms • Correlation of SNPs (single-base DNA variations among individuals) with health and disease • Disease-susceptibility prediction based on gene sequence variation • Genes involved in complex traits and multigene diseases • Complex systems biology including microbial consortia useful for environmental restoration • Developmental genetics, genomics Future Challenges: What We Still Don’t Know U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003

Anticipated Benefits of Genome Research:

Anticipated Benefits of Genome Research Molecular Medicine • improve diagnosis of disease • detect genetic predispositions to disease • create drugs based on molecular information • use gene therapy and control systems as drugs • design “custom drugs” (pharmacogenomics) based on individual genetic profiles Microbial Genomics • rapidly detect and treat pathogens (disease-causing microbes) in clinical practice • develop new energy sources (biofuels) • monitor environments to detect pollutants • protect citizenry from biological and chemical warfare • clean up toxic waste safely and efficiently U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003

Anticipated Benefits of Genome Research-cont.:

Risk Assessment • evaluate the health risks faced by individuals who may be exposed to radiation (including low levels in industrial areas) and to cancer-causing chemicals and toxins Bioarchaeology, Anthropology, Evolution, and Human Migration • study evolution through germline mutations in lineages • study migration of different population groups based on maternal inheritance • study mutations on the Y chromosome to trace lineage and migration of males • compare breakpoints in the evolution of mutations with ages of populations and historical events U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 Anticipated Benefits of Genome Research-cont.

Anticipated Benefits of Genome Research-cont.:

DNA Identification (Forensics) • identify potential suspects whose DNA may match evidence left at crime scenes • exonerate persons wrongly accused of crimes • identify crime and catastrophe victims • establish paternity and other family relationships • identify endangered and protected species as an aid to wildlife officials (could be used for prosecuting poachers) • detect bacteria and other organisms that may pollute air, water, soil, and food • match organ donors with recipients in transplant programs • determine pedigree for seed or livestock breeds • authenticate consumables such as caviar and wine U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 Anticipated Benefits of Genome Research-cont. http://doegenomes.org

Anticipated Benefits of Genome Research-cont.:

Agriculture, Livestock Breeding, and Bioprocessing • grow disease-, insect-, and drought-resistant crops • breed healthier, more productive, disease-resistant farm animals • grow more nutritious produce • develop biopesticides • incorporate edible vaccines incorporated into food products • develop new environmental cleanup uses for plants like tobacco U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 Anticipated Benefits of Genome Research-cont. http://doegenomes.org

Medicine and the New Genetics:

Anticipated Benefits: • improved diagnosis of disease earlier detection of genetic predispositions to disease rational drug design gene therapy and control systems for drugs personalized, custom drugs Medicine and the New Genetics U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 Gene Testing  Pharmacogenomics  Gene Therapy http://doegenomes.org

ELSI: Ethical, Legal, and Social Issues:

ELSI: Ethical, Legal, and Social Issues • Privacy and confidentiality of genetic information . • Fairness in the use of genetic information by insurers, employers, courts, schools, adoption agencies, and the military, among others. • Psychological impact, stigmatization, and discrimination due to an individual’s genetic differences. • Reproductive issues including adequate and informed consent and use of genetic information in reproductive decision making. • Clinical issues including the education of doctors and other health-service providers, people identified with genetic conditions, and the general public about capabilities, limitations, and social risks; and implementation of standards and quality‑control measures. U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org

ELSI Issues (cont.):

ELSI Issues (cont.) • Uncertainties associated with gene tests for susceptibilities and complex conditions (e.g., heart disease, diabetes, and Alzheimer’s disease). • Fairness in access to advanced genomic technologies . • Conceptual and philosophical implications regarding human responsibility, free will vs genetic determinism, and concepts of health and disease. • Health and environmental issues concerning genetically modified (GM) foods and microbes. • Commercialization of products including property rights (patents, copyrights, and trade secrets) and accessibility of data and materials. U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org

Beyond the HGP: What’s Next?:

Beyond the HGP: What’s Next? HapMap Systems Biology Exploring Microbial Genomes for Energy and the Environment Chart genetic variation within the human genome http://doegenomes.org

PowerPoint Presentation:

Genomes to Life: A DOE Systems Biology Program Exploring Microbial Genomes for Energy and the Environment Goals • identify the protein machines that carry out critical life functions • characterize the gene regulatory networks that control these machines • characterize the functional repertoire of complex microbial communities in their natural environments • develop the computational capabilities to integrate and understand these data and begin to model complex biological systems http://doegenomes.org

PowerPoint Presentation:

HapMap An NIH program to chart genetic variation within the human genome • Begun in 2002, the project is a 3-year effort to construct a map of the patterns of SNPs (single nucleotide polymorphisms) that occur across populations in Africa, Asia, and the United States. • Consortium of researchers from six countries • Researchers hope that dramatically decreasing the number of individual SNPs to be scanned will provide a shortcut for identifying the DNA regions associated with common complex diseases • Map may also be useful in understanding how genetic variation contributes to responses in environmental factors http://doegenomes.org

Dideoxy Sequencing:

Dideoxy Sequencing Dideoxy sequencing (also called chain- termination or Sanger method) uses an enzymatic procedure to synthesize DNA chains of varying lengths, stopping DNA replication at one of the four bases and then determining the resulting fragment lengths. Each sequencing reaction tube (T, C, G, and A) in the diagram contains a DNA template, a primer sequence, and a DNA polymerase to initiate synthesis of a new strand of DNA at the point where the primer is hybridized to the template; the four deoxynucleotide triphosphates (dATP, dTTP, dCTP, and dGTP) to extend the DNA strand; one labeled deoxynucleotide triphosphate (using a radioactive element or dye); and one dideoxynucleotide triphosphate, which terminates the growing chain wherever it is incorporated. Tube A has didATP, tube C has didCTP, etc. http://www.ornl.gov/sci/techresources/Human_Genome/publicat/primer/fig12.html

Dideoxy Sequencing:

Dideoxy Sequencing For example, in the A reaction tube the ratio of the dATP to didATP is adjusted so that each tube will have a collection of DNA fragments with a didATP incorporated for each adenine position on the template DNA fragments. The fragments of varying length are then separated by electrophoresis and the positions of the nucleotides analyzed to determine sequence. The fragments are separated on the basis of size, with the shorter fragments moving faster and appearing at the bottom of the gel. Sequence is read from bottom to top http://www.ornl.gov/sci/techresources/Human_Genome/publicat/primer/fig12.html

Dideoxy Sequencing:

Dideoxy Sequencing Polyacrylamide gel with small pores is used to fractionate single-stranded DNA. In the size range 10 to 500 nucleotides, DNA molecules that differ in size by only a single nucleotide can be separated Lane 1- partial replicas terminating in G Lane 2- partial replicas terminating in A Lane 3- partial replicas terminating in T Lane 4- partial replicas terminating in C Alberts et al. Molecular Biology of the Cell.

PowerPoint Presentation:

Brown. Genomes 2

Capillary Electrophoresis:

Capillary Electrophoresis Technique combines the use of gel-filled capillary tubes with a unique laser scanning system to sequence each of the four different types of bases -- adenine, cytosine, guanine, and thymine -- in a sample of DNA. Capillary array electrophoresis cuts the time of the Sanger dideoxy method down by replacing the slab with hundreds of tiny gel-filled capillaries, about 100 microns (four thousandths of an inch) in internal diameter, that can be bundled into a single array for automated detection. http://www.lbl.gov/Science-Articles/Archive/automated-DNA-sequencing.html

Capillary Electrophoresis:

Capillary Electrophoresis The dideoxy method was improved by the use of fluorescent labels. The primer is synthesized and split into four batches, each of which is labeled with a different fluorescent dye. Each dye labeled primer is used in a sequencing reaction with one of the dideoxynucleotides. The reaction products are pooled and analysed in a single lane of a sequencing gel. A four-colour fluorescence detector monitors the DNA as it migrates to the bottom of the gel. The fluorescence signature is used to identify the terminal nucleotide. http://www.lbl.gov/Science-Articles/Archive/automated-DNA-sequencing.html

Capillary Electrophoresis:

Capillary Electrophoresis A method was then developed based on this where fluorescent dideoxynucleotides were used in a single sequencing reaction. The fragments are then separated in a single lane of a sequencing gel and identified by the fluorescent signature. The limitations of gel electrophoresis soon became apparent. Gels take a long time to run and have a limited reproducibility. An automated method was much more desirable, but the automation of gels requires complex robotic handling. The use of capillaries allows much higher electrical fields to be used making the separations faster. Flexible capillaries are also easily incorporated into an automated instrument making sequencing cheap, fast and efficient. However a single capillary is still a bottleneck in the sequencing process. A gel is easily capable of running up to 96 samples simultaneously. To overcome this a instrument fitted with an array of capillaries was developed. In the first instruments the detector moved across the array, but the time lag means some information can be missed. Now all the capillaries are simultaneously monitored using an array of photodiodes. http://www.chemsoc.org/exemplarchem/entries/2003/leeds_chromatography/chromatography/cge.htm

Capillary Electrophoresis:

Capillary Electrophoresis http://elchem.kaist.ac.kr/BK21_SMS.web/2001_instanal/FIG/20011029/0003_ANG_2000_04463_DNA_CAE.pdf

Capillary Electrophoresis:

Capillary Electrophoresis Capillary holds a sieving medium, which allows separation of DNA fragments based on their size Sample is injected into the capillary by placing the end of the capillary in the sample solution, and applying electric current. After injection is complete, the sample is replaced by running buffer and electric field is reapplied to drive the samples through the capillary. Laser-induced fluorescence detector near the end of the capillary records the fluorescent signal in four different channels to resolve the fluorescent signal from the four dyes. http://elchem.kaist.ac.kr/BK21_SMS.web/2001_instanal/FIG/20011029/0003_ANG_2000_04463_DNA_CAE.pdf

Capillary Electrophoresis:

Capillary Electrophoresis Small inner diameter of capillary tube reduces Joule heating to negligible levels, allowing the use of extremely high voltage, for rapid sequencing Provides a 2-fold improvement over slab gel sequencing methods http://elchem.kaist.ac.kr/BK21_SMS.web/2001_instanal/FIG/20011029/0003_ANG_2000_04463_DNA_CAE.pdf

Capillary Electrophoresis:

Capillary Electrophoresis http://ntri.tamuk.edu/ce/ce.html

Automated Sequencing:

Automated Sequencing http://www.ornl.gov/sci/techresources/Human_Genome/publicat/hgn/v10n3/images/megabaces.jpg

PowerPoint Presentation:

http://www.ornl.gov/sci/techresources/Human_Genome/education/images.shtml

PowerPoint Presentation:

Brown. Genomes 2

Shotgun Sequencing:

Shotgun Sequencing Bacteriophage fX174, was the first genome to be sequenced, a viral genome with only 5,368 base pairs (bp). Frederic Sanger, in another revolutionary discovery, invented the method of "shotgun" sequencing, a strategy based on the isolation of random pieces of DNA from the host genome to be used as primers for the PCR amplification of the entire genome. The amplified portions of DNA are then assembled by their overlapping regions to form contiguous transcripts (otherwise known as contigs). The final step involved the utilization of custom primers to elucidate the gaps between the contigs thus giving the completely sequenced genome. Sanger first used "shotgun" sequencing five years later to complete the bacteriophage l sequence that was significantly larger, 48,502 bp. This method allowed sequencing projects to proceed at a much faster rate thus expanding the scope of realistic sequencing venture. Sanger first used "shotgun" sequencing five years later to complete the bacteriophage l sequence that was significantly larger, 48,502 bp. http://bioinfo.mbb.yale.edu/course/projects/final-4/

Shotgun Sequencing:

Shotgun Sequencing A team headed by J. Craig Venter from the Institute for Genomic Research (TIGR) and Nobel laureate Hamilton Smith of Johns Hopkins University, sequenced the 1.8 Mb bacterium with new computational methods developed at TIGR's facility in Gaithersburg, Maryland. Previous sequencing projects had been limited by the lack of adequate computational approaches to assemble the large amount of random sequences produced by "shotgun" sequencing. In conventional sequencing, the genome is broken down laboriously into ordered, overlapping segments, each containing up to 40 Kb of DNA. These segments are "shotgunned" into smaller pieces and then sequenced to reconstruct the genome. Venter's team utilized a more comprehensive approach by "shotgunning" the entire 1.8 Mb H. Influenzae genome. http://bioinfo.mbb.yale.edu/course/projects/final-4/

Shotgun Sequencing:

Shotgun Sequencing Previously, such an approach would have failed because the software did not exist to assemble such a massive amount of information accurately. Software, developed by TIGR, called the TIGR Assembler was up to the task, reassembling the approximately 24,000 DNA fragments into the whole genome. After the H. Influenzae genome was "shotgunned" and the clones purified sufficiently the TIGR Assembler software required approximately 30 hours of central processing unit time on a SPARCenter 2000 containing half a gigabyte of RAM . http://bioinfo.mbb.yale.edu/course/projects/final-4/

Shotgun Sequencing:

Shotgun Sequencing Venter's H. Influenzae project had failed to win funding from the National Institute of Health indicating the serious doubts surrounding his ambitious proposal. It simply was not believed that such an approach could sequence the large 1.8 Mb sequence of the bacterium accurately. Venter proved everyone wrong and succeeded in sequencing the genome in 13 months at a cost of 50 cents per base which was half the cost and drastically faster than conventional sequencing. http://bioinfo.mbb.yale.edu/course/projects/final-4/

Dr. J. Craig Venter:

Dr. J. Craig Venter Earned his Ph.D. in Physiology and Pharmacology from the University of California at San Diego and became a researcher at the National Institutes of Health. While serving first as a Section Chief and then as a Lab Chief in the National Institute of Neurological Disorders and Stroke, he developed expressed sequence tags or EST’s, a revolutionary new strategy for gene discovery. In 1992, he and his wife, Dr. Claire Fraser, founded The Institute for Genomic Research known as TIGR, where he served as President and Chief Scientific Officer until 1998. Dr. Venter and his team at TIGR decoded the genome of the bacterium Haemophilus influenzae, making it the first free-living organism to have its full DNA deciphered and to date have sequenced over 30 genomes. He now serves as Chairman of the Board of Trustees of TIGR. In 1998, he founded Celera Genomics and announced that Celera would decode the human genome faster and more economically than the publicly funded consortium of scientists. That challenge is now credited with creating the climate of urgency that spurred competition and substantially accelerated the project’s successful conclusion. At the White House press conference announcing the sequencing of the human genome, President Bill Clinton called it “the most important, most wondrous map ever produced by mankind.” http://www.harrywalker.com/speakers_template.cfm?spea_id=549

mRNA Sequencing:

mRNA Sequencing An alternative strategy for sequencing was presented during the early 90’s by Craig Venter. The functional portion of the human DNA supposedly accounts for less than 10% (perhaps less than 5%) of the entire human genome. The HGP strategy, i.e. sequencing everything, could be considered as lavishness with resources since the main part of the information lacks relevance. The scope of the strategy by Venter and co-workers is to focus the investigations to messenger ribonucleic acid (mRNA) instead of DNA. The point of using mRNA is that it does not include any non-coding DNA. The mRNA molecule can be isolated and used as a template to synthesize a complementary DNA (cDNA) strand, which can then be used to locate the corresponding genes on a chromosome map. By using Venter´s method an incomplete copy of the gene, called expressed sequence tag (EST), is acquired. ESTs are useful for localizing and orienting the mapping and sequence data reported from many different laboratories and serve as landmarks on the developing physical map of the human genome. http://wcn.ntech.se/history.html

Whole Genome Shotgun Sequencing:

Whole Genome Shotgun Sequencing Venter and co-workers success in 1995 of sequencing the H. influenzae bacterium introduced a method called "whole genome shotgun sequencing". The shotgun method involves randomly sequencing tiny cloned sections of the genome, with no foreknowledge of where on a chromosome the section originally came from. The partial sequences obtained are then reassembled to a complete sequence by use of computers. The advantage with this method is that it eliminates the need for time-consuming mapping. By competing (and cooperating) the governmentally financed human genome project (HGP) and the private biotechnology company Celera has completed a reference DNA sequence of the human genome. Both parties made their information simultaneously available in February 2001, by publishing it in on the Internet and in the scientific journals Nature and Science. http://wcn.ntech.se/history.html

Whole Genome Shotgun Sequencing :

Whole Genome Shotgun Sequencing After the sequence is shotgunned the 10 million fragments of the genomic jigsaw puzzle need to be recompiled into the readable base pairs in the proper order. This method will be completed using a 10x redundancy to eliminate errors and reduce the possibility of having misses any targeted regions. The Celera Assembler is one of the core competencies and makes this Herculean task possible. The first pass through the data the shotgunned fragments are compared against each other and equivalent sequences greater than 40 base pairs long identified. These 40 base pairs matches are statistically impossible to occur by chance. These matches are then determined to be true or repeat induced. True matches are overlapping sections and are the desired fragments; repeat-induced fragments occur in multiple locations of the genome and do not belong together. http://www-management.wharton.upenn.edu/pennings/coursedocuments/executive_education_courses/557/genome%20Paper%201.doc

Whole Genome Shotgun Sequencing:

Whole Genome Shotgun Sequencing The assembler then searches for overlapping fragments that have a common sequence and are not contested elsewhere in the dataset. The uncontested data is assembled into unitigs containing approximately 30 fragments. These assembled unitigs are 99 % accurate and repeats are filtered out using the Discriminator algorithm. Unitigs passing this filter are identified and renamed U-untigs that are ready for ordering. The scaffolding stage starts and the order found by looking at the mate pairs and organizing these into contigs. By constantly looking at these contigs and looking at the orientation the scaffold become complete except for some sequencing gaps. This strategy is repeated until the gaps are filled using the Discriminator algorithm and a method using sequence “rocks” and “pebbles”. http://www-management.wharton.upenn.edu/pennings/coursedocuments/executive_education_courses/557/genome%20Paper%201.doc

Whole Genome Shotgun Sequencing:

Whole Genome Shotgun Sequencing As HGP has been making public the incremental sequence the shotgun approach utilized this data to help eliminate errors and speed the scaffolding process. http://www-management.wharton.upenn.edu/pennings/coursedocuments/executive_education_courses/557/genome%20Paper%201.doc

Sequence Gaps:

Sequence Gaps Brown. Genomes 2

Advances:

Advances The following advances in robotics and automation reduced the labor by 80% while combining the microbiological advances: Development of Perkin-Elmer (ABI PRISM 3700) gene sequence. 1000 sample per day 15 minutes instead of 8 hours for first automated sequencers A parallel system of 300 sequencers ($300,000 each) Use of supercomputers to assemble fragments Development of process support instrumentation to process 100 K template preps and 200 K sequence reactions per day. 24 hour per day unattended operation of sequencers http://www-management.wharton.upenn.edu/pennings/coursedocuments/executive_education_courses/557/genome%20Paper%201.doc

PowerPoint Presentation:

Map of Chromosome 16 http://www.ornl.gov/sci/techresources/Human_Genome/education/images.shtml

Advances:

Advances In addition to the above advances the field of computational biology (bioinformatics) became increasingly important as the software and processors required to assemble a puzzle of this size still needed to be developed. The solution came in advances in processor speeds that have doubled every 18 months and the development of better overlap detection algorithms. It is expected that using 100 networked workstations the entire genome could be assembled in 30-60 computational days. http://www-management.wharton.upenn.edu/pennings/coursedocuments/executive_education_courses/557/genome%20Paper%201.doc

Costs of Human Genomic Sequencing:

Costs of Human Genomic Sequencing Clone by clone $0.30 per finished base $130 million per year for 7 years Total $900 million spent by end of 2003 Shotgun $0.01 per raw base $130 million for 3 years would provide 10× coverage/redundancy plus an additional $90 million for informatics http://www-management.wharton.upenn.edu/pennings/coursedocuments/executive_education_courses/557/genome%20Paper%201.doc

Human Genome Projects Progress:

Human Genome Projects Progress http://www-management.wharton.upenn.edu/pennings/coursedocuments/executive_education_courses/557/genome%20Paper%201.doc

Algorithms:

Algorithms Human Genome Project: GigAssembler Celera: Celera Assembler Euler Algorithm http://www.genome.org/cgi/content/full/11/9/1461 http://www.cs.ucsd.edu/~htang/assembly.html

Gigassemler:

Gigassemler Assembly Process Overview: The assembly proceeds according to the following major steps: Decontaminating and repeat masking the sequence. Alignment of mRNA, EST, BAC end, and paired plasmid reads against genomic fragments. On a cluster of one hundred 800 MhZ Pentium III CPUs running Linux this takes about three days. Creating an input directory structure with using Washington University map and other data. This step takes about an hour on a single computer. For each fingerprint clone contig, aligning the fragments within that contig against each other. This takes about three hours on the cluster. Using the GigAssembler program within each fingerprint clone contig to merge overlapping fragments and to order and orient the resulting sequence contigs into scaffolds. This takes about two hours on the cluster. Combining the contig assemblies into full chromosome assemblies. This takes about twenty minutes on one computer. http://www.cse.ucsc.edu/~learithe/browser/goldenPath/algo.html

Algorithms & Related Material:

Algorithms & Related Material http://portal.acm.org/citation.cfm?id=369190&jmp=citings&dl=GUIDE&dl=ACM http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11504945 http://www.genome.org/cgi/content/full/11/9/1461 http://www.genome.org/cgi/content/full/7/5/401 http://www.pnas.org/cgi/content/full/98/17/9748 http://www.cse.ucsc.edu/~learithe/browser/goldenPath/algo.html http://www.eecs.berkeley.edu/~gene/Papers/greedy.path.merging.pdf --> ***detailed algorithm description***

Homework:

Homework http://www.bioperl.org/GetStarted/tpj_ls_bio.html Lincoln Stein’s classic article on “How Perl Saved The Human Genome Project” http://www.eecs.berkeley.edu/~gene/Papers/greedy.path.merging.pdf Celera Assembler Algorithm