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Encyclopedia > Human Genome Project

The Human Genome Project (HGP) is an international scientific research project. Its goal is to understand the genetic make-up of the human species by determining the sequence of chemical base pairs which make up DNA, and to identify the 20,000-25,000 genes of the human genome. The project also focused on several other nonhuman organisims such as Escherichia coli, the fruit fly, and a laboratory mouse. It was one of the largest investigational projects in modern science.[citation needed] Image File history File links Broom_icon. ... Image File history File links Broom_icon. ... A scientific method or process is considered fundamental to the scientific investigation and acquisition of new knowledge based upon physical evidence. ... Look up Genetic in Wiktionary, the free dictionary. ... This article is about modern humans. ... E. coli redirects here. ...


The project began in 1990 initially headed by James D. Watson. A working draft of the genome was released in 2000 and a complete one in 2003, with further analysis still being published. James Dewey Watson (born April 6, 1928) is an American molecular biologist, best known as one of the co-discoverers of the structure of DNA. Watson, Francis Crick, and Maurice Wilkins were awarded the 1962 Nobel Prize in Physiology or Medicine for their discoveries concerning the molecular structure of nucleic...


A parallel project was conducted by the private company Celera Genomics. Most of the sequencing was performed in universities and research centers from the United States and Great Britain. The term privately held company refers to ownership of a business company in two different ways—first, referring to ownership by non-governmental organizations; and second, referring to ownership of the companys stock by a relatively small number of holders who do not trade the stock publicly. ... Celera Genomics (NYSE: CRA) is a business unit of the Applera Corporation that focuses on genetic sequencing and related technologies. ...


The mapping of human genes is an important step in the development of medicines and other aspects of health care.


The HGP originally aimed to map the nucleotides contained in a haploid reference human genome (more than three billion). Several groups have announced efforts to extend this to diploid human genomes including the International HapMap Project, Applied Biosystems, Perlegen, Illumina, JCVI, Personal Genome Project, and Roche-454. Haploid (meaning simple in Greek) cells have only one copy of each chromosome. ... Diploid (meaning double in Greek) cells have two copies (homologs) of each chromosome (both sex- and non-sex determining chromosomes), usually one from the mother and one from the father. ... The goal of the International HapMap Project is to develop a haplotype map of the human genome, also referred to as the HapMap, which will describe the common patterns of human genetic variation. ... Illumina (NASDAQ: ILMN) has developed a targeted set of instruments and chips for organizations conducting larger-scale research in genotyping and gene expression profiling. ... Aquatic metagenomics is one of the Institutes interests. ... The Personal Genome Project aims to publish the complete genomes and medical records of several volunteers, in order to enable research into personalized medicine. ... 454 Life Sciences is a biotechnology company based in Branford, Connecticut specializing in high-throughput DNA sequencing using a novel massively parallel sequencing-by-synthesis approach. ...


The "genome" of any given individual (except for identical twins and cloned animals) is unique; mapping "the human genome" involves sequencing multiple variations of each gene. The project did not study all of the DNA found in human cells; some heterochromatic areas (about 8% of the total) remain un-sequenced. Fraternal twin boys in the tub The term twin most notably refers to two individuals (or one of two individuals) who have shared the same uterus (womb) and usually, but not necessarily, born on the same day. ... For other uses, see clone. ... There are about 210 distinct human cell types. ... For differently-colored eyes, see Heterochromia. ...

Contents

The Project

Background

Initiation of the Project was the culmination of several years of work supported by the Department of Energy, in particular workshops in 1984 [1] and 1986 and a subsequent initiative the Department of Energy.[2] This 1986 report stated boldly, "The ultimate goal of this initiative is to understand the human genome" and "Knowledge of the human genome is as necessary to the continuing progress of medicine and other health sciences as knowledge of human anatomy has been for the present state of medicine." Candidate technologies were already being considered for the proposed undertaking at least as early as 1985.[3] The United States Department of Energy (DOE) is a Cabinet-level department of the United States government responsible for energy policy and nuclear safety. ... List of bones of the human skeleton Human anatomy is primarily the scientific study of the morphology of the adult human body. ... This article is about the year. ...


James D. Watson was Head of the National Center for Human Genome Research at the National Institutes of Health (NIH) in the United States starting from 1988. Largely due to his disagreement with his boss, Bernadine Healy, over the issue of patenting genes, he was forced to resign in 1992. He was replaced by Francis Collins in April 1993, and the name of the Center was changed to the National Human Genome Research Institute (NHGRI) in 1997. James Dewey Watson (born April 6, 1928) is an American molecular biologist, best known as one of the co-discoverers of the structure of DNA. Watson, Francis Crick, and Maurice Wilkins were awarded the 1962 Nobel Prize in Physiology or Medicine for their discoveries concerning the molecular structure of nucleic... Year 1988 (MCMLXXXVIII) was a leap year starting on Friday (link displays 1988 Gregorian calendar). ... Dr. Bernadine Patricia Healy (b. ... // Introduction Gene patents are patents on specific sequences of genes. ... Year 1992 (MCMXCII) was a leap year starting on Wednesday (link will display full 1992 Gregorian calendar). ... This article needs to be wikified. ... The National Human Genome Research Institute (NHGRI) is a division of the National Institutes of Health, located in Bethesda, Maryland. ... For the band, see 1997 (band). ...


The $3-billion project was formally founded in 1990 by the United States Department of Energy and the U.S. National Institutes of Health, and was expected to take 15 years. In addition to the United States, the international consortium comprised geneticists in China, France, Germany, Japan, and the United Kingdom. Research funding is a term generally covering any funding for scientific research, in the areas of both hard science and technology, and social science. ... Year 1990 (MCMXC) was a common year starting on Monday (link displays the 1990 Gregorian calendar). ... The United States Department of Energy (DOE) is a Cabinet-level department of the United States government responsible for energy policy and nuclear safety. ... The National Institutes of Health is an institution of the United States government which focuses on medical research. ... A consortium is an association of two or more individuals, companies, organisations or governments (or any combination of these entities) with the objective of participating in a common activity or pooling their resources for achieving a common goal. ... A geneticist is a scientist who studies genetics, the science of heredity and variation of organisms. ...


Due to widespread international cooperation and advances in the field of genomics (especially in sequence analysis), as well as major advances in computing technology, a 'rough draft' of the genome was finished in 2000 (announced jointly by then US president Bill Clinton and British Prime Minister Tony Blair on June 26, 2000).[4] Ongoing sequencing led to the announcement of the essentially complete genome in April 2003, 2 years earlier than planned.[5] In May 2006, another milestone was passed on the way to completion of the project, when the sequence of the last chromosome was published in the journal Nature.[6] Genomics is the study of an organisms entire genome; Rathore et al, . Investigation of single genes, their functions and roles is something very common in todays medical and biological research, and cannot be said to be genomics but rather the most typical feature of molecular biology. ... The term sequence analysis in biology implies subjecting a DNA or peptide sequence to sequence alignment, sequence databases, repeated sequence searches, or other bioinformatics methods on a computer. ... Year 2000 (MM) was a leap year starting on Saturday (link will display full 2000 Gregorian calendar). ... William Jefferson Bill Clinton (born William Jefferson Blythe III[1] on August 19, 1946) was the 42nd President of the United States, serving from 1993 to 2001. ... The Prime Minister of the United Kingdom of Great Britain and Northern Ireland is, in practice, the political leader of the United Kingdom. ... For other people of the same name, see Tony Blair (disambiguation) Anthony Charles Lynton Blair (born May 6, 1953)[1] is the Prime Minister of the United Kingdom, First Lord of the Treasury, Minister for the Civil Service, Leader of the Labour Party, and Member of Parliament for the constituency... is the 177th day of the year (178th in leap years) in the Gregorian calendar. ... In genetics and biochemistry, sequencing means to determine the primary structure (or primary sequence) of an unbranched biopolymer. ... Year 2006 (MMVI) was a common year starting on Sunday of the Gregorian calendar. ... Chromosome 1 is, by convention, the designation for the largest human chromosome. ... Nature is a prominent scientific journal, first published on 4 November 1869. ...


There are multiple definitions of the "complete sequence of the human genome". According to some of these definitions, the genome has already been completely sequenced, and according to other definitions, the genome has yet to be completely sequenced. There have been multiple popular press articles reporting that the genome was "complete." The genome has been completely sequenced using the definition employed by the International Human Genome Project. A graphical history of the human genome project shows that most of the human genome was complete by the end of 2003. However, there are a number of regions of the human genome that can be considered unfinished. First, the central regions of each chromosome, known as centromeres, are highly repetitive DNA sequences that are difficult to sequence using current technology. The centromeres are millions (possibly tens of millions) of base pairs long, and for the most part these are entirely un-sequenced. Second, the ends of the chromosomes, called telomeres, are also highly repetitive, and for most of the 46 chromosome ends these too are incomplete. We do not know precisely how much sequence remains before we reach the telomeres of each chromosome, but as with the centromeres, current technology does not make it easy to get there. Third, there are several loci in each individual's genome that contain members of multigene families that are difficult to disentangle with shotgun sequencing methodologies - these multigene families often encode proteins important for immune functions. It is likely that the centromeres and telomeres will remain un-sequenced until new technology is developed that facilitates their sequencing. Other than these regions, there remain a few dozen gaps scattered around the genome, some of them rather large, but there is hope that all these will be closed in the next couple of years. In summary: our best estimates of total genome size indicate that about 92% of the genome has been completed . Most of the remaining DNA is highly repetitive and unlikely to contain genes, but we cannot truly know until we sequence all of it. Understanding the functions of all the genes and their regulation is far from complete. The roles of junk DNA, the evolution of the genome, the differences between individuals, and many other questions are still the subject of intense study by laboratories all over the world. The centromere is a region on chromosomes with a special sequence and structure. ... DNA replication Deoxyribonucleic acid (DNA) is a nucleic acid which carries genetic instructions for the biological development of all cellular forms of life and many viruses. ... Base pairs, of a DNA molecule. ... A telomere is a region of highly repetitive DNA at the end of a chromosome, which functions as an aglet. ... Shotgun sequencing is a method used in genetics for sequencing long DNA strands. ... A scanning electron microscope image of a single neutrophil (yellow), engulfing anthrax bacteria (orange). ... In molecular biology, junk DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified. ...


Goals

The goals of the original HGP were not only to determine more than 3 billion base pairs in the human genome with a minimal error rate, but also to identify all the genes in this vast amount of data. This part of the project is still ongoing, although a preliminary count indicates about 22,000–23,000 genes in the human genome,[citation needed] which is fewer than predicted by many scientists.[citation needed]


Another goal of the HGP was to develop faster, more efficient methods for DNA sequencing and sequence analysis and the transfer of these technologies to industry. In genetics and biochemistry, sequencing means to determine the primary structure (or primary sequence) of an unbranched biopolymer. ... The term sequence analysis in biology implies subjecting a DNA or peptide sequence to sequence alignment, sequence databases, repeated sequence searches, or other bioinformatics methods on a computer. ...


The sequence of the human DNA is stored in databases available to anyone on the Internet. The U.S. National Center for Biotechnology Information (and sister organizations in Europe and Japan) house the gene sequence in a database known as Genbank, along with sequences of known and hypothetical genes and proteins. Other organizations such as the University of California, Santa Cruz[1], and Ensembl[2] present additional data and annotation and powerful tools for visualizing and searching it. Computer programs have been developed to analyze the data, because the data themselves are difficult to interpret without such programs. The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ... This article is about computing. ... The National Center for Biotechnology Information (NCBI) is part of the US National Library of Medicine (NLM), which is a branch of the US National Institutes of Health. ... The GenBank sequence database is an annotated collection of all publicly available nucleotide sequences and their protein translations. ... The University of California, Santa Cruz (UCSC or UC Santa Cruz) is a coeducational public university located in Santa Cruz, California. ... Ensembl is a bioinformatics research project aiming to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. It is run in a collaboration between the Wellcome Trust Sanger Institute and the European Bioinformatics Institute, an outstation of the European Molecular Biology Laboratory. ... A computer program is a collection of instructions that describe a task, or set of tasks, to be carried out by a computer. ...


The process of identifying the boundaries between genes and other features in raw DNA sequence is called genome annotation and is the domain of bioinformatics. While expert biologists make the best annotators, their work proceeds slowly, and computer programs are increasingly used to meet the high-throughput demands of genome sequencing projects. The best current technologies for annotation make use of statistical models that take advantage of parallels between DNA sequences and human language, using concepts from computer science such as formal grammars. Genome annotation is the process of attaching biological information to sequences. ... Map of the human X chromosome (from the NCBI website). ... In computer science and linguistics, a formal grammar, or sometimes simply grammar, is a precise description of a formal language — that is, of a set of strings. ...


Another, often overlooked, goal of the HGP is the study of its ethical, legal, and social implications. It is important to research these issues and find the most appropriate solutions before they become large dilemmas whose effect will manifest in the form of major political concerns.


All humans have unique gene sequences; therefore the data published by the HGP does not represent the exact sequence of each and every individual's genome. It is the combined genome of a small number of anonymous donors. The HGP genome is a scaffold for future work in identifying differences among individuals. Most of the current effort in identifying differences among individuals involves single nucleotide polymorphisms and the HapMap. DNA strand 1 differs from DNA strand 2 at a single base-pair location (a C/T polymorphism). ... The goal of the International HapMap Project is to develop a haplotype map of the human genome, also referred to as the HapMap, which will describe the common patterns of human genetic variation. ...


How it was accomplished

Funding came from the US government through the National Institutes of Health in the United States, and the UK charity, the Wellcome Trust, who funded the Sanger Institute (then the Sanger Centre) in Great Britain, as well as numerous other groups from around the world. The genome was broken into smaller pieces; approximately 150,000 base pairs in length. These pieces are called "bacterial artificial chromosomes", or BACs, because they can be inserted into bacteria where they are copied by the bacterial DNA replication machinery. Each of these pieces was then sequenced separately as a small "shotgun" project and then assembled. The larger, 150,000 base pairs go together to create chromosomes. This is known as the "hierarchical shotgun" approach, because the genome is first broken into relatively large chunks, which are then mapped to chromosomes before being selected for sequencing. The Wellcome Trusts Gibbs Building on Euston Road The Wellcome Trust is a United Kingdom-based charity established in 1936 to administer the fortune of the American-born pharmaceutical magnate Sir Henry Wellcome. ... The Wellcome Trust Sanger Institute (formally the Sanger Centre) is a genome research centre in Cambridgeshire, England. ... A bacterial artificial chromosome (BAC) is a DNA construct, based on a fertility plasmid (or F-plasmid), used for transforming and cloning in bacteria, usually E. coli. ... DNA replication. ...


Celera Genomics HGP

In 1998, a similar, privately funded quest was launched by the American researcher Craig Venter and his firm Celera Genomics. The $300 million Celera effort was intended to proceed at a faster pace and at a fraction of the cost of the roughly $3 billion publicly funded project. Craig Venter, 2007 J. Craig Venter (born John Craig Venter October 14, 1946, Salt Lake City) is an American biologist and businessman. ... Celera Genomics (NYSE: CRA) is a business unit of the Applera Corporation that focuses on genetic sequencing and related technologies. ... Research funding is a term generally covering any funding for scientific research, in the areas of both hard science and technology, and social science. ...


Celera used a riskier technique called whole genome shotgun sequencing, which had been used to sequence bacterial genomes of up to six million base pairs in length, but not for anything nearly as large as the three thousand million base pair human genome. Whole genome shotgun sequencing is a semi-automated technique for shotgun sequencing DNA, in which high-molecular-weight DNA is sheared into random fragments, size selected (usually 2, 10, 50, and 150 kb), and cloned into an appropriate vector. ...


Celera initially announced that it would seek patent protection on "only 200-300" genes, but later amended this to seeking "intellectual property protection" on "fully-characterized important structures" amounting to 100-300 targets. The firm eventually filed preliminary ("place-holder") patent applications on 6,500 whole or partial genes. Celera also promised to publish their findings in accordance with the terms of the 1996 "Bermuda Statement," by releasing new data quarterly (the HGP released its new data daily), although, unlike the publicly funded project, they would not permit free redistribution or commercial use of the data. Year 1996 (MCMXCVI) was a leap year starting on Monday (link will display full 1996 Gregorian calendar). ... The Bermuda Principles are a set of agreements made by researchers involved in the sequencing of the human genome during a meeting on the Bermudas in 1996. ...


In March 2000, President Clinton announced that the genome sequence could not be patented, and should be made freely available to all researchers. The statement sent Celera's stock plummeting and dragged down the biotechnology-heavy Nasdaq. The biotechnology sector lost about $50 billion in market capitalization in two days. 2000 : January - February - March - April - May - June - July - August - September - October - November - December This is a timeline for events in March, 2000. ... William Jefferson Bill Clinton (born William Jefferson Blythe III[1] on August 19, 1946) was the 42nd President of the United States, serving from 1993 to 2001. ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... The structure of insulin Biotechnology is technology based on biology, especially when used in agriculture, food science, and medicine. ... NASDAQ in Times Square, New York City. ... Market capitalization, or market cap, is a measurement of corporate or economic size equal to the stock price times the number of shares outstanding of a public company. ...


Although the working draft was announced in June 2000, it was not until February 2001 that Celera and the HGP scientists published details of their drafts. Special issues of Nature (which published the publicly funded project's scientific paper)[7] and Science (which published Celera's paper[8]) described the methods used to produce the draft sequence and offered analysis of the sequence. These drafts covered about 83% of the genome (90% of the euchromatic regions with 150,000 gaps and the order and orientation of many segments not yet established). In February 2001, at the time of the joint publications, press releases announced that the project had been completed by both groups. Improved drafts were announced in 2003 and 2005, filling in to ~92% of the sequence currently. Nature is a prominent scientific journal, first published on 4 November 1869. ... Academic publishing describes the subfield of publishing which distributes academic research and scholarship. ... Science is the journal of the American Association for the Advancement of Science (AAAS). ... For information on Wikipedia press releases, see Wikipedia:Press releases. ...


The competition proved to be very good for the project, spurring the public groups to modify their strategy in order to accelerate progress. The rivals initially agreed to pool their data, but the agreement fell apart when Celera refused to deposit its data in the unrestricted public database GenBank. Celera had incorporated the public data into their genome, but forbade the public effort to use Celera data. The GenBank sequence database is an annotated collection of all publicly available nucleotide sequences and their protein translations. ...


HGP is the most well known of many international genome projects aimed at sequencing the DNA of a specific organism. While the human DNA sequence offers the most tangible benefits, important developments in biology and medicine are predicted as a result of the sequencing of model organisms, including mice, fruit flies, zebrafish, yeast, nematodes, plants, and many microbial organisms and parasites. Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus). ... part of a DNA sequence A DNA sequence (sometimes genetic sequence) is a succession of letters representing the primary structure of a real or hypothetical DNA molecule or strand, The possible letters are A, C, G, and T, representing the four nucleotide subunits of a DNA strand (adenine, cytosine, guanine... A model organism is one that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workings of other organisms. ... This article is about the animal. ... Species Drosophila melanogaster Drosophila subobscura Drosophila is a genus of small flies whose members are often called fruit flies or more appropriately vinegar flies, wine flies, pomace flies, grape flies, and picked fruit-flies. ... Binomial name Danio rerio (Hamilton-Buchanan, 1822) The Zebra Danio or Zebrafish (Brachydanio rerio or Danio rerio) is a tropical fish belonging to the minnow family (Cyprinidae). ... Typical divisions Ascomycota (sac fungi) Saccharomycotina (true yeasts) Taphrinomycotina Schizosaccharomycetes (fission yeasts) Basidiomycota (club fungi) Urediniomycetes Sporidiales Yeasts are a growth form of eukaryotic microorganisms classified in the kingdom Fungi, with approximately 1,500 species described. ... Classes Adenophora    Subclass Enoplia    Subclass Chromadoria Secernentea    Subclass Rhabditia    Subclass Spiruria    Subclass Diplogasteria The roundworms (Phylum Nematoda) are one of the most common phyla of animals, with over 20,000 different described species. ... Binomial name Arabidopsis thaliana (L.) Heynh. ... A microorganism or microbe is an organism that is so small that it is microscopic (invisible to the naked eye). ... A parasite is an organism that spends a significant portion of its life in or on the living tissue of a host organism and which causes harm to the host without immediately killing it. ...


In 2004, researchers from the International Human Genome Sequencing Consortium (IHGSC) of the HGP announced a new estimate of 20,000 to 25,000 genes in the human genome.[9] Previously 30,000 to 40,000 had been predicted, while estimates at the start of the project reached up to as high as 2,000,000. The number continues to fluctuate and it is now expected that it will take many years to agree on a precise value for the number of genes in the human genome.


History

In 1976, the genome of the virus Bacteriophage MS2 was the first complete genome to be determined, by Walter Fiers and his team at the University of Ghent (Ghent, Belgium).[10] The idea for the shotgun technique came from the use of an algorithm that combined sequence information from many small fragments of DNA to reconstruct a genome. This technique was pioneered by Frederick Sanger to sequence the genome of the Phage Φ-X174, a tiny virus called a bacteriophage that was the first fully sequenced genome (DNA-sequence) in 1977.[11] The technique was called shotgun sequencing because the genome was broken into millions of pieces as if it had been blasted with a shotgun. In order to scale up the method, both the sequencing and genome assembly had to be automated, as they were in the 1980s. Year 1976 Pick up sticks(MCMLXXVI) was a leap year starting on Thursday (link will display full calendar) of the Gregorian calendar. ... This article is about biological infectious particles. ... The bacteriophage MS2 or Bacillus phage M2 (Caudovirales, Podoviridae) infects Bacillus subtilis. ... Walter Fiers was born in Ieper (Belgium) in 1931. ... Ghent University (in Dutch, Universiteit Gent, abbreviated UGent) is one of the two large Flemish universities. ... This article is about the Belgian city. ... In mathematics, computing, linguistics, and related disciplines, an algorithm is a finite list of well-defined instructions for accomplishing some task that, given an initial state, will terminate in a defined end-state. ... Frederick Sanger, OM, CH, CBE, FRS (born 13 August 1918) is an English biochemist and a two time Nobel laureate in chemistry. ... The Phi-X174 phage was the first organism to have its genome sequenced. ... An artists rendering of an Enterobacteria phage T4. ... Also: 1977 (album) by Ash. ... Shotgun sequencing is a method used in genetics for sequencing long DNA strands. ... In genetics and biochemistry, sequencing means to determine the primary structure (or primary sequence) of an unbranched biopolymer. ... Genome assembly refers to the process of taking a large number of short DNA sequences, all of which were generated by a shotgun sequencing project, and putting them back together to create a representation of the original chromosomes from which the DNA originated. ... The 1980s refers to the years from 1980 to 1989. ...


Those techniques were shown applicable to sequencing of the first free-living bacterial genome (1.8 million base pairs) of Haemophilus influenzae in 1995 [12] and the first animal genome (~100 Mbp) [13] It involved the use of automated sequencers, longer individual sequences using approximately 500 base pairs at that time. Paired sequences separated by a fixed distance of around 2000 base pairs which were critical elements enabling the development of the first genome assembly programs for reconstruction of large regions of genomes (aka 'contigs'). Binomial name Haemophilus influenzae (Lehmann & Neumann 1896) Winslow 1917 Haemophilus influenzae, formerly called Pfeiffers bacillus or Bacillus influenzae, is a non-motile Gram-negative coccobacillus first described in 1892 by Dr. Richard Pfeiffer during an influenza pandemic. ... Genome assembly refers to the process of taking a large number of short DNA sequences, all of which were generated by a shotgun sequencing project, and putting them back together to create a representation of the original chromosomes from which the DNA originated. ...


Three years later, in 1998, the announcement by the newly-formed Celera Genomics that it would scale up the shotgun sequencing method to the human genome was greeted with skepticism in some circles. The shotgun technique breaks the DNA into fragments of various sizes, ranging from 2,000 to 300,000 base pairs in length, forming what is called a DNA "library". Using an automated DNA sequencer the DNA is read in 800bp lengths from both ends of each fragment. Using a complex genome assembly algorithm and a supercomputer, the pieces are combined and the genome can be reconstructed from the millions of short, 800 base pair fragments. The success of both the public and privately funded effort hinged upon a new, more highly automated capillary DNA sequencing machine, called the Applied Biosystems 3700, that ran the DNA sequences through an extremely fine capillary tube rather than a flat gel. Even more critical was the development of a new, larger-scale genome assembly program, which could handle the 30-50 million sequences that would be required to sequence the entire human genome with this method. At the time, such a program did not exist. One of the first major projects at Celera Genomics was the development of this assembler, which was written in parallel with the construction of a large, highly automated genome sequencing factory. Development of the assembler was led by Gene Myers. The first version of this assembler was demonstrated in 2000, when the Celera team joined forces with Professor Gerald Rubin to sequence the fruit fly Drosophila melanogaster using the whole-genome shotgun method[14]. At 130 million base pairs, it was at least 10 times larger than any genome previously shotgun assembled. One year later, the Celera team published their assembly of the three billion base pair human genome. This article is about the psychological term. ... The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ... In genetics, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). ... A DNA sequencer is a machine to automatize the DNA sequencing process. ... Genome assembly refers to the process of taking a large number of short DNA sequences, all of which were generated by a shotgun sequencing project, and putting them back together to create a representation of the original chromosomes from which the DNA originated. ... For other uses, see Supercomputer (disambiguation). ... The term DNA sequencing encompasses biochemical methods for determining the order of the nucleotide bases, adenine, guanine, cytosine, and thymine, in a DNA oligonucleotide. ... Capillary Flow Experiment to investigate capillary flows and phenomena onboard the International Space Station Capillary action, capillarity, capillary motion, or wicking is the ability of a substance to draw another substance into it. ... This article does not cite any references or sources. ... Gene Myers is a professor of computer science at the University of California, Berkeley, whose research focuses on algorithms and computational biology. ... Gerald M. Rubin (born 1950) is an American biologist, notable for pioneering the use of transposable P elements in genetics, and for leading the public project to sequence the Drosophila melanogaster genome. ... Binomial name Meigen, 1830[1] Drosophila melanogaster (from the Greek for black-bellied dew-lover) is a two-winged insect that belongs to the Diptera, the order of the flies. ...


How it was accomplished

The IHGSC used pair-end sequencing plus whole-genome shotgun mapping of large (~100 Kbp) plasmid clones and shotgun sequencing of smaller plasmid sub-clones plus a variety of other mapping data to orient and check the assembly of each human chromosome[7].


The Celera group tried “whole-genome shotgun” sequencing without using the additional mapping scaffolding[8], but by including shredded public data raised questions [15].


Whose genome was sequenced?

In the IHGSC international public-sector Human Genome Project (HGP), researchers collected blood (female) or sperm (male) samples from a large number of donors. Only a few of many collected samples were processed as DNA resources. Thus the donor identities were protected so neither donors nor scientists could know whose DNA was sequenced. DNA clones from many different libraries were used in the overall project, with most of those libraries being created by Dr. Pieter J. de Jong. It has been informally reported, and is well known in the genomics community, that much of the DNA for the public HGP came from a single anonymous male donor from Buffalo, New York (code name RP11).[16] < [[[[math>Insert formula here</math>The public sector is that part of economic and administrative life that deals with the delivery of goods and services by and for the [[government </math></math></math></math> Direct administration funded through taxation; the delivering organisation generally has no specific requirement to meet commercial... In molecular biology, a library is a collection of molecules in a stable form that represents some aspect of an organism. ... Nickname: Location of Buffalo in New York State Coordinates: , Country State County Erie Government  - Mayor Byron Brown (D) Area  - City 52. ... A code name or cryptonym is a word or name used clandestinely to refer to another name or word. ...


HGP scientists used white blood cells from the blood of 2 male and 2 female donors (randomly selected from 20 of each) -- each donor yielding a separate DNA library. One of these libraries (RP11) was used considerably more than others, due to quality considerations. One minor technical issue is that male samples contain only half as much DNA from the X and Y chromosomes as from the other 22 chromosomes (the autosomes); this happens because each male cell contains only one X and one Y chromosome, not two like other chromosomes (autosomes). (This is true for nearly all male cells, not just sperm cells.) White Blood Cells redirects here. ... ‹ The template below (Expand) is being considered for deletion. ... The human Y chromosome is one of two sex chromosomes, it contains the genes that cause testis development, thus determining maleness. ... A spermatozoon or spermatozoan ( spermatozoa), from the ancient Greek σπέρμα (seed) and (living being) and more commonly known as a sperm cell, is the haploid cell that is the male gamete. ...


Although the main sequencing phase of the HGP has been completed, studies of DNA variation continue in the International HapMap Project, whose goal is to identify patterns of single nucleotide polymorphism (SNP) groups (called haplotypes, or “haps”). The DNA samples for the HapMap came from a total of 270 individuals: Yoruba people in Ibadan, Nigeria; Japanese people in Tokyo; Han Chinese in Beijing; and the French Centre d’Etude du Polymorphisms Humain (CEPH) resource, which consisted of residents of the United States having ancestry from Western and Northern Europe. The goal of the International HapMap Project is to develop a haplotype map of the human genome, also referred to as the HapMap, which will describe the common patterns of human genetic variation. ... DNA strand 1 differs from DNA strand 2 at a single base-pair location (a C/T polymorphism). ... A haplotype is the genetic constitution of an individual chromosome. ... The Yoruba (Yorùbá in Yoruba orthography) are a large ethno-linguistic group or ethnic nation in West Africa. ... This article does not cite any references or sources. ... Languages Japanese Religions Shinto, Buddhism, large secular groups      The Japanese people ) is the ethnic group that identifies as Japanese by culture or ancestry, or both. ... Language(s) Chinese languages Religion(s) Predominantly Taoism, Mahayana Buddhism, traditional Chinese religions, and atheism. ... Peking redirects here. ... Centre detude du polymorphisme humaine (or the Center for the Study of Human Polymorphisms), now called the Foundation Jean Dausset-CEPH, is an international genetic research center located in Paris, France. ... Northern Europe Northern Europe is the northern part of the European continent. ...


In the Celera Genomics private-sector project, DNA from five different individuals were used for sequencing. The lead scientist of Celera Genomics at that time, Craig Venter, later acknowledged (in a public letter to the journal Science) that his DNA was one of those in the pool[17]. Celera Genomics (NYSE: CRA) is a business unit of the Applera Corporation that focuses on genetic sequencing and related technologies. ... The private sector of a nations economy consists of all that is outside the state. ... Craig Venter, 2007 J. Craig Venter (born John Craig Venter October 14, 1946, Salt Lake City) is an American biologist and businessman. ... Science is the journal of the American Association for the Advancement of Science (AAAS). ...


On September 4th, 2007, a team led by Craig Venter, published his complete DNA sequence[18], unveiling the six-billion-letter genome of a single individual for the first time. Craig Venter, 2007 J. Craig Venter (born John Craig Venter October 14, 1946, Salt Lake City) is an American biologist and businessman. ... On September 4th, 2007, a team led by Craig Venter, published his complete DNA sequence[1], unveiling the six-billion-letter genome of a single individual for the first time. ...


Benefits

The work on interpretation of genome data is still in its initial stages. It is anticipated that detailed knowledge of the human genome will provide new avenues for advances in medicine and biotechnology. Clear practical results of the project emerged even before the work was finished. For example, a number of companies, such as Myriad Genetics started offering easy ways to administer genetic tests that can show predisposition to a variety of illnesses, including breast cancer, disorders of hemostasis, cystic fibrosis, liver diseases and many others. Also, the etiologies for cancers, Alzheimer's disease and other areas of clinical interest are considered likely to benefit from genome information and possibly may lead in the long term to significant advances in their management. For the chemical substances known as medicines, see medication. ... The structure of insulin Biotechnology is technology based on biology, especially when used in agriculture, food science, and medicine. ... Myriad Genetics, based in Salt Lake City, is doing genomic research. ... Breast cancer is cancer of breast tissue. ... Coagulation is the thickening or congealing of any liquid into solid clots. ... For the bird, see Liver bird. ... This article is about the medical term. ... Cancer is a class of diseases or disorders characterized by uncontrolled division of cells and the ability of these to spread, either by direct growth into adjacent tissue through invasion, or by implantation into distant sites by metastasis (where cancer cells are transported through the bloodstream or lymphatic system). ...


There are also many tangible benefits for biological scientists. For example, a researcher investigating a certain form of cancer may have narrowed down his/her search to a particular gene. By visiting the human genome database on the worldwide web, this researcher can examine what other scientists have written about this gene, including (potentially) the three-dimensional structure of its product, its function(s), its evolutionary relationships to other human genes, or to genes in mice or yeast or fruit flies, possible detrimental mutations, interactions with other genes, body tissues in which this gene is activated, diseases associated with this gene or other datatypes. Cancer is a class of diseases or disorders characterized by uncontrolled division of cells and the ability of these to spread, either by direct growth into adjacent tissue through invasion, or by implantation into distant sites by metastasis (where cancer cells are transported through the bloodstream or lymphatic system). ... WWWs historical logo designed by Robert Cailliau The World Wide Web (commonly shortened to the Web) is a system of interlinked, hypertext documents accessed via the Internet. ...


Further, deeper understanding of the disease processes at the level of molecular biology may determine new therapeutic procedures. Given the established importance of DNA in molecular biology and its central role in determining the fundamental operation of cellular processes, it is likely that expanded knowledge in this area will facilitate medical advances in numerous areas of clinical interest that may not have been possible without them. A biological process is a process of a living organism. ...


The analysis of similarities between DNA sequences from different organisms is also opening new avenues in the study of the theory of evolution. In many cases, evolutionary questions can now be framed in terms of molecular biology; indeed, many major evolutionary milestones (the emergence of the ribosome and organelles, the development of embryos with body plans, the vertebrate immune system) can be related to the molecular level. Many questions about the similarities and differences between humans and our closest relatives (the primates, and indeed the other mammals) are expected to be illuminated by the data from this project. This article is about evolution in biology. ... Molecular biology is the study of biology at a molecular level. ... Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). ... Schematic of typical animal cell, showing subcellular components. ... For other uses, see Embryo (disambiguation). ... This article does not cite any references or sources. ... A scanning electron microscope image of a single neutrophil (yellow), engulfing anthrax bacteria (orange). ... Families 15, See classification A primate is any member of the biological order Primates, the group that contains all the species commonly related to the lemurs, monkeys, and apes, with the latter category including humans. ... Subclasses & Infraclasses Subclass †Allotheria* Subclass Prototheria Subclass Theria Infraclass †Trituberculata Infraclass Metatheria Infraclass Eutheria Mammals (class Mammalia) are warm-blooded, vertebrate animals characterized by the presence of sweat glands, including milk producing sweat glands, and by the presence of: hair, three middle ear bones used in hearing, and a neocortex...


The Human Genome Diversity Project, spinoff research aimed at mapping the DNA that varies between human ethnic groups, which was rumored to have been halted, actually did continue and to date has yielded new conclusions. In the future, HGDP could possibly expose new data in disease surveillance, human development and anthropology. HGDP could unlock secrets behind and create new strategies for managing the vulnerability of ethnic groups to certain diseases (see race in biomedicine). It could also show how human populations have adapted to these vulnerabilities. The Human Genome Diversity Project (HGDP) was started by Stanford Universitys Morrison Institute and a collaboration of scientists around the world. ... Clinical surveillance (or Syndromic Surveillance) refers to the systematic collection, analysis, and interpretation of health data about a clinical syndrome that has a significant impact on public health, which is then used to drive decisions about health policy and health education. ... Human development is the process of growing to maturity. ... Anthropology (from Greek: ἀνθρωπος, anthropos, human being; and λόγος, logos, knowledge) is the study of humanity. ... This article is about the medical term. ... Race in Biomedicine refers to an active debate among biomedical researchers about the meaning and importance of race to their research. ...


References

  1. ^ Cook-Deegan R (1989). "The Alta Summit, December 1984". Genomics 5: 661-663. 
  2. ^ Barnhart, Benjamin J. (1989). "DOE Human Genome Program". Human Genome Quarterly 1: 1.  Retrieved 2005-02-03.
  3. ^ DeLisi, Charles (2001). "Genomes: 15 Years Later A Perspective by Charles DeLisi, HGP Pioneer". Human Genome News 11: 3–4.  Retrieved 2005-02-03.
  4. ^ White House Press Release. Retrieved on 2006-07-22.
  5. ^ BBC NEWS. Retrieved on 2006-07-22.
  6. ^ Guardian Unlimited. Retrieved on 2006-07-22.
  7. ^ a b International Human Genome Sequencing Consortium (2001). "Initial sequencing and analysis of the human genome.". Nature 409: 860−921. 
  8. ^ a b Venter, JC, et al (2001). "The sequence of the human genome.". Science 291: 1304−1351. 
  9. ^ IHGSC (2004). "Finishing the euchromatic sequence of the human genome.". Nature 431: 931-945. 
  10. ^ Fiers W, Contreres R, Duerinck F, Haegeman G, Iserentant D, Merregaert J, Min Jou W, Molemans F, Raeymaekers A, Van den Berghe A, Volckaert G, Ysebaert M. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene, Nature. 1976 Apr 8;260(5551):500-7.
  11. ^ Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M., Nucleotide sequence of bacteriophage phi X174 DNA, Nature. 1977 Feb 24;265(5596):687-95
  12. ^ Fleischmann, R. D. et al. (1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.". Science 269: 496−512. 
  13. ^ C. elegans Sequencing Consortium (1998). "Genome sequence of the nematode C. elegans: A platform for investigating biology.". Science 282: 2012–18. 
  14. ^ Adams, MD. et al. (2000). "The genome sequence of Drosophila melanogaster.". Science 287: 2185−2195. 
  15. ^ Waterston RH, Lander ES, Sulston JE (2003). "More on the sequencing of the human genome". Proc Natl Acad Sci U S A. 100: 3022-4. PMID 12631699. 
  16. ^ Osoegawa, Kazutoyo (2001). "A Bacterial Artificial Chromosome Library for Sequencing the Complete Human Genome". Genome Research 11: 483-496. 
  17. ^ Kennedy D (2002). "Not wicked, perhaps, but tacky". Science 297: 1237. PMID 12193755. 
  18. ^ Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. (2007). "The Diploid Genome Sequence of an Individual Human". PLoS Biology 5 (10). 

Year 2006 (MMVI) was a common year starting on Sunday of the Gregorian calendar. ... is the 203rd day of the year (204th in leap years) in the Gregorian calendar. ... Year 2006 (MMVI) was a common year starting on Sunday of the Gregorian calendar. ... is the 203rd day of the year (204th in leap years) in the Gregorian calendar. ... Year 2006 (MMVI) was a common year starting on Sunday of the Gregorian calendar. ... is the 203rd day of the year (204th in leap years) in the Gregorian calendar. ... A representation of the 3D structure of the myoglobin protein. ... April 8 is the 98th day of the year (99th in leap years) in the Gregorian calendar. ... is the 55th day of the year in the Gregorian calendar. ... Binomial name Caenorhabditis elegans Wild-type C. elegans hermaphrodite stained to highlight the nuclei of all cells Caenorhabditis elegans () is a free-living nematode (a roundworm), about 1 mm in length, which lives in a temperate soil environment. ...

External links

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Image File history File links Wikibooks-logo-en. ... Wikibooks logo Wikibooks, previously called Wikimedia Free Textbook Project and Wikimedia-Textbooks, is a wiki for the creation of books. ... The National Human Genome Research Institute (NHGRI) is a division of the National Institutes of Health, located in Bethesda, Maryland. ... NIH can refer to: National Institutes of Health Norwegian School of Sports Sciences: (Norges idrettshøgskole - NIH) Not Invented Here This is a disambiguation page — a navigational aid which lists other pages that might otherwise share the same title. ... Project Gutenberg, abbreviated as PG, is a volunteer effort to digitize, archive and distribute cultural works. ... QuickTime is a multimedia framework developed by Apple Inc. ... RealPlayer, briefly known also as RealOne Player, is a cross-platform media player by RealNetworks that plays a number of multimedia formats including MP3, MPEG-4, QuickTime, Windows Media and multiple versions of proprietary RealAudio and RealVideo formats. ...

See also


  Results from FactBites:
 
Human Genome Project - MSN Encarta (1418 words)
Through a process known as sequencing, the Human Genome Project has identified nearly all of the estimated 20,000 to 25,000 genes (the basic units of heredity) in the nucleus of a human cell.
The project has also mapped the location of these genes on the 23 pairs of human chromosomes, the structures containing the genes in the cell’s nucleus.
The human genome is composed of about 20,000 to 25,000 genes located on the 23 pairs of chromosomes in a human cell.
Origins of the Human Genome Project (6240 words)
The human genome project was borne of technology, grew into a science bureaucracy in the U.S. and throughout the world and is now being transformed into a hybrid academic and commercial enterprise.
The genome project is premised on the claim that genetic maps and new technologies will be among the most useful scientific approaches to highly complex biological phenomena, not that these maps will be the end of biology.
The genome project now embraces three main technical goals: genetic linkage maps to trace the inheritance of chromosome regions through pedigrees; physical maps of large chromosome regions, to enable the direct study of DNA structure in search of genes; and substantial DNA sequence information, enabling the correlation of DNA changes with alterations in biological function.
  More results at FactBites »

 
 

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