Human Genome

The human genome is the genome of Homo sapiens, which is composed of 24 distinct chromosomes (22 autosomal + X + Y) with a total of approximately 3 billion DNA base pairs containing an estimated 20,000-25,000 genes. The Human Genome Project produced a reference sequence of the euchromatic human genome, which is used worldwide in biomedical sciences. The human genome is much more gene-sparse than was initially predicted at the outset of the Human Genome Project, with only about 1.5% of the total length serving as protein-coding exons.There are estimated 20,000-25,000 human protein-coding genes. The estimate of the number of human genes has been repeatedly revised down from initial predictions of 100,000 or more as genome sequence quality and gene finding methods have improved, and could continue to drop further. Protein-coding sequences (specifically, coding exons) comprise less than 1.5% of the human genome. Aside from genes and known regulatory sequences, the human genome contains vast regions of DNA the function of which, if any, remains unknown. These regions in fact comprise the vast majority, by some estimates 97%, of the human genome size. Much of this is comprised of repeat elements, transposons, and pseudogenes, but there is also a large amount of sequence that does not fall under any known classification.Much of this sequence may be an evolutionary artifact that serves no present-day purpose, and these regions are sometimes collectively referred to as "junk" DNA. First, it is important to realize that 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 unsequenced. 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. It is likely that the centromeres and telomeres will remain unsequenced until new technology is developed that allows us to sequence them. 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 we have completed about 92% of the genome. 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 races, and many other questions are still the subject of intense study by laboratories all over the world.

Lupus gene finding prompts call for more DNA samples

Wellcome Trust researchers have identified a key gene involved in the disease Lupus, which affects around 50,000 people in the UK, mostly women. The lead researcher behind the study has called for more patients to volunteer DNA samples to enable them to further study the underlying causes of the disease.

Lupus - or Systemic Lupus Erythematosus (SLE) - is an autoimmune disease which frequently causes skin rash, joint pains and malaise, but can also lead to inflammation of the kidneys and other internal organs. The risk of death in SLE is increased fivefold over that of the general population. However, because the symptoms are often non-specific, diagnosing the condition can be difficult. There is currently no cure for the disease, which can be triggered by viral infections, sunlight, trauma or stress, as well as puberty and childbirth.

In research published online today in the journal Nature Genetics, Professor Tim Vyse from Imperial College London, and colleagues in the US and Canada, have identified a new genetic variant, OX40L, which increases the risk of developing Lupus. The variant, which is carried by one in six people in the UK, increases the risk of developing the disease by 50% per copy.

"Lupus can be a very serious condition, but because its symptoms are often similar to those of other illnesses, it can be difficult and take time to diagnose," says Professor Vyse, a Wellcome Trust Senior Fellow from Imperial College. "Although it appears to have a number of environmental triggers, we are now beginning to get a clearer picture of the role that genetics also plays in the disease."

OX40L is a gene that is important in several different types of cells in the immune system. The work, carried out by members of Prof Vyse's laboratory, shows that the genetic variants in the OX40L gene that amplify the risk of lupus do so by increasing the amount of OX40L present on the surface of lymphocytes, which are key components of the immune system. They are currently studying exactly how this increases the risk of SLE.

"As well as causing problems with diagnosis, Lupus's many symptoms make it difficult to work out which are key to the disease," he says. "Identifying a specific gene will enable us to see at a molecular level what is behind Lupus and develop treatments targeted at inhibiting or blocking the action of those genes."

Prof Vyse's group and other scientists have previously discovered two other genes implicated in Lupus. IRF5 is a gene involved in regulating interferons, of which there appears to be an overabundance in Lupus. Interferons are natural proteins produced by the cells of the immune system in response to challenges by pathogens such as viruses, bacteria and tumour cells. The role of the second of the previously-discovered genes, FCGR3B, in Lupus is unclear.

Professor Vyse is very grateful to everyone who has provided DNA samples for these studies, but stresses the importance of more DNA samples from volunteers and calls for more patients to provide samples. The OX40L gene was identified by studying approximately 1.400 people with Lupus, and other members of their families in the UK and the US.

"Without DNA samples from people with Lupus, we would be unable to study the disease," he says. "Despite the disease being relatively common, DNA samples are in short supply. I would encourage patients to discuss with their GP or consultant about providing a blood sample to help further our understanding."

International HGP

The Project was launched in 1986 by Charles DeLisi, who was then Director of the US Department of Energy's Health and Environmental Research Programs. He was later awarded the Citizen's medal by President Clinton for his seminal role in the Project. The goals and general strategy of the Project were outlined in a two-page memo to the Assistant Secretary in April 1986, which helped garner support from the DOE, the United States Office of Management and Budget (OMB) and the United States Congress, especially Senator Pete Domenici. A series of Scientific Advisory meetings, and complex negotiations with senior Federal officials resulted in a line item for the Project in the 1987 Presidential budget submission to the Congress.Initiation of the Project was the culmination of several years of work supported by the US Department of Energy, in particular a feasibility workshop in 1986 and a subsequent detailed description of the Human Genome Initiative in a report that led to the formal sanctioning of the initiative by the Department of Energy.
This 1987 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. 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.

Celera Genomics & HGP

In 1998, an identical, 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.Celera Genomics was established in May 1998 by the Perkin-Elmer Corporation (and was later purchased by Applera Corporation), with Dr. J. Craig Venter from The Institute for Genomic Research (TIGR) as its first president. While at TIGR, Venter and Hamilton Smith led the first successful effort to sequence an entire organism's genome, that of the Haemophilus influenzae bacterium. Celera was formed for the purpose of generating and commercializing genomic information to accelerate the understanding of biological processes.
The rise and fall of Celera as an ambitious competitor of the Human Genome Project is the main subject of the book The Genome War by James Shreeve, who takes a strong pro-Venter point of view. (He followed Venter around for two years in the process of writing the book.) A view from the public effort's side is that of Nobel laureate Sir John Sulston in his book The Common Thread: A Story of Science, Politics, Ethics and the Human Genome.Celera used a newer, riskier technique called whole genome shotgun sequencing, which had been used to sequence bacterial genomes up to 6 million base pairs in length, but not for anything nearly as large as the 3 billion base pair human genome.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. Contrary to its public promises, the firm eventually filed patent applications on 6,500 whole or partial genes.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) and Science (which published Celera's paper) described the methods used to produce the draft sequence and offered analysis of the sequence. These drafts covered about 90% of the genome, with much of the remaining 10% filled in later. 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 again in 2005, filling in roughly 8% of the remaining sequence.
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.In 2005, 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. 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.

Goals of the original Human Genome Project (HGP)

* identify all the approximately 20,000-25,000 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.

The goals of the original HGP were not only to determine all 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 30,000 genes in the human genome, which is far fewer than predicted by most scientists.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.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, and ENSEMBL 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 them.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.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.


How it was accomplished

The publicly funded groups NIH, the Sanger Institute in Great Britain, and numerous groups from around the world broke the genome into larger 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 replication machinery. Each of these pieces was then sequenced separately as a small "shotgun" project and then assembled. The larger, 150,000 base pair chunks were then stitched 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 whole-genome shotgun (WGS) method is faster and cheaper, and by 2003 - thanks to the availability of clever assembly algorithms - it had become the standard approach to sequencing most mammalian genomes.


Whose genome was sequenced?

In the 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 the state of New York.Technically, it is much easier to prepare DNA cleanly from sperm than from other cell types because of the much higher ratio of DNA to protein in sperm and the much smaller volume in which purifications can be done. Using sperm does provide all chromosomes for study, including equal numbers of sperm with the X (female) or Y (male) sex chromosomes. HGP scientists also used white cells from the blood of female donors so as to include female-originated samples. One minor technical issue is that sperm 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 sperm cell contains only one X or one Y chromosome, but not both. Thus in 100 sperm cells, on average there will be 50 X and 50 Y chromosomes, as compared to 100 copies of each of the other chromosomes.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 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 in Tokyo; Han Chinese in Beijing; and the French Centre d’Etude du Polymorphisme Humain (CEPH) resource, which consisted of residents of the United States having ancestry from Western and Northern Europe.In the Celera Genomics private-sector project, DNAs 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.

The Human Genome Projects - 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.
There are also many tangible benefits for biological scientists. For example, a researcher investigating a certain form of cancer may have narrowed down his 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.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.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.
The Human Genome Diversity Project, spin-off 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.

What's Turning Genomics Vision Into Reality

In "A Vision for the Future of Genomics Research," published in the April 24, 2003 issue of the journal Nature, the National Human Genome Research Institute (NHGRI) details a myriad of research opportunities in the genome era. This backgrounder describes a few of the more visible, large-scale opportunities.

The International HapMap Project

Launched in October 2002 by NHGRI and its partners, the International HapMap Project has enlisted a worldwide consortium of scientists with the goal of producing the "next-generation" map of the human genome to speed the discovery of genes related to common illnesses such as asthma, cancer, diabetes and heart disease.Expected to take three years to complete, the "HapMap" will chart genetic variation within the human genome at an unprecedented level of precision. By comparing genetic differences among individuals and identifying those specifically associated with a condition, consortium members believe they can create a tool to help researchers detect the genetic contributions to many diseases. Whereas the Human Genome Project provided the foundation on which researchers are making dramatic genetic discoveries, the HapMap will begin building the framework to make the results of genomic research applicable to individuals.

ENCyclopedia Of DNA Elements (ENCODE)

This NHGRI-led project is designed to develop efficient ways of identifying and precisely locating all of the protein-coding genes, non-protein-coding genes and other sequence-based, functional elements contained in the human DNA sequence. Creating this monumental reference work will help scientists mine and fully utilize the human sequence, gain a deeper understanding of human biology, predict potential disease risk, and develop new strategies for the prevention and treatment of disease.The ENCODE project will begin as a pilot, in which participating research teams will work cooperatively to develop efficient, high-throughput methods for rigorously and fully analyzing a defined set of target regions comprising approximately 1 percent of the human genome. Analysis of this first 30 megabases (Mb) of human genome sequence will allow the project participants to test and compare a variety of existing and new technologies to find the functional elements in human DNA.

Chemical Genomics

NHGRI is exploring the acquisition and/or creation of publicly available libraries of organic chemical compounds, also referred to as small molecules, for use by basic scientists in their efforts to chart biological pathways. Such compounds have a number of attractive features for genome analysis, including their wide structural diversity, which mirrors the diversity of the genome; their ability in many cases to enter cells readily; and the fact that they can often serve as starting points for drug development. The use of these chemical compounds to probe gene function will complement more conventional nucleic acid approaches.This initiative offers enormous potential. However, it is a fundamentally new approach to genomics, and largely new to basic biomedical research as a whole. As a result, substantial investments in physical and human capital will be needed. NHGRI is currently planning for these needs, which will include large libraries of chemical compounds (500,000 - 1,000,000 total); capacity for robotic-enabled, high-throughput screening; and medicinal chemistry to convert compounds identified through such screening into useful biological tools.

Genomes to Life

The Department of Energy's "Genomes to Life" program focuses on single-cell organisms, or microbes. The fundamental goal is to understand the intricate details of the life processes of microbes so well that computational models can be developed to accurately describe and predict their responses to changes in their environment."Genomes to Life" aims to understand the activities of single-cell organisms on three levels: the proteins and multi-molecular machines that perform most of the cell's work; the gene regulatory networks that control these processes; and microbial associations or communities in which groups of different microbes carry out fundamental functions in nature. Once researchers understand how life functions at the microbial level, they hope to use the capabilities of these organisms to help meet many of our national challenges in energy and the environment.

Structural Genomics Consortium

Structural genomics is the systematic, high-throughput generation of the three-dimensional structure of proteins. The ultimate goal for studying the structural genomics of any organism is the complete structural description of all proteins encoded by the genome of that organism. Such three-dimensional structures will be crucial for rational drug design, for diagnosis and treatment of disease, and for advancing our understanding of basic biology. A broad collection of structures will provide valuable biological information beyond that which can be obtained from individual structures.

RNA genes

RNA genes (sometimes referred to as non-coding RNA or small RNA) are genes that encode RNA that is not translated into a protein. The most prominent examples of RNA genes are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation. However, since the late 1990s, many new RNA genes have been found, and thus RNA genes may play a much more significant role than previously thought. In the late 1990s and early 2000, there has been persistent evidence of more complex transcription occurring in mammalian cells (and possibly others). This could point towards a more widespread use of RNA in biology, particularly in gene regulation. A particular class of non-coding RNA, micro RNA, has been found in many metazoans (from Caenorhabditis elegans to Homo sapiens) and clearly plays an important role in regulating other genes. First proposed in 2004 by Rassoulzadegan and published in Nature 2006.

RNA is implicated as being part of the germline. If confirmed, this result would significantly alter the present understanding of genetics and lead to many question on DNA-RNA roles and interactions.RNA Deatiles,ScienceRibonucleic acid (RNA) is a nucleic acid polymer consisting of nucleotide monomers, that acts as a messenger between DNA and ribosomes, and that is also responsible for making proteins out of amino acids. RNA polynucleotides contain ribose sugars and predominantly uracil unlike deoxyribonucleic acid (DNA), which contains deoxyribose and predominantly thymine. It is transcribed (synthesized) from DNA by enzymes called RNA polymerases and further processed by other enzymes.

RNA serves as the template for translation of genes into proteins, transferring amino acids to the ribosome to form proteins, and also translating the transcript into proteins. Nucleic acids were discovered in 1868 (some sources indicate 1869) by Johann Friedrich Miescher (1844-1895), who called the material 'nuclein' since it was found in the nucleus. It was later discovered that prokaryotic cells, which do not have a nucleus, also contain nucleic acids. The role of RNA in protein synthesis had been suspected since 1939, based on experiments carried out by Torbjörn Caspersson, Jean Brachet and Jack Schultz. Hubert Chantrenne elucidated the messenger role played by RNA in the synthesis of proteins in ribosome.

The sequence of the 77 nucleotides of a yeast RNA was found by Robert W. Holley in 1964, winning Holley the 1968 Nobel Prize for Medicine. In 1976, Walter Fiers and his team at the University of Ghent determined the complete nucleotide sequenceDNA Bases Bio TechnologyDeoxyribonucleic acid, or DNA is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all living organisms. The main role of DNA is the long-term storage of information and it is often compared to a set of blueprints, since DNA contains the instructions needed to construct other components of cells, such as proteins and RNA molecules.
The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Chemically, DNA is a long polymer of simple units called nucleotides, which are held together by a backbone made of alternating sugars and phosphate groups. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription. Most of these RNA molecules are used to synthesize proteins, but others are used directly in structures such as ribosomes and spliceosomes.
Within cells, DNA is organized into structures called chromosomes and the set of chromosomes within a cell make up a genome. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms such as animals, plants, and fungi store their DNA inside the cell nucleus, while in prokaryotes such as bacteria it is found in the cell's cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA, which helps control its interactions with other proteins and thereby control which genes are transcribed Biotechnology Indroduction. The convention recognized for the first time in international law that the conservation of biological diversity is "a common concern of humankind" and is an integral part of the development process.

The agreement covers all ecosystems, species, and genetic resources. It links traditional conservation efforts to the economic goal of using biological resources sustainably. It sets principles for the fair and equitable sharing of the benefits arising from the use of genetic resources, notably those destined for commercial use. It also covers the rapidly expanding field of biotechnology through its Cartagena Protocol on Biosafety, addressing technology development and transfer, benefit-sharing and biosafety issues. Importantly, the Convention is legally binding; countries that join it('Parties') are obliged to implement its provisions .

Apply Bio Technology Science The convention reminds decision-makers that natural resources are not infinite and sets out a philosophy of sustainable use. While past conservation efforts were aimed at protecting particular species and habitats, the Convention recognizes that ecosystems, species and genes must be used for the benefit of humans. However, this should be done in a way and at a rate that does not lead to the long-term decline of biological diversity The convention also offers decision-makers guidance based on the precautionary principle that where there is a threat of significant reduction or loss of biological diversity, lack of full scientific certainty should not be used as a reason for postponing measures to avoid or minimize such a threat. The Convention acknowledges that substantial investments are required to conserve biological diversity. It argues, however, that conservation will bring us significant environmental, economic and social benefits in return.In this situation, your range of choices is very broad and many packages will meet these limited.