Human Genome Projects...

History

The idea for the Human Genome Project (HGP) first arose in the mid-1980s. Several scientific groups met to discuss the feasibility, and various reports were published. The most influential report was prepared by the National Research Council (NRC) of the U.S. National Academy of Sciences. It proposed a detailed scientific strategy that persuaded many scientists that the project was possible. October 1, 1990, was declared the official start time for the HGP in the United States; significant funding had become available and research groups were starting their work. Major contributions to the HGP have been made by the United Kingdom, France, Japan, and Germany, with smaller contributions from many other quarters. Coordination among the countries has been informal, relying largely on scientist-to-scientist collaborations, but has proved to be very effective.

Scientific strategy

First, markers are placed on the chromosomes by genetic mapping, that is, observing how the markers are inherited in families. Second, a physical map is created from overlapping cloned pieces of the DNA. Third, the sequence of each piece is determined, and the sequences are lined up by computer until a continuous sequence along the whole chromosome is obtained. The second and third steps can be reversed or done in parallel. As the pieces are sequenced, the sequences at the overlapping ends can be used to help order the pieces. If the sequencing is done before the pieces are mapped, the process is called whole-genome shotgun sequencing. See also Deoxyribonucleic acid (DNA); Gene.

Because the human genome is so big (human DNA consists of about 3 billion nucleotides connected end to end in a linear array), it was necessary to break the task down into manageable chunks (see illustration).

Steps in analyzing a genome.

Model organisms

An important element of the overall strategy was to include the study of model organisms in the HGP. There were two reasons for this: (1) Simpler organisms provide good practice material. (2) Comparisons between model organisms and humans yield very valuable scientific information. The HGP initially adopted five model organisms to have their DNA sequenced: the bacterium Escherichia coli, the yeast Saccharomyces cerevisiae, the roundworm Caenorhabditis elegans, the fruitfly Drosophila melanogaster, and the laboratory mouse Mus musculus. The mouse genome is just as complex as the human genome, but the mouse offers the advantages that it can be bred and other experiments can be conducted that are not possible on humans.

Findings

How many genes are there is probably the most common question regarding the human genome. The first two human chromosomes to be sequenced, chromosomes 22 and 21, provided some interesting observations. Although the two chromosomes are approximately the same length, chromosome 22 has more than twice as many genes as chromosome 21. Extrapolation of the number of genes found on chromosomes 22 and 21 led to the estimate that the whole human genome contains about 36,000 genes. This is quite a surprise because previous estimates were 80,000 to 100,000 genes. Preliminary examination of the draft sequence of the entire human genome confirmed that the number of genes is much lower than previously thought. This does not necessarily mean that the human genome is less complex, because many genes can produce more than one protein by alternate splicing of their exons (protein-encoding regions of the gene) during translation into the constituents of proteins. See also Chromosome; Genetic code.

Another fascinating feature of the human genome sequence is the large fraction that consists of repeated sequence elements; 40% of chromosome 21 and 42% of chromosome 22 are composed of repeats. The function of any of these repeats is not yet known, but elucidating their distribution in the genome may help to reveal it.

Another statistic that is of interest is the base composition, the percent of the DNA that is made of guanine-cytosine (GC) base pairs as opposed to adenine-thymine (AT) base pairs. Chromosome 22 has a 48% GC content, whereas chromosome 21 has 41% and the average over the genome is 42%. Again, the significance of this is not yet known, but higher GC content seems to correlate with higher gene density.

The type of analysis performed initially on chromosomes 21 and 22 has been extended to the entire human sequence. However, a full understanding will take decades to achieve.

Future research

With the complete sets of genes of organisms available, how genes are turned on and off and how genes interact with each other can be studied. What the different genes do and how they affect human health must also be learned. Consequently, much effort is now directed to studying the regulation of gene expression and annotating the sequence with useful biological information about function.

Another key challenge is to understand how DNA function varies with differences in the DNA sequence. Each human being has a unique DNA sequence which differs from that of any other human being by about 0.1%, regardless of ethnic origin. Yet this small difference affects characteristics such as how humans look and to what diseases they are susceptible. The differences also provide clues about the evolution of the human species and the historical migration patterns of people across the world.

The Human Genome Project (HGP) is an international research program that aims to spell out the complete genetic inheritance of human beings and selected experimental animals. The HGP's goal is to decode the complete DNA inheritance, or genome, of human beings by 2003; following completion of a draft in 2000 that charted 90 percent of the human DNA inheritance. In addition to decoding human and animal DNA, the HGP trains scientists, develops techniques for analyzing genomes, and examines the ethical, legal, and social implications of human genetics research.

DNA is the long thread of a molecule that carries genes. Each strand of DNA, packaged as a chromosome, bears thousands of genes. Each gene contains the instructions for making a single component of the body, usually a protein. The hereditary instructions embedded in DNA are written with a four-letter alphabet (A, G, C, and T). A single misspelling in the DNA code can lead to the production of a defective protein, which can cause disease.

Understanding the human genome, the complete set of genes, sheds light on how the human body works at the fundamental level of molecules. Genes orchestrate the many fantastic and elegant features of life, like the development of embryos, while variations in gene sequence influence each person's susceptibility to diseases, including common illnesses like cancer and heart disease. The HGP will ultimately answer a wide range of scientific and medical questions, including: How do cells work? How do complex organisms develop from single cells? How are living beings related to each other? How do diseases arise?

The HGP was officially launched in 1990, as a joint project of the U.S. government and international partners. It was established as a large-scale, coordinated research project, marshaling the collaborative effort of hundreds of researchers. Between 1990 and 2003, the HGP is expected to reveal the sequence of approximately 3 billion "letters" that make up human DNA to identify all of the approximately 100,000 genes in human DNA, and to make all this information accessible to anyone with access to the Internet. The tools the HGP has built, including increasingly detailed maps of the human genome, helped genetic researchers navigate the genome and discover scores of disease genes in the 1990s. By 2003, a 99.99 percent– accurate listing of the letters that make up the DNA in all the human chromosomes is expected; that readout of the human genome, along with catalogs showing how DNA sequences vary among individuals, will help scientists tease out the genetic basis for complex diseases like diabetes, Alzheimer's disease, cancer, and heart disease— illnesses whose origins can be traced to the effects of multiple genes, as well as social and environmental factors.

By helping reveal the molecular foundations of disease, the HGP is expected by some to transform health care. Genetic technologies are becoming increasingly available. For example, genetic tests are being used to confirm diagnoses for some conditions, and to help define prognoses. Other tests predict the risk for future health problems. In time, more detailed understanding of the molecules involved in disease is expected to promote more rational drug design, making for increasingly precise, in some cases individualized, pharmacologic therapies that will minimize side effects or even avoid them altogether. Ultimately, understanding the molecular origins of disease may reveal ways of preventing many diseases entirely, perhaps by circumventing molecular glitches that can lead to illness or by repairing the altered molecules outright.

While genetic information and technology are likely to create great opportunities for promoting health and preventing disease, some risks are likely to accompany these powerful technologies. Genetic information can be misinterpreted or misused. As knowledge about individuals' genetic backgrounds becomes increasingly widespread, some insurers and employers may use predictions about future health to limit or deny access to health care or employment. Therefore, protecting the privacy of genetic information and preventing genetic discrimination will be crucial. To tap the full benefits of genetics, the medical profession and the public will need to become better equipped to evaluate the meaning of genetic information and to make decisions about the use of the new genetic technologies. At the same time, proper oversight will be necessary to ensure that gene tests and technologies are valid and reliable, sensitive, and specific, and used in appropriate situations.

Genetics, which was largely confined to research laboratories during the twentieth century, is expected to pervade everyday life in the twenty-first century. In the arena of public health, it may be used to access individuals' risks for health problems and to develop programs of preventive health care. Knowing their susceptibility to various health risks, individuals may be able to adopt a schedule of surveillance, perhaps take medications that will prevent health problems, and ideally become motivated to adopt lifestyle measures that will minimize their risks.

Most observers argue that the goal of public health genetics programs should be phenotypic prevention—preventing the emergence of disease—rather than genotypic prevention which is trying to change the genes people inherit. To attempt to prevent the transmission of particular genetic traits to future generations as a public health measure would tread into eugenic territory. Instead, public health goals should be designed to forestall the clinical manifestations of genetic risks.

The genome represents the entire complement of DNA in a cell. The Human Genome Project is the determination of the entire nucleotide sequence of all 3 billion + bases of DNA within the nucleus of a human cell. It is one of the greatest scientific undertakings in the history of mankind. The first draft of the human genome sequence was completed in the year 2001 and published simultaneously in the British journal Nature and the American journal Science.

The data obtained from sequencing the human genome promise to bring unprecedented scientific rewards in the discovery of disease-causing genes, in the design of new drugs, in understanding developmental processes and cancer, and in determining the origin and evolution of the human race. The Human Genome Project has also raised many social and ethical issues with regard to the use of such information.

Origins of the Human Genome Project

One could say that the Human Genome Project really began in 1953, when James Watson and Francis Crick deduced the molecular structure of DNA, the molecule of which the genome is made. (Watson and Crick were awarded the Nobel Prize for this work in 1962.) Since that time, scientists have wanted to know the complete sequence of a gene, and even dreamed that some day it would be possible to determine the complete sequence of all of the genes in any organism, including humans.

The original impetus for the Human Genome Project came almost a decade earlier, however, from the U.S. Department of Energy (DOE) shortly after World War II. The atomic bombs that were dropped on Hiroshima and Nagasaki, Japan, left many survivors who had been exposed to high levels of radiation. The survivors of the bomb were stigmatized in Japan. They were considered poor marriage prospects, because of the potential for carrying mutations, and the rest of Japanese society often ostracized them. In 1946 the famous geneticist and Nobel laureate Hermann J. Muller wrote in the New York Times that "if they could foresee the results [mutations among their descendants] 1,000 years from now …, they might consider themselves more fortunate if the bomb had killed them."

Muller had firsthand experience with the devastating effects of radiation, having studied the biological effects of radiation on the fruit fly Drosophila melanogaster. He predicted similar results would follow from the human exposure to radiation. As a consequence, the Atomic Energy Commission of the DOE set up an Atomic Bomb Casualty Commission in 1947 to address the issue of potential mutations among the survivors. The problem they faced was how to experimentally determine such mutations. At that time there were no suitable methods to study the problem. Indeed, it would be many years before the appropriate technology was available.

During the 1970s molecular biologists developed techniques for the isolation and cloning of individual genes. Paul Berg was the first to create a recombinant DNA molecule in 1972, and within a few years gene cloning became a standard tool of the molecular biologist. Using cloning techniques, scientists could generate large quantities of a single gene, enabling researchers to study its structure and function. In 1977 Drs. Walter Gilbert and Fred Sanger independently developed methods for the sequencing of DNA, for which they received the 1980 Nobel Prize along with Berg. Sanger's group in England was the first to completely sequence a genome, identifying all 5,386 bases of the bacterial virus φχ174.

Table 1

MODEL ORGANISMS SEQUENCED
Date sequenceda	Species	Total basesb
7/28/1995	Haemophilis influenzae (bacterium)	1,830,138
10/30/1995	Mycoplasma genitalium (bacterium)	580,073
5/29/1997	Saccharomyces cerevisiae (yeast)	12,069,247
9/5/1997	Escherichia coli (bacterium)	4,639,221
11/20/1997	Bacillus subtillis (bacterium)	4,214,814
12/31/1998	Caenorhabditis elegans (round worm)	97,283,371
		99,167,964c
3/24/2000	Drosophila melanogaster (fruit fly)	~137,000,000
12/14/2000	Arabidopsis thaliana (mustard plant)	~115,400,000
1/26/2001	Oryza sativa (rice)	~430,000,000
2/15/2001	Homo sapiens (human)	~3,200,000,000
First publication date.
Data excludes organelles or plasmids. These numbers should not be taken as absolute. Scientists are confirming the sequences; several laboratories were involved in the sequencing of a particular organism and have slightly different numbers; and there are some strain variations. Data were obtained from the (NCBI) Web site.
The first number was originally published, and the second is a correction as of June 2000.

Another technological breakthrough occurred in 1985, when the polymerase chain reaction method was developed by Dr. Kary Mullis and colleagues at Cetus Corp. This team devised a method whereby minute samples of DNA can be multiplied a billion-fold for analysis. This technique, which has many applications in diverse fields of biology, is one of the most important scientific breakthroughs in gene analysis. Mullis received the Nobel Prize for this work in 1993.

At this time, however, DNA sequencing was still done by hand. At best, a researcher could manually sequence only a few hundred bases per day. To be able to sequence the human genome, machines would be needed that could sequence a million or more bases per day. In 1986 Leroy Hood developed the first generation of automated DNA sequencers, thereby dramatically increasing the speed with which bases could be sequenced. Thus, by the mid-1980s the stage was set.

With these new techniques, molecular biologists now felt that it might be feasible to sequence the entire human genome. The first serious discussions came in June 1985, when Robert Sinsheimer, chancellor of the University of California at Santa Cruz, called a meeting of leading scientists to discuss the possibility of sequencing the human genome. Sinsheimer was inspired by the success of the Manhattan Project, which was the concerted effort of many physicists to develop atomic weapons during World War II. That project led to rapid development and a massive influx of funding for physicists. Sinsheimer wanted a "Manhattan Project" for molecular biology, to enhance and expand human genome research.

Meanwhile, the DOE continued to be interested in the problem of identifying mutations caused by radiation exposure. Led by associate director Charles DeLisi, the DOE became a strong supporter of the genome-mapping initiative, for it understood that sequencing the entire genome would provide the best way to analyze such mutations. Thus the DOE became the first federal agency to begin funding the Human Genome Project.

Mapping the human genome came to be called the "Holy Grail of Molecular Biology," and many biologists were interested in the project. Most notable among them was Nobel laureate Gilbert who, through his interest, personality, and academic ties, developed enormous enthusiasm for the project. The initial goals set out for the Human Genome Project were threefold: to develop genetic linkage maps; to create a physical map of ordered clones of DNA sequences; and to develop the capacity for large-scale sequencing, because faster and cheaper machines along with other great leaps in technology would be needed to get the job done.

In 1988 the National Institutes of Health (NIH) set up an Office of the Human Genome, and Watson agreed to head the project. It had an estimated budget of approximately $3 billion, and 3 percent of the funding was devoted to the study of the social and ethical issues that would arise from the endeavor. A target date for completion of the project was set for September 30, 2005. By 1990 the Human Genome Project had received the additional endorsement of the National Academy of Sciences, the National Research Council, the DOE, the National Science Foundation, the U.S. Department of Agriculture, and the Howard Hughes Medical Institute. Sequencing of the human genome had now officially begun.

While sequencing the human genome was a primary goal, other sequencing projects were just as important. Many scientists established projects that sought to sequence several organisms of genetic, biochemical, or medical importance (see Table 1). These so-called model organisms, with their smaller genomes, would be useful in testing sequencing methodologies and for providing invaluable information that could be used to identify corresponding genes in the human genome. Sequence databases were established, and computer programs to search these databases were written.

Competition Between the Public and Private Sectors

Dr. Craig Venter, a scientist at the NIH, felt that private companies could sequence genomes faster than publicly funded laboratories. For this reason he founded a biotechnology company called the Institute for Genomic Research (TIGR). In 1995 TIGR published the first completely sequenced genome, that of the bacterium Haemophilus influenzae. TIGR was soon joined by other biotechnology companies that competed directly with the publicly funded Human Genome Project.

Among these other biotech firms is Celera Genomics, founded in 1998 by Venter in conjunction with the Perkin-Elmer Corporation, manufacturer of the world's fastest automatic DNA sequencers. Celera's goal was to privately sequence the human genome in direct competition with the public efforts supported by the NIH and DOE and the governments of several foreign countries. Using 300 Perkin-Elmer automatic DNA sequencers along with one of the world's most powerful supercomputers, Celera sequenced the genomes of several model organisms with remarkable speed and, in April 2000, announced that it had a preliminary sequence of the human genome.

In order eventually to make a profit, these biotech companies were patenting DNA sequences and intended ultimately to charge clients, including researchers, for access to their databases. This issue of patenting had already caused controversy. Watson felt strongly that the sequence data flowing from the Human Genome Project should remain within the public domain, freely available to all. Meeting opposition to this view, he stepped down from his position as director of the NIH-sponsored project in 1992 and was succeeded by Francis Collins.

Other researchers shared Watson's view, and in 1996 the international consortium of publicly funded laboratories agreed at a meeting in Bermuda to release all data to GenBank, a genome database maintained by NIH. The agreement reached by these scientists came to be known as "The Bermuda Principles," and it mandated that sequence data would be posted on the Internet within 24 hours of acquisition. Because the information is freely available to the public, the sequences can not be patented. The dispute between Celera Genomics and the International Human Genome Consortium continues, as scientists now begin the task of searching the genome for valuable information.

Progress in the Human Genome Project

Sequencing the human genome has led to some surprising results. For example, we once thought that highly evolved humans would need a great many genes to account for their complexity, and scientists originally estimated the number of human genes to be about 100,000. The draft of the human genome, however, indicates that humans may have only about 30,000 genes, far fewer than originally expected. Indeed, this is only about one-third more than the number of genes found in the lowly roundworm, Caenorhabditis elegans (approximately 20,000 genes), and roughly twice the number of genes in the fruit fly Drosophila melanogaster (approximately 14,000 genes). Subsequent estimates have placed the number of human genes closer to 70,000; the true number is unknown as of mid-2002. Scientists have learned that most of the genome does not code for proteins, but rather contains "junk DNA" of no known function. In fact, only a small percentage of human DNA actually encodes a gene.

The complete human genome consists of twenty-two pairs of chromosomes plus the X and Y sex chromosomes. On December 2, 1999, more than 100 scientists working together in laboratories in the United Kingdom, Japan, the United States, Canada, and Sweden announced the first completely sequenced human chromosome, chromosome 22, the smallest of the autosomes. To assure the accuracy of the sequence data, each segment must be sequenced at least ten times.

Thousands of scientists, working in more than 100 laboratories and 19 different countries around the world, have contributed to the Human Genome Project since its inception. Thanks to the development of later generations of high-speed automatic sequencers and supercomputers to handle the enormous amount of data generated, work on the project progressed well ahead of schedule and well under budget, a rare phenomenon in government-sponsored projects. In 2001 the first draft of the complete human genome was published. However, considerable work remained to be done, particularly in the sequence of regions of repetitive DNA.

Whose Genome Is It?

Although all humans share more than 99.99 percent of their genome sequences, each human is unique. Geneticists estimate that each person carries many mutations, perhaps hundreds or even thousands of them. Therefore, one of the major questions that has arisen in the Human Genome Project is "whose genome is it?" The final catalog of sequences, whenever it is complete, will have to take into account these individual variations, and ultimately there will be a "consensus sequence," but it will represent no one specific individual.

A related issue arises from the distinct differences that scientists anticipate will occur among different populations. Which sequences should be considered "normal," and which ones should be classed as "mutated"? The Human Genome Diversity Project was proposed in 1997 to catalog and study naturally occurring sequence variations among racial and geographic groups. This project never gained much support, however, because of the social and ethical ramifications to such a catalog. On the other hand, a Human Cancer Genome Anatomy Project was initiated to catalog all the genes that are expressed in cancer cells in order to aid in the detection and treatment of cancers. This project enjoyed much more support.

Patenting the Genome

From the outset there has been considerable debate among scientists, politicians, and entrepreneurs as to whether the human gene sequences can or should be patented. Indeed, this debate was the reason that Watson resigned as the first director of the NIH Human Genome Project program in 1992. Watson's position was opposed by many biotechnology companies, which hoped to recover the cost of their genome research and began patenting short segments of sequenced DNA without any idea as to their function. As of 2000, the U.S. Patent and Trademark Office (PTO) changed its policy, and began granting patents only to genes that have been identified, rather than just the random sequenced fragments. The data that flow from genome sequencing will be an invaluable scientific resource, particularly in the area of developing new medical treatments, but its use will be restricted if individual organizations can claim exclusive use rights to large segments of it. It is thus clear that debate on the patenting of genes will continue for years to come.

At present much of data from genome research are available to scientists and other interested parties. The data generated by participants in the Bermuda Principles agreement can be accessed on-line at the National Center for Biotechnology Information (NCBI) Web site, at www.ncbi.nlm.nih.gov/genome/guide/human. The International Human Genome Consortium Web site provides a current list of genome sites that offer links to most genome databases at www.ensembl.org/genome/central. Information about all the genomes that have been sequenced, as well as information on the sequencing of cancer genes, can be found on the Internet at http://www.ncbi.nlm.nih.gov.

Genomics and Proteomics

The Human Genome Project has given rise to new fields of research. One of these is genomics. This new field combines information science with molecular biology. It is resulting in the "mining of the genome" for valuable sequence data.

An even more recent development is the field of proteomics, the study of protein sequences. Research in this field is rapidly expanding, as protein sequences can be predicted from the gene sequence. The folding of the proteins (secondary and tertiary structures) can be predicted by computers, leading to a three-dimensional view of the protein encoded by a particular gene. Proteomics will be the next big challenge for genetics research. Indeed, Celera is already gearing up for massive protein sequencing.

Ethical Issues

From the very beginning of the Human Genome Project, many from both the scientific and public sector have been concerned with ethical issues raised by the research. These issues include preserving the confidentiality of an individual's DNA information and avoiding the stigmatization of individuals who carry certain genes. Some fear that insurers will deny coverage for "preexisting" conditions to people carrying a gene that predisposes them to particular diseases, or that employers might start demanding genetic testing of job applicants.

There are also concerns that prenatal genetic testing could lead to genetic manipulation or a decision to abort based on undesirable traits disclosed by the tests. In addition, some raise concerns that a full knowledge of the human genome could raise profound psychological issues. For example, individuals who know that they carry detrimental genes may find the knowledge to be too great a burden to bear. All of these ethical issues will ultimately have to be addressed by society as a whole.