A Short History of Mapping

Reading The Human Blueprint

"All human disease is genetic in origin," Nobel laureate Paul Berg of Stanford University told a cancer symposium a few years ago. Berg was exaggerating only slightly. It has become increasingly evident that virtually all human afflictions, from cancer to psychological disorders and susceptibility to infection, are rooted in our genes. "What we need to do now is find those genes," claims James Watson, who shared a Nobel Prize for deciphering the structure of DNA and who now directs the National Center for Human Genome Research at the National Institutes of Health.

The necessary guide will be a map fixing each of the estimated 50,000 to 100,000 human genes to its correct location on the chromosomes. "Like the system of interstate highways spanning our country, the map of the human genome will be completed stretch by stretch," Watson says. He expects that this map, the goal of the federally funded Human Genome Project, will provide the key to understanding the nearly 4,000 known genetic disorders and the countless diseases whose origin may be due in part to genetic malfunctions, as well as the astonishing variety of normal human traits.

Such a map has been on the wish lists of molecular explorers for years. Without it, nailing the culprits responsible for genetic diseases requires not only hard work, ingenuity, and determination, but more than a little luck. Although researchers were aided by luck when they found the general location of the gene for Huntington's disease (HD) on chromosome 4 in 1983, for instance, since that time they have spent eight years painstakingly slogging through the target area at the tip of the chromosome and still have no gene in sight.

Yet single-gene diseases such as HD are relatively easy targets. Disorders that seem to be caused by the interplay of several genes, hypertension, atherosclerosis, and most forms of cancer and mental illness, are much more difficult to track down. Having a map of the entire human genome will make it theoretically possible to identify every gene that contributes to them.

A gene map can also lead researchers to new frontiers in drug development. Once all the genes are identified and their bases are sequenced, it will be possible to produce virtually any human protein-valuable natural pharmaceuticals, such as tissue plasminogen activator, interferon, and erythropoietin - as well as new molecules designed specifically to block disease-producing proteins.

The NIH gene-mapping project officially began in October, 1990. But the map of the human genome has been in the making for a good part of the century. It started in 1911, when the gene responsible for red-green color blindness was assigned to the X chromosome following the observation that this disorder was passed on to sons by mothers who saw colors normally. Some other disorders that affect only males were likewise mapped to the X chromosome on the theory that females, who have two X chromosomes, were protected from these disorders by a normal copy of the gene on their second X chromosome unlike males, who have one X and one Y chromosome.

The other 22 pairs of chromosomes remained virtually uncharted until the late 1960s. Then biologists fused human and mouse cells to create uneasy hybrid cells that cast off human chromosomes until only one or a few remained. Any recognizable human proteins in these hybrid cells thus had to be produced by genes located on the remaining human chromosomes. This strategy allowed scientists to assign about 100 genes to specific chromosomes.

Map-making really took off in the early 1970s, when geneticists discovered characteristic light and dark stripes or bands across each chromosome after it was stained with a chemical. These bands, which fluoresced under ultraviolet light, provided the chromosomal equivalent of latitudes. They made it easier to identify individual human chromosomes in hybrid cells and served as rough landmarks on the chromosomes, leading to the assignment of some 1,000 genes to specific chromosomes.

Around the same time, recombinant DNA technology began to revolutionize biology by allowing researchers to snip out pieces of DNA and splice them into bacteria, where they could be grown, or cloned, in large quantities. This led to two new mapping strategies. In one, in situ hybridization, scientists stop the division of human cells in such a way that each chromosome is clearly visible under a light microscope. Then they use probes to find the location of any DNA fragment on these chromosomes. Originally these probes were radioactively labeled, but chemically-tagged probes that can be made to fluoresce have been found to yield far more accurate and rapid results.

The other strategy is to use DNA variations as markers on the human genome, as proposed by Botstein, White, Skolnick, and Davis in 1980. This has resulted in a flood of new markers and an explosion in the knowledge of genes' chromosomal whereabouts. The number of genes mapped grew from 579 in 1981 to 1,879 in 1991. Gene mappers, who used to meet to coordinate their findings every year or so, now update the map every day via electronic databases.

Meanwhile, scientists learned to sequence the genes they isolated. This became possible in the mid-1970s when Frederick Sanger at Cambridge University and Walter Gilbert and Allan Maxam at Harvard University developed efficient new methods for determining the order of bases in a strand of DNA. Automated high-speed sequencing by machine followed in the 1980s. Now, once a new gene has been identified, it is immediately sequenced to understand the nature of the protein it codes for and to identify mutations that are related to disease.

Sequencing the entire genome, however, means sequencing at least 3 billion base pairs of DNA - a chromosome of each type, or half the total number of chromosomes in a human cell. This remains a daunting project.

Generally the most interesting or accessible genes have been located first, creating a disparity among chromosomal maps. While the map of the X chromosome appears to be as densely populated as the New York coast, for instance, chromosome 18 looks as lonesome as central South Dakota.

The Human Genome Project should even out the map by sending explorers into chromosomal terra incognito. "The project really isn't doing anything new. What it's doing is creating order and accountability," says geneticist Eric Lander of the Whitehead Institute.

This orderly process is expected to produce a genetic linkage map in which the positions of genes for specific traits and diseases are superimposed on a grid of evenly spaced markers along the chromosomes. The project's five-year goal is to cover the entire genome with 1,500 genetic markers placed at equal intervals. Scientists will be able to determine any gene's location relative to these markers.

In addition, the project will create a physical map that shows actual distances along the chromosomes in terms of base pairs.

The physical map probably will be constructed of long overlapping stretches of DNA cloned in yeast and known as yeast artificial chromosomes (YACs). Developed in 1987 by Maynard Olson, now an HHMI investigator at Washington University in St. Louis, YACs make it possible to clone and store very large DNA segments - much larger than those that can be cloned in bacteria. The technique has reduced the number of DNA pieces that need to be placed in the right order from about 100,000 to 10,000. Recently, Olson assembled a YAC library of the entire genome and distributed it for the use of gene mappers.

At least two approaches have been developed to unite the genetic linkage map and the physical map so that a researcher can easily move back and forth between the two. One is to dot both maps with a new kind of marker known as sequence-tagged sites, or STSs - long sequences of DNA that generally occur only once in the whole human genome and can be used as common reference points. The other approach is to plot the position of existing genetic markers onto the physical map by means of in situ hybridization.

Meanwhile, new strategies promise to speed up sequencing significantly. Some researchers have reported that it may not be necessary to sequence every base but to sequence certain pivotal regions of DNA and fill in the blanks later. Moreover, automated sequencing and computer software designed specifically for genome analysis are already reducing sequencing time. As the pace of mapping and sequencing quickens, so does the pace of data collection. The Genome Data Base, developed by The Johns Hopkins University in collaboration with HHMI, integrates various kinds of mapping and sequencing data, as well as the constantly evolving genetic linkage map. The Paris-based Centre d'Etude du Polymorphisme Humain collates data from laboratories around the world to develop a series of consensus maps for each chromosome. Another international body, the Human Genome Organisation, is starting to coordinate gene-mapping efforts in 42 nations.

The Genome Project has often been criticized as the intrusion of "Big Science" on the traditionally "small science" of biology. However, "everyone's beginning to realize this isn't at all like putting up a space station or erecting a supercolliding superconductor," says Glen Evans of the Salk Institute in La Jolla, California. "We're not going to undertake large-scale sequencing until new technology makes it cheap to do," explains James Watson.

If a map of the genome and sets of overlapping clones had been available when researchers set out to find the cystic fibrosis gene, their task would have taken only a fraction of the time and cost, points out Thomas Caskey, of the HHMI unit at the Baylor College of Medicine. "The investigators wouldn't have had to clone region after region looking for the gene," he says. "They could have just reached into the freezer and pulled out two markers flanking it. The same would be true for many other diseases. And remember, once we make this map, we will never have to do it again."

Go to next story: What can we expect from the Human Genome Project

See Graphics Gallery: Comparative Scale of Mapping, Sequences of Base Pairs

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