New Computer Light Technique Creates a Chromosome Rainbow

July 1996

Toto, I have a feeling we're not in Kansas anymore. We must be over the rainbow.
- Dorothy Gale, 1939

BETHESDA, Md. - Nearly 60 years after Dorothy left gray Kansas for the vibrant land of Oz, wizards of a different sort have concocted a powerful new way to visualize the full set of human chromosomes in a rainbow of colors. The new technique, called "spectral karyotyping," translates computer-gathered light waves into a full-color palette and assigns each chromosome its own distinct hue. With all 23 pairs of human chromosomes identified by a different color, scientists can more easily examine the entire group of chromosomes for changes that could lead to disease, such as missing or extra pieces, or parts from different chromosomes that have swapped places.

The technique could prove to be extremely valuable in diagnosis of disease based on chromosome alterations.

"The value of chromosome examination in understanding the changes that take place during disease progression could be greatly enhanced if we could study the entire genome at once, and clearly distinguish genetic material belonging to one chromosome from that of another," said National Human Genome Research Institute (NHGRI) scientist Thomas Ried, M.D., who led the group that developed the technique. They report their findings in the July 26 issue of the journal Science.

The power of the current diagnostic techniques is limited in examining whole chromosome sets, called karyotypes, for changes because the methods rely on chemical stains that reveal only shades of gray. Pieces exchanged from one chromosome to another - a process called "translocation" that is often associated with disease - cannot easily be detected. And in diseased cells containing several badly distorted chromosomes, tracking the multiplication or exchange of genetic material is often impossible with conventional black-and-white banding.

Chromosome banding was first developed in the early 1970s, when it was observed that each human chromosome portrayed a characteristic pattern of bands when exposed to chemical stains. This allowed researchers to identify and sort out human chromosomes under the microscope not only by their size but also by their characteristic staining patterns.

As staining techniques evolved, scientists used them to link chromosome changes to disease: Missing bands indicated a deletion of genetic material, as in some inherited diseases, whereas extra bands, or translocations, indicated altered or additional genetic material, as is the case in many cancers.

Higher-resolution molecular techniques for visualizing chromosome regions, particularly fluorescence in situ hybridization, or FISH, later improved the process. FISH uses DNA probes labeled with fluorescent dyes to identify specific chromosomal regions. Spectral karyotyping is a new way to interpret data from FISH experiments and has distinct advantages over conventional microscopy.

Ried and his coworkers applied spectral imaging, a technology used in remote sensing devices, to chromosomes isolated from cells. First, they applied different molecular "paints" to the chromosomes. The wavelengths of light, or emission spectrum, each painted chromosome emitted provided a unique "thumbprint" for that chromosome. Although to the eye, the thumbprints are difficult to distinguish from one chromosome to the next, computers rapidly detect differences in emission spectra and assign each chromosome its own easy-to-see color. In a spectral karyotype from a healthy cell, for example, computers translate the emission spectrum for chromosome 1 into yellow, chromosome 2 red, 3 gray, 4 turquoise and so on.

Ried and his coworkers have also showed that spectral karyotyping can be used effectively to pinpoint chromosomal changes linked to disease. They identified structural abnormalities in chromosomes from several different samples obtained from diagnostic laboratories, and demonstrated the value of the technique in identifying a breast cancer cell with a large number of broken and rearranged chromosomes and extra genetic material.

In addition to its role in identifying chromosome changes related to the progression of disease, the authors report that spectral karyotyping may be valuable in comparing genomes from different species to determine how genetic composition evolved over hundreds of thousands of years.

Although Dorothy did eventually return to Kansas, the full-color wizardry of spectral karyotyping is here to stay, says Ried. "I receive about one phone call a day from people who want to learn the technique," he says, anticipating the technology will be common in diagnostic and research laboratories in the coming years.

Sharon Durham
Leslie Fink

The National Human Genome Research Institute (NHGRI), a component of the National Institutes of Health (NIH), is a major partner in the Human Genome Project (HGP), the international research effort to map the estimated 50,000 to 100,000 genes and read the complete set of genetic instructions encoded in human DNA. NHGRI also supports research on the application of genome technologies to the study of inherited disease, as well as the ethical, legal and social implications of this research. For more information about NHGRI or the HGP, visit our Web site.

Last updated: May 16, 2010