In the April issue of the journal Nature Genetics, the researchers report that their novel approach, called spectral karyotyping or SKY, is far more accurate in diagnosing leukemia-associated chromosome defects than is the standard, Giemsa- or G-banding method, today’s most widely used medical test for detecting chromosome aberrations.
"This new advance is a gratifying example of how the Human Genome Project, an ambitious effort to map and sequence all of the human DNA by the year 2005, is spinning off technologies with almost immediate benefit to clinical medicine," says NHGRI director, Dr. Francis Collins.
Currently, physicians use G-banding to look for abnormalities in any of a patient’s 46 chromosomes -- coiled strands of DNA carried in nearly every cell that contain all the genetic information necessary for the body’s proper functioning. By staining chromosomes using a substance dye called Giemsa stain, laboratory specialists can produce a karyotype, or arrangement of chromosomes, that shows a distinctive banding pattern for each chromosome.
In patients with certain cancers, such as leukemia, and birth defects, such as Down syndrome, that banding pattern can reveal various types of chromosomal aberrations. Parts of chromosomes can be translocated, or swapped between one chromosome and another. Other chromosomes can be deleted or duplicated either in whole or in part.
Unfortunately, the limited staining in a G-banding karyotype does not always reveal those aberrations. Subtle translocations in chromosomes, for example, are sometimes undetected in G-banding karyotypes, even by the keen eye of a trained specialist because the banding pattern of the "swapped" chromosome ends is identical.
SKY, on the other hand, produces brightly colored chromosomes that can clearly reveal chromosome aberrations that G-banding misses. In a study of 15 patients with different forms of leukemia, teams led by Dr. Thomas Ried at NHGRI and by Dr. Janet Rowley at the University of Chicago found chromosome aberrations in the leukemia cells that went undetected using G-banding in every case.
"Recently, cytogeneticists have used a technique called fluorescence in situ hybridization, or FISH, which enables the scientist to locate the precise position on the chromosome of one or several different DNA probes using different dyes to label each probe. SKY has the enormous advantage in that it can simultaneously uniquely identify all of the chromosomes in a single cell." says Dr. Rowley.
According to Rowley, the question then becomes, are any pieces of chromosomes in the wrong place, i.e., has there been a translocation we did not detect? Moreover, in cancer cells, there are many so called "marker" chromosomes whose size or shape is so unusual that we cannot identify them. SKY can help unravel the composition of these marker chromosomes even when they contain pieces of three or more chromosomes joined together.
SKY is a hybrid technology based on a standard genetics research tool called FISH, short for fluorescence in situ hybridization, combined with another technology called spectral analysis—a technique commonly used in astronomy to separate out the rainbow-like components of light from distant stars. SKY employs molecules called probes that attach themselves to parts of chromosomes and glow when exposed to light. The tagged portion of each chromosome appears in a specific color, creating a multi-color pattern which vividly distinguishes one chromosome from another.
Ried and his colleagues are already testing to see whether SKY can be used to detect chromosome aberrations in other diseases, such as certain birth defects. If the new technology proves successful, the researchers say, it might soon start augmenting or perhaps even replacing the current G-banding method, which is now performed some 500,000 times a year in hospitals and research centers across the United States and Canada to diagnose a wide range of diseases.
Although SKY is still a more expensive technique to carry out compared to G-banding, Ried believes that SKY’s benefits outweigh its extra costs. First, because SKY provides more accurate diagnoses, doctors can better treat patients with appropriate therapies earlier and potentially avoid unnecessary and costly therapies later on. And second, because of the well-defined patterns, SKY could be assessed by computers, which would greatly speed up the diagnoses of certain diseases.
"SKY has the potential to become an important tool in molecular genetics for identifying subtle and complex chromosome aberrations without requiring any preconceived notions of the abnormalities involved," says Ried.
The NHGRI oversees the role of the National Institutes of Health (NIH) in the Human Genome Project, an international research effort to develop tools for gene discovery. The NHGRI is one of 24 institutes, centers, and divisions that make up the NIH, which is part of the U.S. Department of Health and Human Services and the federal government’s primary agency for the support of biomedical research.