Zeroing in on Chromosomes

Genetics is about informationñspecifically, some 3 billion DNA building blocks, forming about 75,000 protein-encoding genes, distributed over 23 pairs of chromosomes. Ferreting out a particular gene or chromosome can be technically challenging, but this is precisely what genetic diagnosis entails. A technique called FISHñfor fluorescence in situ hybridizationñuses fluorescent dye molecules linked to DNA probes to home in on and highlight specific genes among the many. This enables researchers, and soon clinicians, to identify a particular chromosome at a glance.

Consider Down syndrome, a condition involving varying degrees of mental and physical retardation, heart defects, increased leukemia risk and other health problems. It is usually caused by an extra chromosome 21. (Chromosomes are numbered by decreasing size, although 21 is actually smaller than 22. The error in numbering stems from the blurry nature of early chromosome preparations.) Down syndrome is the most common extra-chromosome abnormality because most others end in miscarriage.

Because of Down syndromeís prevalence, prenatal screening for it has become a rite of passage of sorts during pregnancy, especially for women over the age of 35. The tendency to produce an egg cell with an extra chromosome increases with a womanís age, and 35 is the age at which the risk of an extra fetal chromosome having developed equals the risk of the detection procedure (amniocentesis) causing miscarriage.

But getting a peek at fetal chromosomes is labor-intensive, no pun intended. Before FISH, identifying a specific chromosome required constructing a chart called a karyotype, which displays all 23 chromosome pairs in size order. A karyotype is a little like a class of kindergartners lined up in pairs from shortest to tallest.

Before the advent of computerized karyotyping in the mid-1980s, many cytogeneticists would photograph a cell in which the chromosomes were well spread apart, then use old-fashioned scissors and tape to cut out the individual chromosomes and arrange them in size-order pairs. If three tiny chromosome 2ls turned up, then the fetus whose cell was under scrutiny had Down syndrome.

FISH eliminates the need to sift through all of the chromosomes to detect an extra or errant one. A probe consisting of a DNA sequence known to be part of chromosome 21 is linked to a fluorescent dye and applied to fetal cells. The probe binds to its matching sequence among the chromosomesña property of DNA. If two flashes are visualized under a fluorescence microscope, all is well. If there are three flashes, then the fetus has Down syndrome. Another advantage of the technique is that it works on uncultured cells, giving results in days rather than the weeks that it sometimes takes for karyotypes made in the conventional manner.

FISH is also useful in detecting cancers that are associated with chromosomal rearrangements in which one type of chromosome piggybacks on another or two different chromosomes swap parts. Vysis Inc. in Downers Grove, Ill., is one of several biotech companies offering FISH technology to detect either extra or mixedup chromosomes.

"All our probes mark narrowly defined regions of DNA, offering outstanding future potential for clinical use in tests for cancer, prenatal-disease and genetic-disease predisposition," says Dr. Steven Seelig, director of research and development at Vysis. The company recently announced the unveiling of two new FISH products that detect two chromosomal abnormalities and two cancers.

The fluorescent probe with the long-winded name of LSI 13 SpectrumOrange/LSI 21 Indirect SpectrumGreen simultaneously labels chromosome 21 and chromosome 13, which in an extra dose causes the devastating Patau syndrome. In this condition, all organ systems are abnormal, and such pregnancies typically end in miscarriage or stillbirth, or produce an infant that dies within months. It is rare, seen only once in 15,000 births. But like Down syndrome, its incidence increases with maternal age.

In the test, chromosome 13 flashes orange and chromosome 2l flashes green, using company-developed fluorochromes. Three flashes of either indicate the associated condition. While FISH is fast and specific, it does not detect as many chromosomal anomalies as does the standard karyotype, which displays all of the chromosomes.

Vysisí second new FISH product detects a chromosomal jumble that is associated with two types of blood cancersñchronic myelogenous leukemia (CML) and acute lymphocytic leukemia (ALL). Determining the exact type of leukemia early on is important in beginning the most appropriate treatment.

In these leukemias, many patients have an unusual chromosome in which the tip of one chromosome 9 is stuck onto one copy of chromosome 22. The point of breakage on chromosome 9 is an oncogene, or a cancer-causing gene. In its abnormal position on chromosome 22, it is activated, causing the cancer.

Vysisí test consists of two DNA probesñone that binds to the oncogene on chromosome 9, and one that binds to the breakpoint region on chromosome 22. The chromosome 9 probe is linked to a fluorescent dye that flashes orange, and the chromosome 22 probe to a green fluorochrome. If a chromosome preparation flashes green and orange on four different chromosomes, then the diagnosis is not likely to be either CML or ALL. If, however, a green and orange flash appear next to each other on an unusually long chromosome, either of the cancers is diagnosed. The distinction is made on the basis of the type of white blood cell affected and on the symptoms.

With its ability to offer specificity to the sea of information that is the human genome, it looks as if FISH will transition smoothly from the research laboratories of the Human Genome Project to the clinic.

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