A pediatric research team has used commercially available gene chips to scrutinize all of a patient's chromosomes to identify small defects that cause genetic diseases. Because currently used genetic tests usually cannot detect these abnormalities, the new research may lead to more accurate diagnosis of congenital diseases, including puzzling disorders that lead to mental retardation.
"For years, many children who have multiple congenital problems, such as developmental delays, heart defects and facial abnormalities, have gone undiagnosed because they may not have an easily recognizable syndrome," said study leader Tamin H. Shaikh, Ph.D., a molecular geneticist at The Children's Hospital of Philadelphia.
"Until recently, our laboratory technology was not sufficiently refined to detect many of these small rearrangements in chromosomes," added Dr. Shaikh. "Now we have a better tool for finding the abnormal gene or genes that give rise to a disorder." The research is published in the May 2006 issue of Human Mutation.
For many of these rare disorders caused by small errors in chromosomes, improved diagnosis does not mean that physicians can provide more effective treatments, at least not immediately. In the long run, adds Dr. Shaikh, better knowledge of the underlying genetic cause of a disease may provide targets for designing future therapies.
Conventional genetic tests have limited resolving power in detecting many chromosomal arrangements. In karyotyping, chromosomes are stained and examined under microscopes, but only larger rearrangements are visible, such as extensive deletions, or the presence of an extra chromosome, as occurs in Down syndrome. Another technique, subtelomere analysis, finds smaller, submicroscopic abnormalities, but only in the regions directly below the telomeres, at the end of each chromosome.
Recent advances in diagnostic gene chips, used by Dr. Shaikh's team, allow more precise analysis of very small DNA alterations throughout all of a patient's chromosomes.
Gene Chips Detect Tiny Structural Defects in Genomic Diseases
Conditions that originate in alterations of chromosome architecture have been called "genomic diseases." The smallest of these structural defects are microdeletions, a loss of a small amount of genetic material, or microduplications, an excess of genetic material.
Individually, many genomic diseases are rare, but collectively, they may occur in one in 1,000 live births. Frequently the gene aberrations harm multiple organ systems. For example, patients with chromosome 22q11.2 deletion syndrome may have heart defects, impaired immunity and developmental delay. Deletions of several genes in Prader-Willi syndrome may cause obesity and mental retardation.
To seek out miniscule rearrangements in chromosomes, the Children's Hospital team employed the types of gene chips, or microarrays, originally designed to identify genes involved in common, complex diseases like diabetes and hypertension. Microarrays contain short fragments of DNA, called oligonucleotides, that bind to complementary stretches of DNA within a sample being tested. These microarrays hold more than 100,000 DNA oligonucleotides, which allow researchers to rapidly analyze a person's whole genome -- the entire complement of DNA in a cell nucleus.
"These microarrays provide more rapid and precise results than karyotyping, and offer as much as 50 times higher resolution than other, more commonly used microarrays, such as bacterial artificial chromosome arrays," said Dr. Shaikh. "Our study is one of the first to report using these microarrays in a clinical setting to detect constitutional rearrangements which lead to severe birth defects." Constitutional rearrangements occur in all of a person's cells.
As Technology Improves, Smaller Defects Should Be Detectable
In the current paper, the research team first validated the microarray by using it to test samples from two patients with known chromosomal rearrangements and well-characterized genetic diseases. In a blinded analysis, the experiment found the correct location of the abnormal regions.
In the second part of the study, the researchers studied samples from 10 patients with multiple congenital anomalies, all of whom had previously normal results from karyotype and subtelomeric testing. The team identified novel submicroscopic deletions in two patients. These deletions, one on chromosome 1 and the other on chromosome 3, were not detected in the patients' parents, providing strong evidence that the deletions were the underlying cause of the multiple defects seen in the children.
Dr. Shaikh's laboratory has subsequently used the microarray to analyze DNA samples from more than 60 patients, and have detected novel microdeletions and microduplications in 25 percent of the cases. He also has received a grant to investigate chromosomal rearrangements in bipolar disease, a complex disorder thought to involve interactions among multiple genes.
Dr. Shaikh is currently collaborating with other researchers at Children's Hospital to evaluate other, higher-density gene chips (holding more than 500,000 oligonucleotides), which provide greater resolution. His team is also developing better computational tools to evaluate data from these chips. "Our ability to detect even smaller rearrangements will only get better as there are improvements in the resolution of the microarrays and the computational tools required to analyze and mine the data generated," said Dr. Shaikh.
As he pursues ongoing studies to enroll and study more patients with congenital defects, Dr. Shaikh collaborates with Elaine H. Zackai, M.D., director of Clinical Genetics at Children's Hospital. "It is extremely rewarding to finally have tools to identify heretofore undetectable, cryptic rearrangements and to be able to provide a diagnosis for the patients and their families," said Dr. Zackai.
The National Institutes of Health supported this research, as did the Ethel Brown Foerderer Fund at Children's Hospital. Dr. Shaikh's co-authors, all from The Children's Hospital of Philadelphia, are Jeffrey E. Ming, M.D., Elizabeth Geiger, Alison C. James, Karen L. Ciprero, Manjunath Nimmakayalu, Ph.D., Yi Zhang, Andrew Huang, Madhavi Vaddi, Eric Rappaport, Ph.D., and Elaine H. Zackai, M.D. Drs. Shaikh, Ming and Zackai also are faculty members of the University of Pennsylvania School of Medicine.
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