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Speeding the search for elusive chromosomal errors

oarray 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 pa
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Source:Children's Hospital of Philadelphia


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