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High -tech Mitochondrial DNA Sequencing Tool Updated

l read not only the identity of the expected bases of DNA in a process called "base calling" but those of the variations.

The Affymatrix chip enabled laboratories to resequence the mitochondrial genome much faster than the traditional manual and automated strategies. Just as importantly, like an iPod to music lover, the chip served as the broad technological platform for laboratories to customize arrays more attuned to their research interests.

In 2004, Dr. Anirban Maitra and his colleagues at Johns Hopkins did exactly that with the MitoChip v1.0. In addition to nitty-gritty technical innovations that vastly improved the rate and speed of the chip, the v1.0 marked the first mitochondrial resequencing microarray designed as a potential screening tool for cancer. "With mitochondrial DNA, there is a mass advantage," said Dr. Anirban Maitra, an author on this month's paper whose research is supported by the NIH's National Cancer Institute. "Whereas nuclear DNA contains just two copies of every gene, there are literally hundreds of mitochondria in most cells. If you are screening saliva or other bodily fluids with a limited number of cells to analyze, mitochondrial DNA gives you more to work with and a better chance of detecting mutations that might be associated with a developing cancer."

Dr. Maitra said that despite the original Mitochip's 96 percent success rate assigning base calls, there was room for improvement. Led by Drs. Shaoyu Zhou and Keyaunoosh Kassauei, the Hopkins group cobbled together the MitoChip v2.0. reported in this month's Journal of Molecular Diagnostics. It yielded essentially the same base-call success rate as its predecessor, showed near perfect reproducibility in replicate experiments, and detected more variations than the first-generation chip.

As a proof of principle, the Mitochip v2.0 also detected 31 variations in the non-coding D-loop of 14 head and neck tumor samples. Included in this tal
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