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Additional Data for Oligonucleotide Arrays of the p53 Gene in DNA from Formalin-Fixed, Paraffin-Embedded Tissue

¹ BRT Laboratories, Inc., 400 West Franklin St. Baltimore, MD 21201

^aAuthor for correspondence. Fax 410-383-0938; e-mail allen@brtlabs.com.

The first 20% of the full text of this article appears below.

To the Editor:

The report published by Cooper et al. (1) motivated us to report our experience with the Affymetrix® GeneChip^TM (Chip). In its current state, we agree that the Chip cannot be used as a stand-alone test for mutational analysis of the p53 gene. However, it is still a sensitive tool for reducing the need for full-length sequencing. Validation studies in our laboratory have demonstrated that the Chip can detect most mutations in as few as 5% of a cell population; other claims run to as low as 2%.

The limitations of the Chip include a failure to detect insertions, large deletions, and >6 bp of intronic sequence in any direction. Some limitations are attributable to sequence tiling (2). Insertions and large deletions were not tiled at all. As for the intronic sequences, only the splicing junctions were considered to be critical, thus limiting the utility of the Chip.

Failure to detect some missense mutations appears to be attributable to the quality of the DNA and the number of times a sequence has been tiled . . . [Full Text of this Article]

Rita Kandel^R1,a and Thomas Rohan^R2

^R1 University of Toronto, Toronto, Canada
^R2 Albert Einstein College of Medicine, Bronx, NY

^aAddress correspondence to this author at: Pathology and Laboratory Medicine, Mt. Sinai Hospital, 600 University Ave., Toronto, ON M5G1X5 Canada. Fax 416-586-8628; e-mail rkandel@mtsinai.on.ca.