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Vol. 10, Issue 11, 1726-1736, November 2000

LETTER
Detecting Gene Copy Number Fluctuations in Tumor Cells by Microarray Analysis of Genomic Representations

Robert Lucito,1,5 Joseph West,1 Andrew Reiner,1 Joan Alexander,1 Diane Esposito,1 Bhubaneswar Mishra,2 Scott Powers,3 Larry Norton,4 and Michael Wigler1

1 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; 2 Courant Institute, New York University, New York, New York 10012, USA; 3 Tularik, Greenlawn, New York 11740, USA; 4 Memorial Sloan-Kettering, Division of Solid Tumor Oncology, New York, New York 10021, USA

In this work, we explore the use of representations in conjunction with DNA microarray technology to measure gene copy number changes in cancer. We demonstrate that arrays of DNA probes derived from low-complexity representations can be used to detect amplifications, deletions, and polymorphic differences when hybridized to representations of genomic DNA. The method is both reproducible and verifiable, and is applicable even to microscopic amounts of primary tumors. We also present a mathematical model for array performance that is useful for designing and understanding DNA microarray hybridization protocols. The future applications and challenges of this approach are discussed.

5 Corresponding author.

10:1726-1736 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
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