MATRIX-BASED COMPARATIVE GENOMIC HYBRIDIZATION - BIOCHIPS TO SCREEN FOR GENOMIC IMBALANCES

Comparative genomic hybridization (CGH) to metaphase chromosomes has b een widely used for the genome-wide screening of genomic imbalances in tumor cells. Substitution of the chromosome targets by a matrix consi sting of an ordered set of defined nucleic acid target sequences would greatly enhance the resolution and simplify the analysis procedure, b oth of which are prerequisites for a broad application of CGH as a dia gnostic tool. However, hybridization of whole genomic human DNA to imm obilized single-copy DNA fragments with complexities below the megabas e pair level has been hampered by the low probability of specific bind ing because of the high probe complexity. We developed a protocol that allows CGH to chips consisting of glass slides with immobilized targe t DNAs arrayed in small spots. High-copy-number amplifications contain ed in tumor cells were rapidly scored by use of target DNAs as small a s a cosmid. Low-copy-number gains and losses were identified reliably by their ratios by use of chromosome-specific DNA libraries or genomic fragments as small as 75 kb cloned in P1 or PAC vectors as targets, t hus greatly improving the resolution achievable by chromosomal CGH. Th e ratios obtained for the same chromosomal imbalance by matrix CGH and by chromosomal CGH corresponded very well. The new matrix CGH protoco l provides a basis for the development of automated diagnostic procedu res with biochips designed to meet clinical needs. (C) 1997 Wiley-Liss , Inc.