Chapter 36
Microarrays and DNA-Chips in the Analysis
of Genetic Aberrations
UWE R. MULLER, Y. PAUL BAo, GUANGSHAN LI, XINYING XIE,
and NALINI RAGHAVACHARI
Introduction
Fluorescence in situ hybridization (FISH) is a precise technique to determine copy numbers of a particular sequence in individual cells with a resolution better than 30 Kb, but requires a priori knowledge of the target
sequence to be analyzed. Comparative genomic hybridization (CGH) on
the other hand allows a global analysis of the whole genome, but at significant loss in resolution (on the order of 10-15 Mb). DNA chip technology (so called genosensor-based or matrix-based CGH) combines the high
resolution of FISH with the inherent multiplex capability of CGH, and
adds simplicity to the analysis. This technology represents the latest addition to chip based genetic analyses.
Indeed, three classes of DNA chips have been described so far which
vary significantly in their structure, composition, and intended functionality. The feature in common is the small size of their target array, typically
on the order of a few square centimeters (Note: we use the term target for
the DNA on the chip to be consistent with the CGH and gCGH literature,
but realize that an alternative nomenclature has emerged that refers to the
DNA on the chip as the probe). Several different manufacturing technol~ Uwe R. Miiller, Corning Incorporated, Biochemical Technologies, SP-FR-Ol,
Corning, NY, 14831, USA (phone 607-974-9994; fax 607-974-5957;
e-mail MullerU@Corning.com)
Y. Paul Bao, Corning Incorporated, Biochemical Technologies, SP-FR-Ol, Corning, NY,
14831, USA
Guangshan Li, Corning Incorporated, Biochemical Technologies, SP-FR-Ol, Corning,
NY, 14831, USA
Xinying Xie, Corning Incorporated, Biochemical Technologies, SP-FR-Ol, Corning,
NY, 14831, USA
Nalini Raghavachari, Corning Incorporated, Biochemical Technologies, SP-FR-Ol,
Corning, NY, 14831, USA
PROTOCOL
Microarrays and DNA-Chips in the Analysis
of Genetic Aberrations
UWE R. MULLER, Y. PAUL BAo, GUANGSHAN LI, XINYING XIE,
and NALINI RAGHAVACHARI
Introduction
Fluorescence in situ hybridization (FISH) is a precise technique to determine copy numbers of a particular sequence in individual cells with a resolution better than 30 Kb, but requires a priori knowledge of the target
sequence to be analyzed. Comparative genomic hybridization (CGH) on
the other hand allows a global analysis of the whole genome, but at significant loss in resolution (on the order of 10-15 Mb). DNA chip technology (so called genosensor-based or matrix-based CGH) combines the high
resolution of FISH with the inherent multiplex capability of CGH, and
adds simplicity to the analysis. This technology represents the latest addition to chip based genetic analyses.
Indeed, three classes of DNA chips have been described so far which
vary significantly in their structure, composition, and intended functionality. The feature in common is the small size of their target array, typically
on the order of a few square centimeters (Note: we use the term target for
the DNA on the chip to be consistent with the CGH and gCGH literature,
but realize that an alternative nomenclature has emerged that refers to the
DNA on the chip as the probe). Several different manufacturing technol~ Uwe R. Miiller, Corning Incorporated, Biochemical Technologies, SP-FR-Ol,
Corning, NY, 14831, USA (phone 607-974-9994; fax 607-974-5957;
e-mail MullerU@Corning.com)
Y. Paul Bao, Corning Incorporated, Biochemical Technologies, SP-FR-Ol, Corning, NY,
14831, USA
Guangshan Li, Corning Incorporated, Biochemical Technologies, SP-FR-Ol, Corning,
NY, 14831, USA
Xinying Xie, Corning Incorporated, Biochemical Technologies, SP-FR-Ol, Corning,
NY, 14831, USA
Nalini Raghavachari, Corning Incorporated, Biochemical Technologies, SP-FR-Ol,
Corning, NY, 14831, USA
PROTOCOL