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Chapter 4 : Genomics and Chip Technology

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Abstract:

In a short period, the genomics age has shifted a substantial proportion of study to the search for patterns or profiles of expression or genetic variants in specific diseases. Microarray analysis interrogates total RNA or mRNA purified from cell or tissue sources. Harvest of total RNA or mRNA is critical; technical problems or degradation fatally undermines the interpretation of expression data. Naturally, the quality control steps for ensuring that RNA is not degraded must be established, and in circumstances in which insufficient RNA is available, careful amplification of RNA can be performed during the generation of cDNA. Currently, most studies have used cDNA or oligonucleotide-based arrays to identify regions of loss of heterozygosity or gene amplifications. Chip technology was initially applied to single-base pair mutation detection, using a similar hybridization technology but with genomic DNA as a template. Currently, there are four commercial technologies available for large-scale, high-throughput genotype analysis: Affymetrix, ParAllele, Illumina, and Perlegen. The new technologies for single-nucleotide polymorphism (SNP) detection will enable studies to look at genetic variation across all genes of a pathway or biological process as well as across the entire genome. Similar to the analytical challenges of the microarray expression studies, analytical approaches will continue to evolve in SNP research. One of the major goals of the coming decade is the development of high-throughput sequence technologies.

Citation: Chanock S. 2006. Genomics and Chip Technology, p 22-25. In Detrick B, Hamilton R, Folds J (ed), Manual of Molecular and Clinical Laboratory Immunology, 7th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815905.ch4

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Tables

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TABLE 1

Current high-throughput genotype technologies

Citation: Chanock S. 2006. Genomics and Chip Technology, p 22-25. In Detrick B, Hamilton R, Folds J (ed), Manual of Molecular and Clinical Laboratory Immunology, 7th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815905.ch4

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