Sequencing Arrays

 

Conventional nucleic acid sequencing technologies use analytical separation techniques to resolve sequence at the single nucleotide level. High-density oligonucleotide arrays offer the ability to sequence large numbers of loci in parallel using an automated approach. Sequencing by hybridization (SBH) was invented in the late 1980s as an alternative to gel-based sequencing.   Sequencing using high-density oligonucleotide arrays has been described previously (Khrapko et al 1989, Bains and Smith 1988, Drmanac et al, 1989, Pease et al, 1994). This method uses a set of short oligonuceotide probes of a defined sequence to search for complimentary sequences on a longer target strand of DNA. In fact, the first arrays produced by Affymetrix were designed to resequence the HIV genome. Other array-based sequencing applications followed, including polymorphism and mutation detection in the cytochrome p450 and p53 genes and, more recently, the SARS Coronavirus (Wong et al, 2004). Despite these advances, several limitations moderate the enthusiasm for SBH, including difficulty in the detection of deletions.

 

 

The GeneChip® Human Mitochondrial Resequencing Array 2.0 provides detection of germ line and heteroplasmic mutations of the complete 16kb mitochondrial genome.  Analysis of these mutations can be applied to a wide variety of fields, ranging from disease genetics to forensic identification.

 

 

The GeneChip® SARS Array provides a standard assay for complete sequence analysis of the Severe Acute Respiratory Syndrome (SARS). The SARS-CoV array program is part of an ongoing effort by NIAID to promote genomics approaches to improve the understanding of pathogenic microbes and the diseases they cause. For more details, please refer to TIGR's Pathogen Functional Genomics Resource Center.