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Arrays for Genotyping 255
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Oligonucleotide Arrays for Genotyping
Enzymatic Methods for Typing Single Nucleotide Polymorphisms
and Short Tandem Repeats
Stephen Case-Green, Clare Pritchard, and Edwin Southern
1. Introduction
Much of modern genetics is based on analysis of DNA sequence. Therefore, there
is great pressure to scale up sequence analysis while decreasing its cost. The most
promising platforms are based on the use of oligonucleotide arrays (DNA chips), which
perform many analyses in parallel (1). Arrays comprise libraries of oligonucleotides
or polynucleotides attached to solid supports at defined locations. Assays can be
performed on the whole library simultaneously, increasing both the speed and accuracy
of analysis of the target nucleic acid.
In this chapter, we describe the fabrication and some uses of oligonucleotide arrays
that are under development in our laboratory and give an idea of the flexibility of the
array platform. Practical array-based assays will need to be individually optimized to
the desired target nucleic acid. Although arrays can be made from large fragments of
DNA (2), this chapter concentrates on arrays of synthetic oligonucleotides. Analytic
methods for single nucleotide polymorphisms (SNPs) and short tandem repeat (STR)
measurement are described. Other uses have been made of DNA arrays, such as
expression monitoring (3) and antisense oligonucleotide optimization (4).
Most methods for DNA sequence analysis are based on gel electrophoretic separation
of DNA fragments. Automation and miniaturization of these techniques has been
difficult to achieve. A major advantage of arrays is the potential for automation at all
stages of manufacture and application. Figure 1 shows a scheme for an assay using
an oligonucleotide array.
1.1. Fabrication of Arrays
Two methods of array fabrication are in general use, listed as follows:
1. Presynthesized oligonucleotides can be applied to a support.
2. Oligonucleotide synthesis can be performed in situ at specific sites on the support.
From: Methods in Molecular Biology, Vol. 226: PCR Protocols, Second Edition
Edited by: J. M. S. Bartlett and D. Stirling © Humana Press Inc., Totowa, NJ
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