Nucleic Acids Research 2000, Vol.28, No.22:4552-4557
Date: 2001/11/28
Speaker: Chang-Wei Yeh
Abstract:
Microarray technology provides biologists opportunities to observe thousands of gene expressions at the same time. According to the selection of probes, there are two types of microarray, cDNA microarray and oligonucleotide microarray. The major difference between them is the lengths of probes. As probe length is an important factor in hybridization, length variations must have influence on the sensitivity and specificity of microarray experiments.
Concerning about the sensitivity, it should be examined if there are consistent signals of the same gene from these two types of arrays by testing 3-fold change in mRNA of difference arrays. As a result of the experiments, no significant difference between oligonucleotide and cDNA microarrays was observed. On the other hand, if the probe is not specific enough to the target gene, cross-hybridization will be seen. In cDNA microarrays, the lengths of probes are always longer than those of oligonucleotide microarrays. Furthermore, there are many gene family¡¦s mRNA with very similar region expressed in cells at the same time. If the probe is long enough, there would be more chances that probe is with similar region to un-target genes. There will be consequently less cross-hybridization in oligonucleotide microarray. When testing the specificity of oligonucleotide probes, a specific probe should require non-target genes to be <75% similar over the 50 base target region. If the 50 base target region is marginally similar (50-75%), it must not include a stretch of complementary sequences >15 contiguous bases.
Therefore, if having the information of target and probe sequences, a well-designed oligonucleotide microarray with sensitivity and specificity must be more accurate in measuring gene expressions than cDNA microarray.
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