Antisense oligonucleotides are potentially powerful tools for selective control of cellular and viral gene expression. Crucial to successful application of this approach is the specificity of the oligonucleotide for the chosen RNA target. Here we apply DNA array technology to examine the specificity of antisense oligonucleotide treatments. The molecules used in these studies consisted of phosph...

An allele-specific oligonucleotide microarray was developed for rapid typing of pathogens based on analysis of genomic variations. Using a panel of Escherichia coli strains as a model system, selected loci were sequenced to uncover differences, such as single- or multiple-nucleotide polymorphisms as well as insertion/deletions (indels). While typical genomic profiling experiments employ specifi...

BACKGROUND Microdeletions in the NRXN1 gene have been associated with a range of neurodevelopmental disorders, including autism spectrum disorders, schizophrenia, intellectual disability, speech and language delay, epilepsy and hypotonia. RESULTS In the present study we performed array CGH analysis on 10,397 individuals referred for diagnostic cytogenetic analysis, using a custom oligonucleot...

Several hundred microRNAs (miRNAs) have recently been cloned from a wide range of organisms across phylogeny. Despite the high degree of conservation of miRNAs, their functions in general, and in mammals particularly, are just beginning to be defined. Here we show that an oligonucleotide DNA array can be successfully used for the simultaneous analysis of miRNA expression profiles from tissues o...

To examine the utility and performance of 50mer oligonucleotide (oligonucleotide probe) microarrays, gene-specific oligonucleotide probes were spotted along with PCR probes onto glass microarrays and the performance of each probe type was evaluated. The specificity of oligonucleotide probes was studied using target RNAs that shared various degrees of sequence similarity. Sensitivity was defined...

Incorporation of strain-specific synthetic DNA tags into yeast Saccharomyces cerevisiae gene-deletion strains has enabled identification of gene functions by massively parallel growth rate analysis. However, it is important to confirm the sequences of these tags, because mutations introduced during construction could lead to significant errors in hybridization performance. To validate this expe...

Acute promyelocytic leukemia is characterized by the rearrangement of the retinoic acid receptor α (RARA) gene and its fusion with other genes. We report a novel case of variant acute promyelocytic leukemia with the karyotype der (2)t(2;17)(q32;q21). Array comparative genomic hybridization revealed distinct chromosome breakpoints within the RARA and oligonucleotide/oligosaccharide-binding fold ...

With the complete sequence now available, the yeast genome project enters a post-sequencing phase that will concentrate on a comprehensive determination of gene function. Novel techniques have been developed to undertake genome-wide functional analysis at the levels of phenotype, transcript and protein. These include techniques for the efficient deletion of individual genes while tagging the de...

For the analysis of transcriptional tiling arrays we have developed two methods based on state-of-the-art machine learning algorithms. First, we present a novel transcript normalization technique to alleviate the effect of oligonucleotide probe sequences on hybridization intensity. It is specifically designed to decrease the variability observed for individual probes complementary to the same t...

DNA microarray is a powerful technology for parallel analysis of gene expression (Brown and Bostein, 1999). Since microarray technology emerged 5 years ago (Schena et al., 1995), the number of genes that can be monitored by this technology has increased from several hundreds (Yuan et al., 1998; Aharoni et al., 2000; Reymond et al., 2000) to several thousands (Arabidopsis Functional Genomics Con...