Applications of DNA chips for genomic analysis

Abstract

A major frontier in medical genetics is the definition of the molecular basis of multifactorial diseases. This is especially relevant in the field of clinical psychiatry where the majority of common disorders display complex inheritance patterns, and are further influenced by environmental interactions. New technologies are needed to help address the pressing needs for discovering and deciphering the nature of such disease-associated genes. One such technology which has emerged within the past 3 years involves hybridization-based nucleic acid array (DNA chip) analysis. This technology has the potential to have a lasting impact on diverse genomic-based applications such as large-scale gene mapping studies, mutational analysis, and global expression level monitoring of all human genes. In this review we will describe the fundamental principles behind nucleic acid array-based assays, while focusing on their applications towards genome-wide DNA and RNA analysis. The current capabilities and limitations of these technologies will be discussed, with a focus on areas where future development will be needed for DNA chip-based assays to achieve their full potential.

Family-based linkage disequilibrium mapping using SNP marker haplotypes: application to a potential locus for schizophrenia at chromosome 22q11

“…This analysis may be suitable for more extended mapping of linked loci using genebased SNPs, and to genome-wide analysis with the advent of potentially high-throughput methods such as gene-chip analysis. 50 We used transmission distortion analysis implemented by the ETDT 47 and TRANSMIT 48 programs, to attempt to fine-map the COMT/ARVCF locus for susceptibility alleles for schizophrenia. Seven SNP markers, including two novel polymorphisms, and two flanking microsatellite markers were genotyped at the COMT/ARVCF locus and analysed both individually and as haplotypes up to 198 family trios with schizophrenia from Southwest China.…”

Whole rat DNA array survey for candidate genes related to hypertension in kidneys from three spontaneously hypertensive rat substrains at two stages of age and with hypotensive induction caused by hydralazine hydrochloride

“…The polygenic nature of human essential hypertension has made it challenging to isolate the genes involved in the genesis of the disease. DNA microarrays are a potentially powerful tool for studying the genetics of hypertension, as they facilitate the measurement of the expression of thousands of genes simultaneously (6)(7)(8). Inbred homozygous rodent models of human essential hypertension are ideal for microarray research, and animal models of essential hypertension have been studied using microarrays (9).…”

Silanized nucleic acids: a general platform for DNA immobilization

“…Solid phase nucleic acid hybridization has been used in a wide variety of applications including monitoring gene expression (1)(2)(3), polymorphism analysis (4,5), disease screening and diagnostics (6,7), nucleic acid sequencing (8)(9)(10) and genome analysis (11,12). A number of different substances have been tested as the solid support for nucleic acid immobilization (13)(14)(15)(16), but glass slides are generally favored for DNA and oligonucleotide microarrays (17)(18)(19)(20)(21).…”