SNP array: Difference between revisions

Revision as of 03:11, 3 May 2007

Revision as of 02:07, 23 September 2007

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An SNP array is a useful tool to study the whole genome. The most important application of SNP array is in determining disease susceptibility and consequently, in pharmacogenomics by measuring the efficacy of drug therapies specifically for the individual. As each individual has many single nucleotide polymorphisms that together create a unique DNA sequence, SNP-based linkage analysis could be performed to map disease loci, and hence determine disease susceptibility genes for an individual. The combination of SNP maps and high density SNP array allows the use of SNPs as the markers for Mendelian diseases with complex traits efficiently. For example, whole-genome genetic linkage analysis shows significant linkage for many diseases such as rheumatoid arthritis, a common chronic inflammatory disease, prostate cancer, neonatal diabetes. As a result, drugs can be personally designed to efficiently act on a group of individuals or even each individual.

In addition, SNP-array can be used for studying the loss of heterozygosity. [[Loss of heterozygosity]] (LOH). LOH is a form of allelic imbalance that can result from the complete loss of an allele or from an increase in copy number of one allele relative to the other. UsingWhile highother densitychip-based methods (e.g. [[Comparative genomic hybridization]] can detect only genomic gains or deletions), SNP array tohas detectthe additional advantage of detecting copy number neutral LOH allowsdue identificationto of[[uniparental patterndisomy]](UPD). In UPD, one allele or whole chromosome from one parent are missing leading to reduplication of allelicthe imbalanceother withparental potentialallele prognostic(uni-parental and= diagnosticfrom utilitiesone parent, disomy = duplicated). ThisIn usagedisease ofsetting SNPthis arrayoccurence hasmay abe hugepathologic potentialwhen inthe cancerwildtype diagnosticsallelle as(e.g. LOHfrom the mother) is amissing prominentand characteristicinstead two copies of mostthe heterozygous allelle (e.g. from the father) humanare cancerspresent.

Using high density SNP array to detect LOH allows identification of pattern of allelic imbalance with potential prognostic and diagnostic utilities. This usage of SNP array has a huge potential in cancer diagnostics as LOH is a prominent characteristic of most human cancers. Recent studies based on the SNP array technology have shown that not only solid tumors (e.g. gastric, liver etc) but also hematologic malignancies (ALL, MDS, CML etc) have a high rate of LOH due to genomic deletions or UPD and genomic gains. The results of these studies may help to gain insights into mechanisms of these diseases and to create targeted drugs.

== References ==