SNP array: Difference between revisions

Revision as of 09:03, 16 August 2010

Revision as of 20:54, 17 September 2010

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In addition, SNP array can be used for studying the [[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 [[gene copy number|copy number]] of one allele relative to the other. While other chip-based methods (e.g. [[Comparative genomic hybridization]]) can detect only genomic gains or deletions, SNP array has the additional advantage of detecting copy number neutral LOH due to [[uniparental disomy]] (UPD). In UPD, one allele or whole chromosome from one parent are missing leading to reduplication of the other parental allele (uni-parental = from one parent, disomy = duplicated). In a disease setting this occurrence may be pathologic when the wildtype allelle (e.g. from the mother) is missing and instead two copies of the mutant allelle (e.g. from the father) are present.

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 [[tumor]]s (e.g. [[gastric cancer]], [[Hepatocellular carcinoma|liver cancer]] etc) but also [[leukemia|hematologic malignancies]] ([[Leukemia#Acute Lymphocytic Leukemia (ALL)|ALL]], [[Myelodysplastic syndrome|MDS]], [[Leukemia#Chronic Myelogenousmyelogenous Leukemia (CML)leukemia|CML]] etc) have a high rate of LOH due to genomic [[deletion (genetics)|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.