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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 [[genetic 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]], [[prostate cancer]], and neonatal [[diabetes]]. As a result, [[drug]]s can be personally designed to efficiently act on a group of individuals who share a common [[allele]] - or even a single individual.
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
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 Myelogenous Leukemia (CML)|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.
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