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In [[molecular biology]] and [[bioinformatics]], a '''SNP array''' is a type of [[DNA microarray]] which is used to detect [[Polymorphism (biology)|polymorphisms]] within a population. A [[single nucleotide polymorphism]] (SNP), a variation at a single site in [[DNA]], is the most frequent type of variation in the genome. For example, there isare an estimated 5-10 million SNPs in the [[human genome]]. As SNPs are highly conserved throughout [[evolution]] and within a [[population]], the map of SNPs serves as an excellent genotypic marker for research.
==Principles==
The basic principles of SNP array isare the same as the [[DNA microarray]];. whichThese isare the convergence of [[DNA hybridization]], [[fluorescence microscope|fluorescence microscopy]], and solid surface DNA capture. The three mandatory components of the SNP arrays are:
# The array that contains immobilized [[nucleic acid]] sequences or target;
# One or more labeled probes;
# A detection system that records and interprets the [[DNA-DNA hybridization|hybridization]] signal.
To achieve relative concentration independence and minimal cross-hybridization, raw sequences and SNPs of multiple databases are scanned to design the probes. Each SNP on the array is interrogated with different probes. Depending on the purpose of experiments, the amount of SNPs present on an array is considered.
==Applications==
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 polymorphismspolymorphism]]s 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]], a common chronic inflammatory disease, [[prostate cancer]], and neonatal [[diabetes]]. As a result, drugs[[drug]]s can be personally designed to efficiently act on a group of individuals who share a common [[allele]] - or even eacha 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 [[DNA microarray|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 heterozygous 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 tumors[[tumor]]s (e.g. [[gastric cancer]], [[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.
== References ==
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