In molecular biology, SNP array is a type of microarray DNA used to detect polymorphism in a population. Single nucleotide polymorphism (SNP), a variation in one site in DNA, is the most frequent type of variation in the genome. Around 325 million SNPs have been identified in the human genome, 15 million of which are present at a frequency of 1% or higher across different populations around the world.
Video SNP array
Principles
The basic principle of the SNP array is the same as the DNA microarray. This is the convergence of DNA hybridization, fluorescence microscopy, and solid surface DNA removal. The three mandatory components of the SNP array are:
- An array containing a specific immobilized allele oligonucleotide probe.
- The targeted nucleic acid sequence, labeled with fluorescent dye.
- A detection system that records and interprets hybridization signals.
ASO probes are often selected on the order of individual representative panels: positions found varying in the panel at the specified frequency are used as the basis for the probe. SNP chips are generally explained by the number of SNP positions they test. Two probes must be used for each SNP position to detect both alleles; if only one probe is used, the experimental failure will be distinguished from the homozygosity of the unelected allele.
Maps SNP array
Apps
The SNP array is a useful tool for studying slight variations between the entire genome. The most important clinical application of the SNP array is to determine the susceptibility of disease and to measure the efficacy of drug therapy specifically designed for individuals. In the study, SNP arrays are most commonly used for genome association studies. Each individual has many SNPs. SNP-based genetic linkage analysis can be used to map the disease locus, and determine the susceptibility genes of the disease in individuals. The combination of SNP maps and high density SNP arrays allows the SNP to be used as a marker for complex genetic diseases. For example, genome association studies have identified the SNP associated with diseases such as rheumatoid arthritis, prostate cancer, and type 2 diabetes. SNP arrays can also be used to generate virtual karyotype using software to determine the number of copies of each SNP in the array and then align the SNP in sequence of chromosomes.
SNP can also be used to study genetic abnormalities in cancer. For example, the SNP array can be used to study the loss of heterozygosity (LOH). LOH occurs when one gene allele is mutated by destruction and a functional allele is lost. LOH is common in oncogenesis. For example, tumor suppressor genes help prevent cancer developing. If a person has one copy of a mutated and dysfunctional tumor suppressor gene and a functional copy of both genes is damaged, they may become more likely to develop cancer.
Other chip-based methods such as comparative genome hybridization can detect the gain or removal of the genome that leads to LOH. SNP arrays, however, have the added advantage of being able to detect copy-neutral LOH (also called uniparental disomy or gene conversion). Copy-neutral LOH is a form of elliptical imbalance. In a copy-neutral LOH, one allele or whole chromosome of the parent is lost. This issue causes the duplication of other parent alleles. Copy-neutral LOH may be pathological. For example, say that the mother's allele is a wild and fully functional type, and the father's allele mutates. If the mother's allele is lost and the child has two copies of the father's mutant allele, the disease can occur.
High density SNP density helps scientists identify alelic imbalance patterns. These studies have potential prognostic and diagnostic usage. Since LOH is very common in many human cancers, the SNP array has great potential in cancer diagnosis. For example, recent SNP array studies have shown that solid tumors such as gastric cancer and liver cancer show LOH, as do non-denser malignancies such as haematological malignancy, ALL, MDS, CML and others. These studies can provide insight into how the disease develops, as well as information on how to make therapy for them.
Source of the article : Wikipedia
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