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A SNP array can also be used to generate a virtual karyotype using software to determine the copy number of each SNP on the array and then align the SNPs in chromosomal order. [10] SNPs can also be used to study genetic abnormalities in cancer. For example, SNP arrays can be used to study loss of heterozygosity (LOH). LOH occurs when one allele ...
Data analysis for an array-based DNA copy number test can be very challenging though due to very high volume of data that come out of an array platform. BAC (Bacterial Artificial Chromosome) arrays were historically the first microarray platform to be used for DNA copy number analysis. This platform is used to identify gross deletions or ...
Identification of the captured SNPs was performed on genotyping arrays where each spot on the array contained sequences complementary to the locus-specific tags in the probes. Since the DNA array costs is a major contributor to the cost of this technique, the performance of four-chip-one-color detection was compared to two-chip-two
SNP genotyping is the measurement of genetic variations of single nucleotide polymorphisms (SNPs) between members of a species. It is a form of genotyping, which is the measurement of more general genetic variation. SNPs are one of the most common types of genetic variation.
A tag SNP is a representative single nucleotide polymorphism (SNP) in a region of the genome with high linkage disequilibrium that represents a group of SNPs called a haplotype. It is possible to identify genetic variation and association to phenotypes without genotyping every SNP in a chromosomal region.
SNPs are the most common genetic variant found in all individual with one SNP every 100–300 bp in some species. [4] Since there is a massive number of SNPs on the genome, there is a clear need to prioritize SNPs according to their potential effect in order to expedite genotyping and analysis. [5]
Robust, fast short-read alignment. GMAP: longer reads, with multiple indels and splices (see entry above under Genomics analysis); GSNAP: shorter reads, with one indel or up to two splices per read. Useful for digital gene expression, SNP and indel genotyping. Developed by Thomas Wu at Genentech.
Phylogenetic inference and data visualization for allelic/SNP sequences profiles using Minimum Spanning Trees: All [29] SplitsTree: Software for viewing trees, cladograms, NeighborNets, and other graphs All [30] TreeDyn Open-source software for tree manipulation and annotation allowing incorporation of meta information: All [31] Treevolution