Table of Contents
What is SNP and its application?
Abstract. Single nucleotide polymorphisms (SNPs) distribute numerously and high-density throughout rice (Oryza sativa L.) genome. A total of 80,127 SNP sites were identified in rice genome, and one SNP every 154 bp was found between two rice subspecies indica and japonica. The SNP rate is 0.65%.
How many SNPs are on SNP arrays?
In conclusion the high-density 62 K genic-SNP array ‘CcSNPnks’ described here is a unique genotyping platform for pigeonpea. It has 62,053 SNPs from 9629 genes belonging to five different categories with more than 99% sample success rate and 99.9% SNP call rate.
How do SNP chips work?
The principle is the nucleic acid hybridization theory, and the detected sample DNA is hybridized with the DNA microarray and extended. Subsequently, the fragments of the non-complementary binding reaction on the chip are washed away, and the gene chip is subjected to laser confocal scanning.
How do SNP arrays work?
“The SNP array or SNP microarray works on the principle of DNA hybridization in which a single base change can be detected through fluorescence chemistry.” SNP or snip is known as single nucleotide polymorphism.
What does SNP Array test for?
Microarray analysis is performed using a SNP based microarray chip with approximately 850,000 markers. This test is designed to detect chromosomal imbalances throughout the human genome including deletions, duplications, aneuploidy, and regions of homozygosity.
How are SNPs used in forensics?
The most likely forensic use of lineage SNPs is for missing person cases or mass disaster identifications. Successful identification by genetic testing using kinship analysis is limited by the amount of DNA available for analysis, the number of family members for comparison, and the available genetic markers.
Why are SNP arrays used more often?
Single Nucleotide Polymorphism (SNP)-based techniques became the most commonly used genotyping methods for GWAS because SNPs are cheap, numerous, codominant and can be automatically analysed with SNP-arrays or produced by genotyping-by-sequencing (GBS), or sequencing [2,3,4].
How is a SNP array performed?
The basic principles of SNP array are the same as the DNA microarray. These are the convergence of DNA hybridization, fluorescence microscopy, and solid surface DNA capture. The three mandatory components of the SNP arrays are: An array containing immobilized allele-specific oligonucleotide (ASO) probes.
How are SNPs used as genetic markers?
As mentioned previously, SNPs occur frequently throughout the genome. Therefore, they can be used as markers to identify disease-causing genes by an association study (Gray et al. 2000). In such studies, it is assumed that two closely located alleles (gene and marker) are inherited together.
How does SNP mapping work?
SNP mapping has three steps. First, recombinant mutant animals are generated over a polymorphic strain (usually CB4856) using standard genetic techniques. Second, the genotype of these animals at SNP loci is determined using one of a variety of SNP detection technologies.
What are the clinical applications of SNP arrays?
The most important clinical applications of SNP arrays are for determining disease susceptibility and for measuring the efficacy of drug therapies designed specifically for individuals. In research, SNP arrays are most frequently used for genome-wide association studies.
What is the average number of SNPs in a chip array?
This predominantly SC genes based chip array has 4314 SCP genes with an average of 5. 7 SNPs per gene and 4328 CSCSP genes with an average of 6. 3 SNPs per gene (Table 1). Further, it has 156 AGCP genes with an average of 9. 9 SNPs per gene and 746 DRDRP genes with an average of 10. 8 SNPs per gene.
What is breeding by SNP array?
Breeding in a number of animal and plant species has been revolutionized by the emergence of SNP arrays. The method is based on the prediction of genetic merit by incorporating relationships among individuals based on SNP array data. This process is known as genomic selection.
How are SNP microarray chips manufactured?
The SNP array is based on the sequence information, a common SNP based microarray chip is manufactured by chemical spray method, micromechanical printing method or by in situ synthesis method. On a small piece of slide around 1cm, approximately 4,00,000 different sequence-specific probes are immobilized.