How are tag SNPs selected?
How are tag SNPs selected?
Several algorithms have been devised to partition chromosomal regions into haplotype blocks which are based on haplotype diversity, LD, four-gamete test and information complexity and tag SNPs are selected from all SNPs that belong to that block.
What is haplotype tagging?
A tagging set is the set of SNPs in a haplotype set necessary and sufficient to derive all of the SNPs in the set. Among all of the tagging sets, a minimal tagging set is a set containing the minimum number of SNPs, and its members will be called htSNPs.
How can SNP haplotypes be determined?
With the current technology it is possible to get the genotype of an individual and to determine the positions of the SNPs. The genotype gives the bases at each SNP for both copies of the chromosome but loses the information of the origin.
What is SNP characterization?
Single nucleotide polymorphisms, frequently called SNPs (pronounced “snips”), are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block, called a nucleotide.
What is LD in GWAS?
LD is essentially “correlation” between marker alleles due to physical proximity (roughly speaking, they’re alleles that have not undergone genetic recombination over evolutionary time). The upside of LD is that it makes GWAS more efficient (or even possible with chip-based technologies).
What is lead SNP?
Our meta-analysis identified 74 approximately independent genome- wide significant loci. For each locus, we define the ‘lead SNP’ as the SNP in the genomic region that has the smallest P value (Supplementary Information section 1.6. 1).
How do you detect SNP?
There are several methods to detect SNPs: PCR-AS, PCR-RFLP, TaqMan, mPCR-RETINA, etc. Any information about the time required and about the costs of each one is also appreciated!
What are the criteria for a tag SNP selection algorithm?
The criteria that are needed to define each tag SNP selection algorithm is the following:
How are tag SNPs selection dependent on haplotypes?
The selection of tag SNPs is dependent on the haplotypes present in the genome. Most sequencing technologies provide the genotypic information and not the haplotypes i.e. they provide information on the specific bases that are present but do not provide phasic information (at which specific chromosome each of the bases appear).
What happens when a tag SNP has a high correlation coefficient?
If a single highly correlated tag SNP t is found, the alleles are assigned so their frequencies agree with the allele frequencies of t. When multiple tagging SNPs have the same (high) correlation coefficient with n, the common allele of n has advantage.
What happens when a group of SNPs is inherited together?
When a group of SNPs are inherited together because of high LD there tends to be redundant information. The selection of a tag SNP as a representative of these groups reduces the amount of redundancy when analyzing parts of the genome associated with traits/diseases.
How are tag SNPs selected? Several algorithms have been devised to partition chromosomal regions into haplotype blocks which are based on haplotype diversity, LD, four-gamete test and information complexity and tag SNPs are selected from all SNPs that belong to that block. What is haplotype tagging? A tagging set is the set of SNPs in…