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Extra info for Bioinformatics for biomedical science and clinical applications
It is thus important to check the definition before interpreting a result from the literature, particularly when multiple research works are compared. For example, the ORs in Tanaka et al. (2009) are the dominance mode, while those in WTCCC (2007) are heterozygote and homozygote ORs. 4 Sample size and multiple comparisons When genome-wide variants are evaluated in parallel, multiple hypotheses testings, one per a variant, are performed. This comes with the cost that we must tighten the stringency on P-values for each hypothesis.
A chromosomal recombination disrupts the association (and introduces independence) between variants at the two sides of the recombination spot. After several generations, distant variants are no longer associated due to many recombination hotspots between them. The adjacent variants still retain a certain degree of LD, particularly those between two recombination hotspots. LD of a pair of variants can be quantified by r2 or D' values. r2 is a value between 0 and 1, while 0 indicates no association and 1 indicates high association.
Finally, unnecessary variability may be introduced when each SNP is handled at different times and by different persons. A high-density microarray can assay thousands of SNPs in one go, reducing the complexity, cost, time and variability significantly. e. the target sequence). Existence of a particular genotype in the sample will be detected by the signal of hybridization of the probe corresponding to the target sequence. Hybridization will be shown as intensity signals, which are captured by a scanner and stored as digital images.