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Association mapping has been most widely applied to the study of human disease, specifically in the form of a genome-wide association study (GWAS). A genome-wide association study is performed by scanning an entire genome for SNPs associated with a particular trait of interest, or in the case of human disease, with a particular disease of interest.
An interesting observation was a bias in the differences between cases and controls towards non-CpG island probes (which were significantly underrepresented in this array design), arguing strongly for the use of the latterly designed 450k array which does cover non-CpG islands with a higher density of probes.
The candidate gene approach to conducting genetic association studies focuses on associations between genetic variation within pre-specified genes of interest, and phenotypes or disease states. This is in contrast to genome-wide association studies (GWAS), which is a hypothesis-free approach that scans the entire genome for associations between ...
The publication came under scrutiny because of a discrepancy between the type of genotyping array in the case and control group, which caused several SNPs to be falsely highlighted as associated with longevity. [73] The study was subsequently retracted, [74] but a modified manuscript was later published. [75] Now, many GWAS control for ...
QTL location is indicated only by looking at which markers give the greatest differences between genotype group averages, and the apparent QTL effect at a marker will be smaller than the true QTL effect as a result of recombination between the marker and the QTL. Second, we must discard individuals whose genotypes are missing at the marker.
The only considerable difference is that eQTL studies can involve a million or more expression microtraits. Standard gene mapping software packages can be used, although it is often faster to use custom code such as QTL Reaper or the web-based eQTL mapping system GeneNetwork.