By Kung-Hao Liang
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A Manhattan plot is a scatter plot that offers a useful grand-scale visualization of the GWAS result. The assayed SNPs are sorted by chromosome locations in the x-axis. The y-axis shows the negative logarithm of P-values, and as a result the higher dots represent significant hits. 3). GWAS and its subsequent validation render a short-list of SNPs, which are statistically associated to clinical traits. Albeit intriguing, the molecular mechanisms behind the associations are still vague. Thus, it is essential to pursue further functional exploration of detected associations.
The crossover operation is analogous to the chromosomal recombination events occurring in meioses of cell cycles. The rationale for the crossover operation is that if the good performance of two models is mainly due to parts of themselves, then a crossover operation may combine these two parts, resulting in a scrutiny in the proximity of the search space in the previous two models. Using the defined operations, the models with higher fitness scores are randomly mutated and crossed over with each another so as to produce various candidate models, exploring the entire solution space in a systematic manner.
The NGS platforms and high density SNP arrays are two major high throughput platforms to generate the genomic data. 1 Capillary Sanger sequencing and next generation sequencing Conventional capillary sequencers employed the Sanger methodology and served as the major contributors of the human genome project. This method has limitations on sequence reads (∼1000 bases), which is far shorter than the genome of most species. Thus, sequencing of genomic DNA needs to start by breaking the DNA macromolecule into smaller pieces.