Development of shiny dashboard application for “genome-wide association study on analysis of SNPs injected in Homo sapiens genome (snips-HsG)”

Abstract

Human genome information in databases is growing exponentially, and in future, the collection of these data will exceed 5v's (variety, volume, veracity, value, and velocity). Much of genetic variation exist among genomes of human individuals is mostly in the form of SNPs. Therefore, studying SNPs among individuals is important to analyze genetic risk and diversity. In this regard, the present preliminary study has developed an application on human reference genome before and after SNPs injection using R and hosted in https://snip-hsg.shinyapps.io/home/. In it, initially the comparison of nucleotide frequency between two copies of genomes are made and showed the nucleotide bias due to the SNPs sites. Secondly, genes of two copies of genomes are grouped into five different isochore families, L1 (<37% GC), L2 (37–42%), H1 (42–47%), H2 (47–52%), H3 (>52%) based on GC%. The results through histograms showed that there are differences in the GC% distribution among chromosomes and this study may help the biologist to examine the nucleotide frequency including GC% and isochore family differences comparatively between genomes. Thirdly, in the statistical analysis, the Shapiro–Wilk test provided the evidence that the data have non-normal distributions. Therefore, the values are considered for non-parametric test to validate the significance relationship between these two variables. From the Wilcoxon rank sum test and Chi-square test, the significance difference between gene sets of two copies of genome are projected that the two samples of measurements come from different distributions. The present descriptive and inferential analysis on SNPs in human genome may be useful for the biologists to access SNPs comfortably. One can use this application for comparison, easy access, downloading and visualizing.