GENOME-WIDE IDENTIFICATION OF FUNCTIONAL GENETIC VARIANTS ASSOCIATED WITH PHENOTYPIC DIVERSITY

Abstract

The phenotypic diversity is determined by the complicated interactions between genetic variation and the regulation system, although the identification of functionally significant variants is one of the central issues in genomics. This paper is a genome wide study that aims at determining and defining functional genetic variants related to phenotypic diversity using the large scale public genomic data. The high-quality single nucleotide polymorphisms (SNPs) and the insertion deletion variants (InDels) were observed using standardized variant-calling pipelines and interpreted using the genome-wide association approaches. A genome-wide threshold (p < 5 x 10 -8) was used to determine significant genotype phenotype associations, and functional annotation of these associations was done by ANNOVAR and SnpEff. One point two million variants were found, and it was found that 8542 significantly related statistically with phenotypic characteristics. Functional classification showed that 27 percent of major variants were found in the coding regions, wherein there were missense and nonsense mutations and 43 percent of the variants were in the regulatory regions. Gene Ontology and KEGG pathway analysis showed that the biological processes of the importance of signal transduction, metabolic pathways and cellular response mechanisms enriched significantly. These findings offer a logical system of relating genetic variation to phenotypic diversity and also making important functional variants which may have a role in biomarker discovery and precision genomics. The research is valuable to enhancing the interpretation of the global data that relates statistical association with the functional annotation.