Comprehensive in Silico Analyses of Single Nucleotide Variants of the Human Orthologues of 171 Murine Loci to Seek Novel Insights into the Genetics of Human Pigmentation

Ganguly, K and Sengupta, D and Sarkar, N and Mukherjee, N and Dutta, T and Saha, A and Saha, T and Ghosh, B and Chatterjee, S and Brahmachari, P and Kundu, A and Sengupta, M (2022) Comprehensive in Silico Analyses of Single Nucleotide Variants of the Human Orthologues of 171 Murine Loci to Seek Novel Insights into the Genetics of Human Pigmentation. In: Proceedings of the Zoological Society .

PDF pro_zoo_soc_2022.pdf - Published Version Restricted to Registered users only Download (4MB) | Request a copy

Abstract

Modulations in melanin synthesis and distribution caused by underlying genetic variants are considered to be majorly responsible for the inter-personal human pigmentation variation. In the publicly available Color Genes dataset, 171 cloned murine loci are documented to be involved with alterations in mice coat color. We hypothesize that the human orthologues of these 171 loci may also be implicated towards human pigmentation variation through their polymorphic variants. We used several freely available bioinformatic tools and designed a predictive pipeline to prioritize the Single Nucleotide Variants (SNVs) within and in the vicinity of the 171 human orthologues, according to their functional potential. The genes associated with the prioritized SNVs were annotated a potential function in the pigmentation pathway, based on extensive literature review and assessment of protein–protein interaction networks. Our analyses could prioritize 77 candidate SNVs including 10 non-synonymous SNVs, 45 synonymous SNVs and 22 regulatory SNVs associated with 46 genes that can potentially contribute towards human pigmentation variation. Our study, thus outlines a comprehensive bioinformatic pipeline using freely available web-tools that can be utilized in similar kind of studies dealing with other complex human traits and diseases where individual nucleotide variant imparts subtle functional roles in regulating the phenotype.

Item Type:	Journal Article
Publication:	Proceedings of the Zoological Society
Publisher:	Springer
Additional Information:	The copyright for this article belongs to the Springer.
Keywords:	BRCA1; Color Genes; Complex-phenotype; EED; ENCODE; GTEx; In-silico; KRT75; Melanin; SNV
Department/Centre:	Division of Biological Sciences > Molecular Reproduction, Development & Genetics
Date Deposited:	23 Aug 2022 05:16
Last Modified:	23 Aug 2022 05:16
URI:	https://eprints.iisc.ac.in/id/eprint/76158

Actions (login required)

View Item