Meta-analysis and prioritization of human skin pigmentation-associated GWAS-SNPs using ENCODE data-based web-tools View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2019-04

AUTHORS

Kausik Ganguly, Tania Saha, Arpan Saha, Tithi Dutta, Souradeep Banerjee, Debmalya Sengupta, Sreyashi Bhattacharya, Sampurna Ghosh, Mainak Sengupta

ABSTRACT

Skin pigmentation in human is a complex trait, which varies widely, both within and between human populations. The exact players governing the trait of skin pigmentation remain elusive till date. Various Genome Wide Association Studies (GWAS) have shown the association of different genomic variants with normal human skin pigmentation, often indicating genes with no direct implications in melanin biosynthesis or distribution. Little has been explained in terms of the functionality of the associated Single-Nucleotide Polymorphisms (SNPs) with respect to modulating the skin pigmentation phenotype. In the present study, which, to our knowledge, is the first of its kind, we tried to analyze and prioritize 519 non-coding SNPs and 24 3'UTR SNPs emerging from 14 different human skin pigmentation-related GWAS, primarily using several ENCODE-based web-tools like rSNPBase, RegulomeDB, HaploReg, etc., most of which incorporate experimentally validated evidences in their predictions. Using this comprehensive, in-silico, analytical approach, we successfully prioritized all the pigmentation-associated GWAS-SNPs and tried to annotate pigmentation-related functionality to them, which would pave the way for deeper understanding of the molecular basis of human skin pigmentation variations. More... »

PAGES

163-171

Journal

TITLE

Archives of Dermatological Research

ISSUE

3

VOLUME

311

Author Affiliations

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s00403-019-01891-3

DOI

http://dx.doi.org/10.1007/s00403-019-01891-3

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1112095907

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30756169


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