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Article

Understanding the Function of a Locus Using the Knowledge Available at Single-Nucleotide Polymorphisms

1
Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, ON K1Y 4W7, Canada
2
Plastenor Technologies Company, Montreal, QC H2P 2G4, Canada
3
Department of Medicine, Division of Endocrinology, University of Ottawa, The Ottawa Hospital, Ottawa, ON K1Y 4E9, Canada
4
Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, ON K1Y 4W7, Canada
*
Authors to whom correspondence should be addressed.
Academic Editors: Giuseppe Limongelli and Lia Crotti
Cardiogenetics 2021, 11(4), 255-262; https://doi.org/10.3390/cardiogenetics11040024
Received: 1 August 2021 / Revised: 24 November 2021 / Accepted: 6 December 2021 / Published: 7 December 2021
(This article belongs to the Special Issue Cardiogenetics: Feature Papers 2021)
Understanding the function of a locus is an issue in molecular biology. Although numerous molecular data have been generated in the last decades, it remains difficult to grasp how these data are related at a locus. In this study, we describe an analytical workflow that can solve this problem using the knowledge available at the single-nucleotide polymorphism (SNP) level. The underlying algorithm uses SNPs as connectors to link biological entities and identify correlations between them through a joint bioinformatics/statistics approach. We demonstrate its application in finding the mechanism whereby a mutation causes a phenotype and in revealing the path whereby a gene is regulated and impacts a phenotype. We translate our workflow into publicly available shell scripts. Our approach provides a basic framework to solve the information overload problem in biology surrounding the annotation of a locus and is a step toward repurposing GWAS data for new applications. View Full-Text
Keywords: locus annotation; SNPs; rare variants; Mendelian randomization; algorithm locus annotation; SNPs; rare variants; Mendelian randomization; algorithm
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MDPI and ACS Style

Nikpay, M.; Ravati, S.; Dent, R.; McPherson, R. Understanding the Function of a Locus Using the Knowledge Available at Single-Nucleotide Polymorphisms. Cardiogenetics 2021, 11, 255-262. https://doi.org/10.3390/cardiogenetics11040024

AMA Style

Nikpay M, Ravati S, Dent R, McPherson R. Understanding the Function of a Locus Using the Knowledge Available at Single-Nucleotide Polymorphisms. Cardiogenetics. 2021; 11(4):255-262. https://doi.org/10.3390/cardiogenetics11040024

Chicago/Turabian Style

Nikpay, Majid, Sepehr Ravati, Robert Dent, and Ruth McPherson. 2021. "Understanding the Function of a Locus Using the Knowledge Available at Single-Nucleotide Polymorphisms" Cardiogenetics 11, no. 4: 255-262. https://doi.org/10.3390/cardiogenetics11040024

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