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Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis

Authors Suravajhala P, Benso A

Received 30 September 2016

Accepted for publication 29 December 2016

Published 12 June 2017 Volume 2017:10 Pages 57—64

DOI https://doi.org/10.2147/AABC.S123604

Checked for plagiarism Yes

Review by Single-blind

Peer reviewers approved by Dr Colin Mak

Peer reviewer comments 3

Editor who approved publication: Dr Juan Fernandez-Recio

Video abstract presented by Prashanth Suravajhala.

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Prashanth Suravajhala,1 Alfredo Benso2

1Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark; 2Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy

Abstract: Next-generation sequencing technology has provided resources to easily explore and identify candidate single-nucleotide polymorphisms (SNPs) and variants. However, there remains a challenge in identifying and inferring the causal SNPs from sequence data. A problem with different methods that predict the effect of mutations is that they produce false positives. In this hypothesis, we provide an overview of methods known for identifying causal variants and discuss the challenges, fallacies, and prospects in discerning candidate SNPs. We then propose a three-point classification strategy, which could be an additional annotation method in identifying causalities.

Keywords: clinical mastitis, single-nucleotide polymorphisms, variants, associations, diseases, linkage disequilibrium, GWAS

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