Genetic clustering of depressed patients and normal controls based on single-nucleotide variant proportion
Genetic clustering of depressed patients and normal controls based on single-nucleotide variant proportion
Date
2017-11-10
Authors
Yu, Chenglong
Baune, Bernard T
Fu, Ke-Ang
Wong, Ma Li
Licinio, Julio
Journal Title
Journal ISSN
Volume Title
Publisher
Elsevier
Abstract
Background
Genetic components play important roles in the susceptibility to major depressive disorder (MDD). The rapid development of sequencing technologies is allowing scientists to contribute new ideas for personalized medicine; thus, it is essential to design non-invasive genetic tests on sequencing data, which can help physicians diagnose and differentiate depressed patients and healthy individuals.
Methods
We have recently proposed a genetic concept involving single-nucleotide variant proportion (SNVP) in genes to study MDD. Using this approach, we investigated combinations of distance metrics and hierarchical clustering criteria for genetic clustering of depressed patients and ethnically matched controls.
Results
We analysed clustering results of 25 human subjects based on their SNVPs in 46 newly discovered candidate genes.
Conclusions
According to our findings, we recommend Canberra metric with Ward's method to be used in hierarchical clustering of depressed and normal individuals. Futures studies are needed to advance this line of research validating our approach in larger datasets, those may also be allow the investigation of MDD subtypes.
Limitations
High quality sequencing costs limited our ability to obtain larger datasets.
Description
This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/
This author accepted manuscript is made available following 12 month embargo from date of publication (Nov 2017) in accordance with the publisher’s archiving policy
Keywords
Major depressive disorder,
Sequencing,
Distance metric,
Hierarchical clustering,
Candidate gene,
Canberra distance,
Ward's method
Citation
Yu, C., Baune, B. T., Fu, K.-A., Wong, M.-L., & Licinio, J. (2017). Genetic clustering of depressed patients and normal controls based on single-nucleotide variant proportion. Journal of Affective Disorders, 227, 450–454. https://doi.org/10.1016/j.jad.2017.11.023