In:
Journal of Bioinformatics and Computational Biology, World Scientific Pub Co Pte Ltd, Vol. 15, No. 04 ( 2017-08), p. 1750017-
Abstract:
The t-distributed stochastic neighbor embedding t-SNE is a new dimension reduction and visualization technique for high-dimensional data. t-SNE is rarely applied to human genetic data, even though it is commonly used in other data-intensive biological fields, such as single-cell genomics. We explore the applicability of t-SNE to human genetic data and make these observations: (i) similar to previously used dimension reduction techniques such as principal component analysis (PCA), t-SNE is able to separate samples from different continents; (ii) unlike PCA, t-SNE is more robust with respect to the presence of outliers; (iii) t-SNE is able to display both continental and sub-continental patterns in a single plot. We conclude that the ability for t-SNE to reveal population stratification at different scales could be useful for human genetic association studies.
Type of Medium:
Online Resource
ISSN:
0219-7200
,
1757-6334
DOI:
10.1142/S0219720017500172
Language:
English
Publisher:
World Scientific Pub Co Pte Ltd
Publication Date:
2017
SSG:
12
