Application of t-SNE to human genetic data

作者：Li, Wentian^*; Cerise, Jane E.; Yang, Yaning; Han, Henry

来源：Journal of Bioinformatics and Computational Biology, 2017, 15(4): 1750017.

DOI：10.1142/S0219720017500172

• t-SNE
• PCA
• SNP
• dimension reduction

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.

• 出版日期2017-8
• 单位中国科学技术大学; 河北医科大学