Luke Anderson-Trocmé

TL;DR: Uniform manifold approximation and projection (UMAP), a non-linear dimension reduction tool, is applied to three well-studied genotype datasets and discover overlooked subpopulations within the American Hispanic population, fine-scale relationships between geography, genotypes, and phenotypes in the UK population, and cryptic structure in the Thousand Genomes Project data.

TL;DR: An overview of applications of UMAP in population genetics is given, recommendations for best practices are provided, and insights on optimal uses for the technique are offered.

TL;DR: Spatially resolved profiling of the melanoma microenvironment reveals correlates of response to immune checkpoint inhibitors and the potential of multiplexed single-cell technology to quantify spatial cell-cell interactions within the tumor microenvironment to understand immune therapy responses is highlighted.

TL;DR: This work demonstrates using genotype data from the 1000 Genome Project, the Health and Retirement Study, and the UK Biobank that projections using PCA-UMAP effectively cluster individuals who are genetically closely related while placing them in a global continuum of genetic variation.

TL;DR: It is found that the batch effects also lead to incorrect imputation by leading imputation servers and a small number of suspicious GWAS associations, and lower-quality data from the early phases of the 1kGP thus continues to contaminate modern studies in hidden ways.