Project description:Disease activity in patients with systemic lupus erythematosus (SLE) may fluctuate between flares and remissions, complicating effective disease management. The aim of this study is to detect early signs of cellular attributes responsible for flares and to understand dynamic changes in the immune system. Peripheral blood mononuclear cells were collected at different time points throughout the disease course from 6 patients with SLE (n = 19) and 32 healthy donors fromthe Asian Immune Diversity Atlas (AIDA), and subsequently underwent to generate single cell gene expression combined with T cell receptor (TCR) and B cell receptor (BCR) clonotypes data (10X Chromium 5’, TCR sequencing).
Project description:The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection.
Project description:ZIKV strains belong to three phylogenetic lineages: East African, West African, and Asian/American. RNA virus genomes exist as populations of genetically-related sequences whose heterogeneity may impact viral fitness, evolution, and virulence. The genetic diversity of representative ZIKVs (N=7) from each lineage was examined using next generation sequencing (NGS) paired with downstream Shannon entropy calculation and single nucleotide variant (SNV) analysis. This comprehensive analysis of ZIKV genetic diversity provides insight into the genetic diversity of ZKIV and repository of SNV positions across lineages.
Project description:The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients and biomarkers for prognosis and treatment response lack precision. A comprehensive compendium of tumor immune cells is required to pinpoint predictive cellular states and their spatial localization. We generated a single-cell resolved tumor immune cell atlas, jointly analyzing >500,000 cells from 217 patients and 13 cancer types, providing the basis for a patient stratification based on immune cell compositions. Projecting immune cells from external tumors onto the atlas facilitated an automated cell annotation system for a harmonized interpretation. To enable in situ mapping of immune populations for digital pathology, we developed SPOTlight, a computational tool that identified striking spatial immune cell patterns in tumor sections. We expect the atlas, together with our versatile toolbox for precision oncology, to advance currently applied stratification strategies for prognosis and immuno-therapy response.