OLISSIPO was pleased to host the OLISSIPO Workshop on Analysis of single-cell data from tumors, held on April 4, 2023 at INESC-ID, Lisbon. The workshop was given by Pedro Falé Ferreira (INESC-ID alumni, ETH Zürich).

OLISSIPO Workshop on Analysis of single-cell data from tumors

April 4, 2023 | 09:15-15:30 (WEST – Lisbon)

Location: INESC-ID (Lisboa, Portugal), Room 9, Floor -1 (ask at the reception)

Abstract: Cancer is an evolutionary process in which cells acquire mutations that may lead to their uncontrolled proliferation. As a result of spatial constraints, competitiveness between cancer cells and interactions with the immune system, tumors exhibit significant heterogeneity within and across patients. The advent of next-generation sequencing and recent extensions to single-cell level assays at high throughput has enabled practitioners to characterize this heterogeneity with unprecedented detail. Sequencing genomes and transcriptomes of thousands of single cells individually has shed light on mechanisms of tumor progression, metastasis and treatment resistance.
In this course, we provided an overview of how sequencing data can be used to unravel intra-tumor heterogeneity, and highlight the computational methods that transform those data into biological insights. In the first lecture, we overviewed scDNA and scRNA technologies and the questions they allow us to answer in the context of tumor evolution, with a focus on single-nucleotide variant and copy number calling, and event history reconstruction. In the second lecture, we focused on statistical methods and their application to the analysis of these data. In the hands-on session, we analysed scDNA and scRNA data using recent tools for clustering noisy mutational profiles and identifying hierarchical signatures of gene expression.

Programme:

09:15 – 09:30: Welcome and Registration

09:30 – 11:00: Lecture 1 – Introduction to tumor evolution, single-cell data and analysis methods

— Coffee Break —

11:30 – 12:30: Lecture 2 – Statistical inference methods and applications on single-cell data

— Lunch —

14:00 – 15:30: Hands-on session – Clustering and matrix factorization methods for scDNA-seq and scRNA-seq analysis of tumors in Python

15:30: Closing