Single-cell `Omics Seminar

October 19th
02:00 PM - 04:00 PM

Single-cell `Omics Seminar: Using single cell genomics to define mechanisms in autoimmune disease

Date: 10/19 2-4 pm

Location: Boston, Medical Campus or via zoom

Register Here


Single cell profiling of tissue samples offers new opportunities to glean insights about human diseases, including immune-mediated diseases. We will present several strategies to analyze and interpret single cell data in order to understand tissue inflammation and genetic mechanisms of inflammatory disease development. We will focus on rheumatoid arthritis, a prototypical autoimmune disease affecting up to 1% of individuals in the United States in which the immune system attacks the joints leading to long term disability. 

First, we will present strategies to collect complex single cell data sets and remove batch effects. Second, we will present strategies to identify cell states that are expanded or depleted in patients with disease relative to control patients. Third, we will discuss strategies to identify cell states that vary in abundance between subgroups of patients with a shared diagnosis, which represent disease subphenotypes. Finally, we will discuss how single cell data can enable the interpretation of human genetic data. Genome-wide association studies have revealed many genetic variants that alter disease risk. Single-cell profiling from genotyped cohorts enables the identification of tissue changes that associate with disease-risk variants and may illuminate processes of disease development. We discuss single-cell methods to identify genetic variants that associate with gene expression in a cell-state-dependent manner and present a method to identify cell states that change in abundance in association with genetic variants. 

We will demonstrate how case-control and disease sub-phenotyping approaches as well as genetic association testing in single-cell datasets can be used to define key pathogenic cell states.


Soumya Raychaudhuri is a Professor of Medicine and Biomedical Informatics at and Harvard Medical School (HMS) and an Institute Member at Broad Institute. After completing his undergraduate degrees in biophysics and mathematics from SUNY Buffalo in 1997, Raychaudhuri completed his M.D. and Ph.D. at Stanford University in 2004. He pursued clinical training in internal medicine, followed by subspecialty training in rheumatology at BWH. He concurrently completed postdoctoral training in human genetics at the Broad Institute with Mark Daly. In 2010, he launched his laboratory and joined the faculties of the BWH Divisions of Genetics and Rheumatology. He currently Directs the Center for Data Sciences at Brigham and Women’s Hospital (BWH), where he also holds the Coblyn/Brenner Distinguished Chair, and is a clinically active rheumatologist. The Raychaudhuri Lab studies the basis of immune mediated disease using techniques in human genetics, bioinformatics, and systems biology. They use a combination of computational and statistical methods, high-throughput genomic technologies, and systems biology to elucidate the genetic mechanisms of these conditions and their functional implications. 

Laurie Rumker is a graduate student in the Harvard-MIT MD-PhD Program. She is currently pursuing her PhD in the Raychaudhuri lab through the Harvard Biomedical Informatics and Integrative Genomics PhD Program. She is especially interested in developing approaches to study immunologic variation at population scale and single-cell resolution, in order to better understand immune-mediated diseases and ultimately expand prevention and treatment options for patients. Prior to her MD-PhD training, Laurie completed both her undergraduate studies and an M.S. in Biomedical Informatics at Stanford University.


Seminar Format:

  • 2-2:30 Coffee and cookies

  • 2:30-4 Primer and Research Talk


Notes: Attendees should please register separately for each event and specify if they will attend online or in-person. Questions about the workshop can be directed to