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Functional Population Genomics

Our research group studies how genetic variants in humans affect molecular and cellular traits, and how these cellular changes contribute to genetic risk for both common and rare diseases and traits. We analyze these questions both by computational integration analysis of large genomic and transcriptomic data sets and by experimental approaches.


We study functional genetic variation in human populations, and the mechanisms how it affects human traits and disease. Our work combines computational analysis of high-throughput sequencing data, human population genetics approaches, and experimental approaches. We focus in particular on studying genetic effects on the transcriptome traits, which has further applications in other traits at the cellular and individual level.

While some of our projects are closely related to specific diseases, our overall goal is to uncover general rules of the genomic sources of human variation, which is applicable to a variety of different diseases.

The lab is based both at KTH Royal Institute of Technology and SciLifeLab in Stockholm, Sweden, and at New York Genome Center in New York City, USA. We are a highly collaborative lab, and we participate in several consortium projects including GTEx, TOPMed, and MoTrPAC projects as well as many other cohort data sets.

Specific focus areas of the lab include:

  • Characterizing rare  and common  variants that affect the transcriptome, with applications in interpreting disease-associated loci , and in improving our understanding of the regulatory code and interpretation of the personal genome. While genome and transcriptome data from RNA-sequencing are the main data types that we analyze, we also use multi-omic approaches. Analysis of genetic regulatory variants in human populations  and their experimental characterization both by locus  and on a genome-wide scale  allows unique integrated insights.
  • Gene dosage as a fundamental mechanism mediating both genetic and environmental effects on cellular function and human phenotypes. We study this both using large human cohort data and by CRISPR-based modifications of gene expression
  • Regulatory modifiers of coding variant penetrance , where we combine two traditionally separate areas of human genetics ā€“ analysis of rare coding variants in Mendelian disease, and common regulatory variants in complex disease ā€“ under a model of joint effects on gene dosage.
  • Variation of genetic regulatory effects across tissues , cell types , and physiological  states, using interaction mapping in human cohorts with experimental follow-up .
  • Disease-focused projects, where we apply our approaches to study specific diseases ā€“ or use disease cohorts to demonstrate that the phenomena we study are indeed relevant for human health. Some of the disease areas we study are autism, lower respiratory diseases , psychiatric diseases, immune-related traits , and aging.
  • Genetic effects on transcript structure where long-read data provides exciting new opportunities .
  • Computational and experimental methods development to better extract biological insights from complex data sets and experimental model systems, and to scale up RNA-sequencing to larger cohorts.

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Page responsible:Ludvig Larsson
Belongs to: Department of Gene Technology
Last changed: Aug 11, 2021