The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology

no code implementations • 8 May 2024 • Erin E. Gill, Baofeng Jia, Carmen Lia Murall, Raphaël Poujol, Muhammad Zohaib Anwar, Nithu Sara John, Justin Richardsson, Ashley Hobb, Abayomi S. Olabode, Alexandru Lepsa, Ana T. Duggan, Andrea D. Tyler, Arnaud N'Guessan, Atul Kachru, Brandon Chan, Catherine Yoshida, Christina K. Yung, David Bujold, Dusan Andric, Edmund Su, Emma J. Griffiths, Gary Van Domselaar, Gordon W. Jolly, Heather K. E. Ward, Henrich Feher, Jared Baker, Jared T. Simpson, Jaser Uddin, Jiannis Ragoussis, Jon Eubank, Jörg H. Fritz, José Héctor Gálvez, Karen Fang, Kim Cullion, Leonardo Rivera, Linda Xiang, Matthew A. Croxen, Mitchell Shiell, Natalie Prystajecky, Pierre-Olivier Quirion, Rosita Bajari, Samantha Rich, Samira Mubareka, Sandrine Moreira, Scott Cain, Steven G. Sutcliffe, Susanne A. Kraemer, Yann Joly, Yelizar Alturmessov, CPHLN consortium, CanCOGeN consortium, VirusSeq Data Portal Academic, Health network, Marc Fiume, Terrance P. Snutch, Cindy Bell, Catalina Lopez-Correa, Julie G. Hussin, Jeffrey B. Joy, Caroline Colijn, Paul M. K. Gordon, William W. L. Hsiao, Art F. Y. Poon, Natalie C. Knox, Mélanie Courtot, Lincoln Stein, Sarah P. Otto, Guillaume Bourque, B. Jesse Shapiro, Fiona S. L. Brinkman

The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response.

Epidemiology

Reconstructing subclonal composition and evolution from whole genome sequencing of tumors

no code implementations • 27 Jun 2014 • Amit G. Deshwar, Shankar Vembu, Christina K. Yung, Gun Ho Jang, Lincoln Stein, Quaid Morris

Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations.

Inferring clonal evolution of tumors from single nucleotide somatic mutations

no code implementations • 11 Oct 2012 • Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein, Quaid Morris

High-throughput sequencing allows the detection and quantification of frequencies of somatic single nucleotide variants (SNV) in heterogeneous tumor cell populations.