YMAP: A pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens

Darren A. Abbey, Jason Funt, Mor N. Lurie-Weinberger, Dawn A. Thompson, Aviv Regev, Chad L. Myers, Judith Berman

Research output: Contribution to journalArticlepeer-review

31 Scopus citations

Abstract

The design of effective antimicrobial therapies for serious eukaryotic pathogens requires a clear understanding of their highly variable genomes. To facilitate analysis of copy number variations, single nucleotide polymorphisms and loss of heterozygosity events in these pathogens, we developed a pipeline for analyzing diverse genome-scale datasets from microarray, deep sequencing, and restriction site associated DNA sequence experiments for clinical and laboratory strains of Candida albicans, the most prevalent human fungal pathogen. The YMAP pipeline ( http://lovelace.cs.umn.edu/Ymap/ ) automatically illustrates genome-wide information in a single intuitive figure and is readily modified for the analysis of other pathogens with small genomes.

Original languageEnglish (US)
Article number100
Pages (from-to)1-15
Number of pages15
JournalGenome medicine
Volume6
DOIs
StatePublished - Nov 20 2014

Bibliographical note

Funding Information:
We thank Justin Nelson and Rob Schaeffer for technical assistance with web server setup and maintenance, Anja Forche, Noa Wertheimer, Meleah Hickman, and Jane Usher for beta-testing of the YMAP website and Mark McClellan for both technical and computational help. We thank Meleah Hickman and Anja Forche for example strains for analysis and Aleeza Gerstein and other members of the Berman lab for helpful discussions. We thank Joshua Baller and the University of Minnesota Supercomputing Institute for support and computing resources used in early versions of the pipeline. We thank the Broad Institute Genomics Platform for sequencing work. This work was supported by the National Science Foundation (DBI 0953881) and the CIFAR Genetic Networks Program (to CLM); a National Science Foundation Graduate Research Fellowship and, in part, NIH Pre-Doctoral Training Grant T32GM007287 (to JF); Human Frontiers Science Program (to DAT); and the Howard Hughes Medical Institute, a Career Award at the Scientific Interface from the Burroughs Wellcome Fund, a National Institutes of Health PIONEER award, and a Sloan Fellowship (to AR). The work was also supported by the National Institute of Allergy and Infectious Diseases (NIAID) R01 AI-0624273, the People Programme (Marie Curie Actions) and the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement number 303635 and an ERC Advanced Award, number 340087, RAPLODAPT (to JB).

Publisher Copyright:
© 2014 Abbey et al.; licensee BioMed Central Ltd.

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