title: Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach.
abstract: Polymorphism discovery is a routine application of next-generation sequencing technology where multiple samples are sent to a service provider for library preparation, subsequent sequencing, and bioinformatic analyses. The decreasing cost and advances in multiplexing approaches have made it possible to analyze hundreds of samples at a reasonable cost. However, because of the manual steps involved in the initial processing of samples and handling of sequencing equipment, cross-contamination remains a significant challenge. It is especially problematic in cases where polymorphism frequencies do not adhere to diploid expectation, for example, heterogeneous tumor samples, organellar genomes, as well as during bacterial and viral sequencing. In these instances, low levels of contamination may be readily mistaken for polymorphisms, leading to false results. Here we describe practical steps designed to reliably detect contamination and uncover its origin, and also provide new, Galaxy-based, readily accessible computational tools and workflows for quality control. All results described in this report can be reproduced interactively on the web as described at http://usegalaxy.org/contamination.
authors.affiliation: Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA.|Department of Biology, Penn State University, University Park, PA.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Dickins
authors.affiliation: Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA.|Interdisciplinary Graduate Program in BioSciences, Penn State University, University Park, PA.
authors.forename: Boris
authors.initials: B
authors.lastname: Rebolledo-Jaramillo
authors.affiliation: Department of Biology, Penn State University, University Park, PA.
authors.forename: Marcia Shu-Wei
authors.initials: MS
authors.lastname: Su
authors.affiliation: Department of Pediatrics, Penn State College of Medicine, Hershey, PA.
authors.forename: Ian M
authors.initials: IM
authors.lastname: Paul
authors.affiliation: Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Blankenberg
authors.affiliation: Interdisciplinary Graduate Program in BioSciences, Penn State University, University Park, PA.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Stoler
authors.affiliation: Department of Biology, Penn State University, University Park, PA.
authors.forename: Kateryna D
authors.initials: KD
authors.lastname: Makova
authors.affiliation: Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA.
authors.forename: Anton
authors.initials: A
authors.lastname: Nekrutenko
mesh_terms: D059018:DNA Contamination; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics; D020407:Internet; D011110:Polymorphism, Genetic; D015203:Reproducibility of Results; D017421:Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004272:DNA, Mitochondrial
keywords: Galaxy; contamination; next-generation sequencing; re-sequencing; reproducibility