Virus expression detection reveals RNA-sequencing contamination in TCGA
作者: Sara R. SelitskyDavid MarronDaniel HollernLisle E. MoseKatherine A. HoadleyCorbin JonesJoel S. ParkerDirk P. DittmerCharles M. Perou
作者单位: 1Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 27599, Chapel Hill, North Carolina, USA
2Department of Genetics, University of North Carolina at Chapel Hill, 27599, Chapel Hill, North Carolina, USA
3Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
4Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
刊名: BMC Genomics, 2020, Vol.21 (1), pp.25-101
来源数据库: Springer Nature Journal
DOI: 10.1186/s12864-020-6483-6
关键词: Virus detectionBioinformaticsContaminationHuman papilloma virusXenotropic murine leukemia virus-related
原始语种摘要: Abstract(#br)Background(#br)Contamination of reagents and cross contamination across samples is a long-recognized issue in molecular biology laboratories. While often innocuous, contamination can lead to inaccurate results. Cantalupo et al. , for example, found HeLa-derived human papillomavirus 18 (H-HPV18) in several of The Cancer Genome Atlas (TCGA) RNA-sequencing samples. This work motivated us to assess a greater number of samples and determine the origin of possible contaminations using viral sequences. To detect viruses with high specificity, we developed the publicly available workflow, VirDetect, that detects virus and laboratory vector sequences in RNA-seq samples. We applied VirDetect to 9143 RNA-seq samples sequenced at one TCGA sequencing center (28/33 cancer types) over 5...
全文获取路径: Springer Nature  (合作)
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影响因子:4.397 (2012)

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