Browsing by Author "Johnson, Sarah"
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Item StreamLab06: Overview of Experiments, Instrumentation, and Data collection(St. Anthony Falls Laboratory, 2010-11) Marr, Jeff; Wilcock, Peter; Hondzo, Miki; Foufoula-Georgiou, Efi; Johnson, Sarah; Hill, Craig; Leonardson, Rebecca; Nelson, Peter; Venditti, Jeremy; O'Connor, Ben; Ellis, Christopher R.; Mullin, James; Jefferson, Anne; Clark, JeffThis report summarizes the StreamLab06 experimental research program conducted in the St. Anthony Falls Laboratory (SAFL) Main Channel facility from April through October 2006. The experiments were funded through the National Center for Earth-surface Dynamics and involved a host of researchers, graduate students, visitors, and undergraduate students. The experiments were organized into seven phases of work. The first two phases of the project involved testing of conventional and surrogate bedload monitoring technologies (Marr et. al. 2007). The last five phases involved interdisciplinary research of sediment transport and ecohydraulics. This report focuses on the later phases of the project and does not include the bedload monitoring technologies. This report contains information on the organization of the experiments, the methodologies and protocols used to collect data, the types of data collected, data structure and format, and information on data storage and access.Item SVAtools for junction detection of genome-wide chromosomal rearrangements by mate-pair sequencing(2017-06) Johnson, SarahMate-pair sequencing (MPseq), using long-insert, paired-end genomic libraries, is a powerful next-generation sequencing-based approach for the detection of genomic structural variants. SVAtools is a set of algorithms to detect both chromosomal rearrangements and large (>10kb) copy number variants (CNVs) in genome-wide MPseq data. SVAtools can also predict gene disruptions, gene fusions, and characterize the genomic structure of complex rearrangements. To illustrate the power of SVAtools’ junction detection methods to provide comprehensive molecular karyotypes, MPseq data was compared against a set of samples previously characterized by traditional cytogenetic methods. Karyotype, fluorescence in situ hybridization (FISH) and chromosomal microarray (CMA), performed for 29 patients in a clinical laboratory setting, collectively revealed 285 breakpoints in 87 rearrangements. The junction detection methods of SVAtools detected 87% of these breakpoints compared to 48%, 42% and 57% for karyotype, FISH and CMA respectively. Breakpoint resolution was also reported to 1 kb or less and additional genomic rearrangement complexities not appreciable by standard cytogenetic techniques were revealed. For example, 63% of CNVs detected by CMA were shown by SVAtools’ junction detection to occur secondary to a rearrangement other than a simple deletion or tandem duplication. SVAtools with MPseq provides comprehensive and accurate whole-genome junction detection with improved breakpoint resolution, compared to karyotype, FISH, and CMA combined. This approach to molecular karyotyping offers considerable diagnostic potential for the simultaneous detection of both novel and recurrent genomic rearrangements in hereditary and neoplastic disorders.