This is a PLoS Computational Biology software paper.Ĭopy number changes are a useful diagnostic indicator for many diseases, including cancer. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist. The authors of both studies may be contacted at This work was supported by the National Institutes of Health. C0902 cell line raw data from the Botton 2013 study are in the Supporting Information files of that article. Corresponding raw sequencing data for the melanoma samples were deposited in the database of Genotypes and Phenotypes (dbGaP) under accession phs000977.v1.p1, and array CGH copy number data are in the Gene Expression Omnibus (GEO) under accession GSE55150. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: All CNVkit coverage data files are available from GitHub ( ). Received: SeptemAccepted: MaPublished: April 21, 2016Ĭopyright: © 2016 Talevich et al. Ĭitation: Talevich E, Shain AH, Botton T, Bastian BC (2016) CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing. We packaged the components of CNVkit so that it is straightforward to use and provides visualizations, detailed reporting of significant features, and export options for integration into existing analysis pipelines. We compared the performance of CNVkit to copy number changes identified by array comparative genomic hybridization. After normalizing read counts to a pooled reference, we evaluated and corrected for three sources of bias that explain most of the extraneous variability in the sequencing read depth: GC content, target footprint size and spacing, and repetitive sequences. In particular, we successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes. This combination achieves both exon-level resolution in targeted regions and sufficient resolution in the larger intronic and intergenic regions to identify copy number changes. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. Massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. Do alignment of the proteins and give the analysis on the evolutional conservation of GLUT protein.Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are of significant importance in syndromic conditions and cancer. Do some analysis using your knowledge to your level of education for the 3800 level.ġ2. In this new window pick two DNA and RNA sequences and get them aligned. Compare the sequences by doing the alignment of nucleotides: Go to Toolbox, choose Alignment and Trees, and Create alignmentġ1. Do the same thing for the accession number NM_006516 do download GLUT1 RNAġ0. Choose right destination in your folder, keep accession number with your naming,like: NG-0088232 Human GLUT3ĩ. Close the sequence, and the program will ask: Save changes to 'NG_008232' before closing?, choose "YesĨ. DoubleClick on it, the sequence of 40, 802 be will appear in the bottom.ħ. This sequence will appear: NG 008232 Homo sapiens solute carrier family 2 member 1 (SLC2A1), RefseqGene on chromosome 1 40802Ħ. accession number for the human SLC2A1 DNA (NG_008232). In NCBl search site click nucleotide on the top, on the left choose "all field" and copy the Glucose Transporter 1" (SLC2A1). Go Download and click on Search for sequences on NCBI.Ĥ. In the left navigation area click on CLD data, highlight itĢ. CLC SEQUENCE VIEWER 7.7.1 Download this program from the site: cic.sequence-viewer/#downloadġ.
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