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10.1186/s12859-016-1031-8 http://scihub22266oqcxt.onion/10.1186/s12859-016-1031-8 C4847212!4847212 !27121965     free     free     free Warning: file_get_contents(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=27121965 &cmd=llinks): Failed to open stream: HTTP request failed! 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ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data |pdf=|usr=}}{{27121965 }} gab.com Text ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data JO: BMC Bioinformatics http://www.kidney.de/pget.php?&tw=1&pmid=27121965 #FOAvip BACKGROUND: Detection of tandem duplication within coding exons, referred to as internal tandem duplication (ITD), remains challenging due to inefficiencies in alignment of ITD-containing reads to the reference genome. There is a critical need to develop efficient methods to recover these important mutational events. RESULTS: In this paper we introduce ITD Assembler, a novel approach that rapidly evaluates all unmapped and partially mapped reads from whole exome NGS data using a De Bruijn graphs approach to select reads that harbor cycles of appropriate length, followed by assembly using overlap-layout-consensus. We tested ITD Assembler on The Cancer Genome Atlas AML dataset as a truth set. ITD Assembler identified the highest percentage of reported FLT3-ITDs when compared to other ITD detection algorithms, and discovered additional ITDs in FLT3, KIT, CEBPA, WT1 and other genes. Evidence of polymorphic ITDs in 54 genes were also found. Novel ITDs were validated by analyzing the corresponding RNA sequencing data. CONCLUSIONS: ITD Assembler is a very sensitive tool which can detect partial, large and complex tandem duplications. This study highlights the need to more effectively look for ITD's in other cancers and Mendelian diseases. Twit Text FOAVip ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data ????BMC Bioinformatics http://www.kidney.de/pget.php?&tw=1&pmid=27121965 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=27121965 #FOAvip English Wikipedia <ref>{{Cite pmid|27121965 }}</ref> ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data #MMPMID27121965 Rustagi N ; Hampton OA ; Li J ; Xi L ; Gibbs RA ; Plon SE ; Kimmel M ; Wheeler DA BMC Bioinformatics 2016[Apr]; 17 (ä): 188 PMID27121965 show ga BACKGROUND: Detection of tandem duplication within coding exons, referred to as internal tandem duplication (ITD), remains challenging due to inefficiencies in alignment of ITD-containing reads to the reference genome. There is a critical need to develop efficient methods to recover these important mutational events. RESULTS: In this paper we introduce ITD Assembler, a novel approach that rapidly evaluates all unmapped and partially mapped reads from whole exome NGS data using a De Bruijn graphs approach to select reads that harbor cycles of appropriate length, followed by assembly using overlap-layout-consensus. We tested ITD Assembler on The Cancer Genome Atlas AML dataset as a truth set. ITD Assembler identified the highest percentage of reported FLT3-ITDs when compared to other ITD detection algorithms, and discovered additional ITDs in FLT3, KIT, CEBPA, WT1 and other genes. Evidence of polymorphic ITDs in 54 genes were also found. Novel ITDs were validated by analyzing the corresponding RNA sequencing data. CONCLUSIONS: ITD Assembler is a very sensitive tool which can detect partial, large and complex tandem duplications. This study highlights the need to more effectively look for ITD's in other cancers and Mendelian diseases. |*Algorithms [MESH] |*Mutation [MESH] |*Tandem Repeat Sequences [MESH] |Exome [MESH] |Exons [MESH] |Humans [MESH] |Leukemia, Myeloid, Acute/diagnosis/*genetics [MESH] |Molecular Diagnostic Techniques [MESH]ITD assembler: an algorithm for internal tandem duplication discovery (epmc).pdf DeepDyve Pubget Overpricing