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10.1038/ncomms10001 http://scihub22266oqcxt.onion/10.1038/ncomms10001 C4682041!4682041!26647970     free     free     free Deprecated: Implicit conversion from float 229.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 229.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 229.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 229.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 229.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 229.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       Nat+Commun 2015 ; 6 (ä): ä Nephropedia Template TP {{tp|p=26647970|t=2015. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing |pdf=|usr=}}{{26647970}} gab.com Text A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing JO: Nat Commun http://www.kidney.de/pget.php?&tw=1&pmid=26647970 #FOAvip As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ?100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy. Twit Text FOAVip A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing ????Nat Commun http://www.kidney.de/pget.php?&tw=1&pmid=26647970 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=26647970 #FOAvip English Wikipedia <ref>{{Cite pmid|26647970}}</ref> A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing #MMPMID26647970 Alioto TS; Buchhalter I; Derdak S; Hutter B; Eldridge MD; Hovig E; Heisler LE; Beck TA; Simpson JT; Tonon L; Sertier AS; Patch AM; Jäger N; Ginsbach P; Drews R; Paramasivam N; Kabbe R; Chotewutmontri S; Diessl N; Previti C; Schmidt S; Brors B; Feuerbach L; Heinold M; Gröbner S; Korshunov A; Tarpey PS; Butler AP; Hinton J; Jones D; Menzies A; Raine K; Shepherd R; Stebbings L; Teague JW; Ribeca P; Giner FC; Beltran S; Raineri E; Dabad M; Heath SC; Gut M; Denroche RE; Harding NJ; Yamaguchi TN; Fujimoto A; Nakagawa H; Quesada V; Valdés-Mas R; Nakken S; Vodák D; Bower L; Lynch AG; Anderson CL; Waddell N; Pearson JV; Grimmond SM; Peto M; Spellman P; He M; Kandoth C; Lee S; Zhang J; Létourneau L; Ma S; Seth S; Torrents D; Xi L; Wheeler DA; López-Otín C; Campo E; Campbell PJ; Boutros PC; Puente XS; Gerhard DS; Pfister SM; McPherson JD; Hudson TJ; Schlesner M; Lichter P; Eils R; Jones DTW; Gut IG Nat Commun 2015[]; 6 (ä): ä PMID26647970show ga As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ?100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy. äA comprehensive assessment of somatic mutation detection in cancer usi(epmc).pdf DeepDyve Pubget Overpricing