qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data
TLDR
Advanced and universally applicable models for relative quantification and inter-run calibration with proper error propagation along the entire calculation track are outlined in qBase, a free program for the management and automated analysis of qPCR data.Abstract:
Although quantitative PCR (qPCR) is becoming the method of choice for expression profiling of selected genes, accurate and straightforward processing of the raw measurements remains a major hurdle. Here we outline advanced and universally applicable models for relative quantification and inter-run calibration with proper error propagation along the entire calculation track. These models and algorithms are implemented in qBase, a free program for the management and automated analysis of qPCR data.read more
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Journal ArticleDOI
The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments
Stephen A. Bustin,Vladimir Benes,Jeremy A. Garson,Jan Hellemans,Jim F. Huggett,Mikael Kubista,Reinhold Mueller,Tania Nolan,Michael W. Pfaffl,Gregory L. Shipley,Jo Vandesompele,Carl T. Wittwer,Carl T. Wittwer +12 more
TL;DR: The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency.
Journal ArticleDOI
Functional impact of global rare copy number variation in autism spectrum disorders
Dalila Pinto,Alistair T. Pagnamenta,Lambertus Klei,Richard Anney,Daniele Merico,Regina Regan,Judith Conroy,Tiago R. Magalhaes,Tiago R. Magalhaes,Catarina Correia,Catarina Correia,Brett S. Abrahams,Joana Almeida,Elena Bacchelli,Gary D. Bader,Anthony J. Bailey,Gillian Baird,Agatino Battaglia,Tom Berney,Nadia Bolshakova,Sven Bölte,Patrick Bolton,Thomas Bourgeron,Sean Brennan,Jessica Brian,Susan E. Bryson,Andrew R. Carson,Guillermo Casallo,Jillian P. Casey,Brian H.Y. Chung,Lynne E Cochrane,Christina Corsello,Emily L. Crawford,Andrew Crossett,Cheryl Cytrynbaum,Geraldine Dawson,Maretha de Jonge,Richard Delorme,Irene Drmic,Eftichia Duketis,Frederico Duque,Annette Estes,Penny Farrar,Bridget A. Fernandez,Susan E. Folstein,Eric Fombonne,Christine M. Freitag,John Gilbert,Christopher Gillberg,Joseph T. Glessner,Jeremy Goldberg,Andrew Green,Jonathan Green,Stephen J. Guter,Hakon Hakonarson,Elizabeth A. Heron,Matthew Hill,Richard Holt,Jennifer L. Howe,Gillian Hughes,Vanessa Hus,Roberta Igliozzi,Cecilia Kim,Sabine M. Klauck,Alexander Kolevzon,Olena Korvatska,Vlad Kustanovich,Clara Lajonchere,Janine A. Lamb,Magdalena Laskawiec,Marion Leboyer,Ann Le Couteur,Bennett L. Leventhal,Anath C. Lionel,Anath C. Lionel,Xiao-Qing Liu,Catherine Lord,Linda Lotspeich,Sabata C. Lund,Elena Maestrini,William M. Mahoney,Carine Mantoulan,Christian R. Marshall,Helen McConachie,Christopher J. McDougle,Jane McGrath,William M. McMahon,Alison K. Merikangas,Ohsuke Migita,Nancy J. Minshew,Ghazala Mirza,Jeff Munson,Stanley F. Nelson,Carolyn Noakes,Abdul Noor,Gudrun Nygren,Guiomar Oliveira,Katerina Papanikolaou,Jeremy R. Parr,Barbara Parrini,Tara Paton,Andrew Pickles,Marion Pilorge,Joseph Piven,Chris P. Ponting,David J. Posey,Annemarie Poustka,Fritz Poustka,Aparna Prasad,Jiannis Ragoussis,Katy Renshaw,Jessica Rickaby,Wendy Roberts,Kathryn Roeder,Bernadette Rogé,Michael Rutter,Laura J. Bierut,John P. Rice,Jeff Salt,Katherine Sansom,Daisuke Sato,Ricardo Segurado,Ana Filipa Sequeira,Lili Senman,Lili Senman,Naisha Shah,Val C. Sheffield,Latha Soorya,Inês Sousa,Olaf Stein,Nuala Sykes,Vera Stoppioni,Christina Strawbridge,Raffaella Tancredi,Katherine E. Tansey,Bhooma Thiruvahindrapduram,Ann P. Thompson,Susanne Thomson,Ana Tryfon,John Tsiantis,Herman Van Engeland,John B. Vincent,Fred R. Volkmar,Simon Wallace,Kai Wang,Zhouzhi Wang,Thomas H. Wassink,Caleb Webber,Rosanna Weksberg,Kirsty Wing,Kerstin Wittemeyer,Shawn Wood,Jing Wu,Brian L. Yaspan,Danielle Zurawiecki,Lonnie Zwaigenbaum,Joseph D. Buxbaum,Rita M. Cantor,Edwin H. Cook,Hilary Coon,Michael L. Cuccaro,Bernie Devlin,Sean Ennis,Louise Gallagher,Daniel H. Geschwind,Michael Gill,Jonathan L. Haines,Joachim Hallmayer,Judith Miller,Anthony P. Monaco,John I. Nurnberger,Andrew D. Paterson,Margaret A. Pericak-Vance,Gerard D. Schellenberg,Peter Szatmari,Astrid M. Vicente,Veronica J. Vieland,Veronica J. Vieland,Ellen M. Wijsman,Stephen W. Scherer,James S. Sutcliffe,Catalina Betancur +181 more
TL;DR: The genome-wide characteristics of rare (<1% frequency) copy number variation in ASD are analysed using dense genotyping arrays to reveal many new genetic and functional targets in ASD that may lead to final connected pathways.
Journal ArticleDOI
Autism genome-wide copy number variation reveals ubiquitin and neuronal genes
Joseph T. Glessner,Kai Wang,Guiqing Cai,Olena Korvatska,Cecilia E. Kim,Shawn Wood,Haitao Zhang,Annette Estes,Camille W. Brune,Jonathan P. Bradfield,Marcin Imielinski,Edward C. Frackelton,Jennifer Reichert,Emily L. Crawford,Jeffrey Munson,Patrick M. A. Sleiman,Rosetta M. Chiavacci,Kiran Annaiah,Kelly A. Thomas,Cuiping Hou,Wendy Glaberson,James H. Flory,Frederick G. Otieno,Maria Garris,Latha Soorya,Lambertus Klei,Joseph Piven,Kacie J. Meyer,Evdokia Anagnostou,Takeshi Sakurai,Rachel M. Game,Danielle S. Rudd,Danielle Zurawiecki,Christopher J. McDougle,Lea K. Davis,Judith Miller,David J. Posey,Shana M. Michaels,Alexander Kolevzon,Jeremy M. Silverman,Raphael Bernier,Susan E. Levy,Robert T. Schultz,Geraldine Dawson,Thomas Owley,William M. McMahon,Thomas H. Wassink,John A. Sweeney,John I. Nurnberger,Hilary Coon,James S. Sutcliffe,Nancy J. Minshew,Struan F.A. Grant,Maja Bucan,Edwin H. Cook,Joseph D. Buxbaum,Bernie Devlin,Gerard D. Schellenberg,Hakon Hakonarson +58 more
TL;DR: Several new susceptibility genes encoding neuronal cell-adhesion molecules, including NLGN1 and ASTN2, were enriched with CNVs in ASD cases compared to controls, and duplications 55 kilobases upstream of complementary DNA AK123120 indicate that these two important gene networks expressed within the central nervous system may contribute to the genetic susceptibility of ASD.
Journal ArticleDOI
A novel and universal method for microRNA RT-qPCR data normalization
Pieter Mestdagh,Pieter Van Vlierberghe,An-Sofie De Weer,Daniel Muth,Frank Westermann,Frank Speleman,Jo Vandesompele +6 more
TL;DR: It is demonstrated that the mean expression value outperforms the current normalization strategy in terms of better reduction of technical variation and more accurate appreciation of biological changes.
Journal ArticleDOI
5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming
Mark Wossidlo,Toshinobu Nakamura,Konstantin Lepikhov,C. Joana Marques,Valeri Zakhartchenko,Michele Boiani,Julia Arand,Toru Nakano,Wolf Reik,Wolf Reik,Jörn Walter +10 more
TL;DR: The data suggest an important role of 5hmC and Tet3 for DNA methylation reprogramming processes in the mammalian zygote, as detected in mouse, bovine and rabbit zygotes.
References
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