ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
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TLDR
The ANNOVAR tool to annotate single nucleotide variants and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP is developed.Abstract:
High-throughput sequencing platforms are generating massive amounts of genetic variation data for diverse genomes, but it remains a challenge to pinpoint a small subset of functionally important variants. To fill these unmet needs, we developed the ANNOVAR tool to annotate single nucleotide variants (SNVs) and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP. ANNOVAR can utilize annotation databases from the UCSC Genome Browser or any annotation data set conforming to Generic Feature Format version 3 (GFF3). We also illustrate a 'variants reduction' protocol on 4.7 million SNVs and indels from a human genome, including two causal mutations for Miller syndrome, a rare recessive disease. Through a stepwise procedure, we excluded variants that are unlikely to be causal, and identified 20 candidate genes including the causal gene. Using a desktop computer, ANNOVAR requires ∼4 min to perform gene-based annotation and ∼15 min to perform variants reduction on 4.7 million variants, making it practical to handle hundreds of human genomes in a day. ANNOVAR is freely available at http://www.openbioinformatics.org/annovar/.read more
Citations
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A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
Pablo Cingolani,Adrian E. Platts,Le Lily Wang,M. Coon,Tung T. Nguyen,Luan Wang,Susan Land,Xiangyi Lu,Douglas M. Ruden +8 more
TL;DR: It appears that the 5′ and 3′ UTRs are reservoirs for genetic variations that changes the termini of proteins during evolution of the Drosophila genus.
Journal ArticleDOI
The Ensembl Variant Effect Predictor.
William M. McLaren,Laurent Gil,Sarah E. Hunt,Harpreet Singh Riat,Graham R. S. Ritchie,Anja Thormann,Paul Flicek,Fiona Cunningham +7 more
TL;DR: The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.
Journal ArticleDOI
Genetic studies of body mass index yield new insights for obesity biology
Glgc,Icbp,Magic Investigators +2 more
TL;DR: A genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals provide strong support for a role of the central nervous system in obesity susceptibility.
Genetic studies of body mass index yield new insights for obesity biology
Adam E. Locke,Bratati Kahali,Sonja I. Berndt,Anne E. Justice,Tune H. Pers,Felix R. Day,Corey Powell,Sailaja Vedantam,Martin L. Buchkovich,Jian Yang,Damien C. Croteau-Chonka,Tõnu Esko,Tove Fall,Teresa Ferreira,Stefan Gustafsson,Zoltán Kutalik,Jian'an Luan,Reedik Mägi,Joshua C. Randall,Thomas W. Winkler,Andrew R. Wood,Tsegaselassie Workalemahu,Jessica D. Faul,Jennifer A. Smith,Jing Hua Zhao,Wei Zhao,Jin Chen,Rudolf S N Fehrmann,Åsa K. Hedman,Juha Karjalainen,Ellen M. Schmidt,Devin Absher,Najaf Amin,Denise Anderson,Marian Beekman,Jennifer L. Bolton,Jennifer L. Bragg-Gresham,Steven Buyske,Ayse Demirkan,Guohong Deng,Georg Ehret,Bjarke Feenstra,Mary F. Feitosa,Krista Fischer,Anuj Goel,Jian Gong,Anne U. Jackson,Stavroula Kanoni,Marcus E. Kleber,Kati Kristiansson,Unhee Lim,Vaneet Lotay,Massimo Mangino,Irene Mateo Leach,Carolina Medina-Gomez,Sarah E. Medland,Mike A. Nalls,Cameron D. Palmer,Dorota Pasko,Sonali Pechlivanis,Marjolein Peters,Inga Prokopenko,Dmitry Shungin,Alena Stančáková,Rona J. Strawbridge,Yun Ju Sung,Toshiko Tanaka,Alexander Teumer,Stella Trompet,Sander W. van der Laan,Jessica van Setten,Jana V. van Vliet-Ostaptchouk,Zhaoming Wang,Loic Yengo,Weihua Zhang,Aaron Isaacs,Eva Albrecht,Johan Ärnlöv,Gillian M. Arscott,Antony P. Attwood,Stefania Bandinelli,Amy Barrett,Isabelita Bas,Claire Bellis,Amanda J. Bennett,Christian Berne,Roza Blagieva,Matthias Blüher,Stefan Böhringer,Lori L. Bonnycastle,Yvonne Böttcher,Heather A. Boyd,Marcel Bruinenberg,Ida Henriette Caspersen,Yii-Der Ida Chen,Robert Clarke,E. Warwick Daw,Anton J. M. de Craen,Graciela E. Delgado,Maria Dimitriou,Alex S. F. Doney,Niina Eklund,Karol Estrada,Elodie Eury,Lasse Folkersen,Ross M. Fraser,Melissa E. Garcia,Frank Geller,Vilmantas Giedraitis,Bruna Gigante,Alan S. Go,Alain Golay,Alison H. Goodall,Scott D. Gordon,Mathias Gorski,Hans-Jörgen Grabe,Harald Grallert,Tanja B. Grammer,Jürgen Gräßler,Henrik Grönberg,Christopher J. Groves,Gaëlle Gusto,Jeffrey Haessler,Per Hall,Toomas Haller,Göran Hallmans,Catharina A. Hartman,Maija Hassinen,Caroline Hayward,Nancy L. Heard-Costa,Quinta Helmer,Christian Hengstenberg,Oddgeir L. Holmen,Jouke-Jan Hottenga,Alan James,Janina M. Jeff,Åsa Johansson,Jennifer Jolley,Thorhildur Juliusdottir,Leena Kinnunen,Wolfgang Koenig,Markku Koskenvuo,Wolfgang Kratzer,Jaana Laitinen,Claudia Lamina,Karin Leander,Nanette R. Lee,Peter Lichtner,Lars Lind,Jaana Lindström,Ken Sin Lo,Stéphane Lobbens,Roberto Lorbeer,Yingchang Lu,François Mach,Patrik K. E. Magnusson,Anubha Mahajan,Wendy L. McArdle,Stela McLachlan,Cristina Menni,Sigrun Merger,Evelin Mihailov,Lili Milani,Alireza Moayyeri,Keri L. Monda,Mario A. Morken,Antonella Mulas,Gabriele Müller,Martina Müller-Nurasyid,Arthur W. Musk,Ramaiah Nagaraja,Markus M. Nöthen,Ilja M. Nolte,Stefan Pilz,Nigel W. Rayner,Frida Renström,Rainer Rettig,Janina S. Ried,Stephan Ripke,Neil R. Robertson,Lynda M. Rose,Serena Sanna,Hubert Scharnagl,Salome Scholtens,Fredrick R. Schumacher,William R. Scott,Thomas Seufferlein,Jianxin Shi,Albert V. Smith,Joanna Smolonska,Alice Stanton,Valgerdur Steinthorsdottir,Kathleen Stirrups,Heather M. Stringham,Johan Sundström,Morris A. Swertz,Amy J. Swift,Ann-Christine Syvänen,Sian-Tsung Tan,Bamidele O. Tayo,Barbara Thorand,Gudmar Thorleifsson,Jonathan Tyrer,Hae-Won Uh,Liesbeth Vandenput,Frank C. Verhulst,Sita H. Vermeulen,Niek Verweij,Judith M. Vonk,Lindsay L. Waite,Helen R. Warren,Dawn M. Waterworth,Michael N. Weedon,Lynne R. Wilkens,Christina Willenborg,Tom Wilsgaard,Mary K. Wojczynski,Andrew Wong,Alan F. Wright,Qunyuan Zhang,Eoin P. Brennan,Murim Choi,Zari Dastani,Alexander W. Drong,Per Eriksson,Anders Franco-Cereceda,Jesper R. Gådin,Ali G. Gharavi,Michael E. Goddard,Robert E. Handsaker,Jinyan Huang,Fredrik Karpe,Sekar Kathiresan,Sarah Keildson,Krzysztof Kiryluk,Michiaki Kubo,Jong-Young Lee,Liming Liang,Richard P. Lifton,Baoshan Ma,Steven A. McCarroll,Amy Jayne McKnight,Josine L. Min,Miriam F. Moffatt,Grant W. Montgomery,Joanne M. Murabito,George Nicholson,Dale R. Nyholt,Yukinori Okada,John R. B. Perry,Rajkumar Dorajoo,Eva Reinmaa,Rany M. Salem,Niina Sandholm,Robert A. Scott,Lisette Stolk,Atsushi Takahashi,Toshihiro Tanaka,Ferdinand M. van't Hooft,Anna A. E. Vinkhuyzen,Harm-Jan Westra,Wei Zheng,Krina T. Zondervan,Andrew C. Heath,Dominique Arveiler,Stephan J. L. Bakker,John Beilby,Richard N. Bergman,John Blangero,Pascal Bovet,Harry Campbell,Mark J. Caulfield,Giancarlo Cesana,Aravinda Chakravarti,Daniel I. Chasman,Peter S. Chines,Francis S. Collins,Dana C. Crawford,L. Adrienne Cupples,Daniele Cusi,John Danesh,Ulf de Faire,Hester M. den Ruijter,Anna F. Dominiczak,Raimund Erbel,Jeanette Erdmann,Johan G. Eriksson,Martin Farrall,Stephan B. Felix,Ele Ferrannini,Jean Ferrières,Ian Ford,Nita G. Forouhi,Terrence Forrester,Oscar H. Franco,Ron T. Gansevoort,Pablo V. Gejman,Christian Gieger,Omri Gottesman,Vilmundur Gudnason,Ulf Gyllensten,Alistair S. Hall,Tamara B. Harris,Andrew T. Hattersley,Andrew A. Hicks,Lucia A. Hindorff,Aroon D. Hingorani,Albert Hofman,Georg Homuth,G. Kees Hovingh,Steve E. Humphries,Steven C. Hunt,Elina Hyppönen,Thomas Illig,Kevin B. Jacobs,Marjo-Riitta Järvelin,Karl-Heinz Jöckel,Berit Johansen,Pekka Jousilahti,J. Wouter Jukema,Antti Jula,Jaakko Kaprio,John J.P. Kastelein,Sirkka Keinänen-Kiukaanniemi,Lambertus A. Kiemeney,Paul Knekt,Jaspal S. Kooner,Charles Kooperberg,Peter Kovacs,Aldi T. Kraja,Meena Kumari,Johanna Kuusisto,Timo A. Lakka,Claudia Langenberg,Loic Le Marchand,Terho Lehtimäki,Valeriya Lyssenko,Satu Männistö,André Marette,Tara C. Matise,Colin A. McKenzie,Barbara McKnight,Frans L. Moll,Andrew D. Morris,Andrew P. Morris,Jeffrey C. Murray,Mari Nelis,Claes Ohlsson,Albertine J. Oldehinkel,Ken K. Ong,Pamela A. F. Madden,Gerard Pasterkamp,John F. Peden,Annette Peters,Dirkje S. Postma,Peter P. Pramstaller,Jackie F. Price,Lu Qi,Olli T. Raitakari,Tuomo Rankinen,Dabeeru C. Rao,Treva Rice,Paul M. Ridker,John D. Rioux,Marylyn D. Ritchie,Igor Rudan,Veikko Salomaa,Nilesh J. Samani,Jouko Saramies,Mark A. Sarzynski,Heribert Schunkert,Peter Schwarz,Peter S. Sever,Alan R. Shuldiner,Juha Sinisalo,Ronald P. Stolk,Konstantin Strauch,Anke Tönjes,David-Alexandre Trégouët,Angelo Tremblay,Elena Tremoli,Jarmo Virtamo,Marie-Claude Vohl,Uwe Völker,Gérard Waeber,Gonneke Willemsen,Jacqueline C. M. Witteman,M. Carola Zillikens,Linda S. Adair,Philippe Amouyel,Folkert W. Asselbergs,Themistocles L. Assimes,Murielle Bochud,Bernhard O. Boehm,Eric Boerwinkle,Stefan R. Bornstein,Erwin P. Bottinger,Claude Bouchard,Stéphane Cauchi,John C. Chambers,Stephen J. Chanock,Richard S. Cooper,Paul I.W. de Bakker,George Dedoussis,Luigi Ferrucci,Paul W. Franks,Philippe Froguel,Leif Groop,Christopher A. Haiman,Anders Hamsten,Jennie Hui,David J. Hunter,Kristian Hveem,Robert C. Kaplan,Mika Kivimäki,Diana Kuh,Markku Laakso,Yongmei Liu,Nicholas G. Martin,Winfried März,Mads Melbye,Andres Metspalu,Susanne Moebus,Patricia B. Munroe,Inger Njølstad,Ben A. Oostra,Colin N. A. Palmer,Nancy L. Pedersen,Markus Perola,Louis Pérusse,Ulrike Peters,Chris Power,Thomas Quertermous,Rainer Rauramaa,Fernando Rivadeneira,Timo Saaristo,Danish Saleheen,Naveed Sattar,Eric E. Schadt,David Schlessinger,P. Eline Slagboom,Harold Snieder,Tim D. Spector,Unnur Thorsteinsdottir,Michael Stumvoll,Jaakko Tuomilehto,André G. Uitterlinden,Matti Uusitupa,Pim van der Harst,Mark Walker,Henri Wallaschofski,Nicholas J. Wareham,Hugh Watkins,David R. Weir,H-Erich Wichmann,James F. Wilson,Pieter Zanen,Ingrid B. Borecki,Panos Deloukas,Caroline S. Fox,Iris M. Heid,Jeffrey R. O'Connell,David P. Strachan,Kari Stefansson,Cornelia M. van Duijn,Gonçalo R. Abecasis,Lude Franke,Timothy M. Frayling,Mark I. McCarthy,Peter M. Visscher,André Scherag,Cristen J. Willer,Michael Boehnke,Karen L. Mohlke,Cecilia M. Lindgren,Jacques S. Beckmann,Inês Barroso,Kari E. North,Erik Ingelsson,Joel N. Hirschhorn,Ruth J. F. Loos,Elizabeth K. Speliotes +481 more
TL;DR: This paper conducted a genome-wide association study and meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals.
Journal ArticleDOI
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
TL;DR: This work shows that sequence specificities can be ascertained from experimental data with 'deep learning' techniques, which offer a scalable, flexible and unified computational approach for pattern discovery.
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TL;DR: An approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost is reported, effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.
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Adam Siepel,Gill Bejerano,Jakob Skou Pedersen,Angie S. Hinrichs,Minmei Hou,Kate R. Rosenbloom,Hiram Clawson,John Spieth,LaDeana W. Hillier,Stephen Richards,George M. Weinstock,Richard K. Wilson,Richard A. Gibbs,W. James Kent,Webb Miller,David Haussler +15 more
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