Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
TLDR
The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution.Abstract:
Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today’s sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license.read more
Citations
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Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
Bruce J. Walker,Thomas Abeel,Terrance Shea,Margaret Priest,Amr Abouelliel,Sharadha Sakthikumar,Christina A. Cuomo,Qiandong Zeng,Jennifer R. Wortman,Sarah Young,Ashlee M. Earl +10 more
TL;DR: Pilon is a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions, which is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains.
Journal ArticleDOI
Integrative clinical genomics of advanced prostate cancer
Dan R. Robinson,Eliezer M. Van Allen,Eliezer M. Van Allen,Yi-Mi Wu,Nikolaus Schultz,Robert J. Lonigro,Juan Miguel Mosquera,Bruce Montgomery,Mary-Ellen Taplin,Colin C. Pritchard,Gerhardt Attard,Gerhardt Attard,Himisha Beltran,Wassim Abida,Robert K. Bradley,Jake Vinson,Xuhong Cao,Pankaj Vats,Lakshmi P. Kunju,Maha Hussain,Felix Y. Feng,Scott A. Tomlins,Kathleen A. Cooney,David Smith,Christine Brennan,Javed Siddiqui,Rohit Mehra,Yu Chen,Yu Chen,Dana E. Rathkopf,Dana E. Rathkopf,Michael J. Morris,Michael J. Morris,Stephen B. Solomon,Jeremy C. Durack,Victor E. Reuter,Anuradha Gopalan,Jianjiong Gao,Massimo Loda,Rosina T. Lis,Michaela Bowden,Michaela Bowden,Stephen P. Balk,Glenn C. Gaviola,Carrie Sougnez,Manaswi Gupta,Evan Y. Yu,Elahe A. Mostaghel,Heather H. Cheng,Hyojeong Mulcahy,Lawrence D. True,Stephen R. Plymate,Heidi Dvinge,Roberta Ferraldeschi,Roberta Ferraldeschi,Penny Flohr,Penny Flohr,Susana Miranda,Susana Miranda,Zafeiris Zafeiriou,Zafeiris Zafeiriou,Nina Tunariu,Nina Tunariu,Joaquin Mateo,Joaquin Mateo,Raquel Perez-Lopez,Raquel Perez-Lopez,Francesca Demichelis,Francesca Demichelis,Brian D. Robinson,Marc H. Schiffman,David M. Nanus,Scott T. Tagawa,Alexandros Sigaras,Kenneth Eng,Olivier Elemento,Andrea Sboner,Elisabeth I. Heath,Howard I. Scher,Howard I. Scher,Kenneth J. Pienta,Philip W. Kantoff,Johann S. de Bono,Johann S. de Bono,Mark A. Rubin,Peter S. Nelson,Levi A. Garraway,Levi A. Garraway,Charles L. Sawyers,Arul M. Chinnaiyan +89 more
TL;DR: This cohort study provides clinically actionable information that could impact treatment decisions for affected individuals and identified new genomic alterations in PIK3CA/B, R-spondin, BRAF/RAF1, APC, β-catenin, and ZBTB16/PLZF.
Journal ArticleDOI
The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge.
TL;DR: The current status of TCGA Research Network structure, purpose, and achievements are discussed, to provide publicly available datasets to help improve diagnostic methods, treatment standards, and finally to prevent cancer.
Journal ArticleDOI
Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients
Ahmet Zehir,Ryma Benayed,Ronak Shah,Aijazuddin Syed,Sumit Middha,Hyunjae R. Kim,Preethi Srinivasan,Jianjiong Gao,Debyani Chakravarty,Sean M. Devlin,Matthew D. Hellmann,David Barron,Alison M. Schram,Meera Hameed,Snjezana Dogan,Dara S. Ross,Jaclyn F. Hechtman,Deborah DeLair,Jinjuan Yao,Diana Mandelker,Donavan T. Cheng,Raghu Chandramohan,Abhinita Mohanty,Ryan Ptashkin,Gowtham Jayakumaran,Meera Prasad,Mustafa H Syed,Anoop Balakrishnan Rema,Zhen Y Liu,Khedoudja Nafa,Laetitia Borsu,Justyna Sadowska,Jacklyn Casanova,Ruben Bacares,Iwona Kiecka,Anna Razumova,Julie B Son,Lisa Stewart,Tessara Baldi,Kerry Mullaney,Hikmat Al-Ahmadie,Efsevia Vakiani,Adam Abeshouse,Alexander V Penson,Philip Jonsson,Niedzica Camacho,Matthew T. Chang,Helen Won,Benjamin Gross,Ritika Kundra,Zachary J. Heins,Hsiao-Wei Chen,Sarah Phillips,Hongxin Zhang,Jiaojiao Wang,Angelica Ochoa,Jonathan Wills,Michael H. Eubank,Stacy B. Thomas,Stuart Gardos,Dalicia N. Reales,Jesse Galle,Robert Durany,Roy Cambria,Wassim Abida,Andrea Cercek,Darren R. Feldman,Mrinal M. Gounder,A. Ari Hakimi,James J. Harding,Gopa Iyer,Yelena Y. Janjigian,Emmet Jordan,Ciara Marie Kelly,Maeve A. Lowery,Luc G. T. Morris,Antonio Omuro,Nitya Raj,Pedram Razavi,Alexander N. Shoushtari,Neerav Shukla,Tara Soumerai,Anna M. Varghese,Rona Yaeger,Jonathan A. Coleman,Bernard H. Bochner,Gregory J. Riely,Leonard B. Saltz,Howard I. Scher,Paul Sabbatini,Mark E. Robson,David S. Klimstra,Barry S. Taylor,José Baselga,Nikolaus Schultz,David M. Hyman,Maria E. Arcila,David B. Solit,Marc Ladanyi,Michael F. Berger +99 more
TL;DR: A large-scale, prospective clinical sequencing initiative using a comprehensive assay, MSK-IMPACT, through which tumor and matched normal sequence data from a unique cohort of more than 10,000 patients with advanced cancer are compiled and identified clinically relevant somatic mutations, novel noncoding alterations, and mutational signatures that were shared by common and rare tumor types.
Integrative Genomics Viewer
James T. Robinson,Helga Thorvaldsdottir,Wendy Winckler,Mitchell Guttman,Eric S. Lander,Eric S. Lander,Gad Getz,Jill P. Mesirov +7 more
TL;DR: The sheer volume and scope of data posed by this flood of data pose a significant challenge to the development of efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data.
References
More filters
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Integrative genomics viewer
James T. Robinson,Helga Thorvaldsdottir,Wendy Winckler,Mitchell Guttman,Eric S. Lander,Eric S. Lander,Gad Getz,Jill P. Mesirov +7 more
TL;DR: In this article, the authors present an approach for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data.
Journal ArticleDOI
The variant call format and VCFtools
Petr Danecek,Adam Auton,Gonçalo R. Abecasis,Cornelis A. Albers,Eric Banks,Mark A. DePristo,Robert E. Handsaker,Gerton Lunter,Gabor T. Marth,Stephen T. Sherry,Gilean McVean,Richard Durbin +11 more
TL;DR: VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.
Journal ArticleDOI
A Map of Human Genome Variation From Population-Scale Sequencing
Gonçalo R. Abecasis,David Altshuler,David Altshuler,Adam Auton,Lisa D Brooks,Richard Durbin,Richard A. Gibbs,Matthew E. Hurles,Gil McVean +8 more
TL;DR: The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype as mentioned in this paper, and the results of the pilot phase of the project, designed to develop and compare different strategies for genomewide sequencing with high-throughput platforms.
Journal ArticleDOI
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
Roger E. McLendon,Allan H. Friedman,Darrell D. Bigner,Erwin G. Van Meir,Daniel J. Brat,Gena M. Mastrogianakis,Jeffrey J. Olson,Tom Mikkelsen,Norman L. Lehman,Kenneth Aldape,W. K. Alfred Yung,Oliver Bogler,John N. Weinstein,Scott R. VandenBerg,Mitchel S. Berger,Michael D. Prados,Donna M. Muzny,Margaret Morgan,Steve Scherer,Aniko Sabo,Lynn Nazareth,Lora Lewis,Otis Hall,Yiming Zhu,Yanru Ren,Omar Alvi,Jiqiang Yao,Alicia Hawes,Shalini N. Jhangiani,Gerald R. Fowler,Anthony San Lucas,Christie Kovar,Andrew Cree,Huyen Dinh,Jireh Santibanez,Vandita Joshi,Manuel L. Gonzalez-Garay,Christopher A. Miller,Aleksandar Milosavljevic,Lawrence A. Donehower,David A. Wheeler,Richard A. Gibbs,Kristian Cibulskis,Carrie Sougnez,Timothy Fennell,Scott Mahan,Jane Wilkinson,Liuda Ziaugra,Robert C. Onofrio,Toby Bloom,Rob Nicol,Kristin G. Ardlie,Jennifer Baldwin,Stacey Gabriel,Eric S. Lander,Eric S. Lander,Li Ding,Robert S. Fulton,Michael D. McLellan,John W. Wallis,David E. Larson,Xiaoqi Shi,Rachel Abbott,Lucinda Fulton,Ken Chen,Daniel C. Koboldt,Michael C. Wendl,Rick Meyer,Yuzhu Tang,Ling Lin,John R. Osborne,Brian H. Dunford-Shore,Tracie L. Miner,Kim D. Delehaunty,Chris Markovic,Gary W. Swift,William Courtney,Craig Pohl,Scott Abbott,Amy Hawkins,Shin Leong,Carrie A. Haipek,Heather Schmidt,Maddy Wiechert,Tammi L. Vickery,Sacha Scott,David J. Dooling,Asif T. Chinwalla,George M. Weinstock,Elaine R. Mardis,Richard K. Wilson,Gad Getz,Wendy Winckler,Roel G.W. Verhaak,Michael S. Lawrence,Michael J. T. O’Kelly,James A. Robinson,Gabriele Alexe,Rameen Beroukhim,Scott L. Carter,Derek Y. Chiang,Josh Gould,Supriya Gupta,Josh Korn,Craig H. Mermel,Jill P. Mesirov,Stefano Monti,Huy V. Nguyen,Melissa Parkin,Michael R. Reich,Nicolas Stransky,Barbara A. Weir,Levi A. Garraway,Todd R. Golub,Matthew Meyerson,Lynda Chin,Alexei Protopopov,Jianhua Zhang,Ilana Perna,Sandy Aronson,Narayanan Sathiamoorthy,Georgia Ren,Jun Yao,W. Ruprecht Wiedemeyer,Hyun Soo Kim,Won Kong Sek,Yonghong Xiao,Isaac S. Kohane,Jon G. Seidman,Peter J. Park,Raju Kucherlapati,Peter W. Laird,Leslie Cope,James G. Herman,Daniel J. Weisenberger,Fei Pan,David Van Den Berg,Leander Van Neste,Mi Yi Joo,Kornel E. Schuebel,Stephen B. Baylin,Devin Absher,Jun Li,Audrey Southwick,Shannon T. Brady,Amita Aggarwal,Tisha Chung,Gavin Sherlock,James D. Brooks,Richard M. Myers,Paul T. Spellman,Elizabeth Purdom,Lakshmi Jakkula,Anna Lapuk,Henry Marr,Shannon Dorton,Gi Choi Yoon,Ju Han,Amrita Ray,Victoria Wang,Steffen Durinck,Mark D. Robinson,Nicholas J. Wang,Karen Vranizan,Vivian Peng,Eric Van Name,Gerald V. Fontenay,John Ngai,John G. Conboy,Bahram Parvin,Heidi S. Feiler,Terence P. Speed,Terence P. Speed,Joe W. Gray,Cameron Brennan,Nicholas D. Socci,Adam B. Olshen,Barry S. Taylor,Barry S. Taylor,Alex E. Lash,Nikolaus Schultz,Boris Reva,Yevgeniy Antipin,Alexey Stukalov,Benjamin Gross,Ethan Cerami,Qing Wang Wei,Li-Xuan Qin,Venkatraman E. Seshan,Liliana Villafania,Magali Cavatore,Laetitia Borsu,Agnes Viale,William L. Gerald,Chris Sander,Marc Ladanyi,Charles M. Perou,D. Neil Hayes,Michael D. Topal,Katherine A. Hoadley,Yuan Qi,Sai Balu,Yan Shi,Junyuan Wu,Robert Penny,Michael L. Bittner,Troy Shelton,Elizabeth Lenkiewicz,Scott Morris,Debbie Beasley,Sheri Sanders,Ari B. Kahn,Robert Sfeir,Jessica Chen,David Nassau,Larry Feng,Erin Hickey,Anna D. Barker,Daniela S. Gerhard,Joseph G. Vockley,Carolyn C. Compton,Jim Vaught,Peter Fielding,Martin L. Ferguson,Carl F. Schaefer,Jinghui Zhang,Subhashree Madhavan,Kenneth H. Buetow,Francis S. Collins,Peter J. Good,Mark S. Guyer,Brad Ozenberger,Jane Peterson,Elizabeth J. Thomson +233 more
TL;DR: The interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated gliobeasts, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.