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Integrative genomics viewer

Published on Jan 1, 2011in Nature Biotechnology 35.72
· DOI :10.1038/nbt.1754
James Robinson90
Estimated H-index: 90
(Massachusetts Institute of Technology),
Helga Thorvaldsdottir12
Estimated H-index: 12
(Massachusetts Institute of Technology)
+ 4 AuthorsJill P. Mesirov71
Estimated H-index: 71
(Massachusetts Institute of Technology)
Abstract
Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.
  • References (13)
  • Citations (3987)
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References13
Newest
Published on Oct 28, 2010in Nature 41.58
D Altshuler177
Estimated H-index: 177
(Broad Institute),
Richard Durbin103
Estimated H-index: 103
(Wellcome Trust Sanger Institute)
+ 365 AuthorsMichael Egholm68
Estimated H-index: 68
(Pall Corporation)
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. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother...
5,056 Citations Source Cite
Published on Aug 15, 2010in Bioinformatics 5.48
Marc Fiume10
Estimated H-index: 10
(University of Toronto),
Vanessa Williams5
Estimated H-index: 5
(University of Toronto)
+ 1 AuthorsMichael Brudno45
Estimated H-index: 45
(University of Toronto)
Motivation: The advent of high-throughput sequencing (HTS) technologies has made it affordable to sequence many individuals’ genomes. Simultaneously the computational analysis of the large volumes of data generated by the new sequencing machines remains a challenge. While a plethora of tools are available to map the resulting reads to a reference genome, and to conduct primary analysis of the mappings, it is often necessary to visually examine the results and underlying data to confirm predictio...
95 Citations Source Cite
Published on Apr 1, 2010in Genome Research 10.10
Michael F. Berger71
Estimated H-index: 71
(Broad Institute),
Joshua Z. Levin36
Estimated H-index: 36
(Broad Institute)
+ 23 AuthorsCarrie Sougnez69
Estimated H-index: 69
(Broad Institute)
Global studies of transcript structure and abundance in cancer cells enable the systematic discovery of aberrations that contribute to carcinogenesis, including gene fusions, alternative splice isoforms, and somatic mutations. We developed a systematic approach to characterize the spectrum of cancer-associated mRNA alterations through integration of transcriptomic and structural genomic data, and we applied this approach to generate new insights into melanoma biology. Using paired-end massively ...
221 Citations Source Cite
Published on Mar 1, 2010in Nature Methods 26.92
Cydney B. Nielsen18
Estimated H-index: 18
,
Michael N. Cantor6
Estimated H-index: 6
+ 2 AuthorsTing Wang36
Estimated H-index: 36
(Washington University in St. Louis)
As our ability to generate sequencing data continues to increase, data analysis is replacing data generation as the rate-limiting step in genomics studies. Here we provide a guide to genomic data visualization tools that facilitate analysis tasks by enabling researchers to explore, interpret and manipulate their data, and in some cases perform on-the-fly computations. We will discuss graphical methods designed for the analysis of de novo sequencing assemblies and read alignments, genome browsing...
115 Citations Source Cite
Published on Feb 1, 2010in Bioinformatics 5.48
Iain Milne16
Estimated H-index: 16
(Scottish Crop Research Institute),
Micha Bayer19
Estimated H-index: 19
(Scottish Crop Research Institute)
+ 4 AuthorsDavid Marshall20
Estimated H-index: 20
(Scottish Crop Research Institute)
Summary: Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bi...
426 Citations Source Cite
Published on Jan 1, 2010in Cancer Cell 22.84
Roel G W Verhaak3
Estimated H-index: 3
(Harvard University),
Katherine A. Hoadley54
Estimated H-index: 54
(University of North Carolina at Chapel Hill)
+ 30 AuthorsJill P. Mesirov71
Estimated H-index: 71
(Harvard University)
Summary The Cancer Genome Atlas Network recently cataloged recurrent genomic abnormalities in glioblastoma multiforme (GBM). We describe a robust gene expression-based molecular classification of GBM into Proneural, Neural, Classical, and Mesenchymal subtypes and integrate multidimensional genomic data to establish patterns of somatic mutations and DNA copy number. Aberrations and gene expression of EGFR , NF1 , and PDGFRA/IDH1 each define the Classical, Mesenchymal, and Proneural subtypes, resp...
3,279 Citations Source Cite
Published on Oct 1, 2009in Bioinformatics 5.48
John W. Nicol2
Estimated H-index: 2
(University of North Carolina at Charlotte),
Gregg A. Helt1
Estimated H-index: 1
(University of North Carolina at Charlotte)
+ 2 AuthorsAnn E. Loraine24
Estimated H-index: 24
(University of North Carolina at Charlotte)
Summary: Experimental techniques that survey an entire genome demand flexible, highly interactive visualization tools that can display new data alongside foundation datasets, such as reference gene annotations. The Integrated Genome Browser (IGB) aims to meet this need. IGB is an open source, desktop graphical display tool implemented in Java that supports real-time zooming and panning through a genome; layout of genomic features and datasets in moveable, adjustable tiers; incremental or genome-...
445 Citations Source Cite
Published on Jun 15, 2009in Bioinformatics 5.48
Hua Bao11
Estimated H-index: 11
(Sun Yat-sen University),
Hui Guo18
Estimated H-index: 18
(Sun Yat-sen University)
+ 3 AuthorsSuhua Shi29
Estimated H-index: 29
(Sun Yat-sen University)
Summary: We introduce a new visual analytics tool named MapView to facilitate the representation of large-scale short reads alignment data and genetic variation analysis. MapView can handle hundreds of millions of short reads on a desktop computer with limited memory. It supports a compact alignment view for both single-end and paired end short reads, multiple navigation and zoom modes and multithread processing. Moreover, MapView offers automated genetic variation detection. MapView has been us...
70 Citations Source Cite
Published on Mar 1, 2009in Nature 41.58
Mitchell Guttman36
Estimated H-index: 36
(Broad Institute),
Ido Amit51
Estimated H-index: 51
(Broad Institute)
+ 17 AuthorsJohn P. Cassady15
Estimated H-index: 15
(Massachusetts Institute of Technology)
There is growing recognition that mammalian cells produce many thousands of large intergenic transcripts. However, the functional significance of these transcripts has been particularly controversial. Although there are some well-characterized examples, most (>95%) show little evidence of evolutionary conservation and have been suggested to represent transcriptional noise. Here we report a new approach to identifying large non-coding RNAs using chromatin-state maps to discover discrete transcrip...
2,391 Citations Source Cite
Published on Oct 23, 2008in Nature 41.58
Roger E. McLendon90
Estimated H-index: 90
(Duke University),
Allan H. Friedman87
Estimated H-index: 87
(Duke University)
+ 228 AuthorsKenneth Aldape8
Estimated H-index: 8
(University of Texas MD Anderson Cancer Center)
Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas ( TCGA) pilot project aims to assess the value of large- scale multi- dimensional analysis of these molecular characteristics in human cancer and to provide the data rapidly to the research community. Here we report the interim integrative analysis of DNA copy number, gene expression and DNA methylation aberratio...
4,365 Citations Source Cite
Cited By3987
Newest
Published on Mar 20, 2019in Scientific Reports 4.12
Brett W. Stringer15
Estimated H-index: 15
(QIMR Berghofer Medical Research Institute),
Bryan W. Day16
Estimated H-index: 16
(QIMR Berghofer Medical Research Institute)
+ 19 AuthorsSeçkin Akgül (QIMR Berghofer Medical Research Institute)
Low-passage, serum-free cell lines cultured from patient tumour tissue are the gold-standard for preclinical studies and cellular investigations of glioblastoma (GBM) biology, yet entrenched, poorly-representative cell line models are still widely used, compromising the significance of much GBM research. We submit that greater adoption of these critical resources will be promoted by the provision of a suitably-sized, meaningfully-described reference collection along with appropriate tools for wo...
Source Cite
Published on Apr 17, 2019in Nature Communications 12.35
David Sala3
Estimated H-index: 3
(Discovery Institute),
Thomas J. Cunningham14
Estimated H-index: 14
(Discovery Institute)
+ 7 AuthorsAlessandra Sacco13
Estimated H-index: 13
(Discovery Institute)
Metabolic reprogramming is an active regulator of stem cell fate choices, and successful stem cell differentiation in different compartments requires the induction of oxidative phosphorylation. However, the mechanisms that promote mitochondrial respiration during stem cell differentiation are poorly understood. Here we demonstrate that Stat3 promotes muscle stem cell myogenic lineage progression by stimulating mitochondrial respiration in mice. We identify Fam3a, a cytokine-like protein, as a ma...
Source Cite
Published on Mar 19, 2019in Nature Communications 12.35
Ashot S. Harutyunyan2
Estimated H-index: 2
(McGill University),
Brian Krug1
Estimated H-index: 1
(McGill University)
+ 30 AuthorsLeonie G. Mikael5
Estimated H-index: 5
(McGill University)
Lys-27-Met mutations in histone 3 genes (H3K27M) characterize a subgroup of deadly gliomas and decrease genome-wide H3K27 trimethylation. Here we use primary H3K27M tumor lines and isogenic CRISPR-edited controls to assess H3K27M effects in vitro and in vivo. We find that whereas H3K27me3 and H3K27me2 are normally deposited by PRC2 across broad regions, their deposition is severely reduced in H3.3K27M cells. H3K27me3 is unable to spread from large unmethylated CpG islands, while H3K27me2 can be ...
2 Citations Source Cite
Published on Apr 29, 2019in Genome Biology 13.21
Daryl M. Gohl13
Estimated H-index: 13
(University of Minnesota),
Alessandro Magli10
Estimated H-index: 10
(University of Minnesota)
+ 8 AuthorsShana L. McDevitt (University of California)
Quantification of DNA sequence tags from engineered constructs such as plasmids, transposons, or other transgenes underlies many functional genomics measurements. Typically, such measurements rely on PCR followed by next-generation sequencing. However, PCR amplification can introduce significant quantitative error. We describe REcount, a novel PCR-free direct counting method. Comparing measurements of defined plasmid pools to droplet digital PCR data demonstrates that REcount is highly accurate ...
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Published on May 13, 2019in Nature Communications 12.35
Maha R. Farhat13
Estimated H-index: 13
(Harvard University),
Luca Freschi1
Estimated H-index: 1
(Harvard University)
+ 12 AuthorsDevinder Kaur8
Estimated H-index: 8
(University of Massachusetts Medical School)
Drug resistance diagnostics that rely on the detection of resistance-related mutations could expedite patient care and TB eradication. We perform minimum inhibitory concentration testing for 12 anti-TB drugs together with Illumina whole-genome sequencing on 1452 clinical Mycobacterium tuberculosis (MTB) isolates. We evaluate genome-wide associations between mutations in MTB genes or non-coding regions and resistance, followed by validation in an independent data set of 792 patient isolates. We c...
Source Cite
Published on May 10, 2019in BMC Cancer 3.29
Bernt Popp11
Estimated H-index: 11
(University of Erlangen-Nuremberg),
Abbas Agaimy35
Estimated H-index: 35
(University of Erlangen-Nuremberg)
+ 6 AuthorsChristiane Zweier33
Estimated H-index: 33
(University of Erlangen-Nuremberg)
Background Several subunits of the SWI/SNF chromatin remodeling complex are implicated in both cancer and neurodevelopmental disorders (NDD). Though there is no clinical evidence for an increased tumor risk in individuals with NDDs due to germline mutations in most of these genes so far, this has been repeatedly proposed and discussed. A young woman with NDD due to a de novo mutation in ARID1B now presented with a large renal (> 19 cm in diameter) and multiple hepatic angiomyolipomas (AMLs) but ...
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Published on Apr 23, 2019in Nature Communications 12.35
Alessandro Pastore13
Estimated H-index: 13
(Memorial Sloan Kettering Cancer Center),
Federico Gaiti5
Estimated H-index: 5
(Cornell University)
+ 20 AuthorsWendy Béguelin11
Estimated H-index: 11
(Cornell University)
Cancer evolution is fueled by epigenetic as well as genetic diversity. In chronic lymphocytic leukemia (CLL), intra-tumoral DNA methylation (DNAme) heterogeneity empowers evolution. Here, to comprehensively study the epigenetic dimension of cancer evolution, we integrate DNAme analysis with histone modification mapping and single cell analyses of RNA expression and DNAme in 22 primary CLL and 13 healthy donor B lymphocyte samples. Our data reveal corrupted coherence across different layers of th...
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Published on Feb 14, 2019in Nature Communications 12.35
Daniel P. Depledge12
Estimated H-index: 12
(New York University),
Kalanghad Puthankalam Srinivas1
Estimated H-index: 1
(New York University)
+ 5 AuthorsAngus C. Wilson13
Estimated H-index: 13
(New York University)
Characterizing complex viral transcriptomes by conventional RNA sequencing approaches is complicated by high gene density, overlapping reading frames, and complex splicing patterns. Direct RNA sequencing (direct RNA-seq) using nanopore arrays offers an exciting alternative whereby individual polyadenylated RNAs are sequenced directly, without the recoding and amplification biases inherent to other sequencing methodologies. Here we use direct RNA-seq to profile the herpes simplex virus type 1 (HS...
3 Citations Source Cite