Journal ArticleDOI
Sequencing depth and coverage: key considerations in genomic analyses
TLDR
The issue of sequencing depth in the design of next-generation sequencing experiments is discussed and current guidelines and precedents on the issue of coverage are reviewed for four major study designs, including de novo genome sequencing, genome resequencing, transcriptome sequencing and genomic location analyses.Abstract:
Sequencing technologies have placed a wide range of genomic analyses within the capabilities of many laboratories. However, sequencing costs often set limits to the amount of sequences that can be generated and, consequently, the biological outcomes that can be achieved from an experimental design. In this Review, we discuss the issue of sequencing depth in the design of next-generation sequencing experiments. We review current guidelines and precedents on the issue of coverage, as well as their underlying considerations, for four major study designs, which include de novo genome sequencing, genome resequencing, transcriptome sequencing and genomic location analyses (for example, chromatin immunoprecipitation followed by sequencing (ChIP-seq) and chromosome conformation capture (3C)).read more
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Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering.
Yuan You,Aneta Sawikowska,Manuela Neumann,David Posé,Giovanna Capovilla,Tobias Langenecker,Richard A. Neher,Paweł Krajewski,Markus Schmid,Markus Schmid +9 more
TL;DR: The results suggest that regulation of translation might be involved in adjusting meristem function during the induction of flowering, and the importance of tissue-specific epigenomic analyses is emphasized.
Journal ArticleDOI
Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins
Christian Hauer,Jana Sieber,Thomas Schwarzl,Ina Hollerer,Ina Hollerer,Ina Hollerer,Tomaz Curk,Anne-Marie Alleaume,Matthias W. Hentze,Matthias W. Hentze,Andreas E. Kulozik,Andreas E. Kulozik +11 more
TL;DR: Analysis of bona fide EJC binding sites across the transcriptome including all four RNA binding EJC components eIF4A3, BTZ, UPF3B, and RNPS1 shows that EJCs are largely distributed across spliced RNAs in an orthodox fashion, with two notable exceptions.
Journal ArticleDOI
Clinical Actionability of Comprehensive Genomic Profiling for Management of Rare or Refractory Cancers
Kim M. Hirshfield,Denis Tolkunov,Hua Zhong,Siraj M. Ali,Mark N. Stein,Susan Murphy,Hetal Vig,Alexei Vazquez,John Glod,Rebecca A. Moss,Vladimir Belyi,Chang S. Chan,Suzie Chen,Lauri Goodell,David J. Foran,Roman Yelensky,Norma Alonzo Palma,James Sun,Vincent A. Miller,Philip J. Stephens,Jeffrey S. Ross,Jeffrey S. Ross,Howard L. Kaufman,Elizabeth Poplin,Janice M. Mehnert,Antoinette R. Tan,Joseph R. Bertino,Joseph Aisner,Robert S. DiPaola,Lorna Rodriguez-Rodriguez,Shridar Ganesan +30 more
TL;DR: Comprehensive profiling led to implementable clinical action in 35% of tumors with genomic alterations, and utility, feasibility, and limitations of genomic sequencing for genomically guided therapy or other clinical purpose in the setting of a multidisciplinary molecular tumor board.
Journal ArticleDOI
Beyond genomics: understanding exposotypes through metabolomics.
Nicholas J. W. Rattray,Nicole C. Deziel,Joshua D. Wallach,Sajid A. Khan,Vasilis Vasiliou,John P. A. Ioannidis,Caroline H. Johnson +6 more
TL;DR: The evolution and challenges of metabolomics in epidemiologic research, particularly for assessing environmental exposures and providing insights into gene-environment interactions, and mechanism of biological impact are discussed.
Journal ArticleDOI
RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples
Petr V. Nazarov,Arnaud Muller,Tony Kaoma,Nathalie Nicot,Cristina Maximo,Philippe Birembaut,Nhan L. Tran,Gunnar Dittmar,Laurent Vallar +8 more
TL;DR: It is concluded that modern microarrays can still outperform sequencing for standard analysis of gene expression in terms of reproducibility and cost.
References
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI
Differential expression analysis for sequence count data.
Simon Anders,Wolfgang Huber +1 more
TL;DR: A method based on the negative binomial distribution, with variance and mean linked by local regression, is proposed and an implementation, DESeq, as an R/Bioconductor package is presented.
Journal ArticleDOI
RNA-Seq: a revolutionary tool for transcriptomics
TL;DR: The RNA-Seq approach to transcriptome profiling that uses deep-sequencing technologies provides a far more precise measurement of levels of transcripts and their isoforms than other methods.
Journal ArticleDOI
TopHat: discovering splice junctions with RNA-Seq
TL;DR: The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer.