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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Targeted capture in evolutionary and ecological genomics
Matthew R. Jones,Jeffrey M. Good +1 more
TL;DR: This work aims to increase the accessibility of targeted capture to researchers working in nonmodel taxa by discussing capture methods that circumvent the need of a reference genome, and highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy.
Journal ArticleDOI
Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.
TL;DR: This work has updated maSigPro to support RNA-seq time series analysis by introducing generalized linear models in the algorithm to support the modeling of count data while maintaining the traditional functionalities of the package.
Journal ArticleDOI
Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference
Aaron B. A. Shafer,Aaron B. A. Shafer,Claire R. Peart,Sergio Tusso,Inbar Maayan,Alan Brelsford,Christopher W. Wheat,Jochen B. W. Wolf,Jochen B. W. Wolf +8 more
TL;DR: It is recommended that RAD‐seq studies employ reference‐based approaches to a closely related genome, and due to the high stochasticity associated with the pipeline advocate the use of multiple pipelines to ensure robust population genetic and demographic inferences.
Journal ArticleDOI
Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases.
Oscar Franzén,Raili Ermel,Raili Ermel,Ariella Cohain,Nicholas K. Akers,Antonio Fabio Di Narzo,Husain A. Talukdar,Hassan Foroughi-Asl,Claudia Giambartolomei,John F. Fullard,Katyayani Sukhavasi,Sulev Kõks,Li-Ming Gan,Chiara Giannarelli,Jason C. Kovacic,Christer Betsholtz,Bojan Losic,Tom Michoel,Ke Hao,Panos Roussos,Panos Roussos,Josefin Skogsberg,Arno Ruusalepp,Arno Ruusalepp,Eric E. Schadt,Johan Björkegren +25 more
TL;DR: Gene expression traits associated with CMD risk single-nucleotide polymorphism (SNPs) identified by GWAS were more extensively found in STARNET than in tissue- and disease-unspecific gene-tissue expression studies, indicating sharing of downstream cis-/trans-gene regulation across tissues and CMDs.
Journal ArticleDOI
Implementing TMB measurement in clinical practice: considerations on assay requirements
Reinhard Büttner,John W. Longshore,Fernando Lopez-Rios,Sabine Merkelbach-Bruse,Nicola Normanno,Etienne Rouleau,Frédérique Penault-Llorca +6 more
TL;DR: The factors for adoption of TMB measurement into clinical practice are outlined, providing an understanding of T MB assay considerations throughout the sample journey, and principles to effectively implement TMB assays in a clinical setting are suggested to aid and optimise treatment decisions.
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.