RNA-Seq and human complex diseases: recent accomplishments and future perspectives

Costa, Valerio; Aprile, Marianna; Esposito, Roberta; Ciccodicola, Alfredo

doi:10.1038/ejhg.2012.129

Cited by 212 publications

(154 citation statements)

References 95 publications

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“…The application of RNA-seq to study non-model systems is still in its infancy, and care must be taken not to overlook its limitations in the rush to adopt the technology (Costa et al 2013;Todd et al 2016). In this section, we describe some of the experimental, analytical, and conceptual challenges raised specifically by the body of work described herein and highlight some avenues of future exploratory and confirmatory analyses.…”

Section: Challenges and Directions For Future Researchmentioning

confidence: 99%

“…In this section, we describe some of the experimental, analytical, and conceptual challenges raised specifically by the body of work described herein and highlight some avenues of future exploratory and confirmatory analyses. For further detail about technical and analytical issues surrounding RNA-seq experiments in general, we refer the reader to several discussions on the topic (Fang and Cui 2011;Ozsolak and Milos 2011;Sendler et al 2011;Costa et al 2013;Conesa et al 2016).…”

Section: Challenges and Directions For Future Researchmentioning

confidence: 99%

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Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing

Oomen

Hutchings

2017

FACETS

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The need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and that are predicted to be affected by climate change (e.g., salinity, temperature, dissolved oxygen concentration, and pH). Field and laboratory experiments demonstrate the potential for individuals to respond plastically to short-and long-term environmental stress and reveal molecular mechanisms underlying developmental and transgenerational plasticity, as well as adaptation to different environmental regimes. We discuss experimental, analytical, and conceptual issues that have arisen from this work and suggest avenues for future study.

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Section: Challenges and Directions For Future Researchmentioning

confidence: 99%

Section: Challenges and Directions For Future Researchmentioning

confidence: 99%

Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing

Oomen

Hutchings

2017

FACETS

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“…The majority of disease-associated single nucleotide polymorphisms (SNPs) detected in genome-wide association studies are located in non-coding regions of the genome (Freedman et al 2011). This indicates that these genetic variants might influence gene expression levels rather than protein function (Costa et al 2013). And indeed, by comparing gene expression profiles in healthy and diseased individuals we can get a better understanding of what parts of the genome are up-or downregulated during disease, or detect certain disease-causing alterations that might not be observed on a genomic level but can only be detected when looking at the expression of genes.…”

Section: Disease Studiesmentioning

confidence: 99%

Avian transcriptomics: opportunities and challenges

Jax

Kraus

2018

J Ornithol

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Recent developments in next-generation sequencing technologies have greatly facilitated the study of whole transcriptomes in model and non-model species. Studying the transcriptome and how it changes across a variety of biological conditions has had major implications for our understanding of how the genome is regulated in different contexts, and how to interpret adaptations and the phenotype of an organism. The aim of this review is to highlight the potential of these new technologies for the study of avian transcriptomics, and to summarise how transcriptomics has been applied in ornithology. A total of 81 peer-reviewed scientific articles that used transcriptomics to answer questions within a broad range of study areas in birds are used as examples throughout the review. We further provide a quick guide to highlight the most important points which need to be take into account when planning a transcriptomic study in birds, and discuss how researchers with little background in molecular biology can avoid potential pitfalls. Suggestions for further reading are supplied throughout. We also discuss possible future developments in the technology platforms used for ribonucleic acid sequencing. By summarising how these novel technologies can be used to answer questions that have long been asked by ornithologists, we hope to bridge the gap between traditional ornithology and genomics, and to stimulate more interdisciplinary research.

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“…Highthroughput techniques such as microarrays and next generation sequencing allow investigators to observe and compare the transcriptional landscapes of tumor cells in different biological states [13][14][15][16][17][18]. In this work, we integrated multiple gene expression data from several largescale breast cancer studies to improve the assessment of differential gene expression in breast tumor cells and to effectively increase statistical power.…”

Section: Statistical Analysis Of Gene Expression Datamentioning

confidence: 99%

Genome-Wide Gene Expression Analysis to Identify Epistatic Gene-Pairs Associated with Prognosis of Breast Cancer

Lin¹,

Hsu²

2015

A Concise Review of Molecular Pathology of Breast Cancer

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RNA-Seq and human complex diseases: recent accomplishments and future perspectives

Cited by 212 publications

References 95 publications

Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing

Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing

Avian transcriptomics: opportunities and challenges

Genome-Wide Gene Expression Analysis to Identify Epistatic Gene-Pairs Associated with Prognosis of Breast Cancer

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