Evidence map›Paper›PMID 27297499›Full record

ReviewProgress in retinal and eye research2016

Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research.

Vijender Chaitankar, Gökhan Karakülah, Rinki Ratnapriya, Felipe O Giuste, Matthew J Brooks, Anand Swaroop

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Progress in retinal and eye research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.

0numbers the graph read from it
0cells of the map it votes in
37citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

37 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Vijender ChaitankarNeurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA.
Gökhan KarakülahNeurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA.
Rinki RatnapriyaNeurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA.
Felipe O GiusteNeurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA.
Matthew J BrooksNeurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA.
Anand SwaroopNeurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA. Electronic address: swaroopa@nei.nih.gov.

Funding

Regulation of retinal developmentZIAEY000450 · NEI · NATIONAL EYE INSTITUTE · PI SWAROOP, ANAND · 2009 to 2025
$71.0M
Mechanisms, modeling and therapies of retinal and macular neurodegenerationZIAEY000546 · NEI · NATIONAL EYE INSTITUTE · PI SWAROOP, ANAND · 2015 to 2025
$36.3M
Interventional approaches for restoring visionZIAEY000474 · NEI · NATIONAL EYE INSTITUTE · PI SWAROOP, ANAND · 2009 to 2019
$15.5M
Intramural NIH HHS ZIA EY000450Intramural NIH HHS ZIA EY000474Intramural NIH HHS ZIA EY000546
6 · The paper itself

Abstract

The advent of high throughput next generation sequencing (NGS) has accelerated the pace of discovery of disease-associated genetic variants and genomewide profiling of expressed sequences and epigenetic marks, thereby permitting systems-based analyses of ocular development and disease. Rapid evolution of NGS and associated methodologies presents significant challenges in acquisition, management, and analysis of large data sets and for extracting biologically or clinically relevant information. Here we illustrate the basic design of commonly used NGS-based methods, specifically whole exome sequencing, transcriptome, and epigenome profiling, and provide recommendations for data analyses. We briefly discuss systems biology approaches for integrating multiple data sets to elucidate gene regulatory or disease networks. While we provide examples from the retina, the NGS guidelines reviewed here are applicable to other tissues/cell types as well.

Indexed as

Genome-Wide Association StudyComputational BiologyGenomicsHigh-Throughput Nucleotide SequencingHumansRetinal DiseasesChIP-seqChromatinEpigeneticsGene regulatory networkGenomicsHigh throughput dataNetwork analysisNGS data integrationPhotoreceptorRetinaRetinal diseaseRNA-SeqSystems biologyTranscriptomeVisionWhole exome sequencingWhole genome sequencing

Identifiers

PMID27297499
PMCPMC5112143

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.