Evidence map›Paper›PMID 28696412›Full record

ArticleTranslational psychiatry2017

Whole-genome DNA methylation status associated with clinical PTSD measures of OIF/OEF veterans.

R Hammamieh, N Chakraborty, A Gautam, S Muhie, R Yang, D Donohue, R Kumar, B J Daigle, Y Zhang, D A Amara and 11 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Translational psychiatry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
37citing papers in PubMed, 1 pooled it
2.9field-weighted citation impact, top 8% of its field
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, 1 synthesis or guideline pooled it, 55 citations in OpenAlex.

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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

21 authors at 9 institutions in 1 country.

R HammamiehIntegrative Systems Biology, US Army Center for Environmental Health Research, Frederick, MD, USA.
N ChakrabortyUSACEHR, The Geneva Foundation, Frederick, MD, USA.
A GautamIntegrative Systems Biology, US Army Center for Environmental Health Research, Frederick, MD, USA.
S MuhieUSACEHR, The Geneva Foundation, Frederick, MD, USA.
R YangAdvanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
D DonohueUSACEHR, The Geneva Foundation, Frederick, MD, USA.
R KumarAdvanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
B J DaigleDepartments of Biological Sciences and Computer Science, The University of Memphis, Memphis, TN, USA.
Y ZhangSchool of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
D A AmaraSteven and Alexandra Cohen Veterans Center for the Study of Posttraumatic Stress and Traumatic Brain Injury, Department of Psychiatry, NYU School of Medicine, New York, NY, USA.
S-A MillerUSACEHR, The Geneva Foundation, Frederick, MD, USA.
S SrinivasanUSACEHR, The Geneva Foundation, Frederick, MD, USA.
J FloryDepartment of Psychiatry, Mount Sinai School of Medicine, James J Peters Veterans Administration Medical Center, Bronx, NY, USA.
R YehudaDepartment of Psychiatry, Mount Sinai School of Medicine, James J Peters Veterans Administration Medical Center, Bronx, NY, USA.
L PetzoldSchool of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
O M WolkowitzDepartment of Psychiatry, University of California San Francisco, San Francisco, CA, USA.
S H MellonDepartment of Ob/Gyn, Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA.
L HoodInstitute for Systems Biology, Seattle, WA, USA.
F J DoyleSchool of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
C MarmarSteven and Alexandra Cohen Veterans Center for the Study of Posttraumatic Stress and Traumatic Brain Injury, Department of Psychiatry, NYU School of Medicine, New York, NY, USA.
M JettIntegrative Systems Biology, US Army Center for Environmental Health Research, Frederick, MD, USA.
The Geneva Foundation · USCenter for Environmental Health · USHarvard University · USCohen Children's Medical Center · USFrederick National Laboratory for Cancer Research · USIcahn School of Medicine at Mount Sinai · USUniversity of California, San Francisco · USInstitute for Systems Biology · USUniversity of Memphis · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Emerging knowledge suggests that post-traumatic stress disorder (PTSD) pathophysiology is linked to the patients' epigenetic changes, but comprehensive studies examining genome-wide methylation have not been performed. In this study, we examined genome-wide DNA methylation in peripheral whole blood in combat veterans with and without PTSD to ascertain differentially methylated probes. Discovery was initially made in a training sample comprising 48 male Operation Enduring Freedom (OEF)/Operation Iraqi Freedom (OIF) veterans with PTSD and 51 age/ethnicity/gender-matched combat-exposed PTSD-negative controls. Agilent whole-genome array detected ~5600 differentially methylated CpG islands (CpGI) annotated to ~2800 differently methylated genes (DMGs). The majority (84.5%) of these CpGIs were hypermethylated in the PTSD cases. Functional analysis was performed using the DMGs encoding the promoter-bound CpGIs to identify networks related to PTSD. The identified networks were further validated by an independent test set comprising 31 PTSD+/29 PTSD- veterans. Targeted bisulfite sequencing was also used to confirm the methylation status of 20 DMGs shown to be highly perturbed in the training set. To improve the statistical power and mitigate the assay bias and batch effects, a union set combining both training and test set was assayed using a different platform from Illumina. The pathways curated from this analysis confirmed 65% of the pool of pathways mined from training and test sets. The results highlight the importance of assay methodology and use of independent samples for discovery and validation of differentially methylated genes mined from whole blood. Nonetheless, the current study demonstrates that several important epigenetically altered networks may distinguish combat-exposed veterans with and without PTSD.

Indexed as

DNA MethylationAdultAfghan Campaign 2001-CpG IslandsEpigenesis, GeneticHumansIraq War, 2003-2011MaleMiddle AgedPromoter Regions, GeneticStress Disorders, Post-TraumaticVeteransVeterans HealthYoung Adult

Identifiers

PMID28696412
PMCPMC5538114
OpenAlexW2734636077

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

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.