From Penguins to Frogs: The new frontier of wildlife microbiomes

With recent technological advances in DNA sequencing investigating microbiomes from all areas of life has become possible as PLOS ONE Publication Assistant Maija Mallula finds out. With the advancement of DNA sequencing technology, our ability

The PLOS ONE Early Career Researcher Travel Awards in the Physical Sciences

Early career researchers (ECRs) are very much at the heart of what we do at PLOS. Last year alone, PLOS ONE published more than 20,000 research papers, undoubtedly with tens of thousands of ECRs as

PLOS ONE partners with the Children’s Tumor Foundation to trial Registered Reports

Today, the Children’s Tumor Foundation and PLOS ONE are pleased to announce a partnership to trial the integration of Registered Reports in the grant application and publication process:   The Children’s Tumor Foundation (CTF) and

Meta-Analyses of Genetic Association Studies – PLOS ONE’s Approach

Meta-analysis can be a powerful way to reveal otherwise hidden or unclear associations, when done with care. In line with recent trends in biomedical literature (1), PLOS ONE has seen a consistent increase in submissions reporting meta-analyses of genetic association studies over the last few years. These submissions report analyses of potential associations between candidate gene variants (usually single nucleotide polymorphisms, or SNPs) and specific disease risks and outcomes in human populations, based on a search of the literature to identify published reports studying the association and statistical analyses that synthesize the results of the identified studies.

However, researchers in the community, among them members of our editorial board, have raised concerns about some of these meta-analyses, including the risk of false positives due to publication bias, incomplete searches of the literature, redundancy, and an insufficient assessment of the power and quality of the included studies. As noted a decade ago, “Meta-analysis is not a replacement for adequately powered genetic association studies” (2).  Many of these studies focus on a single gene variant, and many do not include data from relevant genome-wide association  studies (GWAS), some of which have failed to replicate previously reported associations between candidate genes and diseases.

While many meta-analyses of genetic association studies are still clinically relevant, especially those studying rare conditions where GWAS data are not available, and well-conducted meta-analyses can provide useful and valid clinical evidence, we strongly feel that meta-analyses of genetic association studies considered by PLOS ONE must have the rationale clearly explained and that authors must report their studies according to high standards.

In order to address these concerns and after consultation with PLOS ONE editorial board members, we are introducing a new process to handle meta-analyses of genetic association studies. Authors will now be asked to provide the following information:

  1. The rationale for conducting the meta-analysis;
  2. The contribution that the meta-analysis makes to knowledge in light of previously published related reports, including other meta-analyses and systematic reviews;
  3. Whether GWASs relevant to the meta-analysis have been published and whether these were included in the analysis;
  4. Full methodological details for the meta-analysis, including completion of a checklist that has been developed with reference to several published guidelines (3, 4, 5) and in consultation with members of the PLOS ONE editorial board.

The information supplied by the authors will be evaluated by the in-house editorial team as part of the checks undertaken on new submissions. Meta-analyses replicating studies in the literature without adequate justification will be rejected. For those manuscripts that proceed to review, PLOS ONE Academic Editors will be consulted on the adequacy of the methodological aspects of the study and the quality of the reporting in the manuscript.

This process underscores our commitment to maintaining high standards of quality and reporting in publications at PLOS ONE. We are grateful for the input we have received from our editorial board that led to this new process, and wish to thank the PLOS ONE Academic Editors who provided advice and guidance.

If you have any questions or feedback, or if you are an author who would like additional information about our requirements for meta-analyses of genetic association studies, please contact us at plosone@plos.org.

Posted on behalf of the in-house editors at PLOS ONE:

Associate Editors Gina Alvino, Meghan Byrne, Christna Chap, Michelle Dohm, Matt Hodgkinson, Alejandra Clark and Nicola Stead and; Senior Editors Eric Martens and Iratxe Puebla; and Editorial Director Damian Pattinson

  1. Ioannidis JPA, Chang CQ, Lam TK, Schully SD, Khoury MJ (2013) The Geometric Increase in Meta-Analyses from China in the Genomic Era. PLOS ONE 8(6): e65602. doi:10.1371/journal.pone.0065602
  2. Marcus R. Munafò and Jonathan Flint (2004) Meta-analysis of genetic association studies. Trends Genet. 20(9):439-44 doi:10.1016/j.tig.2004.06.014
  3. Sagoo GS, Little J, Higgins JPT (2009) Systematic Reviews of Genetic Association Studies. PLOS Med 6(3): e1000028. doi:10.1371/journal.pmed.1000028
  4. Minelli C, Thompson JR, Abrams KR, Thakkinstian A, Attia J: The quality of meta-analyses of genetic association studies: a review with recommendations. Am J Epidemiol. 2009 Dec 1;170(11):1333-43. doi: 10.1093/aje/kwp350
  5. Little J, Higgins JP, Ioannidis JP, Moher D, Gagnon F, et al. (2009) STrengthening the REporting of Genetic Association Studies (STREGA)- An Extension of the STROBE Statement. PLOS Med 6(2): e1000022. doi:10.1371/journal.pmed.1000022

The post Meta-Analyses of Genetic Association Studies – PLOS ONE’s Approach appeared first on EveryONE.

Editorial Highlight: Reporting Standards at PLOS ONE

 PLOS ONE bug

Most readers are by now familiar with the core principle behind PLOS ONE: to publish all papers that are scientifically and technically sound, regardless of their perceived impact or importance. Another publication criterion that has received far less attention until recently is our commitment to the quality and completeness of reporting.

PLOS ONE considers reporting quality to be of importance in two main areas: first in relation to completeness of authors’ descriptions of study methods and results, and second in assuring readers of the ethical basis underlying the work. The rationale for ensuring high standards of reporting and ethical oversight is aligned with our core mission to facilitate the re-use of open-access research; if studies aren’t reported appropriately, or don’t have the necessary ethical oversight, it is much more difficult for others to replicate the work or incorporate the data as part of a larger study.

The natural follow-up question might be: how do we as a journal maintain these standards? Here, we’d like to outline briefly our standards, the reasons for them, and the process for ensuring that authors adhere to them. By doing this, we hope to shed light on some of our internal processes, both for the journal’s community, as well as for interested readers that appreciate sound, well-done science as much as we do.

PLOS ONE is a large, international, open-access scientific journal that considers all manuscripts reporting the results of primary scientific research. Day to day, the journal receives many types of studies, including experimental and observational work on animal and human populations, as well as a range of computational and theoretical work. These are submitted by researchers around the world who are not necessarily bound by common standards of reporting or ethical oversight.

As an international journal, however, PLOS ONE has a responsibility to establish and maintain consistent and high standards for publication. Therefore, we require that authors assure us on submission of appropriate ethical review and approval for experimental work involving animals and human participants; relevant permissions for field studies or observational work; and adherence to appropriate discipline-specific guidelines for the reporting of taxonomic, paleontological, or archaeological specimens. In some areas, there are also more prescriptive guidelines to ensure the full description of study methods and results—including CONSORT for reporting randomized clinical trials and PRISMA for reporting systematic reviews in relation to human participants—and we provide links to many more in our manuscript guidelines.

How do journal staff check for these standards when we receive so many submissions each day? At PLOS ONE, we’ve found that the most effective way to ensure papers meet our requirements is to perform a series of checks at submission. This ensures that by the time articles are assigned to Academic Editors for detailed review, crucial information about ethical oversight and study conduct will be available for their consideration. By screening papers before the formal peer-review process, we provide support to our Editorial Board and reviewers, who volunteer their time and offer an invaluable service to the journal and the scientific community as a whole. Equipping our Academic Editors with additional, important details when they agree to handle a manuscript allows them to focus their specialized expertise where it is most valued: on the scientific and technical quality of the paper.

That said, we consider our Academic Editors as partners in our goal of maintaining high standards for reporting, research ethics, and integrity. We ask our Editorial Board members for advice in difficult situations, and greatly appreciate the expert input that they provide. In certain situations we seek the advice of additional experts in reporting or ethics to provide oversight on specific papers, and are currently setting up dedicated advisory boards to assist us. We also consult Editorial Board members when developing new internal policies, or when robust community guidelines (such as CONSORT for randomized clinical trials or the proposed ARRIVE for experimental animal research) are not yet available for specific study types.

We appreciate the support of PLOS ONE authors, editors, and reviewers in helping us maintain the highest standards possible.

Posted on behalf of the in-house editors at PLOS ONE:

Associate Editors Gina Alvino, Sarah Bangs, Meghan Byrne, Christna Chap, Michelle Dohm, Matt Hodgkinson, Anna Schmidt, and Elizabeth Silva; Senior Editors Eric Martens and Emma Veitch; Consulting Editors Catriona MacCallum and Iratxe Puebla; and Editorial Director Damian Pattinson

Hurricane Sandy and PLOS ONE

On Monday evening, Hurricane Sandy brought destruction to the Mid-Atlantic and Northeast regions of the United States, leaving much of the area without water, electricity, and other basic amenities. In light of the ongoing effects of the damage, PLOS ONE would like to express our deepest sympathies for those dealing with the impacts of the storm and send our best wishes for the recovery efforts.

For our authors who may be waiting for your manuscript to be handled, please note that submissions may be delayed in their review as many of our Editors and reviewers are based in these regions. We appreciate your patience and understanding.

 

Sincerely,

PLOS ONE Staff

New animal species now official when published online

The International Commission for Zoological Nomenclature (ICZN), the body that regulates animal species names, took a big step earlier this week when it announced that electronic publication of a new species name is now sufficient to make that name official.

Prior to the announcement, the ICZN code stated that a new species name only became official once it was printed. The stipulation was intended to ensure that records of species names were securely archived and would remain accessible over the long term, but for an online-only publisher like PLOS, it meant that we had to print and store physical copies of each paper describing a new species in addition to our standard online publication. To put this in perspective, PLOS ONE published 25 papers presenting new animal species in 2011, and has already published 32 in 2012, including the tiny Brookesia chameleons pictured at the top of this post, so this additional printing and archiving is not trivial.

Now, though, the Commission has decided to adjust their standards in response to today’s increasingly electronic environment. According to the ICZN press release about the updated rules, the change “is intended to speed the process of publishing biodiversity information, to improve access to this information, and to help reduce the ‘taxonomic impediment’ that hinders our cataloguing of the living world.”

It won’t be a free-for-all: new species names must be published in journals or books with ISSNs or ISBNs, so purely web options like blogs or Wikipedia are not sufficient, and before publication authors must register their name with ZooBank, the official ICZN online registry for scientific names of animals. Overall, though, the hope is to reduce the barriers to proper nomenclature monitoring and archiving. The updated code is also in line with similar recent changes to the regulations for naming new botanical species.

The update is part of a broader discussion around how to ensure long-term reliability and durability for any type of electronic records, and while this problem may not yet be robustly solved, we at PLOS ONE applaud the ICZN’s efforts to address the changing needs of today’s scientists.

Image citation: Glaw F, Köhler J, Townsend TM, Vences M (2012) Rivaling the World’s Smallest Reptiles: Discovery of Miniaturized and Microendemic New Species of Leaf Chameleons (Brookesia) from Northern Madagascar. PLoS ONE 7(2): e31314. doi:10.1371/journal.pone.0031314

Genetic Signatures of Exceptional Longevity Revisited

Today we published a paper titled “Genetic Signatures of Exceptional Longevity in Humans,” by lead researchers Paola Sebastiani and Thomas Perls of Boston University, which identifies genetic variants associated with exceptional longevity.

This paper is based on work originally reported in the journal Science in July 2010. The authors voluntarily retracted the Science paper in July 2011 due to various technical concerns, as detailed in the retraction notice:

After online publication of our report ‘Genetic Signatures of Exceptional Longevity in Humans’ (1) we discovered that technical errors in the Illumina 610 array and an inadequate quality control protocol introduced false positive single nucleotide polymorphisms (SNPs) in our findings. An independent laboratory subsequently performed stringent quality control measures, ambiguous SNPs were then removed, and resultant genotype data were validated using an independent platform. We then reanalyzed the reduced data set using the same methodology as in the published paper. We feel the main scientific findings remain supported by the available data: (i) A model consisting of multiple specific SNPs accurately differentiates between centenarians and controls; (ii) genetic profiles cluster into specific signatures; and (iii) signatures are associated with ages of onset of specific age-related diseases and subjects with the oldest ages. However, the specific details of the new analysis change substantially from those originally published online to the point of becoming a new report. Therefore, we retract the original manuscript and will pursue alternative publication of the new findings.

The paper published today is the corrected and peer reviewed version of their findings, with additional authors who independently validated the data and methodology, as well as an additional sample of centenarians used for replication purposes. As stated in the retraction notice, the primary findings remain the same, but the SNPs incorrectly identified in the original study have been removed from the model for predicting longevity.

While we recognize that aspects of this study will attract attention owing to the history and the strong claims made in the paper, the handling editor, Greg Gibson, made the decision that publication is warranted, balancing the extensive peer review and the spirit of PLoS ONE to allow important new results and approaches to be available to the scientific community so long as scientific standards have been met.  We trust that publication will facilitate full evaluation of the study.

1. Sebastiani P, Solovieff N, Puca A, Hartley SW, Melista E, et al. Genetic Signatures of Exceptional Longevity in Humans. Science 10.1126/science.1190532 (2010).