Dataset Information

Reproducibility and replicability of rodent phenotyping in preclinical studies.

ABSTRACT: The scientific community is increasingly concerned with the proportion of published "discoveries" that are not replicated in subsequent studies. The field of rodent behavioral phenotyping was one of the first to raise this concern, and to relate it to other methodological issues: the complex interaction between genotype and environment; the definitions of behavioral constructs; and the use of laboratory mice and rats as model species for investigating human health and disease mechanisms. In January 2015, researchers from various disciplines gathered at Tel Aviv University to discuss these issues. The general consensus was that the issue is prevalent and of concern, and should be addressed at the statistical, methodological and policy levels, but is not so severe as to call into question the validity and the usefulness of model organisms as a whole. Well-organized community efforts, coupled with improved data and metadata sharing, have a key role in identifying specific problems and promoting effective solutions. Replicability is closely related to validity, may affect generalizability and translation of findings, and has important ethical implications.

SUBMITTER: Kafkafi N

PROVIDER: S-EPMC6071910 | biostudies-other | 2018 Apr

REPOSITORIES: biostudies-other

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Publications

Reproducibility and replicability of rodent phenotyping in preclinical studies.

Kafkafi Neri N Agassi Joseph J Chesler Elissa J EJ Crabbe John C JC Crusio Wim E WE Eilam David D Gerlai Robert R Golani Ilan I Gomez-Marin Alex A Heller Ruth R Iraqi Fuad F Jaljuli Iman I Karp Natasha A NA Morgan Hugh H Nicholson George G Pfaff Donald W DW Richter S Helene SH Stark Philip B PB Stiedl Oliver O Stodden Victoria V Tarantino Lisa M LM Tucci Valter V Valdar William W Williams Robert W RW Würbel Hanno H Benjamini Yoav Y

Neuroscience and biobehavioral reviews 20180131

The scientific community is increasingly concerned with the proportion of published "discoveries" that are not replicated in subsequent studies. The field of rodent behavioral phenotyping was one of the first to raise this concern, and to relate it to other methodological issues: the complex interaction between genotype and environment; the definitions of behavioral constructs; and the use of laboratory mice and rats as model species for investigating human health and disease mechanisms. In Janu ...[more]

PMID: 29357292

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Project description:There are increasing reports of plasma miRNAs as biomarkers of human disease but few standards in methodologic reporting, leading to inconsistent data. We systematically reviewed plasma miRNA studies published between July 2013-June 2014 to assess methodology. Six parameters were investigated: time to plasma extraction, methods of RNA extraction, type of miRNA, quantification, cycle threshold (Ct) setting, and methods of statistical analysis. We compared these data with a proposed standard methodologic technique. Beginning with initial screening for 380 miRNAs using microfluidic array technology and validation in an additional cohort of patients, we compared 11 miRNAs that exhibited differential expression between 16 patients with benign colorectal neoplasms (advanced adenomas) and 16 patients without any neoplasm (controls). Plasma was isolated immediately, 12, 24, 48, or 72 h following phlebotomy. miRNA was extracted using two different techniques (Trizol LS with pre-amplification or modified miRNeasy). We performed Taqman-based RT-PCR assays for the 11 miRNAs with subsequent analyses using a variable Ct setting or a fixed Ct set at 0.01, 0.03, 0.05, or 0.5. Assays were performed in duplicate by two different operators. RNU6 was the internal reference. Systematic review yielded 74 manuscripts meeting inclusion criteria. One manuscript (1.4%) documented all 6 methodological parameters, while < 5% of studies listed Ct setting. In our proposed standard technique, plasma extraction ?12 h provided consistent ?Ct. miRNeasy extraction yielded higher miRNA concentrations and fewer non-expressed miRNAs compared to Trizol LS (1/704 miRNAs [0.14%] vs 109/704 miRNAs [15%], not expressed, respectively). A fixed Ct bar setting of 0.03 yielded the most reproducible data, provided that <10% miRNA were non-expressed. There was no significant intra-operator variability. There was significant inter-operator variation using Trizol LS extraction, while this was negligible using modified miRNeasy. For standardized reporting, we recommend plasma extraction ? 12 h, using modified miRNeasy extraction and utilizing a 0.03 Ct.

Dataset Information

Reproducibility and replicability of rodent phenotyping in preclinical studies.

Publications

Reproducibility and replicability of rodent phenotyping in preclinical studies.

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