Improving the reliability of peer-reviewed publications: We are all in it together

Abstract

The current, and welcome, focus on standardization of techniques and transparency of reporting in the biomedical, peer-reviewed literature is commendable. However, that focus has been intermittent as well as lacklustre and so failed to tackle the alarming lack of reliability and reproducibly of biomedical research. Authors have access to numerous recommendations, ranging from simple standards dealing with technical issues to those regulating clinical trials, suggesting that improved reporting guidelines are not the solution. The elemental solution is for editors to require meticulous implementation of their journals' instructions for authors and reviewers and stipulate that no paper is published without a transparent, complete and accurate materials and methods section.

Keywords: Biomedicine; Microarrays; Next generation sequencing; Reproducibility; Research; qPCR.

Fig. 1

Comparison of a dualplex qPCR assay targeting Candida dublinensis or Candida glabrata. (1) A PCRmax Eco (http://www.pcrmax.com) was used to amplify 100 pg of C. glabrata (A) and C. dublinensis (B) and DNA. Four replicate reactions were run of 5 μl each using Agilents’s Brilliant III qPCR mastermix, with PCR amplicons detected using FAM-(C. glabrata, A, blue)- or HEX-(C. dublinensis, B, pink) labelled hydrolysis probes. The assays are 98% and 97% efficient, respectively. (2) Plots of the two assays recording average Cqs of 25.16 ± 0.19 and 25.44 ± 0.19 for C. glabrata and C. dublinensis, respectively (Mean ± SD). (3) Conditions as described for 1, except that the replicates contained 1.5 pg of each of the fungal DNAs. (4) Plot of the two assays recording average Cqs of 31.14 ± 0.09 and 33.73 ± 1.64 for C. glabrata and C. dublinensis, respectively (Mean ± SD).

Fig. 2

Analysis of ten papers published in Cell , , Cell Stem Cell , , Cancer Cell , , and Molecular Cell , , between June and November 2015. Materials and methods and supplementary sections were screened for information on seven key parameters required to assess the technical validity of RT-qPCR assays, detailed on the x-axis. The number of papers reporting any one of these parameters are shown on the left hand y-axis. The right hand y-axis shows the number of supplemental pages published with each of the ten papers. The one paper using two reference genes (RG) uses both one and two RG in different experiments without explicit validation of the stability of these targets, either alone or in combination.