The Possibility of Systematic Research Fraud Targeting Under-Studied Human Genes: Causes, Consequences, and Potential Solutions

Abstract

A major reason for biomarker failure is the selection of candidate biomarkers based on inaccurate or incorrect published results. Incorrect research results leading to the selection of unproductive biomarker candidates are largely considered to stem from unintentional research errors. The additional possibility that biomarker research may be actively misdirected by research fraud has been given comparatively little consideration. This review discusses what we believe to be a new threat to biomarker research, namely, the possible systematic production of fraudulent gene knockdown studies that target under-studied human genes. We describe how fraudulent papers may be produced in series by paper mills using what we have described as a 'theme and variations' model, which could also be considered a form of salami slicing. We describe features of these single-gene knockdown publications that may allow them to evade detection by journal editors, peer reviewers, and readers. We then propose a number of approaches to facilitate their detection, including improved awareness of the features of publications constructed in series, broader requirements to post submitted manuscripts to preprint servers, and the use of semi-automated literature screening tools. These approaches may collectively improve the detection of fraudulent studies that might otherwise impede future biomarker research.

Keywords: Biomarkers; cancer; gene knockdown techniques; paper mill; research fraud; salami publication; under-studied gene.

Figure 1.

Five phases of biomarker development, shown as the biomarker research pipeline, adapted from Pepe et al. The number of biomarker candidates within the pipeline (shown above the phase diagram) progressively reduces as candidate biomarkers are sequentially analysed, and a proportion of candidates are discarded. At the same time, the resources required to advance each candidate progressively increase (shown below the phase diagram). The selection of unproductive candidates at phase 1 may prevent more productive candidates from entering the pipeline.

Figure 2.

Diagrammatic representation showing how the availability of research studies that support candidate genes can influence their selection to enter the biomarker research pipeline (phase 1, see Figure 1). Five genes (A-E) are shown. Genes A, B, D, and E are connected to functional studies (surrounding symbols) that support that gene as a candidate biomarker within a particular cancer type. Functional studies performed in different cancer types are shown as distinct symbols, with black symbols denoting bona fide published studies and purple symbols denoting fraudulent published studies. Without an understanding that genes B and E have been systematically targeted for the fraudulent production of manuscripts in series, genes B and E appear to be the best biomarker candidates and would be most likely to be selected for further biomarker studies. This decision could exclude genes A and D, which are supported by bona fide research, and which could in fact represent superior candidates.

Figure 3.

Summary of the conserved series of experimental results shown in 5 TPD52L2 knockdown studies,^– 4 of which have been retracted from the literature.^– The order of conserved figures is shown vertically and figure panels within each figure are shown horizontally. The data that were shown (upper panels) and the purpose of the experiments (lower panels) are described for each individual figure panel.

Figure 4.

Incorrectly identified short hairpin RNA (shRNA) sequences that were described in TPD52L2 knockdown studies^– and other single-gene knockdown publications. Nucleotide sequences are shown 5ʹ-3ʹ. Nucleotides that are identical to their indicated target according to blastn search results are underlined. (A) TPD52L2 shRNA, correctly used as a targeting sequence^,,, and incorrectly used as a non-targeting sequence.^,, (B) NOB1 shRNA, incorrectly used as a non-targeting sequence.^,,

Figure 5.

Overview of the proposed key features of the construction of fraudulent manuscript series by paper mills using a ‘theme and variations’ approach. The ‘theme’ shown is an under-studied human gene which is examined in different cancer types to produce a number of manuscript ‘variations’. The existence of thousands of under-studied human genes means that this process could be repeated many times to produce large numbers of fraudulent manuscripts and ultimately publications.