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Park Y, West RA, Pathmendra P, Favier B, Stoeger T, Capes-Davis A, Cabanac G, Labbé C, Byrne JA. Identification of human gene research articles with wrongly identified nucleotide sequences. Life Sci Alliance 2022; 5:e202101203. [PMID: 35022248 PMCID: PMC8807875 DOI: 10.26508/lsa.202101203] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 01/01/2023] Open
Abstract
Nucleotide sequence reagents underpin molecular techniques that have been applied across hundreds of thousands of publications. We have previously reported wrongly identified nucleotide sequence reagents in human research publications and described a semi-automated screening tool Seek & Blastn to fact-check their claimed status. We applied Seek & Blastn to screen >11,700 publications across five literature corpora, including all original publications in Gene from 2007 to 2018 and all original open-access publications in Oncology Reports from 2014 to 2018. After manually checking Seek & Blastn outputs for >3,400 human research articles, we identified 712 articles across 78 journals that described at least one wrongly identified nucleotide sequence. Verifying the claimed identities of >13,700 sequences highlighted 1,535 wrongly identified sequences, most of which were claimed targeting reagents for the analysis of 365 human protein-coding genes and 120 non-coding RNAs. The 712 problematic articles have received >17,000 citations, including citations by human clinical trials. Given our estimate that approximately one-quarter of problematic articles may misinform the future development of human therapies, urgent measures are required to address unreliable gene research articles.
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Affiliation(s)
- Yasunori Park
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Rachael A West
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, Australia
| | | | - Bertrand Favier
- Université Grenoble Alpes, Translationnelle et Innovation en Médecine et Complexité, Grenoble, France
| | - Thomas Stoeger
- Successful Clinical Response in Pneumonia Therapy Systems Biology Center, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Genetic Medicine, Northwestern University School of Medicine, Chicago, IL, USA
| | - Amanda Capes-Davis
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- CellBank Australia, Children's Medical Research Institute, Westmead, Australia
| | - Guillaume Cabanac
- Computer Science Department, Institut de Recherche en Informatique de Toulouse, Unité Mixte de Recherche 5505 Centre National de la Recherche Scientifique (CNRS), University of Toulouse, Toulouse, France
| | - Cyril Labbé
- Université Grenoble Alpes, CNRS, Grenoble INP, Laboratoire d'Informatique de Grenoble, Grenoble, France
| | - Jennifer A Byrne
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- New South Wales Health Statewide Biobank, New South Wales Health Pathology, Camperdown, Australia
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The thin ret(raction) line: biomedical journal responses to incorrect non-targeting nucleotide sequence reagents in human gene knockdown publications. Scientometrics 2021. [DOI: 10.1007/s11192-021-03871-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractThe capacity of the scientific literature to self-correct is of vital importance, but few studies have compared post-publication journal responses to specific error types. We have compared journal responses to a specific reagent error in 31 human gene knockdown publications, namely a non-targeting or negative control nucleotide sequence that is instead predicted to target a human gene. The 31 papers published by 13 biomedical journals generated 26 published responses (14 retractions, 5 expressions of concern, 7 author corrections which included one resolved expression of concern) as well as 6 stated decisions to take no action. Variations in published responses were noted both between journals and by 4 journals that published different responses to at least 2 papers. A subset of published responses revealed conflicting explanations for the wrongly identified control reagent, despite 30/31 papers obtaining their gene knockdown reagents from the same external supplier. Viewed collectively, different journal responses to human gene knockdown publications with a common reagent error type suggest that editorial staff require more support to interpret post-publication notifications of incorrect nucleotide sequence reagents. We propose a draft template to facilitate the communication, interpretation and investigation of published errors, including errors affecting research reagents.
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Hupfauf S, Etemadi M, Fernández-Delgado Juárez M, Gómez-Brandón M, Insam H, Podmirseg SM. CoMA - an intuitive and user-friendly pipeline for amplicon-sequencing data analysis. PLoS One 2020; 15:e0243241. [PMID: 33264369 PMCID: PMC7710066 DOI: 10.1371/journal.pone.0243241] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/17/2020] [Indexed: 12/23/2022] Open
Abstract
In recent years, there has been a veritable boost in next-generation sequencing (NGS) of gene amplicons in biological and medical studies. Huge amounts of data are produced and need to be analyzed adequately. Various online and offline analysis tools are available; however, most of them require extensive expertise in computer science or bioinformatics, and often a Linux-based operating system. Here, we introduce "CoMA-Comparative Microbiome Analysis" as a free and intuitive analysis pipeline for amplicon-sequencing data, compatible with any common operating system. Moreover, the tool offers various useful services including data pre-processing, quality checking, clustering to operational taxonomic units (OTUs), taxonomic assignment, data post-processing, data visualization, and statistical appraisal. The workflow results in highly esthetic and publication-ready graphics, as well as output files in standardized formats (e.g. tab-delimited OTU-table, BIOM, NEWICK tree) that can be used for more sophisticated analyses. The CoMA output was validated by a benchmark test, using three mock communities with different sample characteristics (primer set, amplicon length, diversity). The performance was compared with that of Mothur, QIIME and QIIME2-DADA2, popular packages for NGS data analysis. Furthermore, the functionality of CoMA is demonstrated on a practical example, investigating microbial communities from three different soils (grassland, forest, swamp). All tools performed well in the benchmark test and were able to reveal the majority of all genera in the mock communities. Also for the soil samples, the results of CoMA were congruent to those of the other pipelines, in particular when looking at the key microbial players.
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Affiliation(s)
- Sebastian Hupfauf
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Mohammad Etemadi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran
| | | | - María Gómez-Brandón
- Department of Ecology and Animal Biology, GEA Group, University of Vigo, Vigo, Spain
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
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Yow MA, Tabrizi SN, Severi G, Bolton DM, Pedersen J, Giles GG, Southey MC. Characterisation of microbial communities within aggressive prostate cancer tissues. Infect Agent Cancer 2017; 12:4. [PMID: 28101126 PMCID: PMC5237345 DOI: 10.1186/s13027-016-0112-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/13/2016] [Indexed: 12/11/2022] Open
Abstract
Background An infectious aetiology for prostate cancer has been conjectured for decades but the evidence gained from questionnaire-based and sero-epidemiological studies is weak and inconsistent, and a causal association with any infectious agent is not established. We describe and evaluate the application of new technology to detect bacterial and viral agents in high-grade prostate cancer tissues. The potential of targeted 16S rRNA gene sequencing and total RNA sequencing was evaluated in terms of its utility to characterise microbial communities within high-grade prostate tumours. Methods Two different Massively Parallel Sequencing (MPS) approaches were applied. First, to capture and enrich for possible bacterial species, targeted-MPS of the V2-V3 hypervariable regions of the 16S rRNA gene was performed on DNA extracted from 20 snap-frozen prostate tissue cores from ten “aggressive” prostate cancer cases. Second, total RNA extracted from the same prostate tissue samples was also sequenced to capture the sequence profile of both bacterial and viral transcripts present. Results Overall, 16S rRNA sequencing identified Enterobacteriaceae species common to all samples and P. acnes in 95% of analyzed samples. Total RNA sequencing detected endogenous retroviruses providing proof of concept but there was no evidence of bacterial or viral transcripts suggesting active infection, although it does not rule out a previous ‘hit and run’ scenario. Conclusions As these new investigative methods and protocols become more refined, MPS approaches may be found to have significant utility in identifying potential pathogens involved in disease aetiology. Further studies, specifically designed to detect associations between the disease phenotype and aetiological agents, are required. Electronic supplementary material The online version of this article (doi:10.1186/s13027-016-0112-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Melissa A Yow
- Genetic Epidemiology Laboratory, Department of Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, VIC, Australia 3010
| | - Sepehr N Tabrizi
- Department of Microbiology and Infectious Diseases, Royal Women's Hospital, Parkville, VIC Australia 3052 ; Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC Australia 3010 ; Murdoch Childrens Research Institute, Parkville, VIC Australia 3052
| | - Gianluca Severi
- Human Genetics Foundation (HuGeF), Via Nizza, 52-10126 Torino, Italy
| | - Damien M Bolton
- Department of Surgery, University of Melbourne, Austin Health, 145 Studley Road, Heidelberg, VIC Australia 3084
| | - John Pedersen
- TissuPath, 92-96 Ricketts Road, Mount Waverley, VIC Australia 3149
| | | | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Epidemiology Centre, Cancer Council Victoria, Level 2, 615 St Kilda Road, Melbourne, VIC Australia 3004 ; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Level 3, 207 Bouverie Street, Carlton, VIC Australia 3053
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, VIC, Australia 3010
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Ni X, Meng H, Zhou F, Yu H, Xiang J, Shen S. Effect of hypertension on bacteria composition of prostate biopsy in patients with benign prostatic hyperplasia and prostate cancer in PSA grey-zone. Biomed Rep 2016; 4:765-769. [PMID: 27284421 DOI: 10.3892/br.2016.655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/04/2016] [Indexed: 11/06/2022] Open
Abstract
Diagnostic prostate cancer (PC) is difficult to diagnose by prostate biopsy, even in patients with markedly elevated PSA levels. Therefore, we aimed to identify a new, better technique to detect PC in a more consistent manner. A variety of steps were employed to validate this proposed method, including DNA extraction, polymerase chain reaction (PCR) amplification, denaturing gradient gel electrophoresis (DGGE) and DGGE band sequencing. Four transperineal prostate biopsy specimens were obtained from male patients. The patients were under the age of 65 and PSA levels were 4-10 ng/ml. We also investigated the bacteria composition of transperineal prostate biopsy in patients with benign prostatic hyperplasia (BPH) and PC by PCR-DGGE profiling. Sequences from selected bands 2 and 4 both matched with Sphingomonas, which is present in lower amounts in PC without hypertension as compared to PC with hypertension, while there were no particular differences in the BPH group. Specific bacteria from the prostate biopsy tissues provide further confidence in PC diagnosis based on a PCR approach as a diagnostic tool, while hypertension was found to be a disturbing factor that can affect the diagnosis of BPH and PC in grey-zone.
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Affiliation(s)
- Xiaofeng Ni
- Department of Food Science and Nutrition, School of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - Hongzhou Meng
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Feng Zhou
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Haining Yu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P.R. China
| | - Jianjian Xiang
- Department of Ultrasonography, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Shengrong Shen
- Department of Food Science and Nutrition, School of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
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Kalle E, Kubista M, Rensing C. Multi-template polymerase chain reaction. BIOMOLECULAR DETECTION AND QUANTIFICATION 2014; 2:11-29. [PMID: 27896140 PMCID: PMC5121205 DOI: 10.1016/j.bdq.2014.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 12/12/2022]
Abstract
PCR is a formidable and potent technology that serves as an indispensable tool in a wide range of biological disciplines. However, due to the ease of use and often lack of rigorous standards many PCR applications can lead to highly variable, inaccurate, and ultimately meaningless results. Thus, rigorous method validation must precede its broad adoption to any new application. Multi-template samples possess particular features, which make their PCR analysis prone to artifacts and biases: multiple homologous templates present in copy numbers that vary within several orders of magnitude. Such conditions are a breeding ground for chimeras and heteroduplexes. Differences in template amplification efficiencies and template competition for reaction compounds undermine correct preservation of the original template ratio. In addition, the presence of inhibitors aggravates all of the above-mentioned problems. Inhibitors might also have ambivalent effects on the different templates within the same sample. Yet, no standard approaches exist for monitoring inhibitory effects in multitemplate PCR, which is crucial for establishing compatibility between samples.
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Affiliation(s)
- Elena Kalle
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Allmas alle 5, 75007 Uppsala, Sweden
| | - Mikael Kubista
- TATAA Biocenter, Odinsgatan 28, 41103 Göteborg, Sweden; Institute of Biotechnology, Czech Academy of Sciences
| | - Christopher Rensing
- Department of Plant and Environmental Sciences, Faculty of Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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Kalle E, Gulevich A, Rensing C. External and semi-internal controls for PCR amplification of homologous sequences in mixed templates. J Microbiol Methods 2013; 95:285-94. [PMID: 24076226 DOI: 10.1016/j.mimet.2013.09.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 09/10/2013] [Accepted: 09/12/2013] [Indexed: 11/30/2022]
Abstract
In a mixed template, the presence of homologous target DNA sequences creates environments that almost inevitably give rise to artifacts and biases during PCR. Heteroduplexes, chimeras, and skewed template-to-product ratios are the exclusive attributes of mixed template PCR and never occur in a single template assay. Yet, multi-template PCR has been used without appropriate attention to quality control and assay validation, in spite of the fact that such practice diminishes the reliability of results. External and internal amplification controls became obligatory elements of good laboratory practice in different PCR assays. We propose the inclusion of an analogous approach as a quality control system for multi-template PCR applications. The amplification controls must take into account the characteristics of multi-template PCR and be able to effectively monitor particular assay performance. This study demonstrated the efficiency of a model mixed template as an adequate external amplification control for a particular PCR application. The conditions of multi-template PCR do not allow implementation of a classic internal control; therefore we developed a convenient semi-internal control as an acceptable alternative. In order to evaluate the effects of inhibitors, a model multi-template mix was amplified in a mixture with DNAse-treated sample. Semi-internal control allowed establishment of intervals for robust PCR performance for different samples, thus enabling correct comparison of the samples. The complexity of the external and semi-internal amplification controls must be comparable with the assumed complexity of the samples. We also emphasize that amplification controls should be applied in multi-template PCR regardless of the post-assay method used to analyze products.
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Affiliation(s)
- Elena Kalle
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Allmas alle 5, 75007 Uppsala, Sweden.
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