Reporting quality of quantitative polymerase chain reaction (qPCR) methods in scientific publications

TL;DR

This study finds that many scientific papers still fail to report critical details needed to reproduce qPCR experiments, despite existing guidelines.

Contribution

A systematic evaluation of qPCR reporting in recent top-tier genetics and plant science journals reveals persistent deficiencies.

Findings

Only 7–10% of studies reported RNA integrity, and 14–16% specified methods for integrity evaluation.

Accession numbers for reference genes were provided in just 11% of genetics and 32% of plant science papers.

Critical reagent details were missing in 7–14% of reports, highlighting poor methodological transparency.

Abstract

Reproducibility remains a major concern in scientific research, particularly in complex methods such as quantitative polymerase chain reaction (qPCR). Stringent reporting standards are essential to ensure reproducibility, validity of data, and trustworthiness of conclusions. The MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines, introduced in 2009, aimed to improve reporting practices. However, a 2013 study highlighted persistent deficiencies. To further assess the transparency and completeness of qPCR reporting, we conducted a systematic evaluation of recently published research.

We systematically reviewed research articles employing qPCR that were published in the top 20 journals in genetics and heredity (n = 186) and plant sciences (n = 246). Articles were assessed for completeness of methodological reporting with respect to RNA quality control, reference gene reporting, and details of RNA extraction, RNA-to-cDNA conversion, and qPCR procedures. Frequencies of reporting deficiencies were recorded and descriptively analyzed.

Our analysis identified frequent omissions and insufficient detail in reporting key information required to evaluate and replicate qPCR experiments. RNA integrity was reported in only 7—10% of studies, and assessment methods or instruments used for integrity evaluation were specified in just 14—16%. While primer sequences were often disclosed (88—93%), the traceability of housekeeping/reference genes was limited: accession numbers were provided in only 11% of genetics/heredity papers and 32% of plant science papers. Critical methodological details—including kit names, catalog numbers, and reagent specifications for RNA extraction, RNA-to-cDNA conversion, and qPCR—were also frequently missing, appearing in only 7—14% of reports.

This study underscores the urgent need for improved reporting practices in qPCR experiments. Greater emphasis should be placed on quality controls, detailed descriptions of reagents and materials, and increased analytical transparency. Addressing these deficiencies is vital to enhance reproducibility and to strengthen the trustworthiness of qPCR-based research. Potential solutions include encouraging the citation of protocols in online repositories, providing structured reporting templates, and developing automated tools to support compliance with MIQE standards.

Not applicable (not a clinical trial). The study was preregistered on the Open Science Framework (OSF): 10.17605/OSF.IO/9ZP5M.

The online version contains supplementary material available at 10.1186/s41073-026-00188-0.

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