Paper 68: Analysis of mutational dynamics at the DMPK (CTG)n locus identifies saliva as a suitable DNA sample source for genetic analysis in myotonic dystrophy type 1

Author

Lee Jones - Senior Biostatistician - Statistical Review

Published

March 7, 2026

References

Corrales E, Vásquez M, Zhang B, Santamaría-Ulloa C, Cuenca P, Krahe R, et al. (2019) Analysis of mutational dynamics at the DMPK (CTG)n locus identifies saliva as a suitable DNA sample source for genetic analysis in myotonic dystrophy type 1. PLoS ONE 14(5): e0216407. https://doi.org/10.1371/journal.pone.0216407

Disclosure

This reproducibility project was conducted to the best of our ability, with careful attention to statistical methods and assumptions. The research team comprises four senior biostatisticians (three of whom are accredited), with 20 to 30 years of experience in statistical modelling and analysis of healthcare data. While statistical assumptions play a crucial role in analysis, their evaluation is inherently subjective, and contextual knowledge can influence judgements about the importance of assumption violations. Differences in interpretation may arise among statisticians and researchers, leading to reasonable disagreements about methodological choices.

Our approach aimed to reproduce published analyses as faithfully as possible, using the details provided in the original papers. We acknowledge that other statisticians may have differing success in reproducing results due to variations in data handling and implicit methodological choices not fully described in publications. However, we maintain that research articles should contain sufficient detail for any qualified statistician to reproduce the analyses independently.

Methods used in our reproducibility analyses

There were two parts to our study. First, 100 articles published in PLOS ONE were randomly selected from the health domain and sent for post-publication peer review by statisticians. Of these, 95 included linear regression analyses and were therefore assessed for reporting quality. The statisticians evaluated what was reported, including regression coefficients, 95% confidence intervals, and p-values, as well as whether model assumptions were described and how those assumptions were evaluated. This report provides a brief summary of the initial statistical review.

The second part of the study involved reproducing linear regression analyses for papers with available data to assess both computational and inferential reproducibility. All papers were initially assessed for data availability and the statistical software used. From those with accessible data, the first 20 papers (from the original random sample) were evaluated for computational reproducibility. Within each paper, individual linear regression models were identified and assigned a unique number. A maximum of three models per paper were selected for assessment. When more than three models were reported, priority was given to the final model or the primary models of interest as identified by the authors; any remaining models were selected at random.

To assess computational reproducibility, differences between the original and reproduced results were evaluated using absolute discrepancies and rounding error thresholds, tailored to the number of decimal places reported in each paper. Results for each reported statistic, e.g., regression coefficient, were categorised as Reproduced, Incorrect Rounding, or Not Reproduced, depending on how closely they matched the original values. Each paper was then classified as Reproduced, Mostly Reproduced, Partially Reproduced, or Not Reproduced. The mostly reproduced category included cases with minor rounding or typographical errors, whereas partially reproduced indicated substantial errors were observed, but some results were reproduced.

For models deemed at least partially computationally reproducible, inferential reproducibility was further assessed by examining whether statistical assumptions were met and by conducting sensitivity analyses, including bootstrapping where appropriate. We examined changes in standardized regression coefficients, which reflect the change in the outcome (in standard deviation units) for a one standard deviation increase in the predictor. Meaningful differences were defined as a relative change of 10% or more, or absolute differences of 0.1 (moderate) and 0.2 (substantial). When non-linear relationships were identified, inferential reproducibility was assessed by comparing model fit measures, including R², Akaike Information Criterion (AIC), and Bayesian Information Criterion (BIC). When the Gaussian distribution was not appropriate for the dependent variable, alternative distributions were considered, and model fit was evaluated using AIC and BIC.

Summary from statistical review

This paper investigated whether saliva is a suitable DNA source for genetic analysis in individuals with myotonic dystrophy type 1. Univariate and multivariable linear regression models were used to examine whether age of onset was modified by allele size transmitted from the affected parent to the affected offspring and by somatic instability. Linearity was assessed by fitting a quadratic term. Data were log-transformed, presumably to address distributional assumptions; however, the rationale for this transformation was not reported. Although the direction of associations was described, interpretation of the linear regression results focused primarily on the proportion of variance explained, rather than on the magnitude or relevance of individual parameter estimates. High correlations between variables were noted, but collinearity was not formally assessed or discussed.

Data availability and software used

The authors provided the data in the supporting information as an Excel file with a data description; however, the dataset’s structure is not readily compatible with standard statistical software and requires reformatting prior to analysis. SPSS was used for the statistical analyses.

Regression sample

Data were potentially available but were not assessed for reproducibility, as reproduction was limited to the first 20 papers with accessible datasets.

Computational reproducibility results

Data were potentially available but were not assessed for computational reproducibility, as reproduction was limited to the first 20 papers with accessible datasets.

Inferential reproducibility results

Data were potentially available but were not assessed for inferential reproducibility, as reproduction was limited to the first 20 papers with accessible datasets.