## Replication Study: _Fusobacterium nucleatum_ infection is prevalent in human colorectal carcinoma <br> **Abstract** As part of the [Reproducibility Project: Cancer Biology][1], we published a Registered Report ([Repass et al., 2016][2]), that described how we intended to replicate an experiment from the paper "_Fusobacterium nucleatum_ infection is prevalent in human colorectal carcinoma" ([Castellarin et al., 2012][3]). Here we report the results. When measuring _Fusobacterium nucleatum_ DNA by qPCR in colorectal carcinoma (CRC), adjacent normal tissue, and separate matched control tissue, we did not detect _F. nucleatum_ in most samples: 5% of matched control tissue, 25% of adjacent normal, and 40% of CRCs were positive. When all samples were included in the analysis, we observed a statistically significant increase in _F. nucleatum_ expression in CRC compared to adjacent normal tissue, similar to the original study (Figure 2; Castellarin et al., 2012). However, when only samples with detectable _F. nucleatum_ in CRC and adjacent normal tissue were compared, the difference was not statistically significant. Finally, we report a meta-analysis of the result, which suggests _F. nucleatum_ expression is increased in CRC, but is confounded by the inability to detect _F. nucleatum_ in most samples. The difference in _F. nucleatum_ expression between CRC and adjacent normal tissues was thus smaller than the original study, and not detected in most samples. ---------- ### Contents **Reports:** Read the [Replication Study][12], or view the [preprint versions][4]. **Note**: In order to successfully run and knit the Replication Study Manuscript R Markdown file, you must install a series of necessary R packages. You can review the necessary packages included in the checkpoint manifest in the markdown file [here][13] or run and knit the following r markdown file and they will be downloaded automatically. To reproduce the Replication Study manuscript text run this in [R Studio][5] (note: downloads [R markdown file][6] directly from osf.io): library(httr) library(rmarkdown) GET("https://osf.io/fmp6u/?action=download", write_disk("Replication_Study_50.Rmd", overwrite = T)) render("Replication_Study_50.Rmd", output_format = "word_document") <br> Also, explore the [Registered Report][7] and materials related to the Registered Report [here][8]. <br> **Data and Material Availability:** All associated data, protocols, analysis scripts, and other digital materials are available within this OSF project. **Experiments replicated:** Reproduce and explore the figures, analyses, data, and methods generated in this replication attempt. - [Quantitative PCR for amplification of F. nucleatum from matched normal and tumor human colon cancer specimens][9] - Replication of Figure 2 in Castellarin et al., 2012. <br> **Meta-analyses:** As a measure of evaluating reproducibility a meta-analysis of each effect was performed. The forest plots, analyses, and data are available [here][10]. <br> Questions about the project can be directed to [contact+rpcb@cos.io][11]. [1]: https://osf.io/e81xl/wiki/home/ [2]: https://elifesciences.org/content/5/e10012 [3]: http://genome.cshlp.org/content/22/2/299 [4]: https://osf.io/j7wgp/ [5]: https://www.rstudio.com [6]: https://osf.io/fmp6u/ [7]: https://elifesciences.org/content/5/e10012 [8]: https://osf.io/yadgq/wiki/home/ [9]: https://osf.io/rb4yq/wiki/home/ [10]: https://osf.io/kup8d/wiki/home/ [11]: mailto:contact+rpcb@cos.io [12]: https://doi.org/10.7554/eLife.25801 [13]: https://osf.io/fmp6u/