A recent article in Molecular Cancer Research, “Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models” (1), describes a computational algorithm for separating human and mouse sequencing reads in xenograft studies. The authors assert that only one other algorithm, “Xenome” by Conway and colleagues (2), has been published with the same aim. However, we would like to inform the authors and readers of two additional algorithms for the same purpose, one of which was published prior to submission of the article by Khandelwal and colleagues (1): our article titled “Disambiguate: An open-source application for disambiguating two species in next generation sequencing data from grafted samples” (3) and a more recent publication by Callari and colleagues (4). However, the algorithm proposed by Khandelwal and colleagues (1) is identical with minor exceptions to the one in ref. 3. Preceding the publications, the code for the “Disambiguate” algorithm has been publicly available as open-source software since 2013 (https://github.com/AstraZeneca-NGS/disambiguate) and has been widely adopted, see for example, ref. 5 and https://github.com/chapmanb/bcbio-nextgen. This highlights a significant risk in scientific publishing that without due diligence, authors and reviewers can often overlook recently published research. For example, as in this case, a previously published algorithm has been republished as novel with minor modifications and without citing the original article.
See the Response, p. 1814
Disclosure of Potential Conflicts of Interest
M.J. Ahdesmaki has ownership interest (including stock, patents, etc.) in AstraZeneca.