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Reply to Artifacts in the data of Hu et al.

Nature Genetics volume 48, pages 3–4 (2016)Cite this article

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Hu et al . reply:

Despite the claim that our integration sites were artifacts generated from random ligation, we believe our human papillomavirus (HPV) integrations sites were genuine. First, many of the 'artifacts' identified by Dyer et al. were successfully validated in our study by performing Sanger sequencing on the original, unamplified DNA sample (Supplementary Table 6 in ref. 1). Second, if the integration sites were artifacts generated by ligation events involving unrelated fragments during sample processing, then every sample to some extent should have background integration sites, which should show similar patterns. However, in contrast to this expectation, the integration patterns varied extensively in the 135 samples of our study (Fig. 2 and Supplementary Table 5 in ref. 1) and nearly 30 samples (including the HaCaT cell line) that tested positive for HPV did not show HPV integrations (Fig. 2 and Supplementary Table 5 in ref. 1). The same argument could be made for the eight samples that did not show any signs of mitochondrial insertion in the analysis of Dyer et al., despite the existence of thousands of copies of mitochondrial DNA per cell.

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Authors and Affiliations

  1. Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China

    Zheng Hu, Da Zhu, Hui Wang & Ding Ma

  2. Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China

    Wei Wang

  3. Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China

    Weiyang Li, Wenlong Jia, Xi Zeng & Xun Xu

  4. School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China

    Weiyang Li

  5. Department of Computer Science, City University of Hong Kong, Hong Kong, China

    Wenlong Jia

Authors
  1. Zheng Hu
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Corresponding authors

Correspondence to Xun Xu, Hui Wang or Ding Ma.

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Hu, Z., Zhu, D., Wang, W. et al. Reply to Artifacts in the data of Hu et al.. Nat Genet 48, 3–4 (2016). https://doi.org/10.1038/ng.3445

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