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Simultaneous Characterization of Somatic Events and HPV-18 Integration in a Metastatic Cervical Carcinoma Patient Using DNA and RNA Sequencing
  1. Winnie S. Liang, PhD*,
  2. Jessica Aldrich, MS*,
  3. Sara Nasser, PhD*,
  4. Ahmet Kurdoglu, MS*,
  5. Lori Phillips, MS*,
  6. Rebecca Reiman, BA*,
  7. Jacquelyn McDonald, BS*,
  8. Tyler Izatt, MS*,
  9. Alexis Christoforides, BS*,
  10. Angela Baker, PhD*,
  11. Christine Craig, MD,
  12. Jan B. Egan, PhD,
  13. Dana M. Chase, MD,
  14. John H. Farley, MD§,
  15. Alan H. Bryce, MD,
  16. A. Keith Stewart, MD,
  17. Mitesh J. Borad, MD,
  18. John D. Carpten, PhD*,
  19. David W. Craig, PhD* and
  20. Bradley J. Monk, MD
  1. *Translational Genomics Research Institute;
  2. Comprehensive Cancer Care, St Joseph’s Hospital and Medical Center, Phoenix;
  3. Mayo Clinic, Scottsdale;
  4. §Department of Obstetrics and Gynecology, St Joseph’s Hospital and Medical Center, and
  5. Division of Gynecologic Oncology, Creighton University School of Medicine, St Joseph’s Hospital and Medical Center, University of Arizona Cancer Center, Phoenix, AZ.
  1. Address correspondence and reprint requests to Winnie S. Liang, PhD, Collaborative Sequencing Center, Translational Genomics Research Institute, 445 N, Fifth St, Phoenix, AZ 85004. E-mail: wliang{at}tgen.org.

Abstract

Objective Integration of carcinogenic human papillomaviruses (HPVs) into the host genome is a significant tumorigenic factor in specific cancers including cervical carcinoma. Although major strides have been made with respect to HPV diagnosis and prevention, identification and development of efficacious treatments for cervical cancer patients remains a goal and thus requires additional detailed characterization of both somatic events and HPV integration. Given this need, the goal of this study was to use the next generation sequencing to simultaneously evaluate somatic alterations and expression changes in a patient’s cervical squamous carcinoma lesion metastatic to the lung and to detect and analyze HPV infection in the same sample.

Materials and Methods We performed tumor and normal exome, tumor and normal shallow whole-genome sequencing, and RNA sequencing of the patient’s lung metastasis.

Results We generated over 1.2 billion mapped reads and identified 130 somatic point mutations and indels, 21 genic translocations, 16 coding regions demonstrating copy number changes, and over 36 genes demonstrating altered expression in the tumor (corrected P < 0.05). Sequencing also revealed the HPV type 18 (HPV-18) integration in the metastasis. Using both DNA and RNA reads, we pinpointed 3 major events indicating HPV-18 integration into an intronic region of chromosome 6p25.1 in the patient’s tumor and validated these events with Sanger sequencing. This integration site has not been reported for HPV-18.

Conclusions We demonstrate that DNA and RNA sequencing can be used to concurrently characterize somatic alterations and expression changes in a biopsy and delineate HPV integration at base resolution in cervical cancer. Further sequencing will allow us to better understand the molecular basis of cervical cancer pathogenesis.

  • HPV integration
  • Cervical carcinoma
  • Next generation sequencing

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Footnotes

  • The last three authors contributed equally to this manuscript.

  • Supplemental digital content is available for this article. Direct URL citation appears in the printed text and is provided in the HTML and PDF versions of this article on the journal’s Web site (www.ijgc.net).

  • The authors declare no conflicts of interest.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License, where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially.

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