Papillomavirus Research (Dec 2015)
Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection
- Michael Cullen,
- Joseph F. Boland,
- Mark Schiffman,
- Xijun Zhang,
- Nicolas Wentzensen,
- Qi Yang,
- Zigui Chen,
- Kai Yu,
- Jason Mitchell,
- David Roberson,
- Sara Bass,
- Laurie Burdette,
- Moara Machado,
- Sarangan Ravichandran,
- Brian Luke,
- Mitchell J. Machiela,
- Mark Andersen,
- Matt Osentoski,
- Michael Laptewicz,
- Sholom Wacholder,
- Ashlie Feldman,
- Tina Raine-Bennett,
- Thomas Lorey,
- Philip E. Castle,
- Meredith Yeager,
- Robert D. Burk,
- Lisa Mirabello
Affiliations
- Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
- Joseph F. Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA; Corresponding author at: Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Room 6E422, Bethesda, MD 20850, USA. Tel.: +1 240 276 7258; Cancer Genomics Research Laboratory, Leidos Biomedical Inc., National Cancer Institute, 8717 Grovemont Circle, Gaithersburg, MD 20877, USA.
- Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Xijun Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
- Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Qi Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
- Zigui Chen
- Department of Epidemiology and Population Health, At Albert Einstein College of Medicine, Bronx, NY, USA
- Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Jason Mitchell
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
- David Roberson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
- Sara Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
- Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
- Moara Machado
- Department de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Sarangan Ravichandran
- Frederick National Laboratory for Cancer Research, Simulation, Analysis and Mathematical Modeling Group Advanced Biomedical Computing Center, Frederick, MD, USA
- Brian Luke
- Frederick National Laboratory for Cancer Research, Simulation, Analysis and Mathematical Modeling Group Advanced Biomedical Computing Center, Frederick, MD, USA
- Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Mark Andersen
- Thermo Fisher Scientific (Formerly Life Technologies), Carlsbad, CA, USA
- Matt Osentoski
- Thermo Fisher Scientific (Formerly Life Technologies), Carlsbad, CA, USA
- Michael Laptewicz
- Thermo Fisher Scientific (Formerly Life Technologies), Carlsbad, CA, USA
- Sholom Wacholder
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Ashlie Feldman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
- Tina Raine-Bennett
- Regional Laboratory and Women’s Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
- Thomas Lorey
- Regional Laboratory and Women’s Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
- Philip E. Castle
- Department of Epidemiology and Population Health, At Albert Einstein College of Medicine, Bronx, NY, USA; Global Coalition Against Cervical Cancer, Arlington, VA, USA
- Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
- Robert D. Burk
- Department of Epidemiology and Population Health, At Albert Einstein College of Medicine, Bronx, NY, USA; Division of Gynecologic Oncology, Department of Obstetrics & Gynecology and Women’s Health, at Albert Einstein College of Medicine, Bronx, NY, USA
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Corresponding author at: Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Room 6E422, Bethesda, MD 20850, USA. Tel.: +1 240 276 7258; Cancer Genomics Research Laboratory, Leidos Biomedical Inc., National Cancer Institute, 8717 Grovemont Circle, Gaithersburg, MD 20877, USA.
- Journal volume & issue
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Vol. 1
pp. 3 – 11
Abstract
For unknown reasons, there is huge variability in risk conferred by different HPV types and, remarkably, strong differences even between closely related variant lineages within each type. HPV16 is a uniquely powerful carcinogenic type, causing approximately half of cervical cancer and most other HPV-related cancers. To permit the large-scale study of HPV genome variability and precancer/cancer, starting with HPV16 and cervical cancer, we developed a high-throughput next-generation sequencing (NGS) whole-genome method. We designed a custom HPV16 AmpliSeq™ panel that generated 47 overlapping amplicons covering 99% of the genome sequenced on the Ion Torrent Proton platform. After validating with Sanger, the current “gold standard” of sequencing, in 89 specimens with concordance of 99.9%, we used our NGS method and custom annotation pipeline to sequence 796 HPV16-positive exfoliated cervical cell specimens. The median completion rate per sample was 98.0%.Our method enabled us to discover novel SNPs, large contiguous deletions suggestive of viral integration (OR of 27.3, 95% CI 3.3–222, P=0.002), and the sensitive detection of variant lineage coinfections. This method represents an innovative high-throughput, ultra-deep coverage technique for HPV genomic sequencing, which, in turn, enables the investigation of the role of genetic variation in HPV epidemiology and carcinogenesis. Keywords: HPV16, HPV epidemiology, HPV genomics
