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 WacholderAshlie Feldman, Tina Raine-Bennett, Thomas Lorey, Philip E. Castle, Meredith Yeager, Robert D. Burk, Lisa Mirabello

Research output: Contribution to journalArticle

31 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)3-11
Number of pages9
JournalPapillomavirus Research
Volume1
DOIs
StatePublished - Dec 1 2015

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High-Throughput Nucleotide Sequencing
Natural History
Genome
Infection
Uterine Cervical Neoplasms
Virus Integration
Coinfection
Single Nucleotide Polymorphism
Protons
Neoplasms
Carcinogenesis
Epidemiology
Ions

Keywords

  • HPV epidemiology
  • HPV genomics
  • HPV16

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases

Cite this

Deep sequencing of HPV16 genomes : A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection. / Cullen, Michael; Boland, Joseph F.; Schiffman, Mark; Zhang, Xijun; Wentzensen, Nicolas; Yang, Qi; Chen, Zigui; Yu, Kai; Mitchell, Jason; Roberson, David; Bass, Sara; Burdette, Laurie; Machado, Moara; Ravichandran, Sarangan; Luke, Brian; Machiela, Mitchell J.; Andersen, Mark; Osentoski, Matt; Laptewicz, Michael; Wacholder, Sholom; Feldman, Ashlie; Raine-Bennett, Tina; Lorey, Thomas; Castle, Philip E.; Yeager, Meredith; Burk, Robert D.; Mirabello, Lisa.

In: Papillomavirus Research, Vol. 1, 01.12.2015, p. 3-11.

Research output: Contribution to journalArticle

Cullen, M, Boland, JF, Schiffman, M, Zhang, X, Wentzensen, N, Yang, Q, Chen, Z, Yu, K, Mitchell, J, Roberson, D, Bass, S, Burdette, L, Machado, M, Ravichandran, S, Luke, B, Machiela, MJ, Andersen, M, Osentoski, M, Laptewicz, M, Wacholder, S, Feldman, A, Raine-Bennett, T, Lorey, T, Castle, PE, Yeager, M, Burk, RD & Mirabello, L 2015, 'Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection', Papillomavirus Research, vol. 1, pp. 3-11. https://doi.org/10.1016/j.pvr.2015.05.004
Cullen, Michael ; Boland, Joseph F. ; Schiffman, Mark ; Zhang, Xijun ; Wentzensen, Nicolas ; Yang, Qi ; Chen, Zigui ; Yu, Kai ; Mitchell, Jason ; Roberson, David ; Bass, Sara ; Burdette, Laurie ; Machado, Moara ; Ravichandran, Sarangan ; Luke, Brian ; Machiela, Mitchell J. ; Andersen, Mark ; Osentoski, Matt ; Laptewicz, Michael ; Wacholder, Sholom ; Feldman, Ashlie ; Raine-Bennett, Tina ; Lorey, Thomas ; Castle, Philip E. ; Yeager, Meredith ; Burk, Robert D. ; Mirabello, Lisa. / Deep sequencing of HPV16 genomes : A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection. In: Papillomavirus Research. 2015 ; Vol. 1. pp. 3-11.
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AU - Wentzensen, Nicolas

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AU - Ravichandran, Sarangan

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AU - Andersen, Mark

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AU - Laptewicz, Michael

AU - Wacholder, Sholom

AU - Feldman, Ashlie

AU - Raine-Bennett, Tina

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