Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection
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...
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| Format: | Article |
| Language: | English |
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Elsevier
2015-12-01
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| Series: | Papillomavirus Research |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405852115000051 |
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doaj-4b988b69d4e94e779997c118e35c056b |
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| record_format |
Article |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
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 |
| spellingShingle |
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 Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection Papillomavirus Research |
| author_facet |
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 |
| author_sort |
Michael Cullen |
| title |
Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection |
| title_short |
Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection |
| title_full |
Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection |
| title_fullStr |
Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection |
| title_full_unstemmed |
Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection |
| title_sort |
deep sequencing of hpv16 genomes: a new high-throughput tool for exploring the carcinogenicity and natural history of hpv16 infection |
| publisher |
Elsevier |
| series |
Papillomavirus Research |
| issn |
2405-8521 |
| publishDate |
2015-12-01 |
| description |
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 |
| url |
http://www.sciencedirect.com/science/article/pii/S2405852115000051 |
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doaj-4b988b69d4e94e779997c118e35c056b2020-11-24T22:28:06ZengElsevierPapillomavirus Research2405-85212015-12-011311Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infectionMichael Cullen0Joseph F. Boland1Mark Schiffman2Xijun Zhang3Nicolas Wentzensen4Qi Yang5Zigui Chen6Kai Yu7Jason Mitchell8David Roberson9Sara Bass10Laurie Burdette11Moara Machado12Sarangan Ravichandran13Brian Luke14Mitchell J. Machiela15Mark Andersen16Matt Osentoski17Michael Laptewicz18Sholom Wacholder19Ashlie Feldman20Tina Raine-Bennett21Thomas Lorey22Philip E. Castle23Meredith Yeager24Robert D. Burk25Lisa Mirabello26Division 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, USADivision 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.Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USADivision 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, USADivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USADivision 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, USADepartment of Epidemiology and Population Health, At Albert Einstein College of Medicine, Bronx, NY, USADivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USADivision 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, USADivision 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, USADivision 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, USADivision 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, USADepartment de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, BrazilFrederick National Laboratory for Cancer Research, Simulation, Analysis and Mathematical Modeling Group Advanced Biomedical Computing Center, Frederick, MD, USAFrederick National Laboratory for Cancer Research, Simulation, Analysis and Mathematical Modeling Group Advanced Biomedical Computing Center, Frederick, MD, USADivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USAThermo Fisher Scientific (Formerly Life Technologies), Carlsbad, CA, USAThermo Fisher Scientific (Formerly Life Technologies), Carlsbad, CA, USAThermo Fisher Scientific (Formerly Life Technologies), Carlsbad, CA, USADivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USADivision 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, USARegional Laboratory and Women’s Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USARegional Laboratory and Women’s Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USADepartment of Epidemiology and Population Health, At Albert Einstein College of Medicine, Bronx, NY, USA; Global Coalition Against Cervical Cancer, Arlington, VA, USADivision 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, USADepartment 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, USADivision 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.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 genomicshttp://www.sciencedirect.com/science/article/pii/S2405852115000051 |