Rational genomic optimization of DNA detection for human papillomavirus type 16 in head and neck squamous cell carcinoma

Yuki Saito; Alexander V. Favorov; Michael Forman; Shuling Ren; Akihiro Sakai; Takahito Fukusumi; Chao Liu; Sayed Sadat; Mizuo Ando; Guorong Xu; Zubair Khan; John Pang; Alex Valsamakis; Kathleen M. Fisch; Joseph A. Califano

doi:10.1002/hed.26041

Rational genomic optimization of DNA detection for human papillomavirus type 16 in head and neck squamous cell carcinoma

Yuki Saito, Alexander V. Favorov, Michael Forman, Shuling Ren, Akihiro Sakai, Takahito Fukusumi, Chao Liu, Sayed Sadat, Mizuo Ando, Guorong Xu, Zubair Khan, John Pang, Alex Valsamakis, Kathleen M. Fisch, Joseph A. Califano

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

Abstract

Background: We aimed to use genomic data for optimizing polymerase chain reaction (PCR) primer/probe sets for detection of human papillomavirus (HPV)-16 in body fluids of patients with HPV-related head and neck squamous cell carcinoma (HPV-HNSCC). Methods: We used genomic HPV-HNSCC sequencing data from a single institutional and a TCGA cohort. Optimized primer/probe sets were designed and tested for analytical performance in CaSki HPV-16 genome and confirmed in salivary rinse samples from patients with HPV-HNSCC. Results: The highest read density was observed between E5 and L2 regions. The E1 region contained a region that was universally present. Among candidate PCR primer/probe sets created, six reliably detected 30 HPV-16 copy number. In a CLIA certified laboratory setting, the combination of two novel primer/probe with E7 sets improved performance in salivary rinse samples with a sensitivity of 96% and specificity of 100%. Conclusions: PCR-based detection of HPV-16 DNA in HPV-HNSCC can be improved using rational genomic design.

Original language	English
Pages (from-to)	688-697
Number of pages	10
Journal	Head and Neck
Volume	42
Issue number	4
DOIs	https://doi.org/10.1002/hed.26041
Publication status	Published - Apr 1 2020
Externally published	Yes

Keywords

DNA primer
head and neck squamous cell carcinoma
human papillomavirus
polymerase chain reaction
whole-genome sequencing

ASJC Scopus subject areas

Otorhinolaryngology

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10.1002/hed.26041

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Saito, Y., Favorov, A. V., Forman, M., Ren, S., Sakai, A., Fukusumi, T., Liu, C., Sadat, S., Ando, M., Xu, G., Khan, Z., Pang, J., Valsamakis, A., Fisch, K. M., & Califano, J. A. (2020). Rational genomic optimization of DNA detection for human papillomavirus type 16 in head and neck squamous cell carcinoma. Head and Neck, 42(4), 688-697. https://doi.org/10.1002/hed.26041

@article{d926c76b3b334a10a1d0b6f1c9513232,

title = "Rational genomic optimization of DNA detection for human papillomavirus type 16 in head and neck squamous cell carcinoma",

abstract = "Background: We aimed to use genomic data for optimizing polymerase chain reaction (PCR) primer/probe sets for detection of human papillomavirus (HPV)-16 in body fluids of patients with HPV-related head and neck squamous cell carcinoma (HPV-HNSCC). Methods: We used genomic HPV-HNSCC sequencing data from a single institutional and a TCGA cohort. Optimized primer/probe sets were designed and tested for analytical performance in CaSki HPV-16 genome and confirmed in salivary rinse samples from patients with HPV-HNSCC. Results: The highest read density was observed between E5 and L2 regions. The E1 region contained a region that was universally present. Among candidate PCR primer/probe sets created, six reliably detected 30 HPV-16 copy number. In a CLIA certified laboratory setting, the combination of two novel primer/probe with E7 sets improved performance in salivary rinse samples with a sensitivity of 96% and specificity of 100%. Conclusions: PCR-based detection of HPV-16 DNA in HPV-HNSCC can be improved using rational genomic design.",

keywords = "DNA primer, head and neck squamous cell carcinoma, human papillomavirus, polymerase chain reaction, whole-genome sequencing",

author = "Yuki Saito and Favorov, {Alexander V.} and Michael Forman and Shuling Ren and Akihiro Sakai and Takahito Fukusumi and Chao Liu and Sayed Sadat and Mizuo Ando and Guorong Xu and Zubair Khan and John Pang and Alex Valsamakis and Fisch, {Kathleen M.} and Califano, {Joseph A.}",

note = "Funding Information: The authors thank the colleagues in the Moores Cancer Center at University of California, San Diego. This work was supported by National Cancer Institute [grant number UH2CA211396]. J.A. Califano received this grant. The project described was partially supported by the National Institutes of Health, Grant UL1TR001442 of CTSA. Funding Information: The authors thank the colleagues in the Moores Cancer Center at University of California, San Diego. This work was supported by National Cancer Institute [grant number UH2CA211396]. J.A. Califano received this grant. The project described was partially supported by the National Institutes of Health, Grant UL1TR001442 of CTSA. Publisher Copyright: {\textcopyright} 2019 Wiley Periodicals, Inc.",

year = "2020",

month = apr,

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doi = "10.1002/hed.26041",

language = "English",

volume = "42",

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T1 - Rational genomic optimization of DNA detection for human papillomavirus type 16 in head and neck squamous cell carcinoma

AU - Saito, Yuki

AU - Favorov, Alexander V.

AU - Forman, Michael

AU - Ren, Shuling

AU - Sakai, Akihiro

AU - Fukusumi, Takahito

AU - Liu, Chao

AU - Sadat, Sayed

AU - Ando, Mizuo

AU - Xu, Guorong

AU - Khan, Zubair

AU - Pang, John

AU - Valsamakis, Alex

AU - Fisch, Kathleen M.

AU - Califano, Joseph A.

N1 - Funding Information: The authors thank the colleagues in the Moores Cancer Center at University of California, San Diego. This work was supported by National Cancer Institute [grant number UH2CA211396]. J.A. Califano received this grant. The project described was partially supported by the National Institutes of Health, Grant UL1TR001442 of CTSA. Funding Information: The authors thank the colleagues in the Moores Cancer Center at University of California, San Diego. This work was supported by National Cancer Institute [grant number UH2CA211396]. J.A. Califano received this grant. The project described was partially supported by the National Institutes of Health, Grant UL1TR001442 of CTSA. Publisher Copyright: © 2019 Wiley Periodicals, Inc.

PY - 2020/4/1

Y1 - 2020/4/1

N2 - Background: We aimed to use genomic data for optimizing polymerase chain reaction (PCR) primer/probe sets for detection of human papillomavirus (HPV)-16 in body fluids of patients with HPV-related head and neck squamous cell carcinoma (HPV-HNSCC). Methods: We used genomic HPV-HNSCC sequencing data from a single institutional and a TCGA cohort. Optimized primer/probe sets were designed and tested for analytical performance in CaSki HPV-16 genome and confirmed in salivary rinse samples from patients with HPV-HNSCC. Results: The highest read density was observed between E5 and L2 regions. The E1 region contained a region that was universally present. Among candidate PCR primer/probe sets created, six reliably detected 30 HPV-16 copy number. In a CLIA certified laboratory setting, the combination of two novel primer/probe with E7 sets improved performance in salivary rinse samples with a sensitivity of 96% and specificity of 100%. Conclusions: PCR-based detection of HPV-16 DNA in HPV-HNSCC can be improved using rational genomic design.

AB - Background: We aimed to use genomic data for optimizing polymerase chain reaction (PCR) primer/probe sets for detection of human papillomavirus (HPV)-16 in body fluids of patients with HPV-related head and neck squamous cell carcinoma (HPV-HNSCC). Methods: We used genomic HPV-HNSCC sequencing data from a single institutional and a TCGA cohort. Optimized primer/probe sets were designed and tested for analytical performance in CaSki HPV-16 genome and confirmed in salivary rinse samples from patients with HPV-HNSCC. Results: The highest read density was observed between E5 and L2 regions. The E1 region contained a region that was universally present. Among candidate PCR primer/probe sets created, six reliably detected 30 HPV-16 copy number. In a CLIA certified laboratory setting, the combination of two novel primer/probe with E7 sets improved performance in salivary rinse samples with a sensitivity of 96% and specificity of 100%. Conclusions: PCR-based detection of HPV-16 DNA in HPV-HNSCC can be improved using rational genomic design.

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KW - human papillomavirus

KW - polymerase chain reaction

KW - whole-genome sequencing

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JF - Head and Neck

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Rational genomic optimization of DNA detection for human papillomavirus type 16 in head and neck squamous cell carcinoma

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