Evidence map›Paper›PMID 31850594›Full record

ArticleHead & neck2020

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 and 5 more

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Head & neck, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.4field-weighted citation impact, top 38% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed, 3 citations in OpenAlex.

  1. Article
  2. Targeting Viral DNA and Promoter Hypermethylation in Salivary Rinses for Recurrent HPV-Positive Oropharyngeal Cancer.Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery · 2020
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors at 4 institutions in 2 countries.

Yuki SaitoMoores Cancer Center, University of California San Diego, San Diego, California.ORCID 0000-0002-4825-7783
Alexander V FavorovDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.
Michael FormanDepartment of Pathology, Johns Hopkins University, Baltimore, Maryland.
Shuling RenMoores Cancer Center, University of California San Diego, San Diego, California.
Akihiro SakaiMoores Cancer Center, University of California San Diego, San Diego, California.
Takahito FukusumiMoores Cancer Center, University of California San Diego, San Diego, California.
Chao LiuMoores Cancer Center, University of California San Diego, San Diego, California.
Sayed SadatMoores Cancer Center, University of California San Diego, San Diego, California.
Mizuo AndoMoores Cancer Center, University of California San Diego, San Diego, California.
Guorong XuCenter for Computational Biology & Bioinformatics, Department of Medicine, University of California San Diego, San Diego, California.
Zubair KhanDepartment of Otolaryngology-Head and Neck Surgery, Johns Hopkins Hospital, Baltimore, Maryland.
John PangMoores Cancer Center, University of California San Diego, San Diego, California.ORCID 0000-0002-4952-6711
Alex ValsamakisDepartment of Pathology, Johns Hopkins University, Baltimore, Maryland.
Kathleen M FischCenter for Computational Biology & Bioinformatics, Department of Medicine, University of California San Diego, San Diego, California.
Joseph A CalifanoMoores Cancer Center, University of California San Diego, San Diego, California.
University of San Diego · USJohns Hopkins University · USUniversity of California San Diego · USJohns Hopkins Hospital · US

Funding

UC San Diego Clinical and Translational Research InstituteUL1TR001442 · NCATS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FIRESTEIN, GARY S, HOGARTH, MICHAEL · 2015 to 2024
$88.3M
Delineating chromatin-related gene expression signatures as a function of HNSCC progressionR01DE027809 · NIDCR · UNIVERSITY OF MARYLAND BALTIMORE · PI GAYKALOVA, DARIA A, IZUMCHENKO, EVGENY (EUGENE) G · 2019 to 2023
$2.6M
Optimizing an assay for high risk HPV DNA in body fluidsUH3CA211396 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI CALIFANO, JOSEPH A · 2019 to 2020
$684k
Optimizing an assay for high risk HPV DNA in body fluidsUH2CA211396 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI CALIFANO, JOSEPH A · 2017 to 2018
$399k
NCATS NIH HHS UL1 TR001442NCI NIH HHS UH2 CA211396NCI NIH HHS UH3 CA211396NIDCR NIH HHS R01 DE027809
6 · The paper itself

Abstract

backgroundWe 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).

methodsWe 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.

resultsThe 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%.

conclusionsPCR-based detection of HPV-16 DNA in HPV-HNSCC can be improved using rational genomic design.

Indexed as

Head and Neck NeoplasmsPapillomavirus InfectionsDNA, ViralGenomicsHuman papillomavirus 16HumansPapillomaviridaeSquamous Cell Carcinoma of Head and NeckDNA, ViralDNA primerhead and neck squamous cell carcinomahuman papillomaviruspolymerase chain reactionwhole-genome sequencing

Identifiers

PMID31850594
PMCPMC7699136
OpenAlexW2996585779

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.