Component Description
The human papillomavirus
(HPV) in oral rinse estimates the prevalence and determinants of oral HPV
infection in the United States population. Oral HPV infection is newly
appreciated as a strong risk factor for a distinct type of oropharyngeal
squamous cell carcinoma that is rising in incidences in the United States. It
has been estimated that oral HPV16 infection confers an approximate 15-fold
increase in risk for oropharyngeal cancer. Despite these strong risks, little
is known about the epidemiology of oral HPV infection. No population-based
surveys of oral HPV infection, type distribution and determinants, have been
performed in any population worldwide.
Eligible Sample
Examined
participants, aged 14-69 years, were eligible. The public-use data file
includes data for persons 18-69 years of age. Please see Analytic
Notes about the release of data for adolescents 14-17 years of age.
Description of Laboratory Methodology
Samples were
centrifuged at 4,000 x g for 10 minutes at 4°C; the pellet was resuspended in 1
ml of Puregene cell lysis solution and incubated at 37°C for 15 min followed by
DNase-free RNase a (5µg/ml) digestion for 30 min at 37°C. Proteinase K (20
mg/ml) digestion will be performed overnight at 55°C followed by heat
inactivation for 10 min at 95°C. Protein precipitation solution (340 µL) will
be added and sample will be further purified according to the Puregene DNA
purification kit protocol.
Purified DNA were
analyzed for 37 types of HPV by means of a multiplex polymerase-chain-reaction
(PCR) assay targeted to the conserved L1 region of the viral genome, using
PGYM09/11 primer pools and primers for ß-globin (33). PCR products were
denatured in 0.13 N NaOH and hybridized to an immobilized HPV probe array
(Roche Diagnostics) using an extended line-blot assay for genotyping of 37 HPV
types, including HPV-6, -11, -16, -18, -26, -31, -33, -35, -39, -40, -42, -45,
-51, -52, -53, -54, -55, -56, -57, -58, -59, -61, -62, -64, -66, -67, -68, -69,
-70, -71, -72, -73, -81, -82 (MM4 and IS39 subtypes), -83, -84 and -89, and
ß-globin (Roche Molecular Systems, Inc., Alameda, CA). Positive controls,
consisting of 10 and 100 HPV-16 (SiHa) or HPV-18 (C4–2)-positive cells diluted
in a background of HPV-negative cells (K562), and a negative control (K562
cells), in addition to the manufacturer’s controls, were included in each
experiment. Samples positive for ß-globin were considered of sufficient quality
for analysis. The HPV type were reported for positive samples.
Refer to the
Laboratory Method Files section for a detailed description of the laboratory
methods used.
There were no
changes to the lab method, lab equipment, or lab site for this component in the
NHANES 2015-2016 cycle.
Laboratory Method Files
Human Papillomavirus - Oral Rinse Laboratory Procedure Manual
(January 2019)
Laboratory Quality Assurance and Monitoring
Oral rinse
specimens were processed, stored, and shipped to The Ohio State University –
Gillison Laboratory, Columbus, Ohio for analysis.
Detailed
instructions on specimen collection and processing are discussed in the NHANES Laboratory
Procedures Manual (LPM). Vials were
stored under appropriate refrigerated (2-8°C) conditions until they were
shipped to The Ohio State University for testing.
The NHANES quality
assurance and quality control (QA/QC) protocols meet the 1988 Clinical
Laboratory Improvement Act mandates. Detailed QA/QC instructions are discussed
in the NHANES LPM.
Mobile Examination
Centers (MECs)
Laboratory team
performance is monitored using several techniques. NCHS and contract
consultants use a structured competency assessment evaluation during visits to
evaluate both the quality of the laboratory work and the quality control
procedures. Each laboratory staff person is observed for equipment operation,
specimen collection and preparation; testing procedures and constructive
feedback are given to each staff. Formal retraining sessions are conducted
annually to ensure that required skill levels were maintained.
Analytical
Laboratories
NHANES uses
several methods to monitor the quality of the analyses performed by the
contract laboratories. In the MEC, these methods include performing blind split
samples collected on “dry run” sessions. In addition, contract laboratories
randomly perform repeat testing on 2% of all specimens.
NCHS developed and
distributed a quality control protocol for all CDC and contract laboratories
when running NHANES specimens. Progress reports containing any problems
encountered during shipping or receipt of specimens, and any special
considerations are submitted to NCHS quarterly. The laboratories are required
to explain any identified areas of concern.
Data Processing and Editing
The data were
reviewed. Incomplete data or improbable values were sent to the performing
laboratory for confirmation.
Analytic Notes
Exam sample weights should be used for analyses for this dataset.
Refer to the 2015-2016
Laboratory Data Overview for general
information on NHANES laboratory data.
Demographic and
Other Related Variables
The analysis of
NHANES 2015-2016 laboratory data must be conducted using the appropriate survey
design and demographic variables. The NHANES 2015-2016
Demographics File contains demographic data, health
indicators, and other related information collected during household interviews
as well as the sample weight variables.
This laboratory data file can be linked to the other NHANES data files using the unique survey participant identifier (i.e., SEQN).
The public release
data file includes Oral HPV data for participants aged 18–69. Data
for youth aged 14–17 years are available through the NCHS Research Data Center (RDC).
Detection Limits
Since this data is
reported as qualitative data the use of lower LLODs isn’t applicable.
Please refer to the NHANES Analytic
Guidelines and the on-line NHANES Tutorial for further details on the use of sample weights and other analytic
issues.