Component Description
Human
papillomavirus (HPV) infection is one of the most common sexually transmitted
infections in the United States. Although HPV can infect men and women, less is
known about HPV prevalence in men. In 2011, routine HPV vaccination was recommended
by the Advisory Committee on Immunization Practices (ACIP) for males aged 11-12
years. Vaccination was also recommended for men through age 21 years if not
previously vaccinated. Information on the national prevalence of HPV infection
is important for planning vaccination strategies and monitoring the impact of
vaccination in the United States.
Eligible Sample
Examined male
participants aged 14-59 years were eligible. This public data file only
includes examined participants aged 18-59 years. See Analytic Notes for information on participants aged 14-17 years.
Description of Laboratory Methodology
DNA from the self-collected
penile swab is extracted for use in the test below: Roche Linear Array.
Roche Linear Array
Assay
This assay uses
Roche Linear Array HPV Genotyping test that is based on HPV L1 consensus
polymerase chain reaction (PCR) with biotinylated PGMY09/11 primer sets. It
also includes biotinylated β-globin primers as an internal control for sample
amplification. The primer mix amplifies essentially all HPV types found in the
genital tract along with the human β-globin gene. After amplification the
samples are typed by hybridization to the typing strips followed by
colorimetric detection. The strip is a linear array of probes specific for 37
HPV types (6, 11, 16, 18, 26, 31, 33, 35, 39, 40, 42, 45, 51, 52, 53, 54, 55,
56, 58, 59, 61, 62, 64, 66, 67, 68, 69, 70, 71, 72, 73, 81, 82, 83, 84, 89, and IS39)
and for the positive β-globin control as well. Types are read by comparing the
reaction pattern to the typing template. Samples that are negative for HPV and
the β-globin control indicate lack of a suitable sample and are considered
inadequate for interpretation.
Refer to the
Laboratory Method Files section for a detailed description of the laboratory methods
used.
Laboratory Method Files
HPV Penile Swab Linear Array Laboratory Procedure Manual
(November 2019)
Laboratory Quality Assurance and Monitoring
Penile swab specimens
are processed, stored, and shipped to the Division of High-Consequence
Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious
Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, GA 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 National Center
for Emerging and Zoonotic Infectious Diseases for testing.
The NHANES quality
control and quality assurance protocols (QA/QC) meet the 1988 Clinical
Laboratory Improvement Act (CLIA) 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 quality assurance
evaluation during unscheduled visits to evaluate both the quality of the
laboratory work and the quality-control procedures. Each laboratory staff
member is observed for equipment operation, specimen collection and
preparation; testing procedures and constructive feedback are given to each staff
member. Formal retraining sessions are conducted annually to ensure that
required skill levels are 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.
Progress reports
containing any problems encountered during shipping or receipt of specimens are
submitted to NCHS. The reports are reviewed and the laboratories are required
to explain any identified areas of concern.
The HPV PCR tests
are research tests. The HPV laboratory followed strict research QC/QA and has
been CLIA certified since August 2008. The analytical methods are described in
the Description of the Laboratory Methodology section.
Data Processing and Editing
The data were
reviewed. Incomplete data or improbable values were sent to the performing
laboratory for confirmation.
Analytic Notes
Refer to the 2015-2016 Laboratory Data Overview for general information on NHANES laboratory
data.
Please refer to the NHANES Analytic Guidelines and
the on-line NHANES Tutorial for details on the use of sample
weights and analytic issues.
Sample Weights
MEC exam sample weights should be used for analyses.
Demographic and
Other Related Variables
The analysis of NHANES 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).
HPV PCR Assay
Summary Variable
HPV PCR Summary variable (LBDRPCR) indicates the following: if at least one
type is positive (LBDRPCR=1); if the sample is negative (LBDRPCR=2); if the
sample is inadequate (LBDRPCR=3); or if the sample is missing (LBDRPCR=.).
If β-globin is
not present in the sample (both LBDRHP and LBDRLP are negative) and an HPV type is
not detected, the sample is coded as inadequate.
If any of the
types on the strips (LBDR06-LBDRPI) are positive, the sample is coded as
positive. If all of the types on the strip are coded as negative, and
β-globin is detected (either LBDRHP or LBDRLP is positive) the sample is
coded as negative.
Variables LBDRHP
through LBDRPI are from the RUO Roche Linear Array HPV typing assay, however,
LBDR52 also includes information from a type-specific assay for HPV 52. The
Linear Array typing strip includes an XR probe that hybridizes with HPV 52 as
well as HPV types 33, 35 and 58. Samples that are positive for the XR probe and
33, 35, or 58 require specific testing to confirm the presence of HPV 52.
Detection Limits
Since this data is reported as qualitative data the use of lower LLODs is not
applicable.
Data Access
The public release data file includes HPV DNA data for males aged 18-59 years.
HPV DNA data for youth aged 14–17 years are available through the NCHS Research Data Center (RDC).