Human papillomavirus (HPV) infection is one of the most common sexually transmitted infections in the United States. Cervical infection with certain types of HPV is a major risk factor for cervical cancer in women. The “high-risk” types of HPV (e.g., HPV 16, 18) are associated with cervical cancer and the “low-risk” types (e.g., HPV 6, 11) with genital warts. No national surveillance system exists to measure the full burden of HPV infection, and no reliable national population estimate of HPV exists. NHANES offers a unique opportunity to assess the prevalence of HPV infection in the general population.
Reducing the prevalence of HPV infection is a Healthy People 2010 objective: “Reducing the number of new HPV cases can help minimize the overall number of cases of high risk subtypes associated with cervical cancer in females...” Detection and typing of HPV DNA in vaginal swabs (in conjunction with testing of NHANES sera for HPV antibody) will allow evaluation of trends in prevalence of type-specific HPV infection by age, sexual behavior, and race/ethnicity. Two HPV vaccines (Gardasil and Cervarix) are licensed and recommended for use in girls and women. Routine vaccination is recommended for girls 11 or 12 years of age, and catch-up vaccination through 26 years. One vaccine (Gardasil) is licensed and available for boys and men. As vaccine becomes more widely used, the national prevalence of HPV infection will be critical for planning vaccination strategies in the United States.
Results of the Digene hc2 HPV DNA Test and HPV typing based on the Roche prototype line blot assay have been previously released. The current data release adds HPV typing results based on the Roche research use only Linear Array (LA) HPV Genotyping kit. The LA typing assay is based upon the same assay principles as the prototype, but includes proprietary refinements to improve sensitivity and reproducibility.
Examined female participants aged 14-59 years were eligible. This public data file includes data for examined participants aged 18-59 years. Please see Analytic Notes about the release of data for adolescents aged 14-17 years.
Description of Laboratory Methodology
Roche Linear Array Assay
This assay uses the Research Use Only (RUO) 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, IS39, and 89) 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.
Laboratory Method Files
HPV Vaginal Swab Linear Array Laboratory Procedure Manual
Laboratory Quality Assurance and Monitoring
samples were processed, stored and shipped to the Chronic Viral Diseases
Branch, Division of High-Consequence Pathogens and Pathology, National Center
for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and
Prevention, Atlanta, GA for analysis.
instructions on specimen collection and processing are discussed in the NHANES
Laboratory Procedures Manual (LPM). Swabs were stored at room
temperature until they were shipped to the National Center for Emerging and
Zoonotic Infectious Diseases for testing.
instructions are discussed in the NHANES LPM.
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 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 were maintained.
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.
containing any problems encountered during shipping or receipt of specimens,
summary statistics for each control pool, QC graphs, instrument calibration,
reagents, and any special considerations are submitted to NCHS quarterly. The
reports are reviewed for trends or shifts in the data. 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.
Refer to the 2003-2004
Laboratory Data Overview for general information on NHANES
MEC exam sample
weights should be used for analyses.
Other Related Variables
The analysis of
NHANES laboratory data must be conducted using the appropriate survey design
and demographic variables. The NHANES 2003-2004
Demographics File contains demographic data, health indicators, and
other related information collected during household interviews as well as the
sample design variables. The recommended procedure for variance estimation
requires use of stratum and PSU variables (SDMVSTRA and SDMVPSU, respectively)
in the demographic data file.
data file can be linked to the other NHANES data files using the unique survey
participant identifier (i.e., SEQN).
data files contain socio-economic data, health indicators, and other related
information collected during household interviews. Certain sensitive data on participants
under 18 years of age (e.g., HPV typing results, sexual behavior variables) are
not included in the public use files. These data may be requested as described
in the NHANES guidelines.
The public release
data file includes HPV vaginal swab data for participants aged 18-59. HPV
vaginal swab data for youth aged 14-17 years are available through the NCHS Research Data Center
HPV DNA detection
and typing results from two assays are provided: the Roche prototype line blot
assay (previously released, Data set name: l37SWA_C) and the Roche research use
only Linear Array (LA) HPV Genotyping kit (Data set name: l37SWR_C). The Roche
prototype reagents were discontinued when the LA assay was released and will
not be available for further use in future NHANES cycles. While based on identical
principles, the LA was refined for commercialization as a research use only
kit. The two assays were comparable, although LA was found to be more sensitive
and detected more types per sample (3, 4, 5). To assure comparability of
results in the ongoing NHANES sampling, residual extracts from 2003-2004 were
retested with LA.
• We recommend
all analysis of HPV DNA PCR be conducted using the Roche LA results (Data set
name: L37SWR_C) in order to provide the most accurate longitudinal information
on HPV detection and typing by PCR.
Note: The two data
sets can also be distinguished by the variable names. The data for the Roche
prototype line blot assay has a fourth letter of the variable name, H. The
Roche LA assay has the fourth letter of the variable name, R.
HPV PCR Assay
The HPV PCR
Summary variable (LBDRPCR) indicates if at least one type is positive
(LBDRPCR=1), the sample is negative (LBDRPCR=2), the sample is inadequate
(LBDRPCR=3), or the sample is missing (LBDRPCR=.).
If beta-globin is
not present, both LBDRHP and LBDRLP are negative in the sample and no HPV type
is 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
beta-globin is detected (either LBDRHP or LBDRLP is positive) the sample is
coded as negative.
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 positive for the XR probe and 33, 35
or 58 requires specific testing to confirm the presence of HPV 52.
If data is qualitative, the use of lower limits of
detection (LLODs) is not applicable.
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.