• Component Description
• Eligible Sample
• Description of Laboratory Methodology
• Laboratory Method Files
• Laboratory Quality Assurance and Monitoring
• Data Processing and Editing
• Analytic Notes
• References
• Codebook
  • SEQN - Respondent sequence number
  • LBDRPCR - Roche HPV linear array summary result
  • LBDRHP - Roche LA high positive globin control
  • LBDRLP - Roche LA low positive globin control
  • LBDR06 - HPV type 6
  • LBDR11 - HPV type 11
  • LBDR16 - HPV type 16
  • LBDR18 - HPV type 18
  • LBDR26 - HPV type 26
  • LBDR31 - HPV type 31
  • LBDR33 - HPV type 33
  • LBDR35 - HPV type 35
  • LBDR39 - HPV type 39
  • LBDR40 - HPV type 40
  • LBDR42 - HPV type 42
  • LBDR45 - HPV type 45
  • LBDR51 - HPV type 51
  • LBDR52 - HPV type 52
  • LBDR53 - HPV type 53
  • LBDR54 - HPV type 54
  • LBDR55 - HPV type 55
  • LBDR56 - HPV type 56
  • LBDR58 - HPV type 58
  • LBDR59 - HPV type 59
  • LBDR61 - HPV type 61
  • LBDR62 - HPV type 62
  • LBDR64 - HPV type 64
  • LBDR66 - HPV type 66
  • LBDR67 - HPV type 67
  • LBDR68 - HPV type 68
  • LBDR69 - HPV type 69
  • LBDR70 - HPV type 70
  • LBDR71 - HPV type 71
  • LBDR72 - HPV type 72
  • LBDR73 - HPV type 73
  • LBDR81 - HPV type 81
  • LBDR82 - HPV type 82
  • LBDR83 - HPV type 83
  • LBDR84 - HPV type 84
  • LBDR89 - HPV type 89
  • LBDRPI - HPV type IS39

National Health and Nutrition Examination Survey

2013-2014 Data Documentation, Codebook, and Frequencies

Human Papillomavirus (HPV) DNA Results from Penile Swab Samples: Roche Linear Array (Youth) (HPVP_H_R)

RDC Only Data File: HPVP_H_R.xpt

First Published: June 2016

Last Revised: NA

Due to disclosure issues, this dataset is not available publicly. Access may be obtained through the NCHS Research Data Center (https://www.cdc.gov/rdc).

Component Description

Human papillomavirus (HPV) infection is one of the most common sexually transmitted infections in the United States. There is no national surveillance system that currently exists to measure the full burden of HPV infection. 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 aged 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 data file only includes examined male participants aged 14 to 17 years with limited access. See Analytic Notes for information on participants aged 18-59 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, 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.

Please refer to the Laboratory Method Files section for detailed laboratory procedure manual(s) of the methods used.

Laboratory Method Files

HPV Penile Swab Linear Array Laboratory Procedure Manual (Updated November 2018)

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 are stored under appropriate refrigerated (2-8°C) conditions until they are shipped to the CDC for testing.

The NHANES quality control and quality assurance protocols (QA/QC) meet the 1988 Clinical Laboratory Improvement Amendments (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. Detailed quality control and quality assurance instructions are discussed in the NHANES Laboratory Procedures Manual (LPM). 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 2013-2014 Laboratory Data Overview for general information on NHANES Laboratory data.

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 2013-2014 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 Beta globin is not present in the sample (both LBDRHP and LBDRLP are negative) and 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 beta-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)

 

References

• Hernandez BY, Wilkens LR, Unger ER, Steinau M, Markowitz L, Garvin K, Thompson PJ, Shvetsov YB, O'Dillon K, Dunne EF. Evaluation of genital self-sampling methods for HPV detection in males. J Clin Virol. 2013; 8:168-75
• Onyekwuluje JM, Steinau M, Swan DC, Unger ER. A real time PCR assay for HPV 52 detection and viral load quantification. Clin Lab 58:61-66, 2012.
• Steinau M, Swan DC, Unger ER. Type-specific reproducibility of the Roche Linear Array HPV genotyping test. J Clin Virol 2008; 42: 412-414.

Codebook and Frequencies