Table of Contents

Locator Record

Title: Human Papillomavirus (HPV) DNA Results from Vaginal Swab Samples: Digene Hybrid Capture and Roche Linear Array (HPVSWR_E )
Contact Number: 1-866-441-NCHS
Years of Content: 2007 - 2008
First Published: August, 2012
Revised: NA
Access Constraints: None
Use Constraints: None
Geographic Coverage: National
Subject:
Record Source: NHANES 2007 - 2008
Survey Methodology: NHANES 2007 - 2008 is a stratified multistage probability sample of the civilian non-institutionalized population of the U.S.
Medium: NHANES Web site; SAS transport files

Component Description

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 Developmental 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. One vaccine is licensed and recommended for use in males (Gardasil). In mid 2006, the Advisory Committee on Immunizations (ACIP), recommended routine vaccination of females aged 11 or 12 years and for those 13-26 years not previously vaccinated. In December, 2011 ACIP recommended routine vaccination of males aged 11 or 12 years and for those aged 13 through 21 years not previously vaccinated. As vaccine becomes more widely used, the national prevalence of HPV infection will be critical for evaluating vaccination strategies in the United States.

Eligible Sample

Vaginal Swab - Females aged 14 to 59 years.
Public data file includes data for persons 18-59 years of age. Please see Analytic Notes for Data Users about the release of data for adolescents 14-17 years of age.

Description of Laboratory Methodology

Vaginal Swab
Vaginal specimens were processed, stored and shipped to Atlanta, Ga. for analysis. Detailed specimen collection and processing instructions are discussed in the NHANES LPM. DNA from the vaginal swab is extracted for use in the tests described below: Digene Hybrid Capture (hc2), and Roche Linear Array.

Digene hc2 HPV DNA Test
LBXH2RL (Hybrid Capture high risk result)
LBXH3RL (Hybrid Capture low risk result)
The vaginal swab is extracted to obtain DNA. The DNA extracts are used in the Digene hc2 HPV DNA Test. This test, using Hybrid Capture 2 technology, is a nucleic acid hybridization microplate assay with signal amplification. It uses chemiluminescence for the qualitative detection of eighteen types of human papillomavirus (HPV) DNA in cervical specimens. The hc2 HPV DNA Test can differentiate between two HPV DNA groups: low-risk HPV types (LR) 6, 11, 42, 43, 44; and high/intermediate-risk HPV types (HR)16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68. It cannot determine the specific HPV type present.

Specimens containing the target DNA hybridize with the HR or LR HPV RNA probe cocktail. The resultant RNA: DNA hybrids are captured onto the surface of a microplate well coated with antibodies specific for RNA: DNA hybrids. Immobilized hybrids are then reacted with alkaline phosphatase conjugated antibodies specific for the RNA: DNA hybrids, and detected with a chemiluminescent substrate. As the substrate is cleaved by the bound alkaline phosphatase, light is emitted which is measured as relative light units (RLUs) on a luminometer. The intensity of the light emitted denotes the presence or absence of target DNA in the specimen. An RLU measurement equal to or greater than the Cutoff Value indicates the presence of HPV DNA sequences in the specimen. An RLU measurement less than the Cutoff Value indicates the absence of the specific HPV DNA sequences tested or HPV DNA levels below the detection limit of the assay. 

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, 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.

Data Processing and Editing

Read the LABDOC file for detailed data processing and editing protocols.

Laboratory Quality Assurance and Monitoring

While HC2 is approved for clinical testing, the self-collected vaginal sample does not meet clinical guidelines. 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/Medical Technologists Procedures Manual (LPM). Read the LABDOC file for detailed QA/QC protocols. The analytical methods are described in the Description of the Laboratory Methodology section.

Analytic Notes

The analysis of NHANES laboratory data must be conducted with the key survey design and basic demographic variables. The Demographic file contains: status variables providing core information on the survey participant including examination status, demographic variables including age, gender, race etc., and interview and examination sample weight variables and survey design variables. The Questionnaire data files contain socio-economic data, health indicators, and other related information collected during household interviews. Certain sensitive data on respondents 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 Phlebotomy file includes auxiliary information such as the conditions precluding venipuncture. These files may be linked to the Laboratory data file using the unique survey participant identifier SEQN.

Vaginal Swab
Digene hc2 HPV DNA Test
An RLU measurement equal to or greater than the Cutoff Value of 1.0 indicates the presence of HPV DNA sequences in the specimen. An RLU measurement less than the Cutoff Value indicates the absence of the specific HPV DNA sequences tested or HPV DNA levels below the detection limit of the assay.

HPV PCR Assay
HPV Summary Variable
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 there is no Beta globin 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.

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 positive for the XR probe and 33, 35, or 58 require specific testing to confirm the presence of HPV 52.

References

Codebook and Frequencies

SEQN - Respondent sequence number

Variable Name:
SEQN
SAS Label:
Respondent sequence number
English Text:
Respondent sequence number.
Target:
Females only 18 YEARS - 59 YEARS

LBDRPCR - Roche HPV linear array summary result

Variable Name:
LBDRPCR
SAS Label:
Roche HPV linear array summary result
English Text:
Roche HPV linear array (LA) summary result
Target:
Females only 18 YEARS - 59 YEARS

LBXH2RL - Digene HPV Swab High Risk RLU/CB

Variable Name:
LBXH2RL
SAS Label:
Digene HPV Swab High Risk RLU/CB
English Text:
Digene HPV Swab High Risk RLU/CB
Target:
Females only 18 YEARS - 59 YEARS

LBXH3RL - Digene HPV Swab Low Risk RLU/CB

Variable Name:
LBXH3RL
SAS Label:
Digene HPV Swab Low Risk RLU/CB
English Text:
Digene HPV Swab Low Risk RLU/CB
Target:
Females only 18 YEARS - 59 YEARS

LBDRHP - Roche LA high positive globin control

Variable Name:
LBDRHP
SAS Label:
Roche LA high positive globin control
English Text:
Roche LA high positive globin control
Target:
Females only 18 YEARS - 59 YEARS

LBDRLP - Roche LA low positive globin control

Variable Name:
LBDRLP
SAS Label:
Roche LA low positive globin control
English Text:
Roche LA low positive globin control
Target:
Females only 18 YEARS - 59 YEARS

LBDR06 - HPV type 6

Variable Name:
LBDR06
SAS Label:
HPV type 6
English Text:
HPV type 6
Target:
Females only 18 YEARS - 59 YEARS

LBDR11 - HPV type 11

Variable Name:
LBDR11
SAS Label:
HPV type 11
English Text:
HPV type 11
Target:
Females only 18 YEARS - 59 YEARS

LBDR16 - HPV type 16

Variable Name:
LBDR16
SAS Label:
HPV type 16
English Text:
HPV type 16
Target:
Females only 18 YEARS - 59 YEARS

LBDR18 - HPV type 18

Variable Name:
LBDR18
SAS Label:
HPV type 18
English Text:
HPV type 18
Target:
Females only 18 YEARS - 59 YEARS

LBDR26 - HPV type 26

Variable Name:
LBDR26
SAS Label:
HPV type 26
English Text:
HPV type 26
Target:
Females only 18 YEARS - 59 YEARS

LBDR31 - HPV type 31

Variable Name:
LBDR31
SAS Label:
HPV type 31
English Text:
HPV type 31
Target:
Females only 18 YEARS - 59 YEARS

LBDR33 - HPV type 33

Variable Name:
LBDR33
SAS Label:
HPV type 33
English Text:
HPV type 33
Target:
Females only 18 YEARS - 59 YEARS

LBDR35 - HPV type 35

Variable Name:
LBDR35
SAS Label:
HPV type 35
English Text:
HPV type 35
Target:
Females only 18 YEARS - 59 YEARS

LBDR39 - HPV type 39

Variable Name:
LBDR39
SAS Label:
HPV type 39
English Text:
HPV type 39
Target:
Females only 18 YEARS - 59 YEARS

LBDR40 - HPV type 40

Variable Name:
LBDR40
SAS Label:
HPV type 40
English Text:
HPV type 40
Target:
Females only 18 YEARS - 59 YEARS

LBDR42 - HPV type 42

Variable Name:
LBDR42
SAS Label:
HPV type 42
English Text:
HPV type 42
Target:
Females only 18 YEARS - 59 YEARS

LBDR45 - HPV type 45

Variable Name:
LBDR45
SAS Label:
HPV type 45
English Text:
HPV type 45
Target:
Females only 18 YEARS - 59 YEARS

LBDR51 - HPV type 51

Variable Name:
LBDR51
SAS Label:
HPV type 51
English Text:
HPV type 51
Target:
Females only 18 YEARS - 59 YEARS

LBDR52 - HPV type 52

Variable Name:
LBDR52
SAS Label:
HPV type 52
English Text:
HPV type 51
Target:
Females only 18 YEARS - 59 YEARS

LBDR53 - HPV type 53

Variable Name:
LBDR53
SAS Label:
HPV type 53
English Text:
HPV type 53
Target:
Females only 18 YEARS - 59 YEARS

LBDR54 - HPV type 54

Variable Name:
LBDR54
SAS Label:
HPV type 54
English Text:
HPV type 54
Target:
Females only 18 YEARS - 59 YEARS

LBDR55 - HPV type 55

Variable Name:
LBDR55
SAS Label:
HPV type 55
English Text:
HPV type 55
Target:
Females only 18 YEARS - 59 YEARS

LBDR56 - HPV type 56

Variable Name:
LBDR56
SAS Label:
HPV type 56
English Text:
HPV type 56
Target:
Females only 18 YEARS - 59 YEARS

LBDR58 - HPV type 58

Variable Name:
LBDR58
SAS Label:
HPV type 58
English Text:
HPV type 58
Target:
Females only 18 YEARS - 59 YEARS

LBDR59 - HPV type 59

Variable Name:
LBDR59
SAS Label:
HPV type 59
English Text:
HPV type 59
Target:
Females only 18 YEARS - 59 YEARS

LBDR61 - HPV type 61

Variable Name:
LBDR61
SAS Label:
HPV type 61
English Text:
HPV type 61
Target:
Females only 18 YEARS - 59 YEARS

LBDR62 - HPV type 62

Variable Name:
LBDR62
SAS Label:
HPV type 62
English Text:
HPV type 62
Target:
Females only 18 YEARS - 59 YEARS

LBDR64 - HPV type 64

Variable Name:
LBDR64
SAS Label:
HPV type 64
English Text:
HPV type 64
Target:
Females only 18 YEARS - 59 YEARS

LBDR66 - HPV type 66

Variable Name:
LBDR66
SAS Label:
HPV type 66
English Text:
HPV type 66
Target:
Females only 18 YEARS - 59 YEARS

LBDR67 - HPV type 67

Variable Name:
LBDR67
SAS Label:
HPV type 67
English Text:
HPV type 67
Target:
Females only 18 YEARS - 59 YEARS

LBDR68 - HPV type 68

Variable Name:
LBDR68
SAS Label:
HPV type 68
English Text:
HPV type 68
Target:
Females only 18 YEARS - 59 YEARS

LBDR69 - HPV type 69

Variable Name:
LBDR69
SAS Label:
HPV type 69
English Text:
HPV type 69
Target:
Females only 18 YEARS - 59 YEARS

LBDR70 - HPV type 70

Variable Name:
LBDR70
SAS Label:
HPV type 70
English Text:
HPV type 70
Target:
Females only 18 YEARS - 59 YEARS

LBDR71 - HPV type 71

Variable Name:
LBDR71
SAS Label:
HPV type 71
English Text:
HPV type 71
Target:
Females only 18 YEARS - 59 YEARS

LBDR72 - HPV type 72

Variable Name:
LBDR72
SAS Label:
HPV type 72
English Text:
HPV type 72
Target:
Females only 18 YEARS - 59 YEARS

LBDR73 - HPV type 73

Variable Name:
LBDR73
SAS Label:
HPV type 73
English Text:
HPV type 73
Target:
Females only 18 YEARS - 59 YEARS

LBDR81 - HPV type 81

Variable Name:
LBDR81
SAS Label:
HPV type 81
English Text:
HPV type 81
Target:
Females only 18 YEARS - 59 YEARS

LBDR82 - HPV type 82

Variable Name:
LBDR82
SAS Label:
HPV type 82
English Text:
HPV type 82
Target:
Females only 18 YEARS - 59 YEARS

LBDR83 - HPV type 83

Variable Name:
LBDR83
SAS Label:
HPV type 83
English Text:
HPV type 83
Target:
Females only 18 YEARS - 59 YEARS

LBDR84 - HPV type 84

Variable Name:
LBDR84
SAS Label:
HPV type 84
English Text:
HPV type 84
Target:
Females only 18 YEARS - 59 YEARS

LBDR89 - HPV type 89

Variable Name:
LBDR89
SAS Label:
HPV type 89
English Text:
HPV type 89
Target:
Females only 18 YEARS - 59 YEARS

LBDRPI - HPV type IS39

Variable Name:
LBDRPI
SAS Label:
HPV type IS39
English Text:
HPV type IS39
Target:
Females only 18 YEARS - 59 YEARS