Table of Contents

Locator Record

Title: Human Papillomavirus (HPV) DNA Results from Vaginal Swab Samples: Digene Hybrid Capture, and Prototype Line Blot Assay (l37swa_c )
Contact Number: 1-866-441-NCHS
Years of Content: 2003 - 2004
First Published: March, 2009
Revised: October, 2010
Access Constraints: None
Use Constraints: None
Geographic Coverage: National
Subject:Human Papillomavirus (HPV) DNA Results from Vaginal Swab Samples: Digene Hybrid Capture, and Prototype Line Blot Assay
Record Source: NHANES 2003 - 2004
Survey Methodology: NHANES 2003 - 2004 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 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 (Dataset name: L37swr_c). The LA typing assay is based upon the same assay principles as the prototype, but includes proprietary refinements to improve sensitivity and reproducibility.

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 three tests described below: Digene Hybrid Capture (hc2), Prototype Line Blot Assay, and Roche Linear Array.

Digene hc2 HPV DNA Test
LBXH2RL (Hybrid Capture high risk result)
LBXH3RL (Hybrid Capture low risk result)
The Digene hc2 HPV DNA 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.  

Prototype Line Blot Assay
This assay uses HPV L1 consensus polymerase chain reaction (PCR) with biotinylated PGMY09/11 primer sets and β-globin as an internal control for sample amplification. The primer mix amplifies essentially all HPV types found in the genital tract. The amplicons are evaluated by gel electrophoresis for the presence of the 450 bp HPV amplicon. Positive samples are typed by hybridization to the Roche prototype line probe 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 do not hybridize to the typing strip are sequenced to determine the HPV type.

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.

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 was CLIA certified 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 2003–2004 laboratory data must be conducted with the key survey design and basic demographic variables. The NHANES 2003–2004 Household Questionnaire Data Files contain demographic data, health indicators, and other related information collected during household interviews. They also contain all survey design variables and sample weights . 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. The household questionnaire and phlebotomy files may be linked to the laboratory data file using the unique survey participant identifier SEQN.

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.

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 (LBDHPCR) indicates if at least one type is positive (LBDHPCR=1), the sample is negative (LBDHPCR=2), the sample is inadequate (LBDHPCR=3), or the sample is missing (LBDHPCR=.).

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

LBXH2RL - Hybrid Capture high risk (RLU) result

Variable Name:
LBXH2RL
SAS Label:
Hybrid Capture high risk (RLU) result
English Text:
Hybrid Capture high risk (RLU)result
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
0 to 1212 Range of Values 1586 1586
. Missing 273 1859

LBXH3RL - Hybrid Capture low risk (RLU) result

Variable Name:
LBXH3RL
SAS Label:
Hybrid Capture low risk (RLU) result
English Text:
Hybrid Capture low risk (RLU)result
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
0 to 924 Range of Values 1586 1586
. Missing 273 1859

LBDHPCR - HPV summary variable

Variable Name:
LBDHPCR
SAS Label:
HPV summary variable
English Text:
HPV summary variable
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 473 473
2 Negative 1044 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH06 - HPV type 06

Variable Name:
LBDH06
SAS Label:
HPV type 06
English Text:
HPV type 06
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 26 26
2 Negative 1491 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH11 - HPV type 11

Variable Name:
LBDH11
SAS Label:
HPV type 11
English Text:
HPV type 11
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 2 2
2 Negative 1515 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH16 - HPV type 16

Variable Name:
LBDH16
SAS Label:
HPV type 16
English Text:
HPV type 16
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 32 32
2 Negative 1485 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH18 - HPV type 18

Variable Name:
LBDH18
SAS Label:
HPV type 18
English Text:
HPV type 18
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 17 17
2 Negative 1500 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH26 - HPV type 26

Variable Name:
LBDH26
SAS Label:
HPV type 26
English Text:
HPV type 26
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 3 3
2 Negative 1514 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH31 - HPV type 31

Variable Name:
LBDH31
SAS Label:
HPV type 31
English Text:
HPV type 31
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 17 17
2 Negative 1500 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH33 - HPV type 33

Variable Name:
LBDH33
SAS Label:
HPV type 33
English Text:
HPV type 33
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 11 11
2 Negative 1506 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH35 - HPV type 35

Variable Name:
LBDH35
SAS Label:
HPV type 35
English Text:
HPV type 35
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 16 16
2 Negative 1501 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH39 - HPV type 39

Variable Name:
LBDH39
SAS Label:
HPV type 39
English Text:
HPV type 39
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 23 23
2 Negative 1494 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH40 - HPV type 40

Variable Name:
LBDH40
SAS Label:
HPV type 40
English Text:
HPV type 40
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 7 7
2 Negative 1510 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH42 - HPV type 42

Variable Name:
LBDH42
SAS Label:
HPV type 42
English Text:
HPV type 42
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 21 21
2 Negative 1496 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH45 - HPV type 45

Variable Name:
LBDH45
SAS Label:
HPV type 45
English Text:
HPV type 45
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 16 16
2 Negative 1501 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH51 - HPV type 51

Variable Name:
LBDH51
SAS Label:
HPV type 51
English Text:
HPV type 51
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 37 37
2 Negative 1480 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH52 - HPV type 52

Variable Name:
LBDH52
SAS Label:
HPV type 52
English Text:
HPV type 52
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 43 43
2 Negative 1474 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH53 - HPV type 53

Variable Name:
LBDH53
SAS Label:
HPV type 53
English Text:
HPV type 53
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 48 48
2 Negative 1469 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH54 - HPV type 54

Variable Name:
LBDH54
SAS Label:
HPV type 54
English Text:
HPV type 54
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 39 39
2 Negative 1478 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH55 - HPV type 55

Variable Name:
LBDH55
SAS Label:
HPV type 55
English Text:
HPV type 55
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 26 26
2 Negative 1491 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH56 - HPV type 56

Variable Name:
LBDH56
SAS Label:
HPV type 56
English Text:
HPV type 56
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 22 22
2 Negative 1495 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH58 - HPV type 58

Variable Name:
LBDH58
SAS Label:
HPV type 58
English Text:
HPV type 58
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 18 18
2 Negative 1499 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH59 - HPV type 59

Variable Name:
LBDH59
SAS Label:
HPV type 59
English Text:
HPV type 59
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 34 34
2 Negative 1483 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH61 - HPV type 61

Variable Name:
LBDH61
SAS Label:
HPV type 61
English Text:
HPV type 61
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 42 42
2 Negative 1475 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH62 - HPV type 62

Variable Name:
LBDH62
SAS Label:
HPV type 62
English Text:
HPV type 62
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 55 55
2 Negative 1462 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH64 - HPV type 64

Variable Name:
LBDH64
SAS Label:
HPV type 64
English Text:
HPV type 64
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 0 0
2 Negative 1517 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH66 - HPV type 66

Variable Name:
LBDH66
SAS Label:
HPV type 66
English Text:
HPV type 66
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 33 33
2 Negative 1484 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH67 - HPV type 67

Variable Name:
LBDH67
SAS Label:
HPV type 67
English Text:
HPV type 67
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 8 8
2 Negative 1509 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH68 - HPV type 68

Variable Name:
LBDH68
SAS Label:
HPV type 68
English Text:
HPV type 68
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 15 15
2 Negative 1502 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH69 - HPV type 69

Variable Name:
LBDH69
SAS Label:
HPV type 69
English Text:
HPV type 69
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 0 0
2 Negative 1517 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH70 - HPV type 70

Variable Name:
LBDH70
SAS Label:
HPV type 70
English Text:
HPV type 70
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 14 14
2 Negative 1503 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH71 - HPV type 71

Variable Name:
LBDH71
SAS Label:
HPV type 71
English Text:
HPV type 71
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 12 12
2 Negative 1505 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH72 - HPV type 72

Variable Name:
LBDH72
SAS Label:
HPV type 72
English Text:
HPV type 72
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 12 12
2 Negative 1505 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH73 - HPV type 73

Variable Name:
LBDH73
SAS Label:
HPV type 73
English Text:
HPV type 73
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 14 14
2 Negative 1503 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH81 - HPV type 81

Variable Name:
LBDH81
SAS Label:
HPV type 81
English Text:
HPV type 81
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 29 29
2 Negative 1488 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH82 - HPV type 82

Variable Name:
LBDH82
SAS Label:
HPV type 82
English Text:
HPV type 82
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 3 3
2 Negative 1514 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH83 - HPV type 83

Variable Name:
LBDH83
SAS Label:
HPV type 83
English Text:
HPV type 83
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 40 40
2 Negative 1477 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH84 - HPV type 84

Variable Name:
LBDH84
SAS Label:
HPV type 84
English Text:
HPV type 84
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 63 63
2 Negative 1454 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDH89 - HPV type 89

Variable Name:
LBDH89
SAS Label:
HPV type 89
English Text:
HPV type 89
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 38 38
2 Negative 1479 1517
3 Inadequate 70 1587
. Missing 272 1859

LBDHPI - HPV type IS39

Variable Name:
LBDHPI
SAS Label:
HPV type IS39
English Text:
HPV type IS39
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 2 2
2 Negative 1515 1517
3 Inadequate 70 1587
. Missing 272 1859

LBXNST - other HPV strip types

Variable Name:
LBXNST
SAS Label:
other HPV strip types
English Text:
other HPV strip types
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 HPV 22 2 2
2 HPV 32 0 2
3 HPV 38 1 3
4 HPV 44 9 12
5 HPV 74 3 15
6 HPV 85 2 17
7 HPV 87 0 17
8 HPV 91 1 18
9 HPV DL285 1 19
10 HPV IA06 1 20
. Missing 1839 1859