Table of Contents

Locator Record

Title: Human Papillomavirus (HPV) DNA Results from Vaginal Swab Samples: Digene Hybrid Capture, and Roche Linear Array (l37swr_c )
Contact Number: 1-866-441-NCHS
Years of Content: 2003 - 2004
First Published: November, 2010
Revised: NA
Access Constraints: None
Use Constraints: None
Geographic Coverage: National
Subject:Human Papillomavirus (HPV) DNA Results from Vaginal Swab Samples: Digene Hybrid Capture, Prototype Line Blot Assay, and Roche Linear Array
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. 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 (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 requires 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
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 781 781
2 Negative 777 1558
3 Inadequate 29 1587
. Missing 272 1859

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
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 1552 1552
2 Negative 35 1587
. Missing 272 1859

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
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 1540 1540
2 Negative 47 1587
. Missing 272 1859

LBDR06 - HPV type 6

Variable Name:
LBDR06
SAS Label:
HPV type 6
English Text:
HPV type 6
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 68 68
2 Negative 1490 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR11 - HPV type 11

Variable Name:
LBDR11
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 8 8
2 Negative 1550 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR16 - HPV type 16

Variable Name:
LBDR16
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 71 71
2 Negative 1487 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR18 - HPV type 18

Variable Name:
LBDR18
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 38 38
2 Negative 1520 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR26 - HPV type 26

Variable Name:
LBDR26
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 4 4
2 Negative 1554 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR31 - HPV type 31

Variable Name:
LBDR31
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 32 32
2 Negative 1526 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR33 - HPV type 33

Variable Name:
LBDR33
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 32 32
2 Negative 1526 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR35 - HPV type 35

Variable Name:
LBDR35
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 27 27
2 Negative 1531 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR39 - HPV type 39

Variable Name:
LBDR39
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 40 40
2 Negative 1518 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR40 - HPV type 40

Variable Name:
LBDR40
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 24 24
2 Negative 1534 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR42 - HPV type 42

Variable Name:
LBDR42
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 42 42
2 Negative 1516 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR45 - HPV type 45

Variable Name:
LBDR45
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 44 44
2 Negative 1514 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR51 - HPV type 51

Variable Name:
LBDR51
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 101 101
2 Negative 1457 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR52 - HPV type 52

Variable Name:
LBDR52
SAS Label:
HPV type 52
English Text:
HPV type 51
Target:
Females only 18 YEARS - 59 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 61 61
2 Negative 1497 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR53 - HPV type 53

Variable Name:
LBDR53
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 105 105
2 Negative 1453 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR54 - HPV type 54

Variable Name:
LBDR54
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 70 70
2 Negative 1488 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR55 - HPV type 55

Variable Name:
LBDR55
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 45 45
2 Negative 1513 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR56 - HPV type 56

Variable Name:
LBDR56
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 41 41
2 Negative 1517 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR58 - HPV type 58

Variable Name:
LBDR58
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 30 30
2 Negative 1528 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR59 - HPV type 59

Variable Name:
LBDR59
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 62 62
2 Negative 1496 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR61 - HPV type 61

Variable Name:
LBDR61
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 85 85
2 Negative 1473 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR62 - HPV type 62

Variable Name:
LBDR62
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 113 113
2 Negative 1445 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR64 - HPV type 64

Variable Name:
LBDR64
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 1 1
2 Negative 1557 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR66 - HPV type 66

Variable Name:
LBDR66
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 69 69
2 Negative 1489 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR67 - HPV type 67

Variable Name:
LBDR67
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 16 16
2 Negative 1542 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR68 - HPV type 68

Variable Name:
LBDR68
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 29 29
2 Negative 1529 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR69 - HPV type 69

Variable Name:
LBDR69
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 7 7
2 Negative 1551 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR70 - HPV type 70

Variable Name:
LBDR70
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 47 47
2 Negative 1511 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR71 - HPV type 71

Variable Name:
LBDR71
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 20 20
2 Negative 1538 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR72 - HPV type 72

Variable Name:
LBDR72
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 26 26
2 Negative 1532 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR73 - HPV type 73

Variable Name:
LBDR73
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 30 30
2 Negative 1528 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR81 - HPV type 81

Variable Name:
LBDR81
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 54 54
2 Negative 1504 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR82 - HPV type 82

Variable Name:
LBDR82
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 11 11
2 Negative 1547 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR83 - HPV type 83

Variable Name:
LBDR83
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 85 85
2 Negative 1473 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR84 - HPV type 84

Variable Name:
LBDR84
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 104 104
2 Negative 1454 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDR89 - HPV type 89

Variable Name:
LBDR89
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 92 92
2 Negative 1466 1558
3 Inadequate 29 1587
. Missing 272 1859

LBDRPI - HPV type IS39

Variable Name:
LBDRPI
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 0 0
2 Negative 784 784
3 Inadequate 29 813
. Missing 1046 1859