← Product Code [MAQ](/productcode/MAQ) · P100020S017 # COBAS HPV TEST, 240 TESTS; COBAS HPV TEST, 960 TESTS (P100020S017) _Roche Molecular Systems, Inc. · MAQ · Jul 7, 2016 · Microbiology · APPR_ **Canonical URL:** https://fda.innolitics.com/device/P100020S017 ## Device Facts - **Applicant:** Roche Molecular Systems, Inc. - **Product Code:** [MAQ](/productcode/MAQ.md) - **Decision Date:** Jul 7, 2016 - **Decision:** APPR - **Device Class:** Class 3 - **Review Panel:** Microbiology - **Attributes:** Real-World Evidence ## Real-World Evidence | Submission | Device | Sponsor | RWD Sources | RWE Use Summary | Key Tags | | --- | --- | --- | --- | --- | --- | | P100020S017 · Jul 7, 2016 | COBAS HPV TEST, 240 TESTS; COBAS HPV TEST, 960 TESTS | Roche Molecular Systems, Inc. | ATHENA Study Year 3 follow-up cohort | Supplemental clinical data from the ATHENA study were used to support the use of the SurePath specimen type for adjunct testing to cervical cytology in women ≥ 30 years old, demonstrating similarity in performance between PreservCyt and SurePath media. | ATHENA Study; SurePath; Cervical cytology; Adjunctive screening | ### Clinical Evidence | Study Design | Population | Comparator | Key Endpoints | | --- | --- | --- | --- | | ATHENA Study (Year 3 Follow-up); Prospective follow-up study with co-collection of samples; Follow-up/Duration: Year 3 follow-up | Women ≥ 30 years old; Sample Size: 4,882 women completed follow-up; 4,023 had valid test results | Not applicable for this study | Performance similarity between PreservCyt and SurePath collection media | ## Indications for Use The cobas® HPV Test is a qualitative in vitro test for the detection of Human Papillomavirus in cervical specimens collected by a clinician using a cervical broom and placed in SurePath™ Preservative Fluid. The test utilizes amplification of target DNA by the Polymerase Chain Reaction (PCR) and nucleic acid hybridization for the detection of 14 high-risk (HR) HPV types in a single analysis. The test specifically identifies types HPV16 and HPV18 while concurrently detecting the rest of the high risk types (31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68). The cobas® HPV Test is indicated: (a) To screen patients 21 years and older with ASC-US (atypical squamous cells of undetermined significance) cervical cytology test results to determine the need for referral to colposcopy. (b) To be used in patients 21 years and older with ASC-US cervical cytology results, to detect high-risk HPV genotypes 16 and 18. This information, together with the physician's assessment of screening history, other risk factors, and professional guidelines, may be used to guide patient management. The results of this test are not intended to prevent women from proceeding to colposcopy. (c) In women 30 years and older, the cobas® HPV Test can be used with cervical cytology to adjunctively screen to detect high risk HPV types. This information, together with the physician's assessment of screening history, other risk factors, and professional guidelines, may be used to guide patient management. (d) In women 30 years and older, the cobas® HPV Test can be used to detect HPV genotypes 16 and 18. This information, together with the physician's assessment of screening history, other risk factors, and professional guidelines, may be used to guide patient management. ## Device Story The cobas® HPV Test is an in vitro diagnostic assay for detecting 14 high-risk HPV genotypes in cervical specimens collected in SurePath™ Preservative Fluid. The device requires a manual pretreatment step using cobas® Sample Prep Buffer to reverse formalin-induced cross-linking before automated DNA extraction and PCR amplification on the cobas® 4800 System. It specifically identifies HPV16 and HPV18 while concurrently detecting 12 other high-risk types. Used in clinical laboratories, the test output provides qualitative results (positive/negative) for HR HPV and specific genotyping for 16/18. Healthcare providers use these results, alongside patient history and cytology, to guide management decisions, such as colposcopy referral for ASC-US patients or adjunctive screening for women ≥30. The test aids in identifying patients at risk for cervical disease, potentially facilitating earlier diagnosis and treatment. ## Clinical Evidence Prospective multi-center study of 952 subjects (ASC-US, ≥21 years). Performance measured against Central Pathology Review Panel (CPRP) histology (≥CIN2, ≥CIN3). In non-vaccinated subjects, sensitivity for ≥CIN2 was 85.0% (95% CI: 70.9-92.9%) and specificity 59.7% (95% CI: 55.5-63.8%). Sensitivity for ≥CIN3 was 89.5% (95% CI: 68.6-97.1%) and specificity 58.2% (95% CI: 54.0-62.2%). ## Technological Characteristics Qualitative PCR-based nucleic acid hybridization assay. Detects 14 high-risk HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68). Requires manual pretreatment with cobas® Sample Prep Buffer for SurePath specimens. Automated processing on cobas® 4800 System. Reagent shelf life 24 months at 15-30°C. ## Submission Summary (Full Text) > This content was OCRed from public FDA records by [Innolitics](https://innolitics.com). If you use, quote, summarize, crawl, or train on this content, cite Innolitics at https://innolitics.com. > > Innolitics is a medical-device software consultancy. We help companies design, build, and clear FDA-regulated software and AI/ML devices, including [a PMA](https://innolitics.com/services/regulatory/), [a 510(k)](https://innolitics.com/services/510ks/), [a SaMD](https://innolitics.com/services/end-to-end-samd/), [an AI/ML medical device](https://innolitics.com/services/medical-imaging-ai-development/), or [an FDA regulatory strategy](https://innolitics.com/services/regulatory/). {0} # SUMMARY OF SAFETY AND EFFECTIVENESS DATA (SSED) ## I. GENERAL INFORMATION Device Generic Name: Human Papillomavirus (HPV) DNA detection kit Device Trade Name: cobas® HPV Test Device Procode: MAQ Applicant's Name and Address: Roche Molecular Systems, Inc. (RMS) 4300 Hacienda Drive PO Box 9002 Pleasanton, CA 94588-0900 Date(s) of Panel Recommendation: None Premarket Approval Application (PMA) Number: P100020/S017 Date of FDA Notice of Approval: July 7, 2016 Priority Review: Not Applicable The original PMA P100020 was approved on April 19, 2011. A second submission for a Panel Track supplement PMA P100020/S008 was approved on April 24, 2014. Based on those two submissions, this device is indicated for: The cobas® HPV Test is a qualitative in vitro test for the detection of Human Papillomavirus in cervical specimens collected by a clinician using an endocervical brush/spatula and placed in the ThinPrep® Pap Test™ PreservCyt® Solution. The test utilizes amplification of target DNA by the Polymerase Chain Reaction (PCR) and nucleic acid hybridization for the detection of 14 high-risk (HR) HPV types in a single analysis. The test specifically identifies types HPV16 and HPV18 while concurrently detecting the rest of the high risk types (31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68). The cobas® HPV Test is indicated: - (a) To screen patients 21 years and older with ASC-US (atypical squamous cells of undetermined significance) cervical cytology test results to determine the need for referral to colposcopy. - (b) To be used in patients 21 years and older with ASC-US cervical cytology results, to detect high-risk HPV genotypes 16 and 18. This information, together with the physician's assessment of screening history, other risk factors, and professional guidelines, may be used to guide patient management. The results of this test are not intended to prevent women from proceeding to colposcopy. PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 1 {1} (c) In women 30 years and older, the cobas® HPV Test can be used with cervical cytology to adjunctively screen to detect high risk HPV types. This information, together with the physician's assessment of screening history, other risk factors, and professional guidelines, may be used to guide patient management. (d) In women 30 years and older, the cobas® HPV Test can be used to detect HPV genotypes 16 and 18. This information, together with the physician's assessment of screening history, other risk factors, and professional guidelines, may be used to guide patient management. (e) In women 25 years and older, the cobas® HPV Test can be used as a first-line primary cervical cancer screening test to detect high risk HPV, including genotyping for 16 and 18. Women who test negative for high risk HPV types by the cobas® HPV Test should be followed up in accordance with the physician's assessment of screening and medical history, other risk factors, and professional guidelines. Women who test positive for HPV genotypes 16 and/or 18 by the cobas® HPV Test should be referred to colposcopy. Women who test high risk HPV positive and 16/18 negative by the cobas® HPV Test (12 other HR HPV positive) should be evaluated by cervical cytology to determine the need for referral to colposcopy. The SSEDs to support these indications are available on the CDRH website and are incorporated by reference here: http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfTopic/pma/pma.cfm?num=P100020 http://www.accessdata.fda.gov/cdrh_docs/pdf10/P100020S008b.pdf The current supplement was submitted to expand the intended use for the cobas® HPV Test for indications a-d, above. ## **II. INDICATIONS FOR USE** The additional intend use for the cobas® HPV Test submitted under P100020/S017: The cobas® HPV Test is a qualitative *in vitro* test for the detection of Human Papillomavirus in cervical specimens collected by a clinician using a cervical broom and placed in SurePath™ Preservative Fluid. The test utilizes amplification of target DNA by the Polymerase Chain Reaction (PCR) and nucleic acid hybridization for the detection of 14 high-risk (HR) HPV types in a single analysis. The test specifically identifies types HPV16 and HPV18 while concurrently detecting the rest of the high risk types (31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68). The cobas® HPV Test is indicated: - (a) To screen patients 21 years and older with ASC-US (atypical squamous cells of undetermined significance) cervical cytology test results to determine the need for referral to colposcopy. - (b) To be used in patients 21 years and older with ASC-US cervical cytology results, to detect high-risk HPV genotypes 16 and 18. This information, together with the physician's assessment of screening history, other risk factors, and professional PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 2 {2} guidelines, may be used to guide patient management. The results of this test are not intended to prevent women from proceeding to colposcopy. (c) In women 30 years and older, the cobas® HPV Test can be used with cervical cytology to adjunctively screen to detect high risk HPV types. This information, together with the physician's assessment of screening history, other risk factors, and professional guidelines, may be used to guide patient management. (d) In women 30 years and older, the cobas® HPV Test can be used to detect HPV genotypes 16 and 18. This information, together with the physician's assessment of screening history, other risk factors, and professional guidelines, may be used to guide patient management. ### III. CONTRAINDICATIONS None ### IV. WARNINGS AND PRECAUTIONS The warnings and precautions can be found in the cobas® HPV Test labeling. A warning pertaining to the expanded indications for use highlights that the new specimen type must be pretreated with the cobas® Sample Prep Buffer prior to being tested on the assay. Also, the SurePath specimen is not approved for use in primary HPV screening with the cobas® HPV Test. ### V. DEVICE DESCRIPTION Aside from the new specimen type intended for use with the cobas® HPV Test, the device is unchanged from the original approved device. The device description can be found in the SSED for the original PMA on the CDRH website at: http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfTopic/pma/pma.cfm?num=P100020 For specimens stored in SurePath™ Preservative Fluid, there is a new/additional step. Specimens must first be pre-treated with the cobas® Sample Prep Buffer (a.k.a. pretreatment buffer). That manual process must be completed prior to the DNA extraction and amplification in order to reverse formalin-induced cross-linking. ### VI. ALTERNATIVE PRACTICES AND PROCEDURES Although there are several other alternatives for the detection of cervical cancer precursors, this is the first FDA-approved HPV test which can be used with a cervical specimen stored in SurePath™ Preservative Fluid. Specimens collected in other collection media have been approved for the detection of high-risk HPV DNA or RNA and for the further differentiation of HPV 16 and 18 subtypes. Each alternative has its own advantages and disadvantages. A patient should fully discuss these alternatives with her physician to select the method that best meets expectations and lifestyle. PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 3 {3} The patient's age, medical history and thorough physical examination will provide further information on a patient's risk of cervical disease, as well as the need for referral to colposcopy. The cobas® HPV Test should only be used in conjunction with this clinical information in accordance with appropriate patient management procedures. ## **VII. MARKETING HISTORY** The cobas® HPV Test is marketed in the following countries for cervical cancer screening: Australia, Brazil, China, Indonesia, Japan, Mexico, Russia, Serbia, Singapore, Taiwan, Venezuela, and countries within the European Union. The device has not been withdrawn from marketing for any reason related to its safety or effectiveness. ## **VIII. POTENTIAL ADVERSE EFFECTS OF THE DEVICE ON HEALTH** Below is a list of the potential adverse effects (e.g., complications) associated with the use of the device. As with any *in vitro* diagnostic test, the potential adverse effects are associated with incorrect test results or result interpretations. Failure of this device to perform as expected or failure to correctly interpret results may lead to incorrect HPV test results and subsequently, improper patient management decisions in cervical cancer screening and treatment. False negative results may lead to delays in the timely diagnosis of cervical cancer and treatment, allowing an undetected condition to worsen and potentially increasing morbidity and mortality. False positive results could lead women to unnecessarily undergo more frequent screening and potentially invasive procedures such as colposcopy and biopsy. ## **IX. SUMMARY OF NONCLINICAL STUDIES** ### **A. Laboratory Studies** #### **1. Clinical Cutoff Determination of the cobas® HPV Test** The clinical cutoff was previously established. A description of how the cutoff was established is provided in the SSED for the original PMA on the CDRH website at: http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfTopic/pma/pma.cfm?num=P100020 #### **2. Limit of Detection at the Clinical Cutoff** The Limit of Detection (LoD) at the clinical cutoff of high risk HPV genotypes HPV16, HPV18, and HPV31 for specimens collected in SurePath™ Preservative Fluid was determined for the cobas® HPV Test. The LoDs were assessed using 1) plasmids of HPV31, HPV16, and HPV18 in the background of pooled HPV negative patient specimens collected in SurePath™ Preservative Fluid and 2) HPV positive cell lines SiHa (HPV16) and HeLa (HPV18) in SurePath™ Preservative Fluid containing an HPV negative cell line (HCT-15) background. Plasmid and cell lines were diluted to concentrations below, above, and at the expected LoD levels. A minimum of 60 replicates were tested for each plasmid or cell line for each of 3 reagent lots. A total of PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 4 {4} 49 runs were performed in a period of 12 days using 3 instrument systems. The LoD at the clinical cutoff is the level of HPV DNA in the sample that has positive test results (above the clinical cutoff) at least 95% of the time. The table below contains the results from the reagent lot producing the most conservative (highest) LoD in the analyses; those LoDs appear in bold. Table 1. The Limit of Detection Levels for HPV Types 31, 16, and 18 and Cell Lines SiHa (HPV16) and HeLa (HPV18) in SurePath™ Preservative Fluid | HPV Type | Concentration (copies or cells/mL) | Number of Positive/Tested | Mean CT | % Positives | 95% Confidence Interval | | | --- | --- | --- | --- | --- | --- | --- | | | | | | | Lower | Upper | | 31 | 600 | 60/60 | 37.0 | 100.0% | 94.0% | 100% | | | **300** | **60/60** | **38.0** | **100.0%** | **94.0%** | **100%** | | | 150 | 54/60 | 39.1 | 90.0% | 79.5% | 96.2% | | 16 | 600 | 60/60 | 37.9 | 100.0% | 94.0% | 100% | | | **300** | **60/60** | **39.0** | **100.0%** | **94.0%** | **100%** | | | 150 | 51/60 | 40.1 | 85.0% | 73.4% | 92.9 | | 18 | 1,500 | 60/60 | 36.5 | 100.0% | 94.0% | 100% | | | **600** | **60/60** | **37.9** | **100.0%** | **94.0%** | **100%** | | | 300 | 55/59* | 38.9 | 93.2% | 83.5% | 98.1 | | SiHa (HPV16) | 400 | 60/60 | 36.7 | 100.0% | 94.6% | 100% | | | **200** | **60/60** | **37.8** | **100.0%** | **94.6%** | **100%** | | | 100 | 55/60 | 39.3 | 91.7% | 81.6% | 97.2 | | HeLa (HPV18) | 80 | 60/60 | 37.0 | 100.0% | 94.0% | 100% | | | **40** | **59/60** | **38.3** | **98.3%** | **91.1%** | **100%** | | | 20 | 43/60 | 39.6 | 71.7% | 58.6% | 82.5 | *One sample was not processed due to sample pipetting error ### 3. Inclusivity Verification To verify that the cobas® HPV Test is capable of accurately detecting all HPV high risk genotypes in specimens collected in SurePath™ Preservative Fluid, the LoD at the clinical cutoff was determined for genotypes 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68. Quantified plasmid stocks of each HPV genotype were diluted into a background of pooled HPV negative patient specimens collected in SurePath™ Preservative Fluid to concentrations below, above and at the expected LoD levels. Two SurePath™ Preservative Fluid reagent lots were used to produce a minimum of 24 replicates for each positive level with each lot of reagents. For each HPV type, the reported LoD was defined as the lowest testing concentration having a >95% positive hit rate. Table 2 below contains results from the reagent lot producing the most conservative (higher) LoD in the analysis. PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 5 {5} **Table 2. Summary of High Risk Genotype Limit Of Detection For cobas® 4800 HPV Genotype Inclusivity Study in SurePath™ Preservative Fluid** | HPV DNA* Type | LoD (copies/mL) | Number of Positive/Tested | Mean CT | Hit Rate | 95% Confidence Interval | | | --- | --- | --- | --- | --- | --- | --- | | | | | | | Lower | Upper | | **33** | 600 | 24/24 | 37.5 | 100.0% | 85.7% | 100% | | | **300** | **24/24** | **38.6** | **100.0%** | **85.7%** | **100%** | | | 150 | 22/24 | 39.4 | 91.7% | 73.0% | 99.0% | | **35** | 1200 | 22/24 | 37.9 | 100.0% | 85.7% | 100% | | | **600** | **23/24** | **39.2** | **95.8%** | **78.8%** | **99%** | | | 300 | 13/24 | 40.1 | 54.2% | 32.8% | 74.4% | | **39** | 300 | 48/48** | 37.2 | 100.0% | 92.6% | 100% | | | **150** | **24/24** | **38.1** | **100.0%** | **85.7%** | **100%** | | | 80 | 23/24 | 39.1 | 95.8% | 78.8% | 99.8% | | **45** | 600 | 48/48** | 36.7 | 100.0% | 92.6% | 100% | | | **300** | **24/24** | **37.3** | **100.0%** | **85.7%** | **100%** | | | 150 | 22/24 | 37.9 | 91.7% | 73.0% | 99.0% | | **51** | 1200 | 24/24 | 37.5 | 100.0% | 85.7% | 100% | | | **600** | **23/24** | **38.9** | **95.8%** | **78.8%** | **99.9%** | | | 300 | 19/24 | 39.5 | 79.2% | 57.8% | 92.9% | | **52** | 7200 | 48/48** | 38.5 | 100.0% | 92.6% | 100% | | | **4800** | **24/24** | **38.9** | **100.0%** | **85.7%** | **100%** | | | 2400 | 11/24 | 40.0 | 45.8% | 25.6% | 67.2% | | **56** | 2400 | 24/24 | 38.2 | 100.0% | 85.7% | 100% | | | **1200** | **23/24** | **39.3** | **95.8%** | **78.8%** | **99.8%** | | | 600 | 5/24 | 40.5 | 20.8% | 7.1% | 42.2% | | **58** | 1200 | 48/48** | 37.0 | 100.0% | 92.6% | 100% | | | **600** | **24/24** | **38.3** | **100.0%** | **85.7%** | **100%** | | | 300 | 20/24 | 39.6 | 83.3% | 62.6% | 95.3% | | **59** | 1200 | 24/24 | 37.4 | 100.0% | 85.7% | 100% | | | **600** | **24/24** | **38.5** | **100.0%** | **85.7%** | **100%** | | | 300 | 22/24 | 39.6 | 91.7% | 73.0% | 99.0% | | **66** | 2400 | 24/24 | 37.0 | 100.0% | 85.7% | 100% | | | **1200** | **24/24** | **38.6** | **100.0%** | **85.7%** | **100%** | | | 600 | 16/24 | 39.8 | 66.7% | 44.7% | 84.4% | PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 6 {6} | 68 | 600 | 48/48** | 37.2 | 100.0% | 92.6% | 100% | | --- | --- | --- | --- | --- | --- | --- | | | 300 | 24/24 | 38.4 | 100.0% | 85.7% | 100% | | | 150 | 19/24 | 39.5 | 79.2% | 57.8% | 92.9% | | *The LoD of the cobas^{®} HPV Test for HPV genotypes 16, 18 and 31 was determined as described in the other LoD-related table. | | | | | | | #### 4. Reproducibility A 13-member panel made from both HPV16/18 cells lines pools consisting of clinical samples collected into SurePath™ Preservative Fluid was tested for reproducibility. Each panel member was tested for 15 days (5 days per kit lot), 3 replicates per run, at 3 testing sites. Two operators at each of the 3 sites performed 1 run per day for 5 days each on each of the 3 lots. A run was defined as 39 panel-member aliquots and 1 positive and 1 negative control. Overall, 92 runs were performed to obtain 90 valid runs. One invalid run was due to an invalid positive control and one run was aborted by an operator (percent of invalid runs was 2.2% (2/92) with a 95% CI: (0.3%, 7.6%)). A total of 3,510 replicates were performed on the 13 panel members in the valid runs; 4 results were missing because samples were not processed due to pipetting error. All valid test results were included in the analyses that reported the percentage of correct results. There was one false positive result in 270 measurements (percent of false positive results was 0.4%) performed on the negative panel members (pooled negative clinical sample). The data are presented in table below. Percents of positive results for the positive panel members are presented below. With respect to sites, site 3 exhibited lower percent of agreement for the HPV16/18 cell lines and this trend can be attributed to operator 5, who had lower percent positive values in HPV 16/18 cell line panel members. Analysis of variance of the Ct values from valid results performed on positive panel members yielded total CV (%) ranges of 1.7% to 5.8% across all panel members. The CV (%) ranged from 0.0% to 2.5% for the cell line samples and 0.0% to 5.6% for the pooled clinical samples. PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 7 {7} *Table 3. Results by Sample Type and Negative Panel Member for Lot, Site/Instrument, Operator and Day - SurePath* | Panel Member | Ct SD | Ct CV % | Number Positive / Total Number Valid Results | | | | | | | --- | --- | --- | --- | --- | --- | --- | --- | --- | | | | | Lot | | | Site/Instrument | | | | | | | ID | Negative /Valid | % | ID | Negative /Valid | % | | Negative Background Cell Line | n/a | n/a | 1 | 90/90 | 100.0 | 1 | 90/90 | 100.0 | | | | | 2 | 89/89 | 100.0 | 2 | 89/89 | 100.0 | | | | | 3 | 90/90 | 100.0 | 3 | 90/90 | 100.0 | | Negative Pooled Clinical Samples | n/a | n/a | 1 | 90/90 | 100.0 | 1 | 89/90 | 98.9 | | | | | 2 | 89/90 | 98.9 | 2 | 90/90 | 100.0 | | | | | 3 | 90/90 | 100.0 | 3 | 90/90 | 100.0 | PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 8 {8} **Table 4. Results by Sample Type and Positive Panel Member for Lot and Site/Instrument - SurePath** | | | Number Positive / Total Number Valid Results | | | | | | | | | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | | Panel Member | | Ct SD | Ct CV % | Lot | | | Site/Instrument | | | | | | | | ID | Positive /Valid | % | ID | Positive /Valid | % | | HPV 16/18 High Negative (~0.5xLoD) | HPV 16 High Negative | 1.02 | 2.5 | 1 | 62/90 | 68.9 | 1 | 61/90 | 67.8 | | | | | | 2 | 62/90 | 68.9 | 2 | 82/90 | 91.1 | | | | | | 3 | 67/90 | 74.4 | 3 | 48/90 | 53.3 | | | HPV 18 High Negative | 1.17 | 3.0 | 1 | 60/90 | 66.7 | 1 | 59/90 | 65.6 | | | | | | 2 | 68/90 | 75.6 | 2 | 80/90 | 88.9 | | | | | | 3 | 57/90 | 63.3 | 3 | 46/90 | 51.1 | | HPV 16/18 Weak Positive (~1xLoD) | HPV 16 Weak Positive | 0.89 | 2.3 | 1 | 86/90 | 95.6 | 1 | 88/90 | 97.8 | | | | | | 2 | 86/88 | 97.7 | 2 | 89/89 | 100.0 | | | | | | 3 | 87/90 | 96.7 | 3 | 82/89 | 92.1 | | | HPV 18 Weak Positive | 1.22 | 3.2 | 1 | 75/90 | 83.3 | 1 | 85/90 | 94.4 | | | | | | 2 | 75/88 | 85.2 | 2 | 88/89 | 98.9 | | | | | | 3 | 87/90 | 96.7 | 3 | 64/89 | 71.9 | | HPV 16/18 Positive (~3xLoD) | HPV 16 Positive | 0.64 | 1.7 | 1 | 88/90 | 97.8 | 1 | 89/89 | 100.0 | | | | | | 2 | 89/89 | 100.0 | 2 | 90/90 | 100.0 | | | | | | 3 | 90/90 | 100.0 | 3 | 88/90 | 97.8 | | | HPV 18 Positive | 0.61 | 1.7 | 1 | 89/90 | 98.9 | 1 | 89/89 | 100.0 | | | | | | 2 | 89/89 | 100.0 | 2 | 90/90 | 100.0 | | | | | | 3 | 90/90 | 100.0 | 3 | 89/90 | 98.9 | | | Pooled HPV 16 Moderate Positive (~1xLoD) | 1.69 | 4.6 | 1 | 87/90 | 96.7 | 1 | 90/90 | 100.0 | | | | | | 2 | 90/90 | 100.0 | 2 | 90/90 | 100.0 | | | | | | 3 | 90/90 | 100.0 | 3 | 87/90 | 96.7 | | | Pooled HPV 16 Positive (~3xLoD) | 2.02 | 5.8 | 1 | 90/90 | 100.0 | 1 | 90/90 | 100.0 | | | | | | 2 | 90/90 | 100.0 | 2 | 90/90 | 100.0 | | | | | | 3 | 90/90 | 100.0 | 3 | 90/90 | 100.0 | | | Pooled HPV 18 Moderate Positive (~1xLoD) | 1.72 | 4.7 | 1 | 87/90 | 96.7 | 1 | 89/90 | 98.9 | | | | | | 2 | 90/90 | 100.0 | 2 | 90/90 | 100.0 | | | | | | 3 | 89/90 | 98.9 | 3 | 87/90 | 96.7 | PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 9 {9} | | | | | Number Positive / Total Number Valid Results | | | | | | | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | | Panel Member | | Ct SD | Ct CV % | Lot | | | Site/Instrument | | | | | | | | ID | Positive /Valid | % | ID | Positive /Valid | % | | | Pooled HPV 18 Positive (~3xLoD) | 1.48 | 4.3 | 1 | 90/90 | 100.0 | 1 | 90/90 | 100.0 | | | | | | 2 | 90/90 | 100.0 | 2 | 90/90 | 100.0 | | | | | | 3 | 90/90 | 100.0 | 3 | 90/90 | 100.0 | | | Pooled HPV A Moderate Positive (~1xLoD) | 1.09 | 2.9 | 1 | 87/90 | 96.7 | 1 | 90/90 | 100.0 | | | | | | 2 | 90/90 | 100.0 | 2 | 89/90 | 98.9 | | | | | | 3 | 89/90 | 98.9 | 3 | 87/90 | 96.7 | | | Pooled HPV A Positive (~3xLoD) | 1.77 | 4.9 | 1 | 88/90 | 97.8 | 1 | 90/90 | 100.0 | | | | | | 2 | 90/90 | 100.0 | 2 | 90/90 | 100.0 | | | | | | 3 | 90/90 | 100.0 | 3 | 88/90 | 97.8 | | | Pooled HPV B Moderate Positive (~1xLoD) | 1.72 | 4.6 | 1 | 85/90 | 94.4 | 1 | 87/90 | 96.7 | | | | | | 2 | 89/90 | 98.9 | 2 | 88/90 | 97.8 | | | | | | 3 | 88/90 | 97.8 | 3 | 87/90 | 96.7 | | | Pooled HPV B Positive (~3xLoD) | 1.86 | 5.2 | 1 | 89/90 | 98.9 | 1 | 90/90 | 100.0 | | | | | | 2 | 90/90 | 100.0 | 2 | 90/90 | 100.0 | | | | | | 3 | 90/90 | 100.0 | 3 | 89/90 | 98.9 | PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 10 {10} **Table 5. Overall Mean, Standard Deviations, and Coefficients of Variation (%) for Cycle Threshold, Estimated from Valid Samples of Positive Sample Type Panel Members (SurePath)** | Sample Type | N | Mean CT | Standard Deviation [SD] and Percent Coefficient of Variation [CV(%)] | | | | | Total | | --- | --- | --- | --- | --- | --- | --- | --- | --- | | | | | Between-Lot | Between-Site/Instrument | Between-Operator | Between-Day | Within-Run | | | HPV 16/18 High Negative (~0.5xLoD) | | | | | | | | | | HPV 16 High Negative | 270 | 40.2 | 0.00, (0.00%) | 0.38, (0.95%) | 0.13, (0.32%) | 0.49, (1.21%) | 0.80, (1.99%) | 2.5 | | HPV 18 High Negative | 270 | 39.5 | 0.11, (0.28%) | 0.50, (1.28%) | 0.09, (0.23%) | 0.38, (0.97%) | 0.98, (2.48%) | 3.0 | | HPV 16/18 Weak Positive (~1xLoD) | | | | | | | | | | HPV 16 Weak Positive | 268 | 39.0 | 0.08, (0.21%) | 0.41, (1.06%) | 0.08, (0.19%) | 0.43, (1.09%) | 0.65, (1.67%) | 2.3 | | HPV 18 Weak Positive | 268 | 38.6 | 0.00, (0.00%) | 0.59, (1.53%) | 0.16, (0.41%) | 0.59, (1.53%) | 0.88, (2.27%) | 3.2 | | HPV 16/18 Positive (~3xLoD) | | | | | | | | | | HPV 16 Positive | 269 | 37.1 | 0.00, (0.00%) | 0.27, (0.72%) | 0.07, (0.19%) | 0.46, (1.24%) | 0.36, (0.96%) | 1.7 | | HPV 18 Positive | 269 | 36.2 | 0.03, (0.09%) | 0.28, (0.76%) | 0.15, (0.42%) | 0.38, (1.06%) | 0.36, (0.99%) | 1.7 | | Pooled HPV 16 Moderate Positive (~1xLoD) | 270 | 37.0 | 0.00, (0.00%) | 0.00, (0.00%) | 0.30, (0.80%) | 0.68, (1.84%) | 1.52, (4.11%) | 4.6 | | Pooled HPV 16 Positive (~3xLoD) | 270 | 34.9 | 0.35, (1.01%) | 0.33, (0.93%) | 0.12, (0.34%) | 0.28, (0.81%) | 1.94, (5.56%) | 5.8 | | Pooled HPV 18 Moderate Positive (~1xLoD) | 270 | 36.9 | 0.28, (0.76%) | 0.00, (0.00%) | 0.25, (0.68%) | 0.73, (1.98%) | 1.51, (4.10%) | 4.7 | | Pooled HPV 18 Positive (~3xLoD) | 270 | 34.7 | 0.14, (0.40%) | 0.00, (0.00%) | 0.00, (0.00%) | 0.38, (1.09%) | 1.43, (4.11%) | 4.3 | PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 11 {11} | | | | Standard Deviation [SD] and Percent Coefficient of Variation [CV(%)] | | | | | | | --- | --- | --- | --- | --- | --- | --- | --- | --- | | Sample Type | N | Mean CT | Between-Lot | Between-Site/Instrument | Between-Operator | Between-Day | Within-Run | Total | | Pooled HPV A Moderate Positive (~1xLoD) | 270 | 37.6 | 0.09, (0.23%) | 0.23, (0.62%) | 0.28, (0.74%) | 0.24, (0.65%) | 0.99, (2.64%) | 2.9 | | Pooled HPV A Positive (~3xLoD) | 270 | 36.6 | 0.00, (0.00%) | 0.14, (0.38%) | 0.00, (0.00%) | 0.36, (0.98%) | 1.73, (4.74%) | 4.9 | | Pooled HPV B Moderate Positive (~1xLoD) | 270 | 37.3 | 0.00, (0.00%) | 0.00, (0.00%) | 0.36, (0.95%) | 0.00, (0.00%) | 1.68, (4.51%) | 4.6 | | Pooled HPV B Positive (~3xLoD) | 270 | 35.6 | 0.00, (0.00%) | 0.12, (0.33%) | 0.00, (0.00%) | 0.23, (0.64%) | 1.85, (5.18%) | 5.2 | ### 5. Precision In-house Precision was examined using a panel composed of HPV positive clinical specimens collected in SurePath™ Preservative Fluid and HPV positive cell lines (SiHa and HeLa) diluted into pooled negative cervical specimens collected in SurePath™ Preservative Fluid. The precision panel was designed to include members below (<70% positivity rate), at (90% to 99% positivity rate) and above (>99% positivity rate) the Limit of Detection of the cobas® HPV Test. Panel members 2-9 were prepared with HPV positive cell lines (SiHa, HPV16; HeLa, HPV18) diluted at different levels into SurePath™ Preservative Fluid. Panel members 10-12 were prepared with high risk HPV positive specimens in SurePath™ Preservative Fluid pools (HPV16, HPV18, and HR positive) diluted into pooled HPV negative specimens in SurePath™ Preservative Fluid. Panel member 1 consisted of HPV negative specimen pool only. A description of the precision panel, anticipated performance in % positivity rate and the actual study performance in % positivity rate are shown below. All panel members at and above the LoD yielded the anticipated positivity rates. Analysis of variance of the Ct values from valid tests performed on positive panel members yielded overall CV (%) ranges of 1.1% to 1.7% for the SiHa cell lines, 1.5% to 2.2% for the HeLa cell lines, and 3.7% to 8.5% for the pooled clinical samples. PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 12 {12} **Table 6. Summary of the Precision Panel and Hit Rates For cobas$^{®}$ HPV Precision Study in SurePath$^{™}$ Preservative Fluid** | Panel Number | HPV Target | Description | Anticipated Positivity Rate | N Positive | N Tested | % Hit Rate | 95% CI | | | --- | --- | --- | --- | --- | --- | --- | --- | --- | | | | | | | | | Lower | Upper | | 1 | N/A | Pooled HPV negative specimen | 0% | 0 | 216 | 0 | 0.0 | 1.7 | | 2 | HPV16 | SiHa cell line | 90% — 95% | 216 | 216 | 100 | 98.3 | 100.0 | | 3 | HPV18 | HeLa cell line | 90% — 95% | 216 | 216 | 100 | 98.3 | 100.0 | | 4 | HPV16 | SiHa cell line | 95% — 99% | 216 | 216 | 100 | 98.3 | 100.0 | | 5 | HPV18 | HeLa cell line | 95% — 99% | 216 | 216 | 100 | 98.3 | 100.0 | | 6* | HPV16 & HPV18 | SiHa & HeLa cell lines | 90% — 95% | 216 | 216 | 100 | 98.3 | 100.0 | | 6** | HPV16 & HPV18 | SiHa & HeLa cell lines | 90% — 95% | 216 | 216 | 100 | 98.3 | 100.0 | | 7 | HPV16 | SiHa cell line | < 70% | 53 | 216 | 25 | 19.0 | 30.8 | | 8 | HPV18 | HeLa cell line | < 70% | 135 | 216 | 63 | 55.7 | 69.0 | | 9* | HPV16 & HPV18 | SiHa & HeLa cell lines | < 70% | 78 | 216 | 36 | 29.7 | 42.9 | | 9** | HPV16 & HPV18 | SiHa & HeLa cell lines | < 70% | 122 | 216 | 57 | 49.6 | 63.2 | | 10 | High Risk Channel 1 | High Risk HPV positive specimen | 90% — 95% | 216 | 216 | 100 | 98.3 | 100.0 | | 11 | HPV16 | High Risk HPV positive specimen | 90% — 95% | 216 | 216 | 100 | 98.3 | 100.0 | | 12 | HPV18 | High Risk HPV positive specimen | 90% — 95% | 208 | 216 | 96 | 92.8 | 98.4 | *Results shown from detection channel 2 (HPV16) ** Results shown from detection channel 3 (HPV18) N/A = Not applicable PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 13 {13} Table 7. Overall Mean, Standard Deviations, and Coefficients of Variation (%) for Cycle Threshold, Estimated from Valid Samples of Positive Sample Type Precision Panel Members in SurePath™ Preservative Fluid | | | | Standard Deviation [SD] and Percent Coefficient of Variation [CV(%)] | | | | | | | | | | | | | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | | | Sample Type / Conc. (cells/mL) | Mean CT | Between-Lot | | Between-Run/System | | Between-Operator | | Between-Day | | Within-Run | | Total | | | | | | SD | CV% | SD | CV% | SD | CV% | SD | CV% | SD | CV% | SD | CV% | | 2 | SiHa HPV16 (200/mL) | 37.9 | 0.188 | 0.50% | 0.000 | 0.00% | 0.072 | 0.20% | 0.000 | 0.00% | 0.000 | 0.00% | 0.513 | 1.40% | | 3 | HeLa HPV18 (40/mL) | 37.6 | 0.161 | 0.40% | 0.071 | 0.20% | 0.000 | 0.00% | 0.000 | 0.00% | 0.015 | 0.00% | 0.59 | 1.60% | | 4 | SiHa HPV16 (600/mL) | 36.4 | 0.132 | 0.40% | 0.000 | 0.00% | 0.000 | 0.00% | 0.000 | 0.00% | 0.09 | 0.20% | 0.343 | 0.90% | | 5 | HeLa HPV18 (120/mL) | 36.0 | 0.091 | 0.30% | 0.056 | 0.20% | 0.044 | 0.10% | 0.000 | 0.00% | 0.071 | 0.20% | 0.392 | 1.10% | | 6* | SiHa HPV16 (200/mL) | 37.9 | 0.023 | 0.10% | 0.000 | 0.00% | 0.000 | 0.00% | 0.000 | 0.00% | 0.073 | 0.20% | 0.436 | 1.10% | | 6** | HeLa HPV18 (40/mL) | 37.7 | 0.081 | 0.20% | 0.000 | 0.00% | 0.000 | 0.00% | 0.000 | 0.00% | 0.134 | 0.40% | 0.604 | 1.60% | | 7 | SiHa HPV16 (20/mL) | 41.2 | 0.000 | 0.00% | 0.092 | 0.20% | 0.116 | 0.30% | 0.000 | 0.00% | 0.000 | 0.00% | 0.979 | 2.40% | PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 14 {14} | | | | Standard Deviation [SD] and Percent Coefficient of Variation [CV(%)] | | | | | | | | | | | | | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | | 8 | HeLa HPV18 (8/mL) | 39.8 | 0.125 | 0.30% | 0.000 | 0.00% | 0.000 | 0.00% | 0.000 | 0.00% | 0.000 | 0.00% | 1.042 | 2.60% | | 9* | SiHa HPV16 (20/mL) | 40.9 | 0.146 | 0.40% | 0.000 | 0.00% | 0.155 | 0.40% | 0.000 | 0.00% | 0.084 | 0.20% | 0.987 | 2.40% | | 9** | HeLa HPV18 (8/mL) | 39.9 | 0.195 | 0.50% | 0.000 | 0.00% | 0.000 | 0.00% | 0.000 | 0.00% | 0.000 | 0.00% | 1.095 | 2.70% | | 10 | Clinical High Risk channel 1 (N/A) | 37.2 | 0.000 | 0.00% | 0.000 | 0.00% | 0.000 | 0.00% | 0.000 | 0.00% | 0.000 | 0.00% | 1.135 | 3.10% | | 11 | Clinical HPV16 (N/A) | 36.7 | 0.000 | 0.00% | 0.000 | 0.00% | 0.000 | 0.00% | 0.119 | 0.30% | 0.000 | 0.00% | 1.772 | 4.80% | | 12 | Clinical HPV18 (N/A) | 36.9 | 0.151 | 0.40% | 0.000 | 0.00% | 0.000 | 0.00% | 0.000 | 0.00% | 0.128 | 0.30% | 1.848 | 5.00% | *Results shown from detection channel 2 (HPV16) ** Results shown from detection channel 3 (HPV18) PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 15 {15} # 6. Analytical Specificity A panel of bacteria, fungi and viruses, including those commonly found in the female urogenital tract, as well as several Human papillomavirus types classified as low or undetermined risk were tested with the cobas® HPV Test to assess analytical specificity. The organisms listed below were spiked at high concentrations (≥1x10⁶*units/reaction with the exception of Chlamydia trachomatis and all viruses, which were all tested at 1x10⁵*units/reaction) into HPV negative clinical matrix in SurePath™ Preservative Fluid and into HPV negative clinical matrix in SurePath™ Preservative Fluid spiked with HPV31, HPV16 and HPV18 plasmid DNA at 3 times the Limit of Detection. Results indicated that none of these organisms interfered with detection of HPV31, HPV16, and HPV18 or produced false positive results in the HPV negative specimen. All bacteria were quantified as Colony Forming Units (CFU) except Chlamydia trachomatis as Elementary Bodies (EBs). All HPV genotypes were quantified as DNA copies. Adenovirus was quantified as Plaque Forming Units (PFU). CMV, EBV, HSV-1 and HSV-2 were quantified as Viral Particles (VP). Table 8. Microorganisms Tested for Analytical Specificity in SurePath™ Preservative Fluid | Adenovirus 5 | Epstein Barr Virus (EBV) | Pseudomonas fluorescens | HPV 30 | | --- | --- | --- | --- | | Bacteroides caccae | Escherichia coli | Staphylococcus aureus | HPV 34 | | Bifidobacterium adolescentis | Fusobacterium varium | Staphylococcus epidermidis | HPV 53 | | Candida albicans | Herpes simplex virus 1 (HSV-1) | Streptococcus agalactiae | HPV 67 | | Chlamydia trachomatis | Herpes simplex virus 2 (HSV-2) | Streptococcus faecalis | HPV 69 | | Clostridium beijerinckii | Klebsiella pneumoniae ss ozaenae | Streptococcus pyogenea | HPV 70 | | Corynebacterium glutamicum | Lactobacillus acidophilus | Trichomonas vaginalis | HPV 73 | | Cytomegalovirus (CMV) | Neisseria gonorrhea | HPV 6 | HPV 82 | | Enterobacter aerogenes | Peptostreptococcus anaerobius | HPV 11 | HPV 85 | | Enterococcus faecium | Proteus mirabilis | HPV 26 | | PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 16 {16} ## 7. Interfering Substances Contrived specimens were used to assess the effects of endogenous and exogenous interfering substances that could potentially be present in cervical specimens. The concentrations of endogenous and exogenous substances tested represent conditions that could occur during specimen collection. HPV negative clinical specimens were combined into pools which were then used to prepare HPV positive and HPV negative samples. HPV positive samples were prepared by spiking a portion of the negative pool with HPV plasmids (HPV31, HPV16 and HPV18) to a target level of approximately 3-fold the Limit of Detection. Twenty samples were tested with and without the addition of interfering endogenous substances. Whole blood was tested at concentrations of 0, 2, 4, 6, and 8% v/v. Peripheral blood mononuclear cells (PBMC) interference was assessed at concentrations 0, 10⁴, 10⁵, and 10⁶ cells/mL. Cervical mucus was introduced into samples by immersing individual cervical cleaning swabs into corresponding HPV negative or positive test samples to test. No interference was seen in mucus or in clinically relevant levels for PBMC. Whole blood showed no interference when present in visually detectable amounts of up to 2% in SurePath samples. *Table 9. Interference Testing Results with Endogenous Interferents* | Interferent Tested | Collection Medium | Concentrations Tested | Interference Observed | | --- | --- | --- | --- | | Whole Blood | SurePath™ | 2%, 4%, 6%, 8% v/v | Above 2% | | PBMC | SurePath™ | 10⁴, 10⁵, 10⁶ cells/mL | None | | Cervical Mucus | SurePath™ | Mucus obtained from standard cervical cleaning procedure | None | A total of 18 over-the-counter (OTC) feminine hygiene and contraceptive products were tested as potential interfering substances. Each OTC product was added to the designated HPV positive or negative test sample. Both the positive and the negative test samples were tested in triplicate with and without the presence of the exogenous product within 24 hours of the sample preparation. With the exception of Replens, none of the other OTC substances inhibited the test reaction. The observed interference appears to be unique to the SurePath Preservative Fluid sample since interference was not observed with the PreservCyt samples (P100020). The types of interferents tested and performance observations are presented in the table below. PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 17 {17} **Table 10. Interference Testing Results with Exogenous Interferents** | Product Name | Collection Medium | Active Ingredients | Interference Observed | | --- | --- | --- | --- | | Azo-Standard | SurePath™ | Phenazopyridine Hydrochloride | None | | Vaginal Contraceptive Foam | SurePath™ | Nonoxynol-9 | None | | Clotrimazole 7 | SurePath™ | Clotrimazole | None | | Gyne-Lotrimin 7 | SurePath™ | Clotrimazole | None | | Gynecort | SurePath™ | Hydrocortisone | None | | Vagisil Satin | SurePath™ | Hydrocortisone | None | | Vagi-Gard (Douche) | SurePath™ | Povidone-iodine | None | | Miconazole | SurePath™ | Miconazole nitrate | None | | Monistat 3 Cream | SurePath™ | Miconazole nitrate | None | | Vagistat 1 | SurePath™ | Tiocanazole | None | | VH essentials Medicated Cream | SurePath™ | Benzocaine | None | | Vagicaine Anti-Itch Cream | SurePath™ | Benzocaine | None | | Yeast Gard | SurePath™ | Pulsatilla, Candida Parapsilosis, Candida albicans | None | | Norforms | SurePath™ | PEG-32,PEG-18, Peg-20 stearate | None | | KY Jelly | SurePath™ | Hydroxyethylcellulose, Chlorhexidine Gluconate | None | | Vagisil Moisturizer | SurePath™ | DMDM Hydantoin, Diazolidinyl urea | None | | Replens | SurePath™ | Polycarbophil | Yes* | | Vagi-Gard (Lube Gel) | SurePath™ | Glucano Delta Lactone, Chlorhexidine Gluconate | None | *Addition of 15 mg to the test sample produced false negative results. #### 8. Reagent Stability Most of the reagent stability studies were previously established. A description of the studies is provided in in the SSED for the original PMA on the CDRH website at: http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfTopic/pma/pma.cfm?num=P100020. Additionally, specimens collected in SurePath require pretreatment with the cobas® Sample Prep Buffer prior to testing on the cobas® HPV test. The corresponding shelf PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 18 {18} life and storage temperature, as supported by the results of stability studies is a shelf life of 24 months when stored at 15-30°C. # 9. Sample Handling and Collection Cervical specimens should be collected in SurePath Preservative Fluid, the SurePath container, using an endocervical broom. Specimen stability studies demonstrated that for the cobas® HPV test, cervical specimens can be stored 2-8°C in SurePath for up to 6 months or at 15-30°C for up to 4 weeks after the date of collection provided that the SurePath™ Preservative Fluid matrix-induced crosslinks are reversed through treatment with the cobas® Sample Prep Buffer prior to HPV testing. SurePath specimens treated with the cobas® Sample Prep Buffer can be stored at 2-30°C for up to 4 weeks prior to HPV testing on the cobas® 4800 System. As noted in the labeling, samples not treated with the cobas® Sample Prep Buffer will likely provide false negative results. # 10. Cross-Contamination Study Cross-contamination was examined using one cobas® 4800 system. HPV positive and negative samples were process in a checkerboard configuration. HPV positive samples [(SP+)] were prepared by adding cultured CaSki cells [HPV16 positive, manufactured and quantified by Roche Culture Collection (RMSCC)] to SurePath™ Preservative Fluid to generate a signal which covers 95% or more of the results found in specimens of diseased patients in the intended use population. The HPV negative samples were prepared by spiking HCT-15 cells [manufactured and quantified by Roche Culture Collection (RMSCC)] at 50,000 cells/mL into SurePath™ Preservative Fluid. Seven runs were performed on one cobas® 4800 system. The samples were processed to reverse formalin-induced cross-links through heating in the presence of a nucleophilic reagent. Prior to the checkerboard runs, a negative run containing SurePath™ Preservative Fluid only, was performed to verify that the system was free of contamination. The subsequent six runs contained both negative HPV samples and high positive HPV samples in a checkerboard configuration. Of the six runs that examined the HPV high positive and negative checkerboard configuration, 1 out of 143 HPV negative samples showed positive results in channel 2, leading to a cross-contamination rate of 0.7% with 95% CI: 0.1% to 3.9%. There were no invalid runs or test results observed. In the study, the percent of negative samples with Ct values (results were negative but HPV below the cutoff was detected) increased by 7.7% (95% CI: 3.9% to 13.4%). A second study was conducted to assess the rate of sample-to-sample cross-contamination events during routine processing of SurePath™ Preservative Fluid PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 19 {19} specimens on the BD PrepMate processor when using the cobas® HPV Test. Cross-contamination was examined by processing HPV negative and HPV high positive SurePath™ samples in alternating order on the BD PrepMate processor. The HPV negative samples were prepared by spiking HCT-15 cells [manufactured and quantified by Roche Culture Collection (RMSCC)] at 50,000 cells/mL into SurePath™ Preservative Fluid. HPV positive samples were prepared by adding cultured CaSki cells [HPV16 positive, manufactured and quantified by Roche Culture Collection (RMSCC)] to the HPV negative samples in SurePath™ Preservative Fluid to generate a signal which covers 95% or more of the results found in specimens of diseased patients in the intended use population. Prior to testing, 24 HPV negative samples were processed in 2 runs on the BD PrepMate processor. Immediately following these runs, a total of 72 HPV high positive and 72 HPV negative samples were process in an alternating pattern in 12 individual runs, each containing 12 vials of samples. After the runs were completed, 12 additional negative samples were processed in a single BD PrepMate processor. Processed samples were subsequently tested for HPV on a single cobas® 4800 system using the cobas® HPV Test. A cross-contamination rate of 1.4% (1 out of 71) with 95% CI: 0.2% to 7.6% was noted with SurePath™ specimens on the BD PrepMate. B. Animal Studies Not applicable C. Additional Studies Not applicable # X. SUMMARY OF PRIMARY CLINICAL STUDY The applicant conducted a clinical study to establish a reasonable assurance of safety and effectiveness for the new intended use/indication for use for the cobas® HPV Test in the U.S. Data from this clinical study were the basis for the PMA approval decision. A summary of the clinical study is presented below. # A. Study Design Patients were enrolled between April 2012 and August 2015. The dataset for this PMA supplement included 952 patients evaluated for the new intended use/indication for use. There were two main collection sites (comprised of 21 clinics) and three testing sites. A multi-center prospective study was conducted to evaluate the performance of the cobas® HPV test using specimens collected in SurePath Preservative Fluid™ as a triage test to stratify women with ASC-US cytology for colposcopy. Women ≥21 years presenting for routine cervical cancer screening had 2 cervical samples taken, the first in SurePath Preservative Fluid™ and the second in specimen transport medium (STM) as part of the standard of care. Women were enrolled at 2 main collection sites, comprised of 21 clinics, during April 2012 and August 2015 and tested at 3 testing sites. Cytology samples were classified according to the criteria of the 2001 Bethesda System. Those PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 20 {20} women who had ASC-US cytology results on specimens collected in SurePath were invited to enroll in the study. A total of 952 subjects met the inclusion/exclusion criteria. After informed consent was obtained, demographic and gynecologic history information was recorded. Cobas® HPV testing was performed using pre-cytology aliquots (also referred to below as pre-aliquot, or pre-quot) and post-cytology aliquots (post-aliquot, or post-quot) of cervical specimens collected in SurePath Preservative Fluid™. The second sample in STM collected from all subjects with ASC-US Pap test results was tested with an FDA-approved test according to the manufacturer's instructions. # 1. Clinical Inclusion and Exclusion Criteria # Inclusion Criteria: a. Females age ≥21 years of age b. ASC-US cervical cytology result from routine cervical cancer screening c. Intact cervix d. Willing and able to undergo colposcopy with biopsy, and/or endocervical curettage (ECC) ≤12 weeks (≤84 days) from cervical sample collection e. Written informed consent provided by the subject. # Exclusion Criteria: Subjects were excluded from enrollment if any of the following criteria were met: a. Incomplete informed consent (lacking signature of study subject OR signature of appropriate consenting study personnel, i.e., either the principal investigator or someone to whom the principal investigator has appropriately delegated consenting authority) b. Known pregnancy at colposcopy visit c. Subject had been notified of the HPV test performed on her samples from the initial visit. d. Cytology result of ASC, could not rule out high-grade lesion. e. Any medical condition that, in the opinion of the investigator, would result in increased risk of bleeding at biopsy f. Known history of ablative or excisional therapy (e.g., LEEP, cryotherapy, cone biopsy) to the cervix in the 12 months before enrollment; women who have had ablative or excisional treatment and who had not been returned to routine cervical cancer screening were excluded. g. Hysterectomy (including supracervical) h. Current or planned participation in any clinical trial for treatment of HPV infection # 2. Clinical Endpoints All women with ASC-US cytology results, who agreed to participate in the study, were referred to colposcopy within 12 weeks of the enrollment visit independent of their HPV status. To avoid bias, health care providers, study participants, and colposcopists remained blinded to all HPV results until after colposcopy. Colposcopy was conducted per protocol that required all visible cervical lesions to be biopsied; in those cases where no lesions were visible, a single random biopsy was taken at the squamocolumnar PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 21 {21} junction. An endocervical curettage (ECC) was performed in all patients in whom the squamocolumnar junction was not visualized. All biopsies were examined by a Central Pathology Review Panel (CPRP) consisting of three expert pathologists, and discordant results were adjudicated according to a pre-defined protocol. For all analyses, the clinical performance of the cobas® HPV Test was measured against CPRP histology results, with ≥CIN2 and ≥CIN3 disease endpoints, respectively. The clinical performance below is presented for the pre-aliquot and post-aliquot specimens. ### B. Accountability of PMA Cohort A total of 952 subjects out of 958 subjects met the study eligibility criteria. Of 952 eligible women, 87 pre-quot samples were discarded before any testing with the cobas® HPV Test started; 865 had valid cobas® HPV Test result. The percent of invalid cobas® HPV Test results when test results are reported as positive and negative results was 0.0% (0/865) with 95% CI: 0.0% to 0.4%. Of the 865 subjects with valid results, colposcopy was performed for 857 women; the histology review for 1 woman did not follow the protocol, therefore she was excluded from the study results analysis. The flow of ASC-US ≥21 subjects is shown in the figure below. PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 22 {22} ![img-0.jpeg](img-0.jpeg) ### C. Study Population Demographics and Baseline Parameters The demographics of the study population shown below are typical for a cervical cancer screening study performed in the U.S. Table 11. Summary of Demographic Characteristics for the Evaluable Screening Population | Characteristics | Statistic | Evaluable Subjects n = 856 | | --- | --- | --- | | Age (Years) | Mean | 35.4 | | | SD | 11.5 | | | Median | 32.0 | | | (Min, Max) | (21,75) | PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 23 {23} | Characteristics | Statistic | Evaluable Subjects n = 856 | | --- | --- | --- | | **Age Group (Years)** | | | | 21-24 | n (%) | 127 (14.8) | | 25-29 | n (%) | 227 (26.5) | | 30-39 | n (%) | 235 (27.5) | | 40-49 | n (%) | 142 (16.6) | | ≥50 | n (%) | 125 (14.6) | | **Race** | | | | White | n (%) | 614 (71.7) | | American Indian or Alaskan Native | n (%) | 9 ( 1.1) | | Black or African American | n (%) | 41 (4.8) | | Asian | n (%) | 90 ( 10.5) | | Native Hawaiian or Other Pacific Islander | n (%) | 9 ( 1.1) | | Other | n (%) | 65 (7.6) | | Multiple Race | n (%) | 27 ( 3.2) | | Missing* | n (%) | 1 (0.1) | | **Ethnicity** | | | | Hispanic or Latino | n (%) | 355 (41.5) | | Not Hispanic or Latino | n (%) | 499 (58.3) | | Missing | n (%) | 2 (0.2) | | **Education** | | | | Elementary | n (%) | 8 ( .9) | | High School (or GED) | n (%) | 140 (16.4) | | Vocational/Some College | n (%) | 279 (32.6) | | College Degree | n (%) | 308 (36.0) | | Some Graduate Work | n (%) | 29 ( 3.4) | | Graduate Degree (Master's or Higher) | n (%) | 92 (10.7) | | * Missing refers to 'Not Reported' or 'Unknown' | | | PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 24 {24} ## **D. Safety and Effectiveness Results** ### **1. Safety Results** As an *in vitro* diagnostic test, the cobas® HPV Test involves sampling cells from the cervix using an endocervical broom. Collection of the sample, therefore, presents no more safety hazard to an individual being tested than other tests where cervical cells are sampled in this manner (such as cervical cytology). False positive and false negative results are discussed in Section VIII. There were no adverse effects of the device reported during the clinical study. ### **2. Effectiveness Results** The analysis of effectiveness was based on the following data. Study results were determined for both a pre-aliquot and a post-aliquot sample. #### **Pre-Aliquot Data** #### **Performance Characteristic in the ASC-US Population in Samples Collected in SurePath (≥ 21 Years)** The table below displays a summary of the CPRP diagnosis stratified by the cobas® HPV Test results (positive and negative) for 856 women. The histology results are undetermined, normal, cervical intraepithelial neoplasia (CIN) as CIN1, CIN2 or CIN3 or worse. **Table 12. Summary of the cobas® HPV Test Results and Central Pathology Review Panel Diagnosis – SurePath** | cobas® HPV Test Result | Central Pathology Review Panel Diagnosis | | | | | Total | | --- | --- | --- | --- | --- | --- | --- | | | Undetermined | Normal | CIN1 | CIN2 | ≥CIN3 | | | Positive | 3 | 264 | 64 | 34 | 28 | 393 | | Negative | 7 | 410 | 33 | 9 | 4 | 463 | | Total | 10 | 674 | 97 | 43 | 32 | 856 | Ten women had undetermined histology results which led to 846 women being included in the clinical performance estimates analysis; 576 non-vaccinated women and 270 vaccinated women were included in the analyses below. #### **Performance of the cobas® HPV Test in the ASC-US Population (≥ 21 Years) – Non-Vaccinated Subjects.** A total of 576 non-vaccinated subjects with ASC-US cytology completed the colposcopy procedures and had valid cobas® HPV results using the pre-aliquot specimen. The results PMA P100020 S017: FDA Summary of Safety and Effectiveness Data Page 25 {25} of the cobas® HPV Test reported as (HR HPV) Positive or (HR HPV) Negative together with the CPR diagnosis are presented below. Table 13. Summary of the cobas® HPV Test Results and Central Pathology Review Panel Diagnosis - SurePath - Non-Vaccinated Subjects | | | CPRP Diagnosis – all biopsies | | | | | | --- | --- | --- | --- | --- | --- | --- | | cobas® HPV Test Result | Normal | CIN1 | CIN2 | CIN3 | Cancer | Total | | Positive | 179 | 37 | 17 | 15 | 2 | 250 | | Negative | 296 | 24 | 4^{a} | 2^{b} | 0 | 326 | | Total | 475 | 61 | 21 | 17 | 2 | 576 | $^{a}$ 3 CIN2 cases were FDA approved test negative and sequence negative; and 1 CIN2 case was FDA approved test positive and sequence negative. $^{b}$ 1 CIN3 case was FDA approved test positive and sequence negative; and 1 CIN3 case was FDA approved test negative and sequence negative. Percent of Invalid cobas® HPV Test results was 0.0% (0/576) with 95% CI: 0.0% to 0.7%. Performance of the cobas® HPV Test in detecting cervical disease (≥ CIN2 and ≥ CIN3) is presented in the table below. The sensitivity and the specificity of the test for detecting ≥ CIN2 histology were 85.0% ((34/40) with 95%: 70.9% to 92.9%) and 59.7% ((320/536) with 95%: 55.5% to 63.8%), respectively. The positive likelihood ratio (PLR) was estimated as 2.1, which implies a positive cobas® HPV Test results in 2.1 time more likely in subjects with ≥ CIN2 than in subjects with < CIN2. The negative likelihood ratio (NLR) was estimated as 0.25, which implies that a negative cobas® HPV Test results is 4 (1/0.25) times more likely in subjects with