Oropharyngeal Cancer with HPV Status Database

Human papillomavirus (HPV) status is a prognostic factor for oropharyngeal squamous cell carcinoma (OPSCC). SEER has collected data about the HPV status since 2010. The specialized database field "HPV recode (Oropharynx 2010+)" is based on 3 data items:

1. Site Specific Factor (SSF) 10, Human Papilloma Virus (HPV) Status, Collaborative Stage (CS) version 02.05, schemas: Oropharynx, Pharyngeal Tonsil, Palate Soft, and Tongue Base effective for cases diagnosed 2010-2017. The data item was recoded into HPV positive, HPV negative and unknown and released in prior version of this database.
2. Schema Discriminator 2: Oropharyngeal p16 (2018+) for Extent of Disease (EOD), schemas Oropharynx HPV-Associated and Oropharynx HPV-Independent for cases diagnosed 2018 and after. This data item collects the results of p16 testing as positive, negative and unknown. The data item is available in SEER Research Plus and this specialized database.
3. SEER Site Specific Factor 1 HPV status (2018+). This data item collects HPV testing for oropharyngeal cancer different from p16 testing (e.g. viral DNA by ISH or PCR, E6/E7 RNA by ISH or PCR).

The "HPV recode (Oropharynx 2010+)" was calculated for cases identified as Oropharynx using EOD Schema Recode (2010+). For cases diagnosed from 2010 to 2017, the recode described in (1) above was used. For cases diagnosed 2018+, if either Schema Discriminator 2 Oropharyngeal p16 or SEER SSF 1 HPV status were positive the HPV recode (Oropharynx 2010+) was coded positive. HPV status was coded negative if both data items above were negative or one of them was negative and the other unknown. The HPV status was coded unknown if both Schema Discriminator 2 Oropharyngeal p16 and SEER SSF HPV status were unknown.

Database Details

There are two Oropharyngeal Cancer with HPV Status databases available to request, one with and one without Census Tract Attributes. The need for Census Tract Attributes should be described in the Research Objectives and Study Design section of the application, and the planned use of the attributes should be explained in the Analytic Plan section of the application.

Both databases are available in the Case Listing, Frequency, Rate, and Survival sessions in SEER*Stat for the November 2024 data submission. They are identical to the SEER Research Plus (17 Registries) database other than the specialized fields.

1. Oropharyngeal Cancer with HPV Status Database
   • This one is linked to county-level attributes, which include county-level SES, rurality, and demographics.
   • It includes all tumor records from 2000-2022 with follow-up through 2022.
2. Oropharyngeal Cancer with HPV Status with Census Tract Attributes Database
   • There are no geographic identifiers included in this database due to confidentiality concerns.
   • It does not include Alaska Native Tumor Registry data.
   • It includes all tumor records from 2006-2022 with follow-up through 2022.
   • For detailed information about census tract-level SES and rurality variables, refer to Census Tract-level SES and Rurality Database.

Please cite the SEER Specialized Database name in any publications. The database name can be found in the approval email and in SEER*Stat.

Data Limitations and Analytical Considerations

Incompleteness of the HPV Status

SEER registries continued to improve with respect to collection of HPV status and the proportion of cases with known status (HPV Positive or HPV Negative) increased significantly between 2010 and 2017 However, the proportion of cases with unknown status was non-negligible especially for cases diagnosed from earlier years. Because the distribution of HPV (positive cases as a proportion of positive cases plus negative cases) is very likely not the same among those with known status as is among those with unknown status, estimation of HPV-positive incidence (rate) or prevalence would be biased for 2010-2017 dx years.

In addition, as the proportion of cases with unknown HPV status varies over time, trends of HPV-positive incidence would likely to be biased. Due to the above reasons, the use of the dataset for estimation of HPV-positive incidence or prevalence, or the trend of incidence by HPV status is strongly discouraged for 2010-2017 diagnosis years.

In 2018, the HPV status became part of tumor staging for oropharyngeal cancer with the implementation of AJCC 8 edition. This led to increased completeness of HPV status.