The site recode variables are derived from the "Primary site" and "Histologic type ICD-O-3" variables after the registries submit the data to SEER (see Site Recode ( These variables are added to the SEER data as a convenience and are used in most SEER publications to define the cancer of interest.

For example, the cancer sites available in SEER*Explorer ( correspond to a value of a site recode variable.

Create a table showing frequencies by primary site for cases with Site recode ICD-O-3/WHO 2008 = lung and bronchus. Include only malignant cases diagnosed in the SEER 21 registries from 2000 through 2018 and exclude cases with unknown age.

Key Points

  • This exercise introduces three variables related to cancer type in the SEER databases (primary site, site recode, histology).
  • In this exercise, you will calculate frequencies for cases diagnosed between 2000 and 2018, the only years for which all 21 registries have cases in the database.
  • You will set primary site as a display variable in order to create a table showing frequencies for the variable's individual values.
  • The Matrix menu provides a variety of options for modifying the layout of the output table. This exercise uses the Hide Zero Count Rows option to suppress the display of primary site codes not relevant to lung and bronchus cancer.

Step 1:  Create a new Frequency Session

  • Start SEER*Stat.
  • From the File menu select New > Frequency Session or use the Frequency button on the toolbar.

Step 2:  Select a Database (Data Tab)

  • On the Data Tab select "Incidence - SEER Research Limited-Field Data, 21 Registries, Nov 2020 Sub (2000-2018)".

Learn More...

Databases distributed with SEER*Stat use names designed to describe the data. The various parts of this exercise's database name indicate the following:
  • Incidence - The database contains cancer incidence data.
  • SEER Research Limited-Field Data - This indicates the database type and which variables are included, as described in the data dictionary available on SEER*Stat Database Details
  • 21 Registries - The database contains data for the "SEER 21" registries as defined in SEER Registry Groupings for Analyses.
  • Nov 2020 Sub - The data was submitted to the SEER program by the registries in November 2020.
  • (2000-2018) - These are the years of diagnosis for the cases included in the database.

Step 3:  Choose the Statistics to Display (Statistic Tab)

  • Move to the Statistic Tab.
  • In the Statistic box, select Frequencies.

Step 4:  Defining the Analysis Cohort (Selection Tab)

  • Move to the Selection Tab.
  • In this exercise, we want a frequency of malignant lung and bronchus cancer cases diagnosed from 2000 through 2018. We do not want to include all of the cancer sites included in the database. Therefore, we need a selection statement based on site and behavior. The database selected on the Data Tab contains cases diagnosed in the SEER 21 registries; therefore selections based on registry are not necessary.
  • The Select Only box provides a shortcut for commonly-used selections. It is very common to select only malignant behavior when analyzing cancer data. For this exercise we want to select malignant cases in the research database and exclude those with unknown age, so make sure that the Malignant Behavior and Known Age options are checked.
  • Click Edit to open the Case Selection window.
  • Using the controls at the top of the window, you will create a selection statement. The variables are listed in categories in the Variable box on the top left of the screen.
  • In the Variable box, use the "+" to expand the "Site and Morphology" category.
  • Select "Site recode ICD-O-3/WHO 2008".
  • Moving to the center of the window, check to see that "is = to" is selected as the Operator.
  • Scroll through the items in the Values box until you find and select "Lung and Bronchus".
  • The following should appear in the Selection Statement box at the bottom of the window:
    {Site and Morphology.Site recode ICD-O-3/WHO 2008} = ' Lung and Bronchus'.
  • Use the OK button to close the Case Selection window.

Learn More...

  • The Problem Statement specified to create a table showing the frequency of primary site for malignant cases with site recode = lung and bronchus. It is possible to select lung and bronchus cases by creating a selection statement that uses primary site and histology. However, it is much easier to use one of the site recode variables if you do not want to include hematopoietic diseases (such as lymphomas and leukemias) in the table.

Step 5:  View the Primary Site Variable Groupings

  • Move to the Table Tab.
  • Use the "+" to expand the "Site and Morphology" category in the Available Variables box.
  • Select "Primary Site - labeled".
  • Open the dictionary editor to view the groupings for "Primary site". In a previous exercise we learned that the dictionary editor could be opened by:
    1. using the Dictionary button on the toolbar,
    2. selecting Dictionary from the File menu, or
    3. double-clicking on the "Primary site" variable.
  • The Dictionary window should now be open.
  • If it is not already selected, select the "Primary site - labeled" variable from the "Site and Morphology" category.
  • The Create button will be enabled when a variable is selected. Use the Create button to open the Edit Variable window to view the groupings and values associated with this variable.
  • The values of the "Primary Site - labeled" variable correspond to ICD-O-3 codes. There is one grouping for each value of the primary site variable.
  • Click Cancel to close the Edit Variable window without making any changes.
  • Click Close to close the dictionary.

Step 6:  Set the Row Variable

  • Use the "+" to expand the "Site and Morphology" category in the Available Variables box at the bottom of the Table Tab.
  • Select "Primary site - labeled".
  • Click Row on the right hand side of the screen.
  • At this time, "Primary site - labeled" should be listed as a row variable in the Display Variables box at the top of the window.

Step 7:  Specify a Title (Output Tab)

  • Move to the Output Tab.
  • Enter the following title:
Primary Site Frequencies for Malignant Lung and Bronchus (Site recode ICD-O-3/WHO 2008)
SEER 21 Registries, 2000-2018
Frequency Exercise 2

Step 8:  Create Matrix and Hide Extraneous Rows

  • Use the Execute button or select Execute from the Session menu to execute the session.
  • A dialog will display the progress of the job. When the job completes a SEER*Stat matrix window will open containing the results.
  • The results matrix contains one line for each value of the primary site variable. The large number of rows makes it difficult to review the relevant frequencies. SEER*Stat has an option that allows you to suppress the display of the rows with a value of zero in each column.
  • Select Options from the Matrix menu.
  • In the Options box check Hide Zero Count Rows.
  • Click OK.
  • The size of the table will be reduced to six rows: one row for each of the primary site ICD-O-3 codes for lung and bronchus.
  • Compare your results to this SEER*Stat matrix file: Exercise Matrix 2 Results.

Learn More...

  • The Options window gives you the opportunity to correct typographical errors in the title. Corrections that you make to the title in the matrix options will appear in the matrix and printed output. However, sessions extracted from the matrix will retain the original, unedited title.
  • Use the Help button on the Options window to learn about the other matrix options.