SEER*Stat Left Truncated Life Tables Exercise 1: Lung and Bronchus

This exercise assumes that you are familiar with using SEER*Stat. If you are just getting started, be sure to do the introductory tutorials first.

Use the Left-Truncated Life Table session to calculate a life table consisting of the probability of dying of causes other than lung cancer, by attained age, for a cohort of lung cancer patients. Create tables by SEER historic stage using SEER 18, 2000-2010 cases for male lung cancer. Use all standard selections/exclusions. Include both the observed and expected survival in both cumulative summary and detailed life pages.

Key Points and Reminders

  • In the left-truncated life tables session, the time axis is attained age rather than time since cancer diagnosis as in standard survival analyses.
  • When using the Modified Product Limit method, the cumulative summary pages will not start until the age at which the number of contributing cases is large enough to produce stable statistics.
  • The expected survival tables used to produce the expected survival statistics are based on all causes of death, rather than other causes. However, this will not be a significant bias unless death attributable to the cancer of interest is a significant portion of all causes of death for the general population, for example, when analyzing all sites combined.
  • Due to inaccuracies in the coding of the cause of death variable, there are various ways to define the appropriate cause of death. SEER provides a user-defined variable with one grouping defining the cause of death for use with left-truncated life table analyses. It is based on a field (SEER other cause of death classification) which was one of two related fields added to the SEER data starting with the November 2008 submission. For information, refer to the SEER Cause-specific Death Classification.

Step 1:  Create a New Left Truncated Life Tables Session

  • Start SEER*Stat.
  • From the File menu select New > Left Truncated Life Tables Session or use the Left Truncated button on the toolbar.

Step 2:  Select a Database (Data Tab)

  • It is extremely important that you select the database as the first step. The other choices you will make in this session will be based on variables in the selected database. The correct database must be selected in order to see the correct list of variables in selection statements, table statements, and the dictionary editor.
  • On the Data Tab select "Incidence - SEER 18 Regs Research Data + Hurricane Katrina Impacted Louisiana Cases, Nov 2013 Sub (1973-2011 varying)".

Learn More...

  • Databases distributed with SEER*Stat use names designed to describe the data. In this case, "(1973-2013 varying)" describes the years of diagnosis for the cases included in the database. They are considered "varying" because the years of diagnoses for cases vary per registry, depending on which year the registry joined the SEER Program. See Registries - Common Terms for more information.

Step 3:  Defining the Analysis Cohort (Selection Tab)

  • Move to the Selection Tab.
  • The Standard Case Selections box on the Selection Tab contains a set of case selection or exclusion criteria commonly associated with Left Truncated Life Tables analyses. When a new session is started, all but two of the active standard selections or exclusions will be automatically selected. These default selections represent the standard selections most commonly used for a survival analysis.
    • Note that you do not need to select malignant cases as it is one of the Standard Case Selections.
    • The Cases in Research Database option will be checked by default. This will exclude the July through December 2005 cases from Louisiana.
  • In this exercise, we need a statement selecting 2000-2010 cases for male lung cancer.
    1. Select Edit next to the Case Selection box to open the Case Selection window.
    2. Using the controls at the top of the Case Selection window, you will create a search statement. The variables are listed in categories in the Variable box on the top left of the screen. The Selection Statement should read:
      {Race, Sex, Year Dx, Registry, County.Sex} = ' Male'
      And {Race, Sex, Year Dx, Registry, County.Year of diagnosis} = '2000','2001,'2002','2003','2004','2005','2006','2007','2008','2009','2010'
      And {Site and Morphology.Site recode ICD-O-3/WHO 2008} = 'Lung'
    3. When finished, click the OK button.

Step 4:  Choose the Statistics to Display (Statistic Tab)

For this problem, no changes are required to the default settings.

  • In the Ages box, Starting Age is "0" and Ending Age is "115+".
  • In the Method box, Actuarial is selected.
  • For Stability, the Use Modified Product Limit option should be checked.
  • Use the default settings for the Time Dependent Variables.
  • The box to Include Expected Survival In Output should be selected.
    • The default Expected Survival Table is "U.S. 1970-2009 by individual year (White,Black,Other (AI/API), Ages 0-99, All races for Other Unspec 1991+ and Unknown)" is selected.
  • In this exercise, we will use "Dead due to other causes using SEER other cause of death classification" for the Definition of Cause of Death

Step 5:  Table Variables (Table Tab)

  • Use the Dictionary Editor to create a variable based on "SEER historic stage A" with the following groupings: Localized, Regional, Distant, Unstaged, and Total (using the 4 individual stages).
  • Set this as the Display (Page) Variable.
  • Move to the Output tab.

Step 6:  Edit Settings on the Output Tab

  • Enter a title for your results matrix.
    Survival of Causes Other Than Lung Cancer
    SEER 18, Male Lung and Bronchus Cancer by Historic Stage
    Includes Cases Diagnosed in 2000-2010
    Left-Truncated Life Tables Exercise 1
  • Display Cumulative Summary (Annual Intervals) and Standard Life (Monthly Intervals) in the output.

Step 7:  Execute SEER*Stat

  • Use the Execute button or select Execute from the Session menu to execute the session. (Execute Offline is a 3rd option available and has been explained in previous exercises.)
  • You will receive a variable warning dialog instructing you to use caution when using the SEER historic stage A variable. Click OK to close the dialog and execute the session.
  • A dialog will display the progress of the job. When the job completes a new window will open containing the output table or matrix.

Learn More...

  • The SEER Program strives to make all Localized/Regional/Distant (L/R/D) stage variables consistent for all cancer sites for the appropriate years. However, there are certain site/year combinations where this is not possible. For example, lung and bronchus cancer has been blanked out in the SEER Historic Stage A variable for all cases diagnosed prior to 1987. Because this exercise includes lung cancer cases from 2000-2010, the warning can be ignored. To see which cancer sites were affected by the stage adjustments, click on the "For More Information..." link located on the warning dialog that appears when you execute this session. This link is also available on the selection dialog and within the dictionary editor when working with the SEER Historic Stage A variable.

Step 8:  The Results Matrix

  • Use the Save As command on the File menu to save the matrix. Enter "Left Truncated Exercise 1" as the filename. SEER*Stat will assign the "ssm" extension to indicate that this is a "SEER*Stat Survival Matrix" file.
  • Compare your results to this SEER*Stat matrix file: Exercise Matrix 1 Results.
  • The results matrix consists of ten pages of output since you selected to display both the Cumulative Summary and Standard Life tables on the Output tab. There are five cummulative summary tables and five life tables, one for each of the groupings in the user-defined historic stage variable. Use the drop down list on the toolbar to select a different page to view.
  • The Survival Results Matrix section of the help system contains more information about the SEER*Stat matrix and its features.