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U.S. National Institutes of Health National Cancer Institute

SEER*Stat Survival Exercise 3

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.

Create a table showing 5-year cause-specific survival rates for regional stage female breast cancer diagnosed between 1996-2004 in the SEER 17 Registries. Include conditional survival rates. That is, calculate the probability of surviving 3 additional years from 3 conditioning points (Diagnosis, 1-year, and 2-years after). Display the results by age with the following groupings:

Age = All Ages, < 50, 50+

Include the detailed life tables and cumulative summary tables with cause-specific survival and standard errors. Calculate the statistics using monthly intervals, but only include annual intervals in the summary pages. Include the special intervals/conditional survival and median survival in the summary pages.

Key Points and Reminders

  • You must define the cause of death to use for the cause-specific survival. This is done by creating a variable with one grouping defining the cause of death. Due to inaccuracies in the coding of the cause of death variable, there are various ways to define the appropriate cause of death. In this exercise, we will define our cause of death as death due to any malignant cancer for those patients with one and only one tumor, or death due to malignant breast cancer for those patients with two or more tumor diagnoses. This variable would only be appropriate when working with first primary breast cancer cases only. Exclude all patients with missing/unknown cause of death from the analysis.
  • Because the survival session does not use census population estimates, you can use any of the age of diagnosis variables when creating the user-defined age variable.
  • For cause-specific survival, the expected rate table is used only for the Expected Rate Table Exclusions on the Selection tab. These exclusions are optional when calculating cause-specific survival, but are convenient when trying to analyze the same cohort as used when calculating survival rates requiring expected rates.
  • Specify the Special Interval/Conditional Survival criteria on the Parameters Tab as: 1-36, 13-48, 25-60.

Step 1:  Create a New Survival Session

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

Step 2:  Select the Database (Data Tab)

  • On the Data Tab select "Incidence - SEER 17 Regs Limited-Use + Hurricane Katrina Impacted Louisiana Cases, Nov 2007 Sub (1973-2005 varying)"

Step 3:  Choose the Statistics (Statistics Tab)

  • In the Cancer Survival Measures box, select Cause-Specific Survival.
    Cause-specific survival is a net survival measure representing cancer survival in the absence of other causes of death. Cause-specific survival estimates the probability of surviving a specific cause of death specified by you using the Definition of Cause of Death.
  • In the Expected Rate Table drop down box, make sure " U.S. 1970,1980,1990,2000 (White, Black, Other (AI/API) All races for Other Unspec 1991+ and Unknown)" is selected. The expected rate table is used only for the Expected Rate Exclusions located on the Selection Tab when calculating cause-specific survival.
  • You will need to create a cause of death variable as described above.
    1. Use the Create button to open the Definition of Cause of Death window.
    2. Using the controls at the top of the window, create a Selection Statement the reads:
      ({Site and Morphology.COD to site recode} = 'All Malignant Cancers'
      AND {Other.Sequence number} = 'One primary only')
      OR ({Site and Morphology.COD to site recode} = ' Breast'
      AND {Other.Sequence number} = '1st of 2 or more primaries')
    3. When finished, be sure that parentheses and conjunctions are used properly in the selection statement. Then click the OK button to open the Survival Specific Cause of Death Definition window.
    4. Edit the Name field with this variable name: "Dead: All mal & seq 0 or breast & seq 1", then click the OK button. Verify that the newly created variable is selected as the Definition of Cause of Death variable.
    5. Set the Missing/Unknown COD to Exclude from Analysis.

Step 4:  Define the Analysis Cohort (Selection Tab)

  • Use the default settings for the Standard Case Selections. These default selections represent the standard selections most commonly used for a survival analysis.
  • Based on the Problem Statement, we want to make selections based on sex, year of diagnosis, cancer site, and stage.
  • Open the Case Selection window to create the search statement. When complete, the Selection Statement should read:
    {Race, Sex, Year Dx, Registry, County.Sex} = ' Female'
    AND {Race, Sex, Year Dx, Registry, County.Year of diagnosis} = '1996','1997','1998','1999','2000','2001','2002','2003','2004'
    AND {Site and Morphology.Site rec with Kaposi and mesothelioma} = ' Breast'
    AND {Stage.SEER historic stage A} = ' Regional'

Step 5:  Set the Table Variables (Table Tab)

  • Set age as a Row variable. You need to create a user-defined variable for age.
  • First, open the Data Dictionary.

  • Select the "Age recode with <1 year olds" variable from the "Age at Diagnosis" category and use the Create button to open the Edit Variable window.
    • Edit the Name field with this variable name, "Age (All, <50, 50+)".
    • Delete all the groupings from the Groupings box.
    • Create an age grouping for "< 50" using the values "00 years" through "45-49 years" in the Values box.
    • Create the "50+" grouping using the Add Rest button to add a grouping with the values "50-54 years" through "85+".
    • Select Added as one grouping (all values combined) on the Add Rest dialog.
    • Use the Add All button to create a combined grouping for all the values and name it "All ages". Move the "All ages" grouping to the top of the list using the Up button.
    • When you are finished, click the OK button.
  • Expand the "User-defined" category in the Available Variables box using the "+" symbol.
  • Add the age variable to the row dimension. The dimensions specified on the Table Tab only apply to the summary tables.

Step 6:  Set the Parameters

  • Use the default settings for the Dates parameters. The Begin Date initiates the calculation of survival time for an individual case, and the End Date ends the calculation of survival time.
  • By default, SEER*Stat calculates statistics using monthly intervals. To show 5-years of survival, in the Intervals box, set the Number to 60. This indicates a maximum number of 60 monthly survival intervals to be displayed in the output rate tables.
  • Check the box "Include 0th Interval" to generate statistics for time zero.
  • Set the Special Intervals/Conditional Survival to 1-36, 13-48, 25-60.
  • Check "Cumulative Summary" and "Standard Life" in the Display Box.
  • Specify the Interval in the Cumulative Summary box as 12,24,36,48,60.
  • Check the boxes to "Include Special Intervals/Conditional Survival" and "Include Median Survival" in the Cumulative Summary pages.

Learn More...

  • These parameters establish how case survival time will be defined and the intervals that will be used in the analysis. The survival time for each case is calculated and then partitioned into the defined survival duration intervals. For every life table, SEER*Stat calculates the number of cases alive at the beginning of each survival interval.
  • This exercise calls for survival statistics for the 17 SEER Registries from 1996-2004, but data for four of the registries is not available prior to 2000. California excluding SF/SJM/LA, Kentucky, Louisiana, and New Jersey contribute cases for diagnosis years 2000-2004.

Step 7:  Edit Setting on the Output Tab

Enter the following title for your results matrix:
5 Year Cause-Specific Survival Rates
SEER 17, Malignant Regional Female Breast Cancer
Includes Cases Diagnosed in 1996-2004 (2000-2004 for 4 expansion registries)
Survival Exercise 3

Step 8:  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.)
  • A dialog will display the progress of the job. When the job completes a new window will open containing the output table or matrix.

Step 9:  The Results Matrix

  • Use the Save As command on the File menu to save the matrix. Enter "Survival Exercise 3" 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 3 Results.
  • The results matrix consists of multiple pages of output since the Standard Life tables use the variables you set on the Table Tab as page variables. Use the drop down list on the toolbar to select a different page to view.
  • There are no values displayed in the Median Cause-Specific column in the Summary Table. This is because the cumulative cause-specific rate did not go below 50% within the first 60 months of survival for any age group. If we calculated rates for distant instead of regional female breast cancer, values for median rates would be available within the first 60 months. See key.survival3_distant.ssm.
  • The Survival Results Matrix section of the help system contains more information about the SEER*Stat matrix and its features.