nci logo
NIH
U.S. National Institutes of Health National Cancer Institute

SEER*Stat Survival Exercise 1

Create a table showing 5-year relative survival rates (calculated using 60 monthly intervals) for regional stage female breast cancer diagnosed between 1999 and 2005 in the SEER 17 Registries.

Display annual observed, expected, and relative cumulative rates in both summary and detailed life tables.

Adjust relative rates that are increasing or greater than 1.0.

Key Points and Reminders

  • Due to the impact of Hurricane Katrina on Louisiana's population for the July - December 2005 time period, Louisiana cases diagnosed for that six-month time period have been excluded from the limited-use database. These cases are provided with the data, but they are considered supplemental data. SEER does not include these cases in most analyses using the November 2008 submission, therefore the default in SEER*Stat is to exclude them with the "Cases in Limited-Use Database" checkbox on the Selection tab. For more information, see Adjustments for Areas Impacted by Hurricanes Katrina and Rita on the SEER Web site.
  • The database used in the exercise contains cases diagnosed from 1973 through 2006, with registries contributing cases from varying years of diagnosis. This exercise calls for survival statistics for the 17 SEER Registries from 1999-2005, 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 2000-2005. The remaining 13 SEER Areas contribute cases for the entire period 1999-2005.
  • Although the statistics are calculated using monthly intervals, in this exercise we are only displaying annual intervals in the cumulative summary tables. Annual statistics calculated monthly will differ from statistics calculated annually.
  • The default expected rate tables, distributed by SEER, now include expected rates for 2000 and values for unknown race. SEER*Stat no longer excludes records with unknown race when calculating relative survival rates. The expected rates used for the two race groups, Other unspecified 1991+ and Unknown, are All races combined expected rates.
  • For survival, there are several standard selections that are available as check boxes for convenience. Some of these are required when using expected rate data in calculations (to calculate relative survival rates or the crude probability of death using expected survival).
  • When calculating relative survival, the rates can be greater than 1.0. This occurs when the observed survival for the cohort has a higher survival rate than the expected rates for that same age, race, sex and date at which age was coded. For example, relative survival rates for in situ female breast cancer are greater than 1.0. This could be attributed to the low mortality of the disease and an increase in medical care, which could lead to earlier diagnosis of other diseases.
  • Sometimes, the cumulative relative survival rates can be increasing over time, making it appear as if people are rising from the dead. This occurs when the observed survival for the cohort decreases more slowly than the expected rates for that same age, race, sex, and year group.

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 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 17 Regs Limited-Use + Hurricane Katrina Impacted Louisiana Cases, Nov 2008 Sub (1973-2006 varying)"

Learn More...

  • Databases distributed with SEER*Stat use names designed to describe the data. In this case, "(1973-2006 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:  Choose the Statistics to Display (Statistic Tab)

  • In the Cancer Survival Measures box, select Relative Survival.
  • Leave the Period Survival option unchecked, and make sure that the Method is set to Actuarial.
  • 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.

Step 4:  Understanding the Selection Tab in a Survival Session

  • 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 survival analyses. When a new Survival Session is started, all but one 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.
  • In this exercise, you will use the default values for the standard case selections. See Survival Selection Tab in the SEER*Stat help system for a complete description of the standard case selections.

Step 5:  Defining the Analysis Cohort (Selection Tab)

  • Specific click-by-click instructions for creating individual selection statements were given in previous tutorials (see Frequency Exercise 1a). Use those techniques to create four selection statements. Be sure to consider the following before making your selections:

    1. Selection statements reduce the number of records included in an analysis based on specific variables. If no selection statements are made on the Selection Tab, all records in the database will be included. In this exercise, we want to calculate survival rates for regional stage female breast cancer, for SEER 17 cases diagnosed from 1999-2005. Therefore, we need a statement selecting regional stage female breast cancer, for the years 1999-2005.
    2. Note that you do not need to select malignant cases as it is one of the Standard Case Selections.
    3. The Cases in Limited-Use Database option in the Standard Case Selections box will be checked by default. This will exclude the July through December 2005 cases from Louisiana.
  • Select Edit next to the Case Selection box to open the Case Selection window.
  • 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} = ' Female'
    And {Race, Sex, Year Dx, Registry, County.Year of diagnosis} = '1999','2000','2001','2002','2003','2004','2005'
    And {Site and Morphology.Site rec with Kaposi and mesothelioma} = 'Breast'
    AND {Stage.Summary stage 2000 (1998+)} = 'Regional'
  • When finished, click the OK button.

Step 6:  Table Variables (Table Tab)

  • There are no table variables for this exercise. Move to the Parameters tab.

Step 7:  Set the Parameters (Parameters Tab)

  • Use the default setting for all parameters except the Display parameters.
  • The default number of intervals setting of 60 and the months per interval of 1 in the Intervals box will result in 5-years of survival. The five-year survival rates are shown if the number of intervals is 60 or greater. Always set the number of intervals to the largest one of interest to simplify the output and to reduce processing time.
  • Check Cumulative Summary and Standard Life in the Display box and use the default Cumulative Summary settings.

Step 8:  Edit Settings on the Output Tab

  • Enter a title for your results matrix.
    5 Year Survival Rates
    SEER 17, Malignant Regional Female Breast Cancer
    Includes Cases Diagnosed in 1999-2005 (2000-2005 for 4 expansion registries)
    Survival Exercise 1
  • The options to adjust relative rates that are increasing or greater than 1.0 should be checked by default.

Learn More...

As of SEER*Stat version 5.3, survival defaults to displaying statistics as percents. You may specify whether rates in the results matrix will be displayed as percents or proportions, and to how many decimal places they will be rounded. Once you have made your selection, you may click the Set Defaults button if you want to use these settings automatically each time you create new Survival Session.

Step 9:  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 Summary stage 2000 (1998+) variable. This variable is coded for breast cancer for 1998+, therefore the warning does not apply for this analysis. 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. 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 Summary stage 2000 (1998+) variable.

Step 10:  The Results Matrix

  • Use the Save As command on the File menu to save the matrix. Enter "Survival 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 two pages of output since you selected to display both the Cumulative Summary and Standard Life tables on the Parameters tab. 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.

Step 11:  Using the Results in Other Software

Two methods can be used to take results from a SEER*Stat matrix and use them in another program:

  1. Copy data from the matrix to the Windows clipboard. In the other program, paste the contents of the clipboard to the work space. This technique would work well for programs that allow the pasting of data, including most graphing packages such as Excel and PowerPoint. Please refer to the SEER*Stat help system for instructions.
  2. Export the data from the matrix to a delimited text file. Some programs, such as Excel, will allow you to open a delimited text file. In other programs, such as Joinpoint and DevCan, you must select the delimited text file as the input file. Please refer to Exporting Results in the SEER*Stat help system for instructions.