SEER*Stat Survival Exercise 1: Relative Survival

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 relative survival (calculated using 60 monthly intervals) for regional stage female breast cancer diagnosed between 2004 and 2010 in the SEER 18 Registries.

Display annual observed, expected, and relative cumulative survival in both summary and detailed life tables. Include age standardized statistics in your analysis. This will include additional statistics in the summary page and additional age-specific detailed life pages.

Use the International Cancer Survival Standard 1 - Ages 15+ for the Std Case Distribution and the default age variable (Age Standard for Survival (15-44,45-54,55-64,65-74,75+)). This is the appropriate standard for breast cancer. Standard 1 was developed for cancer sites with increasing incidence by age (most cancer sites). For more information about the three available standards, see Age Standards for Survival on the SEER web site.

Adjust relative survival that is increasing or greater than 1.0.

For more information about relative survival and an overview of cancer survival statistics, see Measures of Cancer SurvivalExternal Web Site Policy on the Surveillance Research Program web site.

Key Points and Reminders

  • Starting with the November 2013 data submission, there are new default expected survival life tables. The new life tables are for 1970-2009 by individual year for ages 0-99. The previous default life tables had a maximum age of 119 and were provided for years 1970-2007. With the new expected life tables, all patients with an age at diagnosis greater than 99 will be excluded from the analysis. See the Expected Survival Life Tables on the SEER website for more information.
  • Starting with SEER*Stat 8.1.4, there's a new option on the Parameters tab for censoring cases when their attained age exceeds the expected rate table max. This option will default to on for November 2013 and later databases.
  • The survival calculation can be based on either pre-calculated survival duration variables or begin and end dates, starting with SEER*Stat 8.0.4. The pre-calculated survival duration option is the default in SEER databases starting with the November 2012 submission. Begin and end dates are still associated with the pre-calculated duration field, but duration has been calculated using complete dates (day, month, year) rather than just month and year. By using complete dates the pre-calculated duration is more precise than using begin and end dates which do not have day available. For example, a patient with diagnosis = 7/31/2000 and last contact 8/1/2000, the duration would be 1 day, which translates to 0 months of survival. Using begin and end date fields without day, this would be 7/2000 to 8/2000 and would result in 1 month of survival.
  • SEER includes age standardization for survival analyses, starting with SEER*Stat 7.0.9. Survival generally depends on age at diagnosis, and the age distribution of cancer patients may vary over time or differ among geographical areas. Age standardized survival is used to compare survival across time or different cancer populations with different age distributions. The standards provided are the International Cancer Survival Standard (ICSS) derived in Corazziari et al. (2004) for the adult population (ages 15+). By using this standard, cases with age at diagnosis < 15 will automatically be excluded from the analysis.
  • 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.
  • For survival, there are several standard selections that are available as check boxes for convenience. Some of these are required when using expected survival data in calculations (to calculate relative survival or the crude probability of death using expected survival tables).
  • When calculating relative survival, it can be greater than 1.0. This occurs when the observed survival for the cohort has a higher survival than the expected survival for that same age, race, sex and date at which age was coded. For example, relative survival for in situ female breast cancer is 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 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 survival 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.
  • One or two warnings may be displayed, depending on your SEER*Stat preferences:
    • The first is a linked database alert to warn you that the selected database contains data from multiple sources for the county attributes. Click OK to continue.
    • The second warns that the default censoring age for survival calculations has changed from 119 to 99 years when using the new expected survival life tables. This is the default starting with the November 2013 data submission. Click OK to continue.

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, "(1973-2011 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.
  • In the Cum Expected Method box, Ederer II should be selected.
  • Leave the Period Survival option unchecked, and make sure that the Method is set to Actuarial.
  • Check the box to Age Standardize.
    • Since we are calculating breast cancer survival, the Std Case Distribution should be set to "International Cancer Survival Standard 1 - Age 15+".
    • Use the default selection for the Age Variable, "Age Standard for Survival (15-44, 45-54, 55-64, 65-74, 75+)". Cases less than 15 years of age will be excluded from your analysis.
    • The Age Standards for Survival web page has more information about the standards and age variables.
  • In the Expected Survival Table drop down box, make sure "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.

Learn More...

  • Starting with the November 2010 data submission, SEER uses the Ederer II method when calculating relative survival. Previously the Ederer I method was used, but not shown in the SEER*Stat interface. The new Cum Expected Method box allows you to switch from Ederer II to other available methods. The Hakulinen (exact and simplified) adjustment methods were options that appeared on the Survival Session Output tab prior to SEER*Stat version 7.

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 for regional stage female breast cancer, for SEER 18 cases diagnosed from 2004-2010. Therefore, we need a statement selecting regional stage female breast cancer, for the years 2004-2010.
    2. Note that you do not need to select malignant cases as it is one of the Standard Case Selections.
    3. The Cases in Research 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} = '2004','2005','2006','2007','2008','2009','2010'
    And {Site and Morphology.Site recode ICD-O-3/WHO 2008} = 'Breast'
    AND {Stage - LRD (Summary and Historic).Summary stage 2000 (1998+)} = 'Regional'
  • When finished, click the OK button.

Step 6:  Set the Parameters (Parameters Tab)

  • Use the default setting for all parameters except the Display parameters.
    • The Survival Calculation should be set to "Pre-calculated Duration" and the Duration set to "Survival months (from completed dates)"
    • The "Censor When Attained Age Exceed Expected Table Max" should be checked by default.
    • 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 is 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.

Learn More...

  • Starting with the November 2013 data submission, the default selection is to Censor When Attained Age Exceed Expected Table Max. This is used to match the statistics published throughout the SEER website. If you switch your analysis from a previous database to use a November 2013 database, the new expected survival life tables are the default and age censor selection will be enabled by default. If you are working with data prior to the November 2013 submission and use the new expected survival life tables, the option will not be enabled.

Step 7:  Table Variables (Table Tab)

  • There are no table variables for this exercise.

Step 8:  Edit Settings on the Output Tab

  • Enter a title for your results matrix.
    5 Year Survival
    SEER 18, Malignant Regional Female Breast Cancer
    Includes Cases Diagnosed in 2004-2009
    Survival Exercise 1
  • The options to adjust relative survival that is increasing or greater than 1.0 should be checked by default.

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 seven pages of output since you selected to display both the Cumulative Summary and Standard Life tables on the Parameters tab. There are six standard life tables, one for each of the age groupings in the "Age Standard for Survival (15-44, 45-54, 55-64, 65-74, 75+)" variable, and one that includes "All Included Ages". 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.