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APA BrCa RAM ReadMe

APA_BrCa_RAM:    (A)sian-(P)acific-(A)merican (BrCa) (R)isk (A)ssessment (M)acro

Installing the Asian-Pacific-American BrCa Risk Assessment Macro    Ver 1.0   05/12/11

  "Projecting Individualized Absolute Invasive Breast Cancer Risk in Asian and
   Pacific Islander American Women"   Matsuno, Costantino, Ziegler et al.   JNCI 2011

This module pertains to Windows 2000, Windows XP, Windows Vista and Windows 7
operating systems for desktop/laptop PCs with installed SAS 9 software.

Contents of the Zip file "APA_BrCa_RAM.zip":

(a) APA_BrCa_RAM          sas macro which performs abs risk and 95% CI calculations
                         for Asian-Pacific-American women based on the Asian-American
                         Breast Cancer Study (AABCS) Relative Risk (RR) model.

                         the first 350 lines of the sas macro  "APA_BrCa_RAM"  contains
                         extensive documentaion/clarification on the use and operation
                         of this macro.

(b) APA_BrCa_example.sas  a simple demonstration sas program which reads in raw data,
                         involkes the sas macro  "APA_ABrCa_RAM"  and obtains abs risk
                         and 95% CI.

                         the first 30 lines of this sas program contains a brief
                         description of what this program accomplishes.  additional
                         clarification is scattered throughout the program.

(c) APA_RR.fil            raw data file for input to  "APA_BrCa_example.sas"

(d) APA_BrCa_example.out  sample output from  "APA_BrCa_example.sas"

(e) ReadMe.fil            this file you are reading

After unzipping  "APA_BrCa_AbsRsk.zip",  check to see that all files listed above are
included.  At this point, a cursory examination of  "APA_BrCa_RAM",  "APA_BrCa_example.sas"
and "APA_RR.fil"  will prove helpful.  These files can be veiwed using your favorite text
editor or  Notepad  which is included with Windows.

Installation and operation of the sas macro  "APA_BrCa_RAM":

(a) unzip the entire contentes of the zip file "APA_BrCa_RAM.zip" into a folder on
   your hard drive.

(b) execute the provided demonstration sas program  "APA_BrCa_example.sas".

(c) compare the output  "APA_BrCa_example.lst"  with the provided file
  "APA_BrCa_example.out".  The two files should be identical.  If so, congratulations,
   you have successfully installed the software.

Characteristics of the input sas file for the Asian-Pacific-American Risk Assessment SAS Macro:

(a) the input sas file name and output sas file name are provided by the user upon the
   invocation of the sas macro  "APA_BrCa_RAM".

(b) the input sas file must contain the following 9 quantities.  any additional variables
   on the input sas file are ignored.  No particular ordering is required.

   (1) ID unique ID                      (non-negative integer 1,2,3....9999999)

   (2) current age in years in the age interval [20, 90)           e.g. 35.8

   (3) projctn age in years in the age interval (current age, 90]  e.g. 58.9
       constraint of:  20 =< current age < projctn age <= 90

   (4) # of breast biopsies              (non-negative integer counts 1,2,3...)

   (5) age at menarche in years          (non-negative integer years)

   (6) age of first live birth in years  (non-negative integer years)
       constraint of:  age menarche <= age at first live birth

   (7) # of first degree relatives with breast cancer
      (non-negative integer counts 1,2,3...)

   (8) biopsy displays atypical hyperplasia?
       0  = no
       1  = yes
       99 = unk or not applicable response

       IF # breast biopsies = 0,  hyperplasia         MUST BE 99 (not applicable)
       IF # breast biopsies > 0,  hyperplasia  can be  0,1 or 99 (unknown)

   (9) race of women
       1=Chinese  2=Japanese  3=Filipino 4=Hawaiian 5=Other Pacific Islander 6=Other Asian
       for records where race is not 1 or 2 or 3 or 4 or 5 or 6
       projected  abs risk  defaults to the sas missing value "." .

   more detailed documentation is provided in the first 350 lines of the SAS macro
  "APA_BrCa_RAM"

   in the above [) represents an interval closed on the left and   open on the right
                (] represents an interval   open on the left and closed on the right

   this program will categorize the raw values of # breast biopsies, age menarche,
   age first live birth and # 1st degree relatives with brca into risk categories
   according to the rules outlined in the JNCI 2011 manuscript listed at the beginning
   of this document.

   note that the program, being an analytical tool, will make the most rudimentary
   checks for logical consistency between the input variables.  It is the user's
   responsibility to make sure that all input covariate values are logically
   consistent and correct within each person.  As a final step, the program
   will generate a missing projected Absolute Risk for records which it deems to
   be in error.  The user should examine the output file for any records with a
   missing Absolute Risk and rectify the error(s) for these records.

     e.g. if NBiops equals zero than atypical hyperplasia must be 99 (not applicable)
      or  Projection Age in years must be greater than Current Age

Contacts:
Dr. Mitchell Gail     gailm@exchange.nih.gov      Scientific/Statistical issues
Mr. David    Pee      peed@imsweb.com             Technical/software problems

Terms & Conditions

Source Code for APA model: Asian-Pacific American Women Breast Cancer Risk Calculation Module

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Provider: National Institutes of Health (NIH), National Cancer Institute (hereinafter "NCI")

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The APA model risk calculator may be updated periodically as new data or research becomes
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