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BCRA R Package

BCRA is an R package that projects absolute risk of invasive breast cancer according to NCI’s Breast Cancer Risk Assessment Tool (BCRAT) algorithm for specified race/ethnic groups and age intervals.

This package is to project absolute risk of invasive breast cancer according to NCI’s Breast Cancer Risk Assessment Tool (BCRAT) algorithm for specified race/ethnic groups and age intervals. The updated version 2.0 includes the new Hispanic model.

This package can be used to estimate the risk of developing breast cancer over a predetermined time interval with risk factors. As the same as Breast Cancer Risk Assessment SAS Macro, the users can specify the time interval as appropriate, not only limited to the 5 years risk prediction available with BCRAT. 

The main function in this package is absolute.risk, which is defined based on a statistical model known as the "Gail model". Parameters and constants needed in this function include initial and projection age, recoded covariates using function recode.check, relative risks of BrCa at age "<50" and ">=50" obtained from function relative.risk as well as other known constants listed from function list.constants like BrCa composite incidences, competing hazards, 1-attributable risk using in NCI BrCa Risk Assessment Tool (NCI BCRAT). With risk factors and projection interval ages for a group of women, the function absolute.risk will return the corresponding absolute risk projections. If the function returns any missing values, the function error.table or error.table.all is used to find where the errors occured. The function check.summary can give a quick check for errors of input file and missing values of risks.  For further analysis, a data frame is created from the function risk.summary, which includes age, duration of the projection time interval, covariates and the projected risk.

The version 2.0 includes absolute risk projections for Hispanic women (US born and Foreign born) based on race specific RR risk models developed on the San Francisco Bay Area Breast Cancer Study (SFBCS). Race specific attributable risks, breast cancer composite incidences and competing hazards are added to the updated package.

Any changes/modifications to the package would be at the user’s own discretion and risk.

Software Download:

This package is also available on the Comprehensive R Archive Network (CRAN) - BCRA

References:

  • Gail MH, Brinton LA, Byar DP, Corle DK, Green SB, Shairer C, Mulvihill JJ. Projecting individualized probabilities of developing breast cancer for white females who are being examined annually. JNCI 1989; 81(24): 1879-86. [Pubmed Abstract]
  • Costantino J, Gail MH, Pee D, Anderson S, Redmond CK, Benichou J, Wieand HS. Validation studies for models to project the risk of invasive and total breast cancer. JNCI 1999; 91:1541-8. [Pubmed Abstract]
  • Gail MH, Costantino JP, Pee D, Bondy M, Newman L, Selvan M, Anderson GL, Malone KE, Marchbanks PA, McCaskill-Stevens W, Norman SA, Simon MS, Spirtas R, Ursin G, Berstein L. Projecting individualized absolute invasive breast cancer risk in African American women. JNCI 2007; 99:1782-92. [Pubmed Abstract]
  • Matsuno RK, Costantino JP, Ziegler RG, Anderson GL, Li H, Pee D, Gail MH. Projecting individualized absolute invasive breast cancer risk in asian and pacific islander american women. JNCI 2011; 103:951-61. [Pubmed Abstract]
  • Banegas MP, John EM, Slattery ML, Gomez SL, Yu M, LaCroix AZ, Pee D, Chlebowski RT, Hines LM, Thompson CA, Gail MH.  Projecting Individualized Absolute Invasive Breast Cancer Risk in US Hispanic Women. JNCI 2016; 109.

Support:

Statistical issues should be directed to: Dr. Mitchell Gail

Technical details should be directed to: Fanni Zhang (zhangf@imsweb.com)