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Import and Export

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Export a pedigree as a BOADICEA file

BOADICEA (Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm, Antoniou et al., 2004, 2008) is a risk model for familial breast and ovarian cancer. The model can be used to compute BRCA1 and BRCA2 mutation carrier probabilities and age specific risks for breast and ovarian cancer.

An introduction to BOADICEA can be found here

Be sure to follow all the links from the BOADICEA Project home page. Please also read the BWA user guide. Appendix A shows the BOADICEA pedigree data format.

The BOADICEA data format (just for reference)

  1. FamID: Family/pedigree ID, character string (maximum 13 characters)
  2. Name: First name/ID of the family member, character string (maximum 8 characters)
  3. Target: The family member for whom the BOADICEA risk calculation is made, 1 = target for BOADICEA risk calculation, 0 = other family members. There must only be one BOADICEA target individual.
  4. IndivID: Unique ID of the family member, character string (maximum 7 characters)
  5. FathID: Unique ID of their father, 0 = no father, or character string (maximum 7 characters)
  6. FathID: Unique ID of their father, 0 = no father, or character string (maximum 7 characters)
  7. MothID: Unique ID of their mother, 0 = unspecified, or character string (maximum 7 characters)
  8. Sex: M or F
  9. Twin: Identical twins, 0 = no identical twin, any non-zero character = twin.
  10. Dead: The current status of the family member, 0 = alive, 1 = dead
  11. Age: Age at last follow up, 0 = unspecified, integer = age at last follow up
  12. Yob: Year of birth, 0 = unspecified, or integer (consistent with Age if the person is alive)
  13. 1BrCa: Age at first breast cancer diagnosis, 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
  14. 2BrCa: Age at contralateral breast cancer diagnosis, 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
  15. OvCa: Age at ovarian cancer diagnosis, 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
  16. ProCa: Age at prostate cancer diagnosis 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
  17. PanCa: Age at pancreatic cancer diagnosis 0 = unaffected, integer = age at diagnosis, AU = unknown age at diagnosis (affected unknown)
  18. Gtest: Genetic test status, 0 = untested, S = mutation search, T = direct gene test
  19. Mutn: 0 = untested, N = no mutation, 1 = BRCA1 positive, 2 = BRCA2 positive, 3 = BRCA1 and BRCA2 positive
  20. Ashkn: 0 = not Ashkenazi, 1 = Ashkenazi

1. Draw and export a pedigree

Before you start: make the BOADICEA symbols and labels available.

1. In Input mode select BOADICEA symbols from the Phenotype menu:

> > > > > > > > > >

If you right click on a symbol, you will also notice the change in the Text dialog:

Now we draw the simple pedigree whose data are available in Appendix A of the BWA user guide:

There is nothing new. Nevertheless, let's take alook at the three sisters Sarah, Amy, and Clare.

Right click on Clare, and enter the data, Select "arrow" because she will be the target of the risk calculation.

Sarah and Amy are identical twins, so you have to enter an asterisk in the second text field for Amy:

Sarah also gets an asterisk(identical twin). Select 'deceased' and 'breast cancer', and enter age, year of birth, and age at first breast cancer diagnosis:

If you are done with drawing you should always export your pedigree as a PIP file. Just in case, because a DAT file cannot be re-imported in PED. Now press the 'Export' button again:

This time you select the BOADICEA DAT format:

Press the 'Save' button, and enter a name (suffix 'DAT') in the Windows save dialog

2. Upload the exported data to the BOADICEA Web Application (BWA)

Register at the BWA. It may take some time to get an access key.

From the BOADICEA Project home page select 'Run BOADICEA on-line', and log in:

Select 'Upload a pedigree file from your computer', select the file you just saved, and continue.

You will get a family summary.

ALWAYS CONTROL THESE DATA BEFORE YOU PROCEED !

Now press 'Compute Risks', and you will get computed results. You will receive a comprehensive report with all the details you need. For simple pedigrees, BOADICEA will outline your pedigree:

In PED, if you use the Edit window, the pedigree can be editet and saved, e.g., as a wmf file:

Thank you for reading this short manual.


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