Breast cancer risk assessment using PED 6 and BOADICEApresented at the 20th Conference of the German Society of Humangenetics, 1 - 3rd April 2009, Aachen
There are a number of models available to assess both breast cancer risk and the chances of identifying a BRCA1/2 mutation. In a recent investigation of five different carrier prediction models only the BOADICEA model predicted the overall observed number of mutations detected accurately (Antoniou et al., J Med Genet. 2008, 45:425-31). The current version of BOADICEA has been implemented as a Web-based program where users can upload a pedigree file or create a pedigree online. The online pedigree building application appears quite complicated and enables to build only simple pedigrees. However, the authors of BOADICEA claim their program will process pedigrees of any size and structure.
PED 6 (www.medgen.de) is a Windows application for creating, drawing, and editing of pedigrees. All of the pedigree drawing features conform to the Pedigree Standardization Task Force recommendations. PED 6 enables the user to export family information not only as LINKAGE or CSV (comma separated values) file, but also as a BOADICEA data file. The data files created by PED can be uploaded to the BOADICEA Web Application (BWA; www.srl.cam.ac.uk/genepi/boadicea/boadicea_home.html) to estimate the risks of breast and ovarian cancer and the probability to be a carrier of any cancer-associated mutations in the BRCA1 or BRCA2 gene.
PED 6 appears to be a valuable tool to complement the BWA. In single pedigrees risks calculated by this combination of programs differ significantly from those received by the combination of Cyrillic / LINKAGE programs currently used by the Deutsches Konsortium für Brust- und Eierstockkrebs.
PED 5 Pedigree Software(Presented at the European Congress of Human Genetics 2005)
PED is a fast interactive Pedigree Software for Windows 98 (R) and above. PED was introduced at the ESHG Conference in 1997 and now has a continuously growing user community with researchers and clinicians in over 30 countries worldwide. PED complies with the "Recommendations for standardized human pedigree nomenclature" proposed by the PSTF (Bennet RL et al, Am J Hum Genet 56:745-752,1995). Apart from fully sizable printed output, pedigrees can be exported as Windows metafiles (WMF) to virtually any Windows Office or drawing program.
Among other enhancements, PED 5 now can fetch family information from a data file with LINKAGE or CSV (comma separated values) format, where each line describes an individual by the pedigree ID, the individual's ID, the IDs of his/her father and mother, the gender, the phenotype or affection status, and any other data related to the individual (like haplotypes, or clinical characteristics). Imported pedigrees can virtually be of any size; also descendants with a second, third, or even tenth partner or any descendants of the probands' ancestors will be correctly displayed. Currently, marriage loops are not handled; they must be edited in the edit window. Pedigree charts can also be exported to these standard file formats. With each open/edit/save cycle, all IDs will be preserved. So pedigree data can easily be imported into a spreadsheet, a database, or further be used in linkage calculations or risk assessment. A demonstration program is available at www.medgen.de/ped.
PED complies with the "Recommendations for standardized human pedigree nomenclature" proposed by the PSTF (Bennet RL et al, Am J Hum Genet 56:745-752,1995):
Import pedigree from a LINKAGE or CSV file:
Interactive pedigree drawing
PED provides two drawing windows:
- Input window
- Layout window
Auto-drawing: the input window
- In Input mode all drawing is done by pressing one button
- Click on a symbol, press Ctrl+S, Ctrl+D, or Ctrl+U (or click on the appropriate button at the top of the window) to draw a child (son, daughter, unknown gender) with the partner chosen in the partner drop down listbox (top left). To add a "new" partner: choose the last partner in the partner list box. Ancestors: Click on button Ancestors to draw parents, grandparents, great-grandparents... of the consultands.
- Right click on a symbol to enter text surrounding the symbol
- Change a symbol to one of the predefined (or one of hundreds of other possible) symbols.
- Default symbols as well as their corresponding menu items may be edited by the user:
- or use BOADICEA symbols and labels:
- Many display options are user-defined:
Export your pedigree from Input pane
You may export your pedigree chart from Input pane as a *.PIP (Ped InPut), as a LINKAGE (*.TXT), as a Comma Separated Values (*.CSV) file, or as a BOADICEA DAT file:
Perfect layout: the edit window
Paste your pedigree to the layout ("edit") window:
Add the legend automatically, fine tune the layout manually, and print your pedigree: