Angeline M Loh, Kim W Carter, Steven Wiltshire, Lyle J Palmer

Celestial3D v1.0.1 is now available for download!

Celestial3D is a software tool for the graphical display of familial information. It is being developed by the Laboratory for Genetic Epidemiology at the Western Australian Institute for Medical Research.

If you can see white lines on a black background, then you have installed BS Contact VRML/X3D successfully. Click and drag to rotate. Zoom with the scroll wheel.

Background

With the ever-growing size of genealogical and family-based datasets around the world, there is an increasing need for software tools to analyse, manage and record the data. Graphical techniques are becoming essential for analysing large amounts of data, to improve upon the limitations of traditional text-based techniques, particularly in representing complex data interrelationships. A graphical presentation of familial data (e.g. phenotypic, genotypic or demographic) and pedigree structures can show important information in a far less cluttered fashion, enabling rapid analysis and interpretation of results.

Two Dimensional Pedigree Visualisation

A number of software packages have been developed to visualise pedigrees in 2D. A selection are listed below.

Software	Citation	URL
CoPE	Brun-Samarcq et al. (1999)
CraneFoot	Makinen et al. (2005)	users.tkk.fi/~vmakine2/s1200/cranefoot.html
Cyrillic 2		www.cyrillicsoftware.com/
FamilyTree Builder		www.myheritage.com/FP/Company/family-tree-builder.php
kinship, gap, graphvis	Zhao (2006)	www.cran.r-project.org
KINDRED
Lineage		www.ansci.cornell.edu/lineage/
Madeline 2.0 PDE	Trager et al. (2007)	kellogg.umich.edu/madeline/
PED5	Plendl	www.medgen.de/ped5/
Pedhunter	Agarwala et al. (1998)	www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/pedhunter.html
PediDraw	He, Li (2007)	pedidraw.genet.org.cn
Pedigraph	Garbe et al. (2004)	animalgene.umn.edu/pedigraph/
Pedigree-Draw 6		www.pedigree-draw.com/descPD60.html
Pedigree-Query	Kirichenko (2004)	mga.bionet.nsc.ru/soft/pedquery/pedigreequery.html
PedNavigator	Mancosu et al (2003)	Available from author
PEDPACK	Geyer (1988)	www.stat.washington.edu/thompson/Genepi/Pedpack.shtml
PEDRAW		www.smd.qmul.ac.uk/statgen/dcurtis/software.html
PELICAN	Dudbridge et al.	www.mrc-bsu.cam.ac.uk/personal/frank/software/pelican/
Progeny		www.progenygenetics.com/clinical/pedigree.html
PVin	Wernet, Lakshmipathy (2005)
The Pedigree Tool	Lachmund et al. (2004)	Contact the authors

Current limitations and new solutions

Current 2D techniques for visualising pedigrees are limited in the number of individuals that can be displayed simultaneously, particularly for large pedigrees, due to the exponential expansion of generations. 3D pedigree visualisation is superior to 2D in many ways. 3D techniques can display many more individuals in a given area. Closely related individuals are more easily displayed near each other, allowing trends within families to be clearly seen. In addition, it is possible to display families or individuals of interest in the context of the entire population. To our knowledge, no other tool currently exists to visualise large pedigrees in 3D. However, recent advances in consumer graphics technology allow such a tool to be created and used on most personal computers.

New software

Celestial3D was created as a proof of concept for 3D pedigree visualisation techniques. An alpha version of the software is capable of importing data in the standard Linkage Pedigree format, and displaying all pedigrees simultaneously. The software was used to display and navigate through all known families from the Busselton Health Study, along with their phenotypic data. We welcome suggetions from potential collaborators to enhance Celestial3D's functionality. The software is freely available to academic researchers worldwide.

Screenshots

Multiple pedigrees visualised in Celestial3D. Each sphere contains a distinct pedigree. Here, colours are used to summarise phenotypic information in each family. Pedigree numbers are shown in white.	A large number of pedigrees can be shown.	Top view of a pedigree. The portion above each circular 'shadow' represents a clade - the individuals descended from a pair of founders. Lines that cross over multiple shadows show how people have married into the pedigree.
Large, extensive families are displayed such that individual relationships are clearly seen.	View of a pedigree from an oblique angle. Generations are shown in the vertical axis. The software allows users to navigate through the pedigree and zoom into individuals of interest.	Gender is depicted using shape with men shown as cubes and women as spheres. Disease status can be depicted using icon colour: e.g. red for affected, green for unaffected and grey for unknown.

Coming Soon

The next version of Celestial3D will allow you to display pedigrees with consanguineous loops as seen in this 3D example of a large, inbred pedigree overlaid with bipolar phenotypes. Below is a static version of this pedigree.

Version History

14/01/2008	Celestial3D v1.0.1 release
05/10/2007	Celestial3D v1.0.0 release

Contact

For further information, please contact:

Dr Becky Webster
celestial3d@genepi.org.au

References

1. Agarwala R, Biesecker LG, Hopkins KA, Francomano CA, Schäffer AA (1998): Software for Constructing and Verifying Pedigrees Within Large Genealogies and an Application to the Old Order Amish of Lancaster County. Genome Research 8:211-221,1998.
2. Brun-Samarcq L, Gallina S, Philippi A, Demenais F, Vaysseix G, Barillot E (1999) CoPE: a collaborative pedigree drawing environment. Bioinformatics Applications Note: 15:345-346.
3. Dudbridge F, Carver T, Williams GW. Pelican: Pedigree Editor for Linkage Computer Analysis. Bioinformatics 20:2327-8.
4. Garbe, J. R. and Y. Da (2004) Pedigraph user manual Version 2.0 trial version. Department of Animal Science, University of Minnesota.
5. Garbe, J. R. and Y. Da. (2004) Pedigraph 2.0, a software tool for the graphing and analysis of large complex pedigrees. Abstract book, p. 242, ADSA-ASAS-PSA Joint Annual Meeting, St. Louis, July 25-29, 2004.
6. Geyer CJ (1988) "Software for calculating gene survival and multigene descent probabilities, and for pedigree manipulation and drawing". Technical Report #153.
7. He M, Li W (2007) PediDraw: a web-based tool for drawing a pedigree in genetic counselling. BMC Medical Genetics 8:31 doi:10.1186/1471/2350-8-31.
8. Lachmund P, Nebel I-T, Fuhrer D, Paschke R (2004) The Pedigree Tool: web-based visualisation of a family tree. Human Mutation 23:103-105.
9. Mäkinen et al. (2005), High-throughput pedigree drawing, European Journal of Human Genetics 13, 987-989.
10. Mancosu G, Ledda G, Melis PM (2003) PedNavigator: a pedigree drawing servlet for large and inbred populations. Bioinformatics Applications Note: 19:669-670.
11. Martel J, Butterfield J, Skousen G, Lawyer D, Rice J (2007) A highly interactive pedigree viewer. www.fht.byu.edu/prev_workshops/workshop07/ Family History technology workshop.
12. Plendl H, Caliebe A, Grote W (2005) Proceedings of the European Congress of Human Genetics. 2005.
13. Trager EH, Khanna R, Marrs A, Siden L, Branham KEH, Swaroop A, Rihcards JE (2007) Madeline 2.0 PDE: a new program for local and web-based pedigree drawing. Bioinformatics Applications Note: 23:1854-1856.
14. Wernet EA, Lakshmipathy J (2005) PVin - a scalable and flexible system for visualising pedigree databases. Proceedings of the ACM Symposium on Applied Computing 2005. 115-122.
15. Zhao JH (2006) Pedigree-drawing with R and graphviz. Bioinformatics Applications Note 22:1013-1014.

 

This work is part of an Asthma Foundation Research Project.