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Familial Cancer Database Online | FaCD September 4, 2008

Posted by ramunas in bio-software, cancer genetics, familial cancer, hereditary cancer, Resources, technology.

Familial Cancer Database Online is a very useful online tool for experts in cancer genetics to assist in making a genetic differential diagnosis in cancer patients as well as remind tumor spectrum associated with certain hereditary disorders.

And its dynamic cyberinfrastructure already brings the most updated content in the field of clinical cancer genetics with intention to develop further.

The content was created and is edited by dr. Rolf Sijmons (on the left – during poster presentation at ESHG meeting in Barcelona this year), clinical geneticist and associate professor clinical oncogenetics at the Dept. of Genetics of the University Medical Center Groningen (UMCG), the Netherlands. However, other experts who want to contribute to particular syndrome files are invited to contact the editor; these authors will be listed in the syndrome files they contributed to.

And I’m pleased of being included in the list of contributors for the contribution to rare hereditary disorder called Mosaic Variegated Aneuploidy syndrome, where in addition to other symtomes the risk for several cancers (leukemia, rhabdomyosarcomas and embrional kidney cancers) is increased.

FaCD is intended for free of charge use by health professionals with at least basic knowledge of clinical cancer genetics.


BOADICEA Final Version Released December 15, 2007

Posted by ramunas in bio-software, breast cancer, cancer genetics, familial cancer, genetic testing, hereditary cancer, ovarian cancer, technology.
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Here is probably the most accurate breast&ovarian cancer risk/mutation probability calculation web-application released from Cambridge University Genetic Epidemiology UnitBOADICEA.

BOADICEA is a computer program that enables the user to estimate BRCA1/BRCA2 mutation carrier probabilities and breast/ovarian cancer risks based on polygenic model. The BOADICEA Web Application (BWA) has been designed in collaboration with clinical geneticists and researchers, in order to make BOADICEA risk estimations much quicker and easier.

It differs from available (BRCAPRO, Gail, Couch, Frank, Manchester model etc.), since it assumes not only high penetrance genes (eg. BRCA) for risk calculation, but also contribution of other low penetrance genes, most not yet identified (thus polygenic).

For more than a year lot of users tested beta phase (I am grateful to Alex Cunningham, the main developer and programmer, for letting to participate during this phase) and the final version was released. Excellent work, I would say!

The approach was first described by Antoniou AC et al. in 2004 and it was shown that overall familial risks of breast cancer predicted by this model were close to those observed in epidemiological studies.

Anyone can register to use the program including researchers, healthcare professionals and the public. However, if you are a member of the public and you are concerned about your family history, it is strongly advised that you seek guidance first from your general practitioner (see Advice for members of the public).

N.B. Be aware, however, that current model is based on genetic epidemiology of UK population. For other populations it may give not correct risk estimation.

P.S. I would like to apologize my readers for not posting long – I’m completely drowned in the final year of my residency and end of a year…

Nomogram vs GeneSearch Genetic Test | Breast Cancer August 23, 2007

Posted by ramunas in bio-software, breast cancer, cancer genetics, GeneSearch.
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Several days ago an article from Memorial Sloan-Kettering Cancer Center, NY, USA, presented a user-friendly prediction model (nomogram) based on a large data set to assist in predicting the presence of sentinel lymph node (SLN) metastasis for a specific patient, which is important prognostic factor.

After multivariate analysis with SLN metastasis were associated several factors: age, tumor size, tumor type, lymphovascular invasion, tumor location, multifocality, and estrogen and progesterone receptors [ref.]. The nomogram was accurate, discriminating and properly validated (a model was subsequently applied to 1,545 sequential SLN biopsies.)

Because newly diagnosed breast cancer patients are increasingly interested in information about their disease, this validated nomogram for risk estimation could be useful tool for physicians and patients to accurately predict the likelihood of SLN metastasis.

A nice computerized version (Macromedia Flash 6.0) of the nomogram is available on their website.

This tool, known as a nomogram, can be used to calculate the likelihood that breast cancer that has spread to the sentinel lymph nodes has also spread to additional lymph nodes under the arm (axilla). It is designed to individualize the risk estimate for each patient — a key factor in deciding whether additional surgery is likely to be beneficial, website states.

Obviously, it is not a substitute for medical advise, diagnosis or treatment but seems to be quite useful addition for risk estimation.

Researchers recommends that this tool should be used by physicians only. Patients should use this tool only in consultation with their physicians.

Also, I think it would be of great interest to compare this Breast Cancer Nomogram results with recently FDA approved Johnson&Johnsons GeneSearch™ Breast Lymph Node (BLN) assays results, which claims to detect the spread of breast cancer into the lymph nodes by analyzing the level of metastatic tumor expression markers.

Virtual Cancer Information And Services | Second Life July 31, 2007

Posted by ramunas in bio-software, cancer genetics, media, technology.
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Cyberspace now become more and more widespread phenomena. A Virtual world Second Life, created by Linden Research, Inc , ScienceRoll sees as a new creative education environment. Personally, I have to do a lot in my first (real) life, before I can join a Second Life, but anyway, this environment reminds me a lot of SF’s ideas, I’d read before – William Gibson’s cyberspace, Matrix and S. Lukjanenko’s DeepTown. Interestingly, lot of corporations and real-world institutions are opening their offices in this virtual world, and American Cancer Society’s (ACS) is not an exception. Forbes announces, that on July 27 and 28, almost 2,500 people gathered online in the world of Second Life and run a virtual relay race to raise money for cancer research.

The third annual virtual “Relay for Life” marks the grand opening of the American Cancer Society’s (ACS) virtual headquarters in the Second Life community, which is a co-sponsor of the relay.

Well, I would better join a bicycle ride to raise a funds, but anyway:

The new virtual building, which opened June 1, is designed to provide the same cancer information and services to people in the virtual world as the organization provides in the real world. The building includes presentation and meeting rooms for cancer education sessions and fund-raising meetings, and will soon feature a staffed link to the group’s National Cancer Information Center. The headquarters also features green space and gardens to showcase user-created art that expresses the personal fight against cancer.

“Already, we have existing peer-to-peer Second Life cancer support groups coming to us to use the facility and our resources. We are certain that, going forward, the community will find untold uses for our office space in terms of education, advocacy, fund raising and community support,” said Moss.

It is interestingly whether they have genetic counseling room there? I think that kind of service would be great, especially if you’d implement a portable hyper-DNA-collection-USB device 🙂

BioBar Is like PowerBar | The Guide To Bio-Databases July 18, 2007

Posted by ramunas in bio-software.
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If FDA approved software for diagnostic use, Biobar – a free open-source bioinformatics power-browsing toolbar for Mozilla-based browsers (Firefox/Flock/Mozilla/Netscape & Seamonkey) – would be my suggestion. It is developed by Jawahar Swaminathan from European Bioinformatics Institute (EBI) and Wellcome Trust Genome Campus.

Although Biobar is intented for “biologists and bioinformatics people”, as clinician I use it almost for two years as quickl and very efficient access tool for NCBI Databases, GoogleScholar, Scirus, OMIM, Ensembl (etc.) search and BLASTn’ing (sequence alignment) purposes. Current version (1.5.2 , released 25 Oct 2006) provides browsing and data retrieving access to over 46 different databases (Genomic, Proteomic, Functional, Literature, Taxonomic, Structural, Plant and Animal-specific databases) and is fully customizable.

Other related bio-application is BioFox (by Saleem Mohammed).

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