CancerGEM KB|Home - searchable database/online resource

Blogger's Note: see the results of the search using 'Lynch Syndrome' as a test per example below:

CancerGEM KB|Home


About CancerGEM KB
CancerGEM KB is a continuously updated searchable online resource that provides access to scientific information on the use of genomic information in cancer care and prevention. more

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162 abstracts in HuGE published Literature

No GWAS/meta-analysis entry

1 evidence review/recommendation entries

1 genomic tests in transition to practice 

Office of Public Health Genomics/CDC launches the CancerGEM KB : CDC Office of Public Health Genomics in collaboration with NCI Division of Cancer Control and Population Sciences launches the CancerGEM KB: CancerGEM KB is an online resource for researchers, public health professionals, policy makers, and health care providers interested in the use of genomic information in cancer care and prevention. CancerGEM KB provides objective synthesis and timely dissemination of information on cancer human genome epidemiology (genetic associations, gene-environment interactions and gene prevalence information) and aggregated evidence on cancer genomic tests in transition to clinical and public health practice. CancerGEM KB also offers summary information on Genomic Tests through PLoS Currents Evidence on Genomic Tests, an open-access journal for systematic reviews and structured short summaries of evidence for the validity and utility of genetic tests. Read more about CancerGEM KB

 

bloggers: Gregory D. Pawelski on Genomics And Targets For The Treatment Of Cancer: Is Our New World Turning Into "Pharmageddon" Or Are We On The Threshold Of Great Discoveries?

Gregory D. Pawelski on Genomics And Targets For The Treatment Of Cancer: Is Our New World Turning Into "Pharmageddon" Or Are We On The Threshold Of Great Discoveries?

"I was telling your old colleague, Dr. Herman Kattlove, who posted about this on his blog, I thought his "genetic heterogeneity" terminology was more befitting than what was used in the title of the British study (Intratumor Heterogeneity). "Taking one biopsy sample of a tumor may not be enough to reveal its full genetic identity," was described by Medical News Today's Catharine Paddock, PhD. The study is significant because it suggests relying on one sample could overlook (other) important biomarkers that help make tailored treatments effective, explaining perhaps why personalized cancer therapy has been less successful than expected. Dr. Robert Nagourney, Medical and Laboratory Director at Rational Therapeutics, Inc., Long Beach, California, pointed out the disturbing news regarding the predictive validity and clinical applicability of human tumor genomic analysis for the selection of (targeted) chemotherapeutic agents. He also pointed out the accompanying editorial by Dr. Dan Longo, which made several points worth noting. First, he states that "DNA is not the whole story." This should be familiar to those who follow cell function analysis. Dr. Longo references Albert Einstein, who said, "Things should be made as simple as possible, but not simpler." Dr. Nagourney appreciates and applauds Dr. Long's comments for they echo his sentiments completely. The article of the study is only the most recent example of a growing litany of observations that call into question molecular biologist's preternatural fixation on genomic analyses. Human biology is not simple and malignantly transformed cells more are more complex still. Investigators who insist upon using genomic platforms to force disorderly cells into artificially ordered sub-categories, have once again been forced to admit that these oversimplifications fail to provide the needed insights for the advancement of cancer therapeutics. Those laboratories and corporations that offer "high price" genomic analyses for the selection of "high price" chemotherapy drugs take notice of this and related articles carefully as these reports portend a troubling future for their current business model ("personalized" cancer treatment)."

Editorial: Realizing Genomic Medicine — NEJM

"Although patience is said to be a virtue, it is a commodity that many patients cannot afford, since there is much demand for an immediate clinical return on investment in genomics research. However, biology and health care systems are complex, and it is unrealistic to expect that the march of clinical progress will accelerate at the same rate as technological advances. That said, the advances described in the second Genomic Medicine review series show that genomics has made great strides toward improving human health."

(repost) Genomethics - background and Questionnaire UK

Questionnaire

This ethics and genomics study is being conducted by two Ethics Researchers. The team consists of:
Dr Anna Middleton, Ethics Researcher and Registered Genetic Counsellor,
and
Prof Mike Parker, Professor of Bioethics and Director of the Ethox Centre, University of Oxford
The two Ethics Researchers are part of the Deciphering Developmental Disorders (DDD) Study based at the Wellcome Trust Sanger Institute, Cambridge, UK. More information about the DDD study can be found here: www.ddduk.org
The DDD study involves a large team of scientists and informaticians and the Principal Investigators are:

• Dr Nigel Carter, molecular cytogeneticist, Wellcome Trust Sanger Institute, Cambridge, UK
• Dr Helen Firth, consultant clinical geneticist, Addenbrooke's Hospital, Cambridge, UK
• Dr Matt Hurles, molecular geneticist, Wellcome Trust Sanger Institute, Cambridge, UK
• Dr Jeff Barrett, statistical geneticist, Wellcome Trust Sanger Institute, Cambridge, UK
• Prof David Fitzpatrick, consultant clinical geneticist, Western General Hospital, Edinburgh, UK
• Prof Mike Parker, professor of bioethics, Director of Ethox, University of Oxford, UK

Genetics education and resources for social scientists

Genetics vs. Genomics

In popular media and common speech, the words "genetic" and "genomic" are often used interchangeably. However, to a geneticist, these terms have specific meanings. To appreciate the difference, we must first understand something about the structure of genetic material.
Genetic information is stored in the molecule DNA, which consists of a string of chemicals called bases. The order of bases on the string, called the "sequence", determines the meaning of the genetic message. A gene is a specific stretch of bases that provides instructions for making a particular product, such as a piece of a hormone or enzyme. Humans have many thousands of genes, spaced across the entire set of DNA, which is packaged into 23 pairs of chromosomes. However, there are many DNA sequences in-between genes that do not directly encode specific products. Some of these sequences modify the way that genes are expressed. Other sequences do not have a known function.

Read the full story

Genomics|Update|Current

Does it run in the family? Toolkit will soon be available at federal health centers nationwide, Genetic Alliance, June 2



New Blog Post (click on image below)

What is Public Health Genomics? A Day in the Invisible Life of Public Health Genomics.



  

abstract: Genomic Analysis Reveals the Molecular Heterogeneity of Ovarian Clear Cell Carcinomas

CONCLUSIONS:  
OCCCs constitute a heterogeneous disease at the genomic level despite having similar histological features. The pattern of genomic aberrations in subgroups of OCCCs is of clinical significance.

Educating Physicians on Genomic Medicine: Topol on Genomics (video/transcript/physician feedback)

Genomics Law Report: The Business Effects of Regulatory Uncertainty in Genetic Testing

Genomics in our own hands : The Lancet Neurology

Note: the paper is freely accessible (requires registration (free)

Technology Review: Fine-tuning Cancer Treatments

Scientists at the Wellcome Trust Sanger Institute and Massachusetts General Hospital will test 400 compounds, including chemotherapy drugs and molecularly targeted treatments, on 1,000 cancer cell lines containing cancer-related genetic mutations in an effort to advance personalized medicine. The findings are expected to help drugmakers design clinical studies that include only patients who are most likely to benefit from experimental cancer drugs.
 
"...While a number of molecularly targeted cancer drugs, such as gleevec and herceptin, are already on the market, the effectiveness of most of these drugs depends on a single genetic mutation or molecular marker in the tumor. Scientists say that incorporating the diversity of cancer genomics in much greater detail will enable more personalized treatment for a broader number of patients...cont'd

The Big Flap About Pathway Genomics and Walgreen's: Topol on Genomics

A few weeks ago, Pathway Genomics, a consumer genomics company, had planned to have its saliva kits at all US Walgreen's drug stores. The FDA put a stop to it. Congress is now investigating the matter. What is going on here?
http://www.nytimes.com/2010/06/12/health/12genome.html?scp=1&sq=pathway%20genomics&st=cse

A genomic and transcriptomic approach for a differential diagnosis between primary and secondary ovarian carcinomas in patients with a previous history of breast cancer.

ABSTRACT:
BACKGROUND: The distinction between primary and secondary ovarian tumors may be challenging for pathologists. The purpose of the present work was to develop genomic and transcriptomic tools to further refine the pathological diagnosis of ovarian tumor after a previous history of breast cancer.

METHODS: Sixteen paired breast-ovary tumors from patients with a former diagnosis of breast cancer were collected.. ... A hierarchical clustering of these samples was performed, combined with a dataset of well-identified primary and secondary ovarian tumors.

RESULTS: In 12 of the 16 paired tumors analyzed, the comparison of genomic profiles confirmed the pathological diagnosis of primary ovarian tumor (n = 5) or metastasis of breast cancer (n = 7). Among four cases with uncertain pathological diagnosis, genomic profiles were clearly distinct between the ovarian and breast tumors in two pairs, thus indicating primary ovarian carcinomas, and showed common patterns in the two others, indicating metastases from breast cancer.
CONCLUSIONS: In patients with ovarian carcinoma and a previous history of breast cancer, SNP array analysis can be used to distinguish primary and secondary ovarian tumors. Transcriptomic analysis may be used when primary breast tissue specimen is not available.

full access: Cancer Genomics: Conducting Exemplary Trials With Biospecimen and Biomarker Components

Note: long article regarding efforts in progress

One specific area of importance to patients:

"As clinical trials become more complex, so do the concerns researchers must address. Original correlative trials have now led to a new generation of clinical trials, some of which exclude patients who do not possess the specific biomarker being studied. When these biomarker tests must be completed before enrollment onto a clinical trial, it is important that the study budget provide reimbursement for testing of individuals who are afterward deemed ineligible. Additionally, because biomarker testing is generally completed at a central laboratory designated by the sponsor, it is important that physicians know how long it will take to receive the results. If the turnaround time is 3 to 4 weeks, it should be considered whether patients will agree to wait that long to begin treatment, especially if they may ultimately be excluded from the clinical trial on the basis of the test results. Considerations such as these should be discussed in advance with the sponsor, so efforts can be made to expedite testing. The research site should also be aware of all options that can be provided to patients who are excluded from the clinical trial. Sometimes sponsors will offer an expanded access option or suggest alternative trials using the medication, important factors when enrollment onto the clinical trial is the only remaining treatment option for a patient."

Consumers Slow to Embrace the Age of Genomics - NYTimescom Andy Pollack