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Mammaprint TIME’s November 30, 2007

Posted by ramunas in breast cancer, cancer genetics, genetic testing, MammaPrint.
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Amsterdam based Agendia’s 70 gene expression test MammaPrint® was awarded by TIME Magazine as one of five best innovations of the year 2007 in the health category.

“With MammaPrint, a genetic test of a tumor’s DNA, patients and doctors can get a better handle on how likely it is that the cancer will spread”

It’s also the first microarray test approved by the FDA.

As you may noticed, there are several guys (aka doctors) on the corporate page design. Accidentally, when I was browsing our local website about COPD, I was surprised to find the same “template-doctors” there 🙂

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deCODE’ing Predisposition to Cancer November 17, 2007

Posted by ramunas in breast cancer, cancer genetics, colon cancer, deCODE, genetic testing, prostate cancer.
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Today launched personal genomics service of Icelandic company de CODEdeCODEme – totally surprised me. That was a smash for 23andMe and Navigenics, I think. For a promotional price for the Genetic Scan for $985 (plus sales tax / VAT) users can receive a bunch of information regarding personal genome variation, or SNP’s (discovered mainly in companies own studies and replicated by others), which can predispose to as much as 17 common disease (colorectal, prostate and breast cancers included), eye color, your hair color and many other physical attributes and also discover the origin of ancestry. Wow, kind of social-genomic-network!

I’ve jumped inside deCODEme portal, and will briefly summarize oncological side of this service (disclaimer: most of the text bellow can be found inside deCODEme portal after logging).

The deCODEme genome scan test for these common genetic variants related to these onco-disease:

– Breast cancer. It includes the variants on chromosomes 2 and 8, as well as those in the FGFR2, the TNRC9/TOX3, the LSP1, the MAP3K1 and the CASP8 genes and interpretation of their associated risk to the development of breast cancer.

Note: Strongly acting mutations (like in BRCA1/2 genes) comprise a small percentage of breast cancer cases (2-5%). Variants that are more common but carry less risk play a role in a much larger proportion of cases, perhaps in almost all breast cancer cases. Such variants may individually be quite common with each one alone having little effect on breast cancer risk. However if a person inherits many of these variants, the risks from them might combine to produce a substantial increase in the individual’s overall risk. Combinations of these common breast cancer risk variants may or may not show up as an obvious family history of breast cancer.

– Colorectal cancer. Includes the variants on chromosome 8 and in the SMAD7 gene and interpretation of their associated risk for the development of colorectal cancer.

Note: It has been estimated that up to 30% of colorectal cancers may be due to genetic factors. A fraction (~5%) of colorectal cancer cases occur in families with multiple cases of the disease and appear to be inherited in a dominant manner. An example of such condition is multiple polyposis of the colon, where the inner surface of the colon is covered with thousands of polyps. These cases are in some instances known to be caused by specific mutations in genes that increase the risk of the disease substantially (up to 100%). Individuals belonging to such families should seek counselling about preventive measures. The deCODEme genome scan does not include the rare highly familial cancer genes such as APC, MLH1, MSH2, MSH6, and PMS2. Variants that are more common, but confer less risk, play a role in a much larger proportion of colorectal cancer cases. Such variants may individually be quite common with each one alone having little effect on the colorectal cancer risk. However if a person inherits many of these variants, the risks from them might combine to produce a substantial increase in the individual’s overall risk. To date two common genetic variants have been found that increase the risk of developing colorectal cancer. These are variants on chromosome 8, not close to any known gene, and in the SMAD7 gene on chromosome 18.

– Prostate cancer. Includes the three variants from the 8q24 region and the two from chromosome 17 and an interpretation of their associated risk of developing prostate cancer.

Note: Prostate cancer has been shown to have the strongest genetic component of all cancers. To date several genetic variants have been discovered to increase the risk of developing prostate cancer. These are three variants in the chromosome 8q24 region that lacks any know genes, and two on chromosome 17, one of which is in the TCF2 gene.

Other reviews (updated):

Dangers of Gene Patents | American College of Pathologists November 10, 2007

Posted by ramunas in cancer genetics, genetic testing, media, personal.
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Currently over 20% of 25-30000 human genes are patented most of which do not have yet exact function defined. Even more yet are under the way. Research and identification of a new genes predisposing to the cancer, which affects 1 in 4 person in the population, is of high priority worldwide.

Patents for low/medium penetrance susceptibility genes and sequence variants which can serve as genetical markers of all cancers as well as commercialization of common methods for a common germline mutation detections in particular human cancer genes could seriously suspend the wide public availability of such tests, especially in a developing and limited resources countries where current health care system is bellow good quality standards and further make inequalities in the health care service.

This is an excerpt of my opinion, which I’ve published a year ago on BioForgeNet, an open source biological community portal.

This year on Oct. 30 American College of Pathologists submitted a statement Oct. 30 to the U.S. House of Representatives Judiciary Committee s Subcommittee on Courts, the
Internet and Intellectual Property, stressing that current practices in the patenting and licensing of genetic sequences must be reexamined to ensure that gene-based diagnostic tests are widely available and affordable for the greatest public benefit.
The statement, provided for a hearing titled Stifling or Stimulating The Role of Gene Patents In Research and Genetic Testing, outlined the impact of gene patents on medicine and healthcare and urged support for recently introduced legislation that would prohibit patents from being obtained that would harm patient access, quality of care and training of health providers.
According to the College s statement, when patents are granted, subsequent exclusive license agreements, excessive licensing fees, and other restrictive licensing conditions prevent physicians and laboratories from providing genetic-based clinical testing services.
Consequently, it continues, patient access to care is limited, quality of patient care is jeopardized, clinical observations as the basis for new discoveries are compromised, and training of health care providers is restricted.
The Frist Ganske Law protects physicians from patent infringementlawsuits, but does not extend the same protection to laboratory personnel. The College supports efforts to amend Frist Ganske to provide this protection to pathologists and other laboratory.
The Genomic Research and Accessibility Act, H.R. 977 would prohibit patents from being obtained for a nucleotide sequence, or its functions or correlations, or the naturally occurring products it specifies.
The College declared its support for H.R. 977, and will continue to work with lawmakers on recommendations for legislation that would prevent intellectual copyright protections from limiting laboratory physicians access to genetic information and impeding potential breakthroughs in genomic and proteomic research.

Feel free to express your opinion in a comment field.

Guidelines on Risk Assessment for Hereditary GynCa November 4, 2007

Posted by ramunas in BRCA, breast cancer, cancer genetics, colorectal cancer, genetic testing, hereditary cancer, HNPCC, ovarian cancer.
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Recently guidelines on risk assessment for inherited gynecologic cancer (Hereditary Breast/Ovarian Cancer (HBOC) and the Lynch/Hereditary Non-Polyposis Colorectal (HNPCC)) predispositions were published by The Society of Gynecologic Oncologists (SGO).

Hereditary cancer risk assessment is a process that includes assessment of risk, education and counseling conducted by a provider with expertise in cancer genetics, and may include genetic testing after appropriate consent is obtained (ref).

Genetic risk assessment enables physicians to provide individualized evaluation of the likelihood of having one of these gynecologic cancer predisposition syndromes, as well the opportunity to provide tailored screening and prevention strategies such as surveillance, chemoprevention, and prophylactic surgery that may reduce the morbidity and mortality associated with these syndromes (ref).

Up to 10% of breast cancer and 10-15% of ovarian cancer cases are related to BRCA 1/2 genes mutations (“faulty genes”), so called HBOC syndrome.

Mutations in BRCA1 genes confers a 39% to 46% chance of a woman developing ovarian cancer and a 65% to 85% risk of a woman developing breast cancer by age 70 years. The BRCA2 gene is associated with an ovarian cancer risk for 10% to 27% and a breast cancer risk for 45% to 85% by age 70 years (ref., subscription needed).

For comparison, overall life time breast cancer risk in the western population is 10-12%, and ovarian 1,5-2%.

The SGO guidelines recommend genetic risk assessment for women with a 20% to 25% likelihood of having BRCA1 or BRCA2 mutations. For patients whose probability of predisposition is greater than 5% to 10%, the guidelines suggest that genetic risk assessment “may be helpful.”(ref.)

It is a new thing (“20-25%”) for me, because to my knowledge, a guidelines in USA set by the American Society of Clinical Oncology (ASCO) suggested a 10% likelihood of finding BRCA1/2 mutations to undertake genetic testing. A stringent 20% likelihood threshold of having BCRA mutations is already applied in UK.

Lynch/HNPCC syndrome is caused by germline mutations in genes that oversee DNA mismatch repair. The family predisposition conferred by mutations in genes MLH1, MSH2, or MSH6 includes not only colorectal cancer and cancers of the endometrium but also cancers of the ovary, stomach, small intestine, and other organs. Women with one of these mutations have a 42% to 60% likelihood of developing endometrial cancer and a 9% to 12% chance of developing ovarian cancer by the age of 70 years. Their lifetime risk for colorectal cancer is 40% to 60 (via).

The SGO statement divides the Lynch/HNPCC guidelines into those for patients with a 20% to 25% chance of having the inherited predisposition and those with a greater than 5% to 10% chance. The guidelines reflect both personal and family profiles, with the “revised Amsterdam criteria” included for the higher-risk group.

“revised Amsterdam criteria” for HNPCC are as follows (ref.):

  • Patients have at least 3 relatives with a Lynch/HNPCC-associated cancer (colorectal cancer, cancer of the endometrium, small bowel, ureter, or renal pelvis) in 1 lineage,
  • One affected individual should be a first-degree relative of the other 2,
  • At least 2 successive generations should be affected, and
  • At least 1 HNPCC-associated cancer should be diagnosed before age 50 years.

Performing the genetic testing and finding out that a patient does or does not have a genetic mutation can allow us to reduce risks for other related cancers, and can have tremendous impact for the patient’s family members if a mutation is found.

When assessments identify women at high risk for these cancers, they could receive magnetic resonance imaging breast screening, colorectal screening with colonoscopy, and preventive surgery, but the medical community must become aware of the importance of these strategies in improving individual outcomes. (ref.)

Thanks November 1, 2007

Posted by ramunas in personal.
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Thank you Hsien @ EyeOnDNA for Venter’s book! I will be happy to read it.

P.S. Meanwhile, do not forget to visit the websites of my proud “sponsors” at NicoMarket and SellMyDNA (from New Line Genetics) 🙂

(Learn more here and there).