Here's an excellent explanation of how information provided by personalised genetic testing, e.g. from a company such as 23andMe, can be used to explore your past, present and future, by David Glance. David is the Director of Innovation, Faculty of Arts, Director of Centre for Software Practice at University of Western Australia:
Most would know that the FDA forced 23andMe to cease providing a health advisory service based on the genetic testing in December 2013. "23andMe has still not succeeded in resuming its health advisory service, but it has continued in the meantime with its genetic testing and offers genetic-based ancestry reports instead. It does offer the raw genetic data from the test however, and this can be used to provide health-related information for those who are still interested in that information."
Neil
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Thank you for sharing this interesting article. As a former genetic counselor, I would like to caution readers that it is extremely unlikely at this time that a full genome scan by a company like 23andMe would provide any useful information about CLL. The reason is explained in this recent article from the New York Times:
While learning about your ancestry is very interesting and a positive outcome of genome testing, it is also possible to receive results suggesting that that you are at increased risk for a disease (like Rheumatoid arthritis) for which nothing can be done except worry. Those of us on watch and wait already know what that feels like!
Although the article you shared is a legitimate article, it somehow feels to me like a hidden advertisement for 23andMe. Or maybe for Promethease, which is the company that can do the SNP analysis and generate the report that the FDA no longer allows 23andMe to provide. If anyone takes advantage of these services and has any questions or concerns, I recommend that they consult a genetic counselor to interpret the results. In the US, genetic counselors can be found at nsgc.org/p/cm/ld/fid=164. Outside the US, you can search for a genetics clinic here: genetests.org/clinics/
THANK YOU Roberta for that fantastic response and your referral to that excellent New York Times article.
A few key quotes from the NYT article:
"Despite the exaggerated claims of some entrepreneurs and lab owners, we can’t predict patients’ cancer risk and advise them appropriately just by sequencing their genome. At least not yet.
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The genetic tests that are clearly valuable at this point for predicting cancer risk are those for the specific mutations that we understand. But even then there can be other mutations in the same genes that are of unknown clinical significance.
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There is a good chance that mutations of unknown clinical significance will be found that will increase anxiety without illuminating any known risks."
Any regular reader of the more technical submissions to this community, is well aware of the constant flow of research papers turning up yet more proposed genetic predictors for CLL prognosis and how a supposedly bad marker can sometimes be countered by another marker. Also, as the NYT article points out, we need to differentiate between germ line genome testing and in our case clonal B-cell (tumour) genome testing. There are presumably many as yet undiscovered CLL related markers out there that are needed to account for the extremes of survival times in patients with recognised good or bad markers. If CLL researchers are still finding new genetic markers for a relatively rare cancer like CLL, what hope does a genetic testing company have of keeping across all the new knowledge for all the genetic based diseases and cancers? The final warning flag is that for the FDA to step in - and this is in a country where private business is allowed far more latitude than elsewhere - then we too need to be on guard.
OK, this will be a long reply. It's a hot topic for me as a CLL patient and 23andMe customer.
There's almost a thousand cousins on my 23andMe relatives list. I've been able to document common ancestors with cousins having very short, single segments in common with me. I've met some nice people. It's uncanny. It really works, and you don't have to share anything with anyone if you don't want to.
23andMe does not provide full genome scans. They provide samples of DNA called SNPs ("snips") - specific pairs in the 3 Billion base pairs of human DNA. The SNPs they choose are currently known to be related to particular genes and other DNA segments of medical and genealogical interest. They currently provide results for between 500,000 and 600,000 SNPs. Older versions of their chip provided more SNPs - about 900,000. The new V4 chip provides similar statistical "coverage" of key genes, but is faster to process, because they felt many of the V3 chip SNPs were redundant.
The technology and lab that 23andMe uses is no different from the technology used on medical tests costing thousands of dollars, and genetic tests costing hundreds. Those expensive tests simply do not have to be as expensive as they are.
Interpreting the results of ANY genetic medical test is the sticky point - for everyone involved - patient, doctor, and genetic counselors. 23andMe's raw results are likely to be as good as some tests ordered by your doctor. If you knew the error rates of particular common tests, you might be appalled.
If you get a result from 23andMe, you should certainly have it confirmed via full sequencing. It's also a question of putting the result into perspective given many other factors and desires of patient and doctor. Whether you use 23andMe or not, there are not enough qualified genetic counselors in the world, and most of them are focused on pre-natal advice.
For those of us lucky enough to still have the full reports because we bought our tests before December, 2013, 23andMe does report on several well known CLL risk alleles. For others, you can upload your raw results to a growing number of sites, and get some ... interesting interpretations. Some of the sites have links to 1 or more journal articles regarding individual SNPs. Very technical.
On the other hand, 23andMe's health reports are a model of a good health report - explaining genetic vs lifestyle risks, terminology, and research. They are orders of magnitude better than what you get from your lab or even your doctor. But 23andMe had not filed paperwork the FDA says is now necessary for these new consumer genetic tests. They are filing those papers now - test by test, syndrome by syndrome.
I already have CLL. This test can not diagnose it, though it showed I had increased risk. It certainly might shed some light in the future on course of care. But medical knowledge just isn't there yet regarding that - so many variables. Currently practicing doctors have a ton of education ahead of them on the benefits and pitfalls of Personalized Medicine.
In addition, the 23andMe spit sample may or may not contain B-cells - neither you nor 23andMe can say. So it's not necessarily testing the same cells as the well known CLL tests most of us currently get. My CLL is trisomy 12. No standard DNA sequencing or sampling that I've heard of deals with trisomies. They deal with pairs or even single strands of DNA. CLL trisomy tests are done by eye using fluorescence of entire chromosomes. I continue to ask and search regarding this.
What 23andMe is really, really good for is compiling a database of DNA and survey results to match combinations of SNPs with particular symptoms of currently mysterious syndromes and diseases. It is by far the largest database of its kind in the world. FDA, government, commercial, and academic researchers all know this. 23andMe has recently been granted a contract for research by NIH.
I'm glad you are happy with the results of your 23andMe testing. Ancestry testing is fascinating, and finding previously unknown relatives must be great fun! When I worked in the field of medical genetics, 23andMe had just started up, and "establishment" medical geneticists and genetic counselors did not approve of the concept of direct to consumer genetic testing with no access to a geneticist expert to interpret the information. I left my job in 2010, and haven't carefully kept up with the field. Apparently things have changed.
SNP analysis is done to look for germline mutations - ones that can be passed from parent to child. There are some known germline mutations that can predispose to cancer: for example, Angelina Jolie's story highlighted the BRCA1 and BRCA2 mutations for hereditary breast and ovarian cancer. These can be found by SNP analysis as well as other standard (and more expensive) methods. Still, if I were going to have a prophylactic mastectomy based on the results of such testing, I'd want to have it confirmed by another lab and I'd want to talk to a genetic counselor to make sure I really understood what my risk of getting breast cancer was. And I'm not sure I'd want to learn if I had a high risk for getting Alzheimer's disease if there is nothing that can be done about it. But perhaps you can opt out of receiving that information.
The FISH testing we had to learn more about our CLL prognosis is a type of genetic testing that looks at DNA in a different way. It can find chromosome deletions and trisomies. The testing of the IgVh gene for mutated or non-mutated status is yet another type of genetic testing. These tests are done on the abnormal B-cells only, and look at "somatic" mutations rather than germline mutations. Somatic mutations are acquired by the cell and are what cause them to grow in a crazy way and become cancerous. You are correct that SNP analysis can't diagnose these genetic abnormalities. So 23andMe doesn't offer testing for these mutations.
I still think that it is important for a genetic counselor or at least a doctor who is knowledgeable about genetics (and you'd be surprised how few of them are around) to be available to interpret results if people have questions. And certainly if people are going to make major health decisions based on the results.
Wishing you good health and happy meetings with all your relatives!
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