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Personal Genomics Age Begins


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#31 manofsan

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Posted 20 November 2007 - 04:36 AM

Here's a critique of MS Health Vault:

http://www.worldheal...ical-community/

#32 manofsan

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Posted 20 November 2007 - 05:50 AM

GATC is now also offering full genome sequencing

http://www.gatc-biot...om/en/index.php

I imagine it will be similarly expensive

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#33 niner

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Posted 20 November 2007 - 06:06 AM

GATC is aiming for a 500 Euro full sequence in ten years. If exchange rates continue on their present path, that will probably be about $349,000.00...

#34 manofsan

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Posted 20 November 2007 - 07:07 AM

I notice that these services mention they can get data on your mtDNA

So if I picked 23andme with their offer for 30,000 custom SNPs, does that mean I can pick my own custom selection that includes lots of mtDNA? After all, the mitochondria are important for longevity.

#35 apoptosos

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Posted 20 November 2007 - 11:06 AM

I notice that these services mention they can get data on your mtDNA

So if I picked 23andme with their offer for 30,000 custom SNPs, does that mean I can pick my own custom selection that includes lots of mtDNA? After all, the mitochondria are important for longevity.


23andme use the Illumina chip array:
http://www.illumina.com/
http://www.illumina....0_DataSheet.pdf

The "custom" SNPs are the ones they have chosen to include in addition to the 550 chip - these are not customizable by the customer.

The chip retails for $290 but the Beadstation (which analyzes the chip) is about $300K. 23andme have a joint venture with Illumina for the provision of genotyping services. In comparison, Navigenics is a subsidiary of Affymetrix, the other leading gene chip provider.

#36 eon fathom

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Posted 20 November 2007 - 12:47 PM

Genotyping now seems fairly useless, especially with the low percentages of risk probability. You guys are right about it being useful when it's correlated with MANY peoples' genotype/phenotype.

first people in history to be fully sequenced


That's ridiculous, unless church's group has just come out with a brand new technology, there are real limits to what can be sequenced with known techniques. Repeats, centromere regions, telomers, etc. The HGP only sequenced 92% of the 'full' genome.

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#37 adamb

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Posted 20 November 2007 - 09:19 PM

Since 23andme.com only deals with US customers, and Navigenics charges $1,515 more, I might order at decodeme.com. FYI,

Dear ---,
Thank you for your interest in deCODEme

Regarding your inquiries:

Concerning the safety,

1) We use the FED-EX and rely on their safety procedures.

2) We have tested the collection procedure and are confident in the safety and accuracy of the method.


3) Very briefly our services provide the following (for 985 USD):
1) Looking at about 1 million variants in your genome and providing you with the raw results (the actual variant in formation at every spot looked at).
2) Information on certain of these variants of yours that may have been associated with increased likely hood of the development of diseases, which currently are the 17 diseases listed below.
3) Information regarding ancestry/ethnicity.
4) Information on your eye and hair color markers.

The following are the disease we are currently providing information on: Age-related macular degeneration, Asthma, Atrial fibrillation, Breast Cancer, Celiac Disease, Colorectal Cancer, Chrons's disese, Exfoliation Glaucoma XFG, Inflammatory Bowel Disease, Multiple sclerosis, Myocardial Infarction, Obesity, Prostate cancer, Psoriasis, Restless legs, Rheumatoid arthritis, Type 1 Diabetes, Type 2 Diabetes.
Information on Alzheimer disease is not provided.

deCODEme will provide a report on the www.decodeme.com website.The report will contain your actual genotypes for the SNPs in question. Additionally you will be provided with the raw data of the complete scan, i.e. about 1 mill. SNP genotypes. Reference to the relevant publications will also be a part of the report, specifically linked to each marker being analyzed.

The report will tell you what relative number of people who have the same genetic results as you have the disease in question, compared to the normal population. This is to say that the report is a risk assessment for a group of people and applies only as such to individuals. This is exactly the same as the fact that we know that not everyone who has high cholesterol or is over weight will get myocardial infarction (MI) but that MI is more common amongst people that have high cholesterol and/or are over weight than in the population at large.

We provide assistance for explaining the relevance of the findings reported on in our disease specific reports. This can be anything from an e-mail to one on one phone conversation.

The report will contain a disclaimer that although a SNP is individually associated with disease risk in deCODE´s own population studies, deCODE cannot predict how that SNP will interact with variants at other SNPs in any particular person.

Please contact us again for further information.

Best regards
deCODEme customer services.



#38 eon fathom

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Posted 21 November 2007 - 04:42 AM

I wonder if any of these test for the HER-2 gene amplification for taking the drug herceptin. I believe it costs about $3k for the one gene test. It sure would be nice if the these three covered that and others in one swoop.

#39 forever freedom

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Posted 21 November 2007 - 05:09 AM

It's nice to see and live the tips of what the future is going to look like, especially when we know about all the huge things that are still to come.

#40 John Schloendorn

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Posted 21 November 2007 - 05:55 AM

I wonder if any of these test for the HER-2 gene amplification for taking the drug herceptin

I thought that's something you do on the actual tumor cells. If you have one of these, you probably don't want to wait all these weeks for the snp chip results to come back...

#41 manofsan

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Posted 24 November 2007 - 09:12 AM

Got an email from Decodeme:


---------

Dear ...,

Thank you for being one of the first visitors to deCODEme,
the world's first globally available service that enables individuals
to get a detailed look at their own genome - presented by the
scientists who found the genes.

It has been an exciting week since our launch and we would
like to share some news with you about new and improved
features on the deCODEme website:

**No restrictions on availability in the US**
We are happy to announce that we have now lifted any
restrictions on the availability of our service in certain
US states. You can now purchase our service anywhere on
Earth no matter where you live or want your sample kit shipped.

Visit https://www.decodeme...rdering?src=m1s to order a sample kit
today.

**More payment methods on our website**
There are now two ways to pay for your order on our website.
We are still supporting PayPal secure services. We have also
added a new payment method through our secure payment
services, where we can accept all major credit cards.

Visit https://www.decodeme...rdering?src=m1p to order with the new
method.

It has been a thrilling and exciting week as the response to
deCODEme has been extremely strong and positive. Orders
keep flowing in and our web servers are chugging away,
happily accepting the enormous load of daily visitors from
all corners of the world. We rushed kits to our first customers
on Monday morning and are thrilled to report that the first
customer samples have already been received by our laboratories.

Thank you for your continuing support. We welcome your
feedback and look forward to presenting more exciting
discoveries and new features in the coming days and weeks.

The deCODEme team.

Visit our website: http://www.decodeme.com
Questions/Feedback? Please e-mail mailto:support@decodeme.com

#42 maestro949

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Posted 24 November 2007 - 12:28 PM

Nice. This'll be common procedure in a few years and I'm sure the number of genes scanned/software tools will increase/progress fairly rapidly. What would be better is a personal device where you can scan your own DNA and as manofsan mentions, have software for doing the analysis so your insurance company and employer doesn't have access to the data for discrimination reasons.

How are doctors going to keep up with this? Patients will completely bypass them as mail-in "services" and website diagnosis websites like these emerge.

#43 ilanso

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Posted 25 November 2007 - 05:35 AM

Would you care to post a sample of their fees?

#44 manofsan

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Posted 25 November 2007 - 07:20 AM

Hi, it's on their website, www.decodeme.com

They're charging $986 for the scanning of your genome, which will get you 1 million genotypes from it.
I think that's a lot of info. Sounds like a pretty decent price for a first-time offering.

#45 manofsan

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Posted 03 December 2007 - 01:00 AM

Here's another article on Knome.com's offering for whole-genome sequencing:

http://www.technolog.../editors/21935/

It's good to know that even they are fully booked up, despite their $350K pricetag. There are plenty of people out there who can afford that pricetag, and they'll be getting back a wealth of information in return.

To me, this is money better spent than a trip to outer space.

But just think of the powerful acceleration that science will undergo, as a result of these new genomes being sequenced.
And as more procedures are done, hopefully new efficiencies will be achieved in the sequencing techniques.

I'm wondering if we'll hit the $1000 genome by 2015?

Edited by manofsan, 03 December 2007 - 01:08 AM.


#46 infundibulum

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Posted 08 December 2007 - 05:09 AM

Interesting that DecodeMe.com won't provide information on Alzheimer's. The question is, will they still provide the raw polymorphism data on the SNP's related to the APOE4, APP, PSEN1, PSEN2, GAB2 and SORL1 genes (known/suspected Alzheimer's disease influencing gene variations)?

Having the data on a million variations is cool but not if they're going to restrict reporting on some variations..

Or do you think that Alzheimer's data (as well as that for certain other diseases) should be classified?

There are indications now that lifestyle factors can influence the progress of Alzheimer's.

Edited by infundibulum, 08 December 2007 - 05:16 AM.


#47 John Schloendorn

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Posted 08 December 2007 - 06:14 AM

This sounds like an IP issue to me. I would guess that they can't say these are Alzheimer's genes, because somebody else patented them as diagnostic markers?

Interesting that DecodeMe.com won't provide information on Alzheimer's. The question is, will they still provide the raw polymorphism data on the SNP's related to the APOE4, APP, PSEN1, PSEN2, GAB2 and SORL1 genes (known/suspected Alzheimer's disease influencing gene variations)?

Having the data on a million variations is cool but not if they're going to restrict reporting on some variations..

Or do you think that Alzheimer's data (as well as that for certain other diseases) should be classified?

There are indications now that lifestyle factors can influence the progress of Alzheimer's.



#48 missminni

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Posted 08 December 2007 - 06:01 PM

Interesting that DecodeMe.com won't provide information on Alzheimer's. The question is, will they still provide the raw polymorphism data on the SNP's related to the APOE4, APP, PSEN1, PSEN2, GAB2 and SORL1 genes (known/suspected Alzheimer's disease influencing gene variations)?

Having the data on a million variations is cool but not if they're going to restrict reporting on some variations..

Or do you think that Alzheimer's data (as well as that for certain other diseases) should be classified?

There are indications now that lifestyle factors can influence the progress of Alzheimer's.

My mom had Alzheimers. I am convinced it was a lifestyle issue due to the various anti-depressants
she was prescribed during the 1960's as well as having novicaine injected into her neck in the 70's to
mitigate pain from a severe whip-lash injury she had in a car accident. It was after that car accident
that The Alzheimers symptoms started, but wasn't diagnosed until 7 years later. She was involved as a subject in a research
project on alzheimers at John Hopkins in the mid 80's where they used nicotine patches and gum.
It was working, but the program was discontinued and unfortunately for my mom, my dad was not
into alternative medicine and wouldn't allow me to help. Very sad. She died in 1999 from it. She lived
with it diagnosed for 15 years, but I am positive it started in the late 70's after the car accident.
At one point, I spoke with the Dr. at John Hopkins who was head of the program my Mom was in
and told him what I suspected, and he thought it was as valid as any explanation he knew of
.

#49 ilanso

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Posted 10 January 2008 - 11:32 PM

Here is the general critique:

Genomewide Single-Nucleotide Polymorphism Analyses: Boon or Bane for Clinical Medicine?

Jacquelyn K. Beals, PhD

January 9, 2008 — The role of personal genome analysis in current medical practice is the topic of a Perspective article in the January 10 issue of the New England Journal of Medicine. Considering the clinical value of direct-to-consumer genomics services, the authors conclude that the tests may have high analytic validity but are "not ready for prime time."

Coauthor Muin J. Khoury, MD, PhD, director of the National Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, was interviewed for an online NEJM supplement by Rachel Gotbaum, an independent producer based in Boston, Massachusetts.

"These are exciting methodologies for research," Dr. Khoury said, "because they're essentially beginning to narrow down the list of genes that have something to do with...common diseases. And once you know what the genes are, and you can study their gene products and interactions, you might be able to develop interventions...that essentially begin to counteract the abnormal gene functions related to these genes. But that's not where we are today."

Today, however, there are 2 companies (soon to be 3) offering personal genome analyses directly to consumers. To receive a personal genome analysis, a client submits a DNA sample to the company, which analyzes arrays of 500,000 to 1 million single-nucleotide polymorphisms (SNPs), using tools employed by researchers to scan the whole genome. The client then receives a printout indicating his or her risk for certain medical conditions.

The article identifies 3 major areas of concern with this direct-to-consumer process. First, there is the question of the test's analytic validity, which is rarely addressed, although researchers generally consider the validity to be quite high. Errors still may occur in handling samples, however, and even low error rates could have an appreciable effect when applied across the 500,000 to 1 million SNPs analyzed.

Second, when determining the test's validity for clinical detection or for prediction of a given medical problem, one must weigh its sensitivity, specificity, and both positive and negative predictive capacity.

"Most of the diseases that we get in adults...are very complicated," said Dr. Khoury. Many gene variants exist and interact with each other, as well as with environmental exposures. "When you take 1 gene at a time and measure its relationship or association with that disease, you get a very incomplete picture of the complex array of associations...the amount of information or extra risk that you measure is very weak at best. And therefore, by itself, it has no clinical value for the prediction of that disease."

Finally, the test's clinical utility must consider the advantages — and disadvantages — of introducing the test into medical practice. A fundamental question is, What can be done for a patient identified as being at risk for a given disease? The article states that few data are available on the value (or risk) of screening for gene variants. One basic, but unverified, assumption is that patients who are considered to be genetically at risk will respond to interventions proven effective in the broader population.

Other potential disadvantages are that patients who test negative for disease risk may be less likely to follow preventive health measures. Dr. Khoury also noted that the current lack of legal protection for genetic information could lead to "potential psycho-social and ethical issues...and potentially discrimination.... So we may end up with more harm at this point, given that the science is incomplete."

Steven L. Salzberg, PhD, director, Center for Bioinformatics and Computational Biology, and Horvitz Professor of Computer Science, University of Maryland, College Park, told Medscape Pathology via email: "Personal genomics has tremendous potential, but I think we're not there yet.... [T]o make useful clinical predictions, we need to collect SNP data from thousands of individuals." Further, to identify " 'weak' correlations between SNPs and disease, we might need tens of thousands of individual samples," Dr. Salzberg said.

"It is far too early to start telling people that they have SNPs that indicate a tendency to get one or another genetic disease — we just don't have that data, except for a very few markers such as BRCA1," observed Dr. Salzberg. "This being said, I think it's a positive sign that scientists are trying to commercialize genotyping technology."

Wylie Burke, MD, PhD, professor and chair, Department of Medical History and Ethics, University of Washington, Seattle, also commented by email to Medscape Pathology: "Does it help to know that your risk for diabetes is 1.5 times higher than the population risk, for example? Not necessarily, particularly if the proper steps to reduce risk are to improve dietary and exercise habits."

Testing is only beneficial if it motivates behavioral change or leads to proper treatment. "Clinical studies are needed to see what happens when people get their test results...whether [or not] the test in fact leads to healthy change. Or...to determine whether health outcomes are truly improved after testing and appropriate changes in treatment," said Dr. Burke. The health benefits of these tests remain to be proven.

For the present, when patients walk in with genetic printouts, Dr. Khoury advises physicians to tell them politely that "the information is not predictive...[and] not of sufficient magnitude to warrant concern.... Then proceed to advise them about health promotion and disease-prevention messages related to those diseases on the printout, regardless of whether the person is positive or negative for these genes."

He concluded, "Family history is probably a much more useful tool for clinical practice today than most of these genes on the chip that people are selling right now."

Dr. Khoury, Dr. Salzberg, and Dr. Burke have disclosed no relevant financial relationships.

N Engl J Med. 2008;358(2):105–107.



#50 Houstonian

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Posted 14 March 2008 - 07:44 PM

FYI, The Today Show (NBC) had a segment about the 23andMe. Would like to hear back from anyone who signed up and got their results back from any of the various companies who offer this service.

#51 personalgenome

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Posted 20 March 2008 - 10:10 PM

Hi everyone,

We are researching personal genome tests and the opinions of people who use them or people who might use them. If you have a few minutes, please take our survey about personal genome tests. This is not market research- we are university researchers. The survey is anonymous and you do not have to answer any questions that you do not want to answer. We are trying to reach people who have heard of these personal genome companies (23andMe, deCODEme, Navigenics, etc) but who are not scientists- if you have any ideas as to where else we might find these people (i.e., certain forums), please let me know. Thanks!

https://www.surveymo...nt66qaJtw_3d_3d

#52 Mind

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Posted 19 April 2009 - 04:44 PM

I don't want to throw cold water on the whole genetic testing biz, firstly because it is still in it's nascent stages, secondly because there is some seriously useful technology being developed, but... so far the results are less than spectacular:

Genes Show Limited Value in Predicting Diseases

One issue of debate among researchers is whether, despite the prospect of diminishing returns, to continue with the genomewide studies, which cost many millions of dollars apiece, or switch to a new approach like decoding the entire genomes of individual patients.

The unexpected impasse also affects companies that offer personal genomic information and that had assumed they could inform customers of their genetic risk for common diseases, based on researchers’ discoveries.

These companies are probably not performing any useful service at present, said David B. Goldstein, a Duke University geneticist who wrote one of the commentaries appearing in the journal.

“With only a few exceptions, what the genomics companies are doing right now is recreational genomics,” Dr. Goldstein said in an interview. “The information has little or in many cases no clinical relevance.”

Unlike the rare diseases caused by a change affecting only one gene, common diseases like cancer and diabetes are caused by a set of several genetic variations in each person. Since these common diseases generally strike later in life, after people have had children, the theory has been that natural selection is powerless to weed them out.


The reason why geonomewide studies have not turned up results in cancer and diabetes (not to mention heart disease and alzheimers) is that for the average person it boils down to lifestyle and diet, not genes. This is a no-brainer for me. These are primarily AGE-RELATED diseases. The damage (also epigenetic changes) that occurs during the process of aging causes these diseases. Still, as we learn more about how the whole "system" functions together (genes, metabolism, epigenetics), I suspect the pure genetic analysis will be very valuable.

#53 kismet

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Posted 19 April 2009 - 07:25 PM

Another take on the same issue: Genes to Diseases: Hard Work, You Say? (don't forget to read the comments)
One poster interestingly points out: "And when you consider that 20K+ genes may code for over 1 million proteins [1], any or all of which may be post-translationally modified to become active or inactive...well, is it any wonder that GWAS have fallen short?"

Edited by kismet, 19 April 2009 - 07:25 PM.


#54 AgeVivo

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Posted 30 April 2009 - 09:30 AM

While genetic information is not everything (eg it doesn't tell you if you had an accident that will endanger you) it is far from nothing neither. Epigenetics, while quite random at the molecular level, is surely much less random at the level of a cell, and much less random at the level of a tissue, and much less random at the level of the body.

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#55 PiMZ

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Posted 01 May 2009 - 03:52 AM

Information about genetic diseases, say, can be very useful from preventive point of view.

On the basis of 23andme I found that I have Pi MZ -type mild alpha-1 antitrypsin deficiency. This came totally out of the blue. (However, one of my grandparents died of some sort of chronic lung disease.) Perhaps 3% of US population carry one Z type mutation.

The MZ genotype is mostly harmless and, in fact, probably provides some lung infection resistance. However, with smoking or other persistent pollution, MZ increases lung disease risks enormously. I prefer to know this type of information.




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