GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2008-06 > 1212602148


From: Bill Howard <>
Subject: Re: [DNA] SNPs on chip
Date: Wed, 04 Jun 2008 13:55:48 -0400
References: <5273979.2673741212595562209.JavaMail.www@wwinf2623>
In-Reply-To: <5273979.2673741212595562209.JavaMail.www@wwinf2623>


Hi, Didier,

I'm afraid that I can give you no more information than was included
in my previous note. I rather suspect that the details of how it does
its job is proprietary to each company that uses it, but I am not sure.

One way to smoke out the answer is to write Illumina or DeCode
Genetics directly and ask. You may have a higher probability of
success with Illumina since they want to market their chips whereas
DeCode uses them as a moneymaker.

Good luck and let us all know if you gain any valuable information
about the process.
- Bye from Bill Howard

On Jun 4, 2008, at 12:06 PM, Didier VERNADE wrote:

>
>
>
> Hi Bill,
>
>
> Thanks for your long and detailed answer. I had heard of the
> illumina- deCODEme joint venture. My point is : how does it work ?
> For example I can quickly summarize the principle of the testing at
> FTDNA : DNA primers are used to amplify a specific DNA fragment and
> this amplified DNA is then sequenced and a particular SNP is
> detected (or not). How do they succeed to detect single base pair
> changes without any amplification process ?
>
>
> By the way, I had posted previously that one member of R1b1c6
> project is still waiting for his SNP result from batch 250 and he is
> still waiting... (kit N° 89260) .
>
>
> Didier
>
>
>>
>> Hi, Didier,
>>
>> I think I can shed some light on your question.
>>
>> I have followed the fortunes of DeCode Genetics located in Iceland
>> (deCodeme) and their rival 23andME (privately owned and located in
>> Mountain View, CA). The former company uses chips and methodology in
>> cooperation with a company called Illumina (see URL: http://www.decode.com/Pipeline/Alliances.php)
>> .
>>
>> In their web site they state:
>> ----------------
>> "In May 2006 deCODE and Illumina announced the formation of a
>> strategic alliance to co-develop and commercialize DNA-based
>> diagnostic tests in several major disease areas. The alliance employs
>> Illumina’s platform for high-multiplex single-nucleotide polymorphism
>> (SNP) genotyping to develop tests for gene variants deCODE has
>> previously shown to have impact on the risk of a growing number of
>> common diseases with major public health impact. The alliance will
>> initially focus on the development, validation and commercialization
>> of specific diagnostic tests for variants in genes conferring risk of
>> heart attack, type 2 diabetes and breast cancer.
>> As part of the agreement, Illumina installs its SNP genotyping
>> platform at deCODE, enabling deCODE to expand its contract genotyping
>> business to offer Illumina platform and assay technologies together
>> with deCODE’s proprietary analytical services for customers."
>>
>> ------------------
>>
>> DeCode's efforts employ detailed scans but in areas related to
>> disease
>> (presumably not our DNA "junk" area) that are probably not as related
>> to the interests of this list. These scans are extremely rapid and
>> can
>> explore critical areas so fast that there have been many attempts to
>> capitalize on those capabilities to offer diagnostic tests to the
>> public.
>>
>> I'll bet that the testing agencies that work in our area of interest,
>> particularly in the fields of Y and mitochondrial DNA scanning, are
>> well aware of these types of scanning ability, and they are probably
>> already using similar approaches.
>>
>> Hope this helps.
>>
>> - Bye from Bill Howard
>>
>>
>>
>> On Jun 3, 2008, at 6:06 PM, Didier VERNADE wrote:
>>
>>>
>>> List,
>>>
>>> Is there anyone on this list who could explain is some details the
>>> principle of these DNA chips used by deCODEme and 23andME ? Only on
>>> the basis of those SNPs of the Y chromosome I am impressed : all
>>> those SNPs in such a short time. But I also find the explanations
>>> that came with the results very limited ; someone with no background
>>> would get only a general picture. I don't know if a "tiny" chip not
>>> too expensive could be devised for Y and mitochondrial DNA but
>>> Genographic would have provided so much more with this technology...
>>> I s it a dream or is it the future ?
>>>
>>> Didier
>>
>>
>>
>
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