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Author Topic: Discussion with Scientists at 23andme about Plans for the X  (Read 2142 times)
DKF
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« on: February 07, 2009, 03:13:36 AM »

I had a phone conversation with Dr. Mike Macpherson at 23andme, who, with Dr. Joanna Mountain (my schedule would not permit a conference call but she will be informed as to the substance of the discussion) are the two scientists in charge of autosomal and X ancestry work.

Actually we talked about many subjects but I will confine things to only matters which bear on the X.

Of course my first question was, "when will the X be painted".  Apparently 23andme is working on a major upgrade to the present "Ancestry Painting".  which only uses the 4 HapMap populations as reference samples (those groups were what was available when the project was conceived).  Dr. Macpherson described to me the algorithm that is used and how it makes a first pass getting a view of the major ancestry and makes adjustments accordingly, with the use of simulations that they have done in house with "real people" and the type of blocks that would result after so many meioses. 

I think that they were at one time using SABER but now finding that BEAGLE is faster and more flexible for the phasing work to assign diploid nucleotide bases (e.g., CG) to the correct chromosome - in the case of the X that is only for females. 

Their updated version will include 12 reference populations.  As to a timetable, the X is not going to be painted until incorporated into the Version 2.  As to when we can expect this upgrade, it will be a while - perhaps 6 months to a year.  In the meanwhile there will be a few surprises installed that will move us in the right direction, so stay tuned. 

Dr. Macpherson said that he understands the desire many of us have to control the parameters (to set the bar ourselves).  I mentioned that it would probably be fine to have a default version which 23andme believes is the most likely estimate, but with that caveat in place then we could look at establlishing the bar at 1 Mb, 3 Mb, 5 Mb, 10 Mb and so on.  If we want these features we may have to write to 23andme or the Community pages to express precisely what we would like to see.  My impression is that they need to "make a case" to the brass for establishing these bells and whistles.   I have gone on record as wanting at least what decodeme offers, but not just with one reference sample from each of the 52 populations - all 1049 or so.  So, an e-mail campaign would be in order.  We are only likely to get what we gently insist upon.  They have resource allocation issues as do all companies and people more interested in the disease aspect of the test will be asking for different features.  They need to know that there are lots of us out there and we all want pretty much the same thing.

Again, it could be 2010 before we get the major features that we want in relation to the X, but if we don't make specific requests we might be rather disappointed in what is offered.  Still, over the next few months they will be flying a few trial balloons so there is something to look forward to in the more immediate future.

David.
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X-chromosome:  56.25% England; 12.5% Scotland; 12.5% Ireland; 12.5% Germany; 6.25% North America (Lower Mohawk, Six Nations)
Seán MacGorman Powell
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« Reply #1 on: February 07, 2009, 11:25:40 AM »

Wow, David, that's some great information that you were able to share, thanks!  I'm very encouraged to hear that they are moving toward painting the X, though a bit dismayed by the timeline.  A year is an eternity with respect to the field of genetic genealogy (I'm thinking back to the state of this science a year ago today, and how far we've come).

You're sure right that making our wishes directly known to 23andMe can only help.
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tomcat
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« Reply #2 on: February 07, 2009, 12:02:34 PM »

DKF,

Did you get any sense that 23andMe was planning a chip upgrade in the immediate future? I note that they are offering a special price till 28 February 09 and wondered what was going to happen after that date?
« Last Edit: February 07, 2009, 12:04:26 PM by tomcat » Logged

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DKF
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« Reply #3 on: February 07, 2009, 01:18:10 PM »

DKF,

Did you get any sense that 23andMe was planning a chip upgrade in the immediate future? I note that they are offering a special price till 28 February 09 and wondered what was going to happen after that date?
As best as I could tell tomcat, the answer is probably no.  I can't say for sure no, but Dr. M did not mention any such development.  I did ask specifically about a new Y chip and that question will be forwarded to Dr. Underhill.

David.
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Maria_W
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« Reply #4 on: February 07, 2009, 09:29:32 PM »

David,

Thank you so very much!  Really apprecaite the effort you have made on behalf of all of us!  That would be so amzing! So the 23andme test will go up Feb 28 I best go ahead and order it.  I don't want to wait till 2010.  I could always redo the test again when they paint the X!


Maria
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DeCodeMe: Autosomal: African 2%, Asian 6%,  European 92%.  X: African 4%, Asian 9%, European 87%.
23andme: pending.
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kathlingram
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« Reply #5 on: February 07, 2009, 10:17:36 PM »


Hi David
What is Painting the X? has it been done yet at all? Is it for males  and females?
Does it give any insight into both parents ? My Dad's father was unknown to us and much of what I do is to try to illuminate that part of my ancestry..which autosomally looks Polish and German in addition to my mostly Irish heritage.

Thanks for sharing this with us..
Kathleen
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Kathlingram

X chromosome ancestry % 62.50 Irish,Colonial Admixture of Eng/Irish/Welsh 37.50%.Father 25% Irish,25 % Colonial admix.Mother 37.50% Irish 12.50% Colonial Admix
kathlingram
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« Reply #6 on: February 08, 2009, 12:44:30 PM »


David
I went to 23andMe and looked at it..so I understand better now.
Of course that means I will have another question.. you said this:

"I have gone on record as wanting at least what decodeme offers, but not just with one reference sample from each of the 52 populations "
and I agree..who should we e-mail? Dr.McPherson?

also I think that if we did our testing now we might not be able to get all the reference populations retroactively.? Is that correct?
Again thank you..I for one am excited..
Kathleen
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Kathlingram

X chromosome ancestry % 62.50 Irish,Colonial Admixture of Eng/Irish/Welsh 37.50%.Father 25% Irish,25 % Colonial admix.Mother 37.50% Irish 12.50% Colonial Admix
DKF
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« Reply #7 on: February 08, 2009, 02:19:25 PM »


David
I went to 23andMe and looked at it..so I understand better now.
Of course that means I will have another question.. you said this:

"I have gone on record as wanting at least what decodeme offers, but not just with one reference sample from each of the 52 populations "
and I agree..who should we e-mail? Dr.McPherson?

also I think that if we did our testing now we might not be able to get all the reference populations retroactively.? Is that correct?
Again thank you..I for one am excited..
Kathleen
First thanks for the great detail in the X signature line Kathleen.  It is so helpful to have this information.

In answer to your question, I would write to the contact e-mail at 23andme and they will forward it on.  I get the sense that things will work best with that route.  Also laying out everything on the Community pages will get results because 23andme has assigned Chia to coordinate things here and she will report back to the brass and the scientists.  So perhaps a "two pronged attack" - but of course always pleasant.  We have to realize that they have their own agenda and priorities and that their resources are not unlimited.  If they sense that their customer base is more interested in the ancestry features than disease components they will move in that direction.  I really got the opinion that Mike was very receptive to learning what it was we wanted, and he would do his best to put in place something - even if it was a compromise.

David.
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X-chromosome:  56.25% England; 12.5% Scotland; 12.5% Ireland; 12.5% Germany; 6.25% North America (Lower Mohawk, Six Nations)
kathlingram
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« Reply #8 on: February 08, 2009, 02:48:14 PM »


Hi David
Thanks for the reply.I will look at their message forum.I DID get a trial membership.

My signature involved  a lot of head scratching..I do have some names on Dad's Colonial Delaware  ancestry and they go back to New Sweden times or shortly thereafter but no-one is clear where they all come from.
My Dad's great grandmother on his Mom's side was Edenfield and that man came from Yorkshire.
I find it amazing that Dad's Irish side has been easier to document than  the Colonial Delmarva folks..
and amazing that they are such a large part of my  X ancestry.
Kathleen
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Kathlingram

X chromosome ancestry % 62.50 Irish,Colonial Admixture of Eng/Irish/Welsh 37.50%.Father 25% Irish,25 % Colonial admix.Mother 37.50% Irish 12.50% Colonial Admix
warwick
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« Reply #9 on: February 13, 2009, 10:24:41 AM »

Fascinating.  I've now uploaded my sister's data to the Ben's spreadsheet as well.  Keep us posted.
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Svaale
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« Reply #10 on: February 14, 2009, 05:45:27 PM »

It appears that both 23andme and deCODEme may have underestimated the genetic geneology and genetic ancestry market demand, and now recently also an increased demand from more advanced users for more sophisticated analysis, that advanced users have moved into the "home brewed"/"garage development" to compensate demonstrate to what extend they are actually lagging in their development.
« Last Edit: February 14, 2009, 05:48:37 PM by Svaale » Logged
Maria_W
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« Reply #11 on: February 18, 2009, 04:53:12 AM »

I just ordered 23andme so in about 10 weeks I will have results to share with everyone...Sure hope they will paint the X soon...

Maria
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DeCodeMe: Autosomal: African 2%, Asian 6%,  European 92%.  X: African 4%, Asian 9%, European 87%.
23andme: pending.
United States (Native American: Potowomecke from Virginia and European(Ireland, Scotland, Wales, England, Germany, Switzerland and France)
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