Tuesday, July 31, 2012

More information from Spencer Wells on Geno 2.0

Dr. Spencer Wells provided me with additional information on Geno 2.0 again today, including a link to a recently published interview with him in BioArray News on GenomeWeb, "National Geographic to Use Illumina Chips in Next Phase of Genographic Project". You must register to read the article, but it is free to do so.

In the article, Dr. Wells discusses the community aspect of the new Geno 2.0 and emphasizes that although Geno 2.0's focus is on learning about one's ancestral origins, the test will support genealogical goals:

While National Geographic's project is focused on offering participants the ability to learn more about their deep ancestry, it will support genealogical activities, Wells said.
As it has done to date, National Geographic will allow Genographic participants to transfer their results to Family Tree DNA for free, where they will be able to network with other researchers. Additionally, they can opt to join a National Geographic-sponsored online community of Genographic participants to share their results. And, Wells noted, National Geographic will make participants' results free to them to download. 

He also clarifies Family Tree DNA's role:

Wells said that testing will be done at Family Tree DNA's Genomics Research Center in Houston. He noted that while Family Tree DNA helped design the chip and is processing the samples, Geno 2.0 remains a National Geographic project.

Perhaps, most importantly, the story quotes Dr. Wells' restating his belief that the raw data should always be returned to the customer:

"Your data belongs to you," he said. "We feel that this is a cornerstone of ethical DTC genetic testing."

I took this opportunity to ask him a couple of questions that I have received from readers:

Q: Will the Walk Through the Y customers whose samples were used for vetting the new chip receive their results?

A: Yes, the WTY and whole-mtDNA genome customers used in the validation process will receive their results when the results section of the website goes live for all Geno 2.0 participants this fall. As I said in the story, your data belongs to you.  There will be no charge to them for this, and we hope that they enjoy the new Geno 2.0 experience and will become cheerleaders for the project.

I am so happy to hear this news that the participants whose samples were used for vetting, including the mtDNA full sequence samples, will receive their results in concordance with Dr. Wells' belief that your data belongs to you.

Q: Can you comment on the inclusion of Native American samples in your research for Geno 2.0?

A: We have genotyped lots of Native American samples, though most are admixed to various degrees.  The reference populations were drawn from 1000 Genomes samples, as well as samples collected by the Genographic team in Mexico, the Caribbean, and South America, and we'll be expanding our reference set over the next year.  I don't want to discuss the analytical methods in detail until we finish writing the papers, but we have developed an innovative way of analyzing admixture that is capable of distinguishing Native American ancestry very accurately.

This is all for now, but I have no doubt, we will be hearing more about Geno 2.0 very soon.


  1. As a FYI. I assisted one of my Journalist Friends (see his email below to me)in putting together this well written story and the additional information from Spencer Wells about Geno 2.0 as well as FTDNA.

    Personally, I think this is a Consumer Friendly "DTC DNA Tipping Point" for the Genetic Genealogy Community and hopefully it will assist Consumers / Researchers / Academics / Journalists / Opinion Leaders FTDNA Project Leaders / ISOGG Leaders distinguish the new Geno 2.0 DNA Test from other DNA Tests such as those at 23andMe & Ancestry.com & Various Research Groups (i.e. as with the POBI Study funded by a Pharmaceutical Company) who are presently using "old fashion / out dated / non consumer friendly" DNA Array Chips which also test areas of DNA which are medically relevant.

    Here is the piece on National Geographic. "National Geographic to Use Illumina Chips in Next Phase of Genographic Project"
    Thanks for your help.
    Justin Perrone
    July 31, 2012

  2. I have had my full mitochondrial dna scanned by FTDNA and placed in Genbank. I have had part of my Y chromosome dna scanned by FTDNA via WTY; a new SNP L829 was found and is of particular relevance to my surname and geographical origin.

    It looks like Geno 2.0 will include my data, and will produce no results which will be of benefit to me. I could be wrong in this assumption.

    1. Ponto,

      I am about 100% certain the Version 1 of the Geno 2.0 Illumina Chip WILL NOT INCLUDE the Y-DNA SNP J-L829.

      You are in the "J" Haplogroup.

      Do you have a RS# for J-L829?

      What's your FTDNA Kit# or http://www.ysearch.org/ ID#?

      What's your Y-DNA related Paternal Surnames ... your current Surname and ones prior to your current Surname if known?

      What's your likely Y-DNA J-L829 Countries of Origin?

      The criteria for a "Public" Y-DNA SNP to be included on in the Geno 2.0 version Chip is discovery and treeing at ISOGG & FTDNA / Other Groups PRIOR to November 1, 2012.

      The same goes for mtDNA ... it has has to be PRIOR to November 1, 2012

      What date did you get results notice for the WTY FTDNA test?

      Besides you ... I find only 1 other male who is TESTED POSITIVE as J-L829+.

      Of course, one can always develop a Y-STR Signature Profile J-L829 likely males in the J Haplogroup and at various degrees of certainty say they are PREDICTED POSITIVE for J-829

      For more information on J-L829 see: FTDNA YMPAP of J-L829: http://ymap.ftdna.com/cgi-bin/gb2/gbrowse/hs_chrY/?name=L829

      I do not see J-L829 here:
      ISOGG 2012 J Tree: http://www.isogg.org/tree/ISOGG_HapgrpJ.html

      Perhaps the Blog Admin can make inquiries to the Y-DNA team for Geno 2.0 and verify this November 1, 2012 cutoff date. I think that will be helpful for others going through your scenario ... where they believe ALL Y-DNA SNPs and ALL mtDNA SNPs are on version 1 of the Geno 2.0 Chip.


    2. Revision: My message above should be the version 1 Geno 2.0 cutoff date is thought to be November 1, 2011.

  3. I am just going from what I read, which seemed to imply that all the mtDNA results on Genbank will be included and that all the results of WTY will be included on the Geno 2.0 chip.

    My WTY result, L829, does not have an rs# assigned to it, just a position number on the Y chromosome. Yes, I am of the J haplogroup, specifically, J-147.1 My kit number is 118385 and my Genbank number is HM804482.1 You won't find J-L829 on Isogg 2012, the SNP is still fairly new (October 2011) and you will need to look up http://ytree.ftdna.com/ That link contains all the new SNPs found by WTY.

    The SNP is localized to Southern Italy and Malta, the other positive is an Italian American whose ancestor is from Calabria, so is mine, but my ancestor immigrated to Malta in 1505. We are not related for at least 500 years. Both the American and I have the same surname, his is the Italian version and mine is Maltese.

  4. Ponto,

    I still think you are out of luck with having J1-L829 on the Geno 2.0 Chip this year because of the 11/1/11 cutoff date. Perhaps you should email Thomas Krahn at FTDNA and ask him about being on Geno 2.0 since you were a 2011 WYY Participant.

    BTW, have you pushed the ISOGG "J" Y-DNA coordinators to get J1-L829 treed? It's a "process" and you may have to test other known and close SNPs on the J1 tree to see if they are J1-l829-.

    For FTDNA Kit# 118385 it appears you have your Autosomal DNA results uploaded to GedMatch.com.

    Here's your eye color for F118385 at GedMatch: http://goo.gl/ihROa When's it back up and running I advise you to look for RARE AUTOSOMAL SNPS on Gedmatch with origins in your J1-L829+ homeland region.

    ?1 Have you tried to Phase your atDNA into Paternal and Maternal groupings? It could make it easier to ID RARE AUTOSOMAL SNPs and hence look for cousins that way also.

    ?2 Does the other J1-L829 Italian American (Kit #16525)have his atDNA results? (If not ... try to convince him to do it on his own or tell him you will pay X% of it) Once you have his atDNA ... I would do a comparison at Gedmatch between your 2 atDNA results and look for matching segments. Set the parameters as >1cM! For 4th and more distant cousins you are looking at matches in the area of 1-4 cMs to get to a MRCA in the 1500s.

    ?3 Have you downloaded your Autosomal DNA into an Excel Spreadsheet? Then Color Code the markers when matching others. I use GREEN - FIR 100% Match; YELLOW - HIR 50% Match; RED - 0% Match; Gray No Call / No Info. Doing that way eventually help to find some Rare SNPs unique to your paternal homeland in Malta - Calabria Italy - Etc.

    I see that indeed there are only 2 J1-L829+ persons .... with 70 persons as J1-L829-.

    Have you considered trying to get 5 "best probable" males with your surname or variant tested via Y-DNA 37 at FTDNA?

    You can search in the USA for Moscato or other Surname at Intellius. Just design some postcards and send them out.

    Length: 1
    ISOGG_haplogroup: not listed
    Mutation: C to A
    YCC_haplogroup: Approx. hg: J-L147.1
    allele_anc: C
    allele_der: A
    comments: Found in a hg J-L147.1 WTY participant
    count_derived: 2
    count_tested: 72
    primer_f: L469_F
    primer_r: L469_R
    primary_id: 44998
    gbrowse_dbid: ymap:database

  5. Is the Geno 2.0 test the same or similar to Ancestry's DNA test they're offering? Can you advise the difference between the two, in Laymen's terms and which you'd recommend to be part of? I've been on the waiting list at www.ancestry.com and it's been revealed via customer service reps that they are choosing people at random and not "customer seniority" which is fine by me seeing as I've only been a member about a year. What I am primarily interested in is my ethnicity.

  6. Hi,

    I wondering the same thing about haplogroup R1a1a SNP L579 being included in Geno 2.0.
    It was scored in May, 2011 and Hungary is the country of origin.

    Hoping it is included.


    Name: L579
    Type: snp
    Source: other
    Position: ChrY:13536848..13536848 (+ strand)
    Length: 1
    ISOGG_haplogroup: R1a (Inv)
    Mutation: A to G
    YCC_haplogroup: Approx. hg: R-M417
    allele_anc: A
    allele_der: G
    comments: Found in a hg R-M417 WTY participant
    count_derived: 1
    count_tested: 559
    primer_f: M379M201M261M377M378L259_F
    primer_r: M379M201M261M377M378L259_R
    primary_id: 43955
    gbrowse_dbid: ymap:database
    >L579 class=Sequence position=ChrY:13536848..13536848 (+ strand)