More on Geno 2.0: Third Party Resources and Images from a Second Set of Results

It turns out that an additional correspondent of mine received her National Geographic Geno 2.0 results in the last batch and she has kindly given me permission to share them. I have also received word that several third party tools are ready to accept GenoChip (Geno 2.0) raw data.

THIRD PARTY TOOLS
Mitochondrial DNA researcher James Lick's mthap tool (mtDNA haplogroup predictor) is now capable of processing the new GenoChip raw data. In fact, his tool returns an even more detailed subclade for the K1a1b1 result (shown below) than Geno 2.0 currently reports (K1a1b1f). This was also true for a K1 sample that was extended to K1e with Jim's tool.

Happily, reversing his earlier statements, Dr. Doug McDonald has successfully adapted his admixture analysis program to be able to work with the Geno 2.0 files. However, as expected, he reported that the results are inferior when compared to using 23andMe and Family Finder files due to the lower number of SNPs that he is able to incorporate in his program.

Dienekes announced today that he has created a converter to run Geno 2.0 files on his DIYDodecad tool.

After working with a raw data file, Mike Cariaso, cofounder of SNPedia, tells me that versions of Promethease 0.1.149 and later will be able to read the Geno 2.0 files directly.

Leon Kull reports that he is accepting Geno 2.0 files for inclusion in his HIR Search autosomal DNA matching database.

Y-DNA researcher David Reynolds compiled a list of Y-SNPs on the GenoChip from the raw data file. He explains on the ISOGG Facebook page, "While we don't know the exact location yet of most of the 12,000+ (e.g., the CTS, F, PF SNPs), this will answer the questions about which DF/L/Z etc SNPs are included."

Dr. Tim Janzen, 23andMe Ancestry Ambassador and ISOGG Y-SNP Tree Committee Member, is currently working on creating a file that will include the SNP positions for all of the SNPs on the GenoChip that are also found on the 23andMe v3 chip. I will add the link here when it is completed (probably tomorrow).

Dr. Ann Turner (we all know who she is and needs no introduction from me!) has informed me that she is ready to share the spreadsheet method that she has been working on to facilitate Geno 2.0 raw data usage with third party applications. She tells me, "GenoConvertTemplate.xlsm contains a macro to convert the GenoChip raw data download to the format used by 23andMe, which many 3rd party utilities can handle. It uses Build 37 numbers for the chromosomal locations of the SNPs." She would like to test it with additional Geno 2.0 data files, especially from people who have also tested at 23andMe and are willing to share both files with her. Please contact Ann directly for access or to donate your raw data (you can write to me for her email address if you don't have it).

Mitochondrial DNA researcher and mtDNA Haplogroup K Project administrator  Bill Hurst has spent quite a bit of time examining the data as well. After working with two files, he commented (in agreement with Jim Lick) that so far he "was impressed by the full coverage of the test, even while testing only 19% of the mtDNA."

I had full confidence that our amazing community of researchers/citizen scientists would come through for us and they have, even more quickly than imagined! Thank you to all those who have contributed so far to this groundbreaking project. (There's a long way to go yet!) I would be remiss if I didn't note that this expedient work could not have happened without the generosity of both Sharon and Anna in sharing their early data. Thanks go out to both of them from all of the community!

The researchers listed above are still looking to examine more raw data files, so if anyone reading this has received their results and would like to contribute to the cause, please contact me or any of the researchers directly. If you have a third party tool that is accepting Geno 2.0 raw data and is not listed, please comment below or email me to be added. I will continue to update this list as I receive more info, so please check back periodically.

**To access your Geno 2.0 raw data for use with these tools, go to "Expert Options" under the Profile tab and download the .CSV file to your desktop.**


MORE RESULTS FROM GENO 2.0:

YOUR MATERNAL LINE
Here are the newest set of mtDNA results:

WHO AM I?
These are her autosomal results:

Note: Clicking on a percentage brings up information about that population

National Geographic has recently clarified that the matching reference populations listed as first and second (shown in this screen shot) are not in order of closest matching, but simply the top two.

Interestingly, her Denisovan ancestry component is significantly lower than the other account that I reviewed.

OUR STORY
It looks like there are a few more "stories" in the community section now:

There are a total of 30 as of today (more than when I looked yesterday!).


TRANSFERS
I tried to transfer her data to Family Tree DNA (found in Expert Options under the "Download Data" button),

but I got this:

"The kit you entered already has a Population Finder, new PopFinder data cannot be transferred"

It appears that if you already have a Family Finder test from FTDNA (which includes the Population Finder feature), then you cannot transfer your Geno 2.0 results at this time. I'm surprised by this since Family Finder (PopFinder) and Geno 2.0 are very different products. Further, this customer does not have a mtDNA test in her FTDNA account, so she should be able to transfer her mtDNA results at the very least. One project administrator has already reported that a woman has transferred her results into an FTDNA Project, so contrary to earlier reports, women are not automatically blocked from transferring their Geno 2.0 results to FTDNA. I'm quite confident that National Geographic or FTDNA will clarify this issue for us soon.

MORE TO COME...
I'm sure this will be only one of my many future posts on Geno 2.0, so stay tuned.

Family Tree DNA Adds New RSRS Reporting for Mitochondrial DNA

STAYING AHEAD OF THE GAME

Family Tree DNA is staying on top of the latest advancements in genetic genealogy, adding a new way of reporting our mitochondrial DNA.

PAPER

In April of this year a paper by Doron Behar (et al) was published proposing a new method of reporting mtDNA. This method uses mutations referenced to a Reconstructed Sapiens Reference Sequence (RSRS) instead of the traditional revised Cambridge Reference Sequence (rCRS). In the author's own words:

In this study, we propose a “Copernican” reassessment of the human mtDNA phylogeny by switching to a Reconstructed Sapiens Reference Sequence (RSRS) as the phylogenetically valid reference point. We aim to trigger the radical but necessary change in the way mtDNA mutations are reported relative to their ancestral/derived status, thus establishing an intellectual cohesiveness with the current consensus of shared common ancestry of all contemporary human mitochondrial genomes.

 NEW RESULTS

In line with this proposal, FTDNA has added the new RSRS values in a tab next to the rCRS values that we are used to seeing.  Here is what it looks like in my account:

rCRS Values (old mutation list)

RSRS Values (new mutation list)

  

IMPROVEMENT OVER rCRS

This new method is an improvement over the old method (based on the 1981 sequence which is now being classified as belonging to the haplogroup H2a2a1), in part, because it uses the root of the tree as the base from which to count mutations rather than the differences from the random sample that has been used in the past. More from the authors:

Mutational events along the human mitochondrial DNA (mtDNA) phylogeny are traditionally identified relative to the revised Cambridge Reference Sequence (rCRS), a contemporary European sequence published in 1981. This historical choice is a continuous source of inconsistencies, misinterpretations and errors in medical, forensic and population genetic studies. Here, after having refined the human mtDNA phylogeny to an unprecedented level by adding information from 8,216 modern mitogenomes, we propose switching the reference to a Reconstructed Sapiens Reference Sequence (RSRS), which was identified by considering all available mitogenomes from Homo neanderthalensis. 

mtDNA Phylogeny - found under "Resources" tab

NEW SITE

 

With this change, FTDNA has also launched a new website:
mtDNACommunity.org is brought to you as a free public service, aiming to facilitate the further understanding of the human mtDNA phylogeny. 

New mtDNA Community Website

Its stated goal is:
This website is committed to the support of the "Copernican" reassessment of the human mtDNA phylogeny and to the establishment of computational tools meant to facilitate phylogenetic analysis and comparison of complete mtDNA sequences. 

It appears that Dr. Behar will be actively involved in the site:

TOOLS TO EASE THE TRANSITION

There are two new tools to help us ease into the transition:
To facilitate data transition from an rCRS to an RSRS based nomenclature we release the tool "FASTmtDNA". Additionally, the tool "mtDNAble" automatically labels haplogroups, performs a phylogeny based quality check and identifies private substitutions. These noted features are fully supported in this website or as standalone versions, which can be freely downloaded from the website including their manual and example files.

MORE DETAILED HAPLOGROUP

On FTDNA's website, I am still listed as haplogroup U5b1, but on mtDNA Community, my full U5b1b2 Haplogroup is reported. That is the same haplogroup reported by 23andMe for me and my matrilineal relatives, so it is nice to see it confirmed here.

More detailed haplogroup

 OUR CITIZEN SCIENTISTS

It is exciting to see that the contributions of genetic genealogists and "citizen scientists" Rebekah Canada and William R. Hurst were acknowledged in this paper and, as we in the genetic genealogy community know, this is well deserved. However, Ian Logan's earlier paper with similar ideas published in 2007 by the Journal of Genetic Genealogy was also deserving of acknowledgement and, perhaps, mistakenly, overlooked.

 MATCHES

Matches can be accessed under the "Community" heading on the new site. I uploaded my results, but I don't have any matches there, so hurry up and add your full sequence so mine isn't so lonely!

**Update - Ann Turner shared the following information in a comment below. I thought it was important enough to add it to the body of this post:
mtDNACommunity is indeed restricted to full mitochondrial sequences. I agree that upgrading would not be informative in terms of finding matches, but you would learn a more detailed haplogroup assignment if that is of interest to you.
All who have tested at 23andMe: you can learn your differences from the RSRS by going to Ancestry Labs / Haplogroup Tree Mutation Mapper. 23andMe doesn't test every position, but all the positions listed will be differences from "mtEve." I did a quick check, and it looks like 73 and 16311 would be the only positions missing along the route between the RSRS and the CRS. Thanks Ann!
And Bill Hurst (the same William R above) posted on the ISOGG list this new info: FTDNA has listed your "NCBI Number" or GenBank accession number beside your haplogroup designation on your personal page. For me it wasn't there because I submitted to GenBank through Ian Logan, but for anyone who submitted through FTDNA, you should be able to see it. Thanks, Bill!

This is as new to me as it is to the rest of you, so we will learn together as we go. Rebekah Canada has kindly posting an extremely informative "tutorial" on the ISOGG Facebook page, so follow along to learn more.**

"Finding Your Roots with Henry Louis Gates, Jr." - DNA in the Sixth Episode

The sixth episode of Finding Your Roots with Henry Louis Gates, Jr., investigating the mixed ancestry of Robert Downey, Jr and Maggie Gyllenhaal, aired last night on PBS. These two actors not only share a profession, but both have a mixture of Eastern European Jewish ancestry as well as deep American roots. Because of these commonalities, I thought their stories worked well together. I was thoroughly entertained by this episode for three reasons: 1) I love Robert Downey, Jr., 2) I discovered that Maggie is my cousin through our shared 10th great grandfather John Lothrop and 3) The appearance of Bennett Greenspan, President of Family Tree DNA (or as Professor Gates called it "FamilyTreeDNA.com", which I am sure was much appreciated).

Bennett Greenspan on "Finding Your Roots with Henry Louis Gates, Jr."

Unfortunately, the DNA portion was only about five minutes long again this week (starting at 43:00), nevertheless it felt a bit more substantial to me than last time. I was happy to see a number of different tests featured: 23andMe's Ancestry Painting, FTDNA's Population Finder and mtDNA testing.

Robert Downey, Jr.'s "Ancestry Painting" from 23andMe

First, Robert Downey, Jr., whose father is half Jewish, was presented with a pie chart of his 23andMe Ancestry Painting, which breaks down a person's genetic ancestral origins into three populations - European, African and Asian. (Note - this test is included in the 23andMe Personal Genome Service and is presented as a chromosomal chart rather than a pie chart.) Dr. Gates has repeatedly stated that this test reveals "European, African and Native American ancestry", however I would like to remind readers that the Asian reference population simply "stands in" for Native American. 23andMe does this because the genetic makeup of the two populations is similar, but in reality, this is not quite the same as having reference samples from Native Americans and the two should not be confused with each other. For instance, a person could show Asian DNA on their Ancestry Painting, but one should not automatically reach the conclusion that they have Native American ancestry because they may have ancestors from China, Japan, Korea or any other Asian region. If a person has reason to suspect that they possess Native American ancestors and knows of no other Asian ancestry, then this test is useful for that purpose. As is typical of most people, RDJ guessed that his ancestry would be more "interesting" than it was and seemed disappointed to learn that his Ancestry Painting showed 100% European ancestry. As I have mentioned before, this actually encompasses all of Europe, including the Middle East, so it doesn't rule out RDJ's Jewish ancestry.

Robert Downey, Jr.'s "Population Finder" from Family Tree DNA

Next, Dr. Gates presented RDJ with what I believe was his Population Finder admixture from Family Tree DNA. (The PopFinder feature is included with the Family Finder test.) This test broke down RDJ's ancestral origins a bit more, showing that he is about 20% Middle Eastern or Jewish.  That is slightly under what we might expect for him with a father who is half Jewish, so his one Jewish grandparent may have had a little something else mixed into his/her ancestral origins.

Later, Dr. Gates sat down with Maggie to discuss her mitochondrial DNA (mtDNA) which is inherited straight down the maternal line, passed from mother to child as far back "as you can think" enthused Maggie. Maggie's mom is Jewish, so it makes perfect sense that Maggie's mtDNA has been inherited from one of four Jewish founding mothers who lived thousands of years ago. The voiceover explained, "Scientists have concluded that 40% of Eastern European Jews share genetic lineages that reach back two to three thousand years, remarkably to just four women...today about 3.5 million people descend from one of these four maternal ancestors." Haplogroup Project Administrator and genetic genealogist Vince Tilroe points out that Bennett Greenspan and Professor Gates were most likely speaking of mtDNA Haplogroups K1a1b1a, K1a9, K2a2a, and N1b when referring to the four Jewish maternal lines. These were identified in the 2006 study by Dr. Behar, "The Matrilineal Ancestry of Ashkenazi Jewry: Portrait of a Recent Founder Event".

Bennett Greenspan of FTDNA explaining Jewish DNA to Dr. Gates

Bennett further explained that Maggie had "hit the jackpot" with about 150 exact matches in Family Tree DNA's mtDNA database.  Bill Hurst, Administrator of the mtDNA Haplogroup K Project and a leading expert on this haplogroup, theorizes that if Maggie's mtDNA haplogroup is K, she likely falls into the K1a1b1a ancestral haplotype. Hurst explains that this haplotype's match numbers most closely coincide with the those that Bennett cited from FTDNA's database. At the HRV1/HRV2 level of testing, this haplotype now has 194 exact matches, but at the time of filming may have had closer to 150. He also notes that K2a2a is now called K2a2a1 due to recent discoveries. (There are three levels of mtDNA testing offered by Family Tree DNA which you can read about here.)

At the end of the episode Professor Gates discussed the question of "nature versus nurture" with his guests and asked Robert Downey, Jr. if he feels that his ancestral past has shaped who he is today. In answer, RDJ insightfully commented, "I don't see how it couldn't...it's informing you whether you're conscious of it or not, so probably better to be conscious." The episode ended with RDJ expressing his feelings about this experience with Dr. Gates, explaining that he felt that this was just the beginning of his journey of self-discovery.

I hope this show has also inspired all of you to begin (or continue) the journey into your ancestral roots. See you next week when we review the genetics of Samuel Jackson, Condoleezza Rice and Ruth Simmons. The television listing says that the show will be using DNA to "determine which parts of Africa their ancestors came from." That sounds promising!


I have been writing a review of the DNA testing used in each episode:
Week 1- Episode 1 & Episode 2 - Harry Connick Jr. & Branford Marsalis; Cory A. Booker & John Lewis
Week 2- Episode 3 - Barbara Walters & Geoffrey Canada
Week 3- Episode 4 - Kevin Bacon & Kyra Sedgwick
Week 4- Episode 5 -  Rick Warren, Angela Buchdahl & Yasir Qadhi