Showing posts with label Family Tree DNA. Show all posts
Showing posts with label Family Tree DNA. Show all posts

Saturday, 4 January 2020

New lower pricing structure at FamilyTreeDNA

The FTDNA sale has now ended but the good news is that the prices haven’t gone back up to the old pricing levels and the new prices are now much lower. When ordering direct from the FTDNA home page there are now only five tests available:
  • Y-37 $119 (previously $169)
  • Y-111 $249 (previously $359)
  • BigY-700 $449 (previously $649)
  • mtDNA full sequence $159 (previously $199)
  • Family Finder autosomal DNA test $79 (no change)
The old price of the BigY-700 test included access to the raw data file (the BAM file). However, most people did not want the raw data file which meant that the price was artificially inflated for the benefit of the few. If you do want your BAM file you can now purchase it as an add on for $100.

Shipping costs $9.95 in the US and $12.95 to most international destinations.

The 25-marker test and the 67-marker test have now been discontinued. The 12-marker test is still available for $59 but can only be ordered through a project. You can access the project search menu here.

There used to be discounts available when ordering kits through projects but these discounts are no longer available. However, with the new lower prices I would hope that all of us with projects at FTDNA will see renewed interests in our projects in 2020.

In addition to the reduced prices for new tests there are also big reductions in the upgrade prices for Y-DNA tests. Dave Nicolson compiled a spreadsheet showing the new pricing which he shared in the Only FTDNA Project Administrators Group on Facebook. He has kindly given me permission to reproduce his chart below.


Discounts for members of the Guild of One-Name Studies
If you are a member of the Guild of One-Name Studies note that you can buy 37-marker tests and Family Finder tests at discounted prices from the Guild.

The Y-DNA test is currently £88 from the Guild. The cost from FTDNA is £91 at current exchange rates. Postage rates are calculated individually by the Guild and you would need to pay return postage for the kit to Texas but for most people, especially outside the US, it is likely to be cheaper to buy a 37-marker test from the Guild, and especially so if you can pick up a kit at one of the Guild events. 

You can also buy FTDNA Family Finder kits direct from the Guild for £40. This is a considerable saving on the current price of $79 from FTDNA which works out at £60 at current exchange rates. Postage would again be extra.

For further details see the page on the Guild website on DNA kits available from the Guild.

Wednesday, 2 August 2017

Three generations of FTDNA MyOrigins 2.0 results from Family Tree DNA

In April this year Family Tree DNA rolled out a new version of their myOrigins report. I've tested three generations of my family at FTDNA so I thought it would be interesting to do a multi-generation comparison. I did this exercise with the first version of the myOrigins test, and you can read about our previous results here.

I've provided below a summary of the genealogical ancestry for each family member tested together with a screenshot of their results. Click on the images to enlarge them.

Debbie's dad
  • Four grandparents born in England: Bristol, Gloucestershire, London (x2).
  • Eight great-grandparents born in England: Bristol (x2), Devon, Essex, Gloucestershire, Hertfordshire, London (x2).
  • Fifteen great-great grandparents born in England: Devon (x2), Bristol, Essex, Gloucestershire, Hertfordshire (x 2), London. One great-great grandparent born in Scotland (location not known). The birthplace of seven of his English great-great-grandparents is unknown. Four were probably born in Bristol or in a nearby county. Three were Londoners who could have moved to London from anywhere in England.

Debbie's mum
  • Four grandparents born in England: London (x2), Hampshire (x2).
  • Eight great-grandparents born in England: Berkshire, Hampshire, London (x3), Somerset, Wiltshire. The birthplace of one great-grandparent is not known but he was probably born in London.
  • Fifteen great-great-grandparents born in England: Bedfordshire, Berkshire (x2), Gloucestershire, Hampshire (x2), Hertfordshire, London (x2), Somerset (x2), Wiltshire. One great-great-grandparent born in Ireland: County Kerry. The birthplace of three of her English great-great-grandparents is unknown. One was probably born in Hampshire. The other two were probably Londoners who could have come from anywhere in the country.

Debbie
  • Four grandparents born in England: Bristol, London (x3).
  • Eight great-grandparents born in England: Bristol, Gloucestershire, Hampshire (x2), London (4).
  • Sixteen great-great-grandparents born in England: Berkshire, Bristol (2), Devon, Essex, Gloucestershire, Hampshire, Hertfordshire, London (x 5), Somerset and Wiltshire. The one great-great-grandparent with an unknown birth location was probably born in London.
  • Twenty-four great-great-great grandparents born in England: Berkshire (x2), Bristol, Devon (x2), Essex, Gloucestershire (x2), Hampshire (x2), Hertfordshire (x3), London (x5), Somerset (x2), Wiltshire. One great-great-great grandparent born in Ireland: County Kerry. One great-great-great grandparent born in Scotland (location not known). The birthplace of the remaining eight English great-great-great-grandparents is unknown but they were probably born in Bristol, London and Hampshire.

Debbie's husband
  • Four grandparents born in England: Cambridgeshire (x2), Cumberland, Devon.
  • Eight great-grandparents born in England: Cambridgeshire (x3), Devon (x2), Dorset, Somerset, Surrey.
  • Sixteen great-great grandparents born in England: Cambridgeshire (x3), Devon (x4), Hampshire, Herefordshire, Hertfordshire, Huntingdonshire (x2), Somerset (x2), Surrey (x2).
  • Twenty-six great-great-great grandparents born in England: Cambridgeshire (6), Devon (x8), Hampshire, Herefordshire (x2), Huntingdonshire, Somerset (x4), Surrey (x3), Sussex. The birthplace of the remaining six English great-great-great-grandparents is unknown. Three were probably born in Cambridgeshire, two in Hertfordshire and one in Surrey.

Debbie's eldest son


Discussion
It's interesting that four out of five of my family have now come out as 100% British Isles with myOrigins 2.0. This does correspond with our known genealogical ancestry in the last few hundred years. However, it's somewhat surprising that my husband, who also has an all-British genealogy, is now dramatically less "British" than he was before.

I've compiled a table showing our percentages of "British Isles" DNA with the old and new myOrigins test:

Tester myOrigins 1.0 MyOrigins 2.0
Debbie's dad 40% 99%
Debbie's mum 7% 100%
Debbie 57% 100%
Debbie's husband 38% 15%
Debbie's son 75% 100%

With the new results both my dad and my husband have tiny percentages of what Family Tree DNA call trace percentages. My dad has <2% South Central Asia. My husband has <1% Oceania. FTDNA advise that "a trace percentage indicates a very small amount of shared DNA in common with the corresponding population. In some cases this minor percentage could be attributed to background noise."

I've seen mixed reports for the updated myOrigins reports. Some people say that their results are much better and others say that their results are a lot worse. For the results I've seen for people in the UK in my various projects at FTDNA I've noticed that the percentages of British Isles in general now appear to be much higher than before, but my husband's results show that this is not always the case. I would continue to urge caution when interpreting admixture results.

Further reading

Saturday, 29 July 2017

Comparing match tallies for family members with Family Tree DNA's Family Finder test

I've taken a look at the total number of matches for all my family members who have taken a Family Finder test at Family Tree DNA. I've also done a comparison with the data I extracted on 26th May 2016 just before Family Tree DNA updated their matching algorithms. The results are shown in the table below. Note that I have excluded immediate family members from the totals.

Relation Number of matches
 28 July 2017
Number of matches
 26 May 2016
% increase
Debbie 1217 592 51%
Debbie's dad 1344 643 52%
Debbie's mum 1038 495 52%
Debbie's husband 905 443 51%
Debbie's eldest son 1138 542 52%

If my matches are representative of the wider Family Finder database then there has been over a 50% increase in the size of the database in the last 14 months.

I've also looked at the number of matches I share with my parents and taken stock of the number of matches which don't match either parent.

I share 501 matches with my dad. Of these, 320 were assigned to the paternal side with FTDNA's Family Matching tool. The remaining 181 matches were in common with my dad but did not meet the threshold for Family Matching.

I share 402 matches with my mum. Of these, 276 were assigned to the maternal side with the Family Matching tool. The remaining 126 matches did not meet the threshold for Family Matching.

I therefore have a total of 903 matches (74%) which match my mum or my dad. However, this means that 314 of my 1217 matches (26%) do not appear in the match lists of either of my parents.

All the matches that don't match my parents have a longest segment under 15 cMs. This is the breakdown.

Longest block  Number
10-14 cMs 28
7-9 cMs 286

The last time I did a comparison of parent and child matches I found that 23% of my matches did not match either of my parents.

These matches are either false positives or false negatives but without further investigation it is not possible to tell.

Have you tested both of your parents at Family Tree DNA? What are your statistics?

Related blog posts

Saturday, 25 March 2017

The updated mtDNA tree at Family Tree DNA and an upgrade sale

Family Tree DNA have finally updated the mitochondrial DNA haplogroup assignments for all their customers to Build 17, the latest version of the mtDNA tree. The mtDNA tree is documented by scientists on the Phylotree website. Build 17 of the mtDNA was introduced in February 2016, but until this week FTDNA were using Build 14, which dates back to April 2012, so this update is long overdue. Here is what FTDNA have said about the upgrade in an e-mail to group administrators:
You or your members may have received an email about the update of the mitochondrial DNA database from Build 14 to Build 17, which is the most recent phylogenetic build for mtDNA. This update has been in the works for several months while the scientific team tested and verified the programming and results. We were able to release it this week, so some of you may have seen a change to your mtDNA haplogroup. 
To give you an idea of the scope of this project, Build 14 was based on the analysis of 8,216 modern mitogenomes, while Build 17 was designed using 24,275 mtDNA sequences - almost three times as much information! Build 17 increased to 5437 nodes from 3550 in Build 14, an increase of 1887 haplogroups. Obviously, the update provides a much finer resolution in terms of haplogroup assignment. 
In a very few cases haplogroups may have reverted to a higher branch on the tree. Usually, this is because in Build 14, some of the branches of the tree were predicted, not confirmed. The additional sequences added between Build 14 and Build 17 did not provide supporting data to justify their existence, so these branches have been removed.
What this means in practice is that some people who have taken a full mitochondrial sequence (FMS) test with Family Tree DNA will now find that they have extra letters and numbers in their haplogroup name reflecting the latest discoveries in mtDNA research. For example if you were previously a U4a1a you might learn that you are now either a U4a1a1, a U4a1a2 or a U4a1a3. This is because, as more and more full sequences have become available, it is possible to identify new subclades or branches on the tree.

You can see an updated list of the mtDNA haplogroup-defining mutations on the FTDNA website. Not all subclades have been updated this time but it is always possible your subclade could be refined the next time the tree is updated.

To see where you belong on the mtDNA tree go to the Phylotree website and navigate to your branch of the tree. In the screenshot from Phylotree below you can see the three new daughter clades of U4a1a. Next to the subclade names there is a list of the mutations that define these subclades. The letter and number codes on the far right represent the GenBank IDs of the sequences that were used to define these new subclades.









For a sequence to be used to build the tree it has to be published in the GenBank database. Sequences appearing in scientific papers are uploaded to GenBank on publication. In addition, many Family Tree DNA customers have uploaded their sequences to GenBank so that they can contribute their results to science. If your sequence is used to identify a new subclade you might have the honour of having your sequence listed as one of the two references for that subclade. You might even find that your sequence gets used in a scientific paper! My own personal mtDNA sequence has already appeared in two scientific papers to date.

If you are interested in uploading your mtDNA sequence to GenBank you can find further information on the ISOGG Wiki page on GenBank

It's important to remember that you will share your mtDNA sequence with your siblings, your mother, and any cousins who descend in an all-female line from your matrilineal ancestors. There are 37 genes in the mtDNA molecule and in some cases people will have mutations that have medical significance so any mutation that potentially affects you will also affect your other matrilineal relatives. It's very rare to find such mutations but it's always a good idea to get your sequence checked out before sharing it publicly. If you are technically minded you can look up your own mutations on Mitomap. Alternatively you can order a custom mtDNA report from Dr Ann Turner for a small and very reasonable fee. I ordered a report for myself and I can highly recommend this service. 

If you want to find out more about your haplogroup have a look at Rebekah Canada's wonderful Encyclopedia of mtDNA Origins. If you type in the name of your subclade you can pull up a list of all the sequences in your subclade on GenBank and in the Genographic Project database together with a list of relevant publications from the scientific literature, and an estimate of the age of your subclade.

There are some cases where the haplogroup names have not yet been updated. We have a few examples in the mtDNA Haplogroup U4 Project. These have occurred where the subclade-defining mutation is an insertion or deletion. An example of an insertion is 965.2C. This means that, in comparison to the reference sequence, the person has two extra Cs at position 965. An example of a deletion is 301-  or T310d. The way the deletion is reported depends on which reference sequence is being used  – the revised Cambridge Reference Sequence or the Reconstructed Sapiens Reference Sequence. What this deletion means is that there is a letter T in the reference sequence but this letter T is not present in the person who has tested. The FTDNA algorithms currently seem to be unable to handle these insertions and deletions but hopefully this will be sorted out in due course.

In the meantime if you want to check your own haplogroup assignment you can use James Lick's mtHap tool, which is equipped to handle insertions and deletions. It's also a good idea to join the relevant mtDNA Haplogroup Project. Some of the volunteer haplogroup project admins will be able to check the haplogroup assignment for you.

FMS upgrade sale
To coincide with the update to the mtDNA tree FTDNA have announced an upgrade sale. For the next week only you can upgrade to the full sequence from HVR1 or HVR1+HVR2 for just $99. You will only get the detailed haplogroup assignment with the full sequence test. The FMS upgrade is particularly useful if you have a lot of matches at the lower testing levels. mtDNA can also be used at FTDNA in combination with autosomal DNA testing to rule matches in or out on the matriline. Remember too that FTDNA is the only company where you can use your mtDNA results for genealogical matching purposes.They have the world's largest database of full mitochondrial sequences. As of today's date there are 99,847 FMS records in their database. It's only a matter of time before the 100,000 milestone is reached.

Thursday, 16 February 2017

Family Tree DNA are now accepting autosomal DNA transfers from new AncestryDNA and 23andMe tests

Family Tree DNA are now accepting transfers from AncestryDNA v2 kits (all tests processed after mid May 2016) and 23andMe v4 kits (all tests taken from about November 2013 onwards). As before, the transfer is free but you have to pay a small fee to unlock the rest of the FTDNA features. The good news is that the fee has now been reduced from $39 to just $19.

There are many advantages to being in different databases because each company has its own unique database and only a subset of people have tested across all three companies. You will therefore pick up matches at FTDNA that won't be found in the other databases.

At Family Tree DNA you can benefit from additional features such as the chromosome browser, which provides a visual representation of the segments of DNA that you share with your genetic cousins. This is a great way of understanding the inheritance process, especially if you are also able to test lots of other family members.

FTDNA offer Y-DNA and mitochondrial DNA tests which means that you can combine the results of all three tests when interpreting your results.

FTDNA also have the advantage of a much more international database than AncestryDNA and 23andMe. They host a wide range of geographical DNA projects. If you have recent ancestry from Devon I would very much like to welcome you to my Devon DNA Project. .

To transfer your results and to find out more click on this link:

https://www.familytreedna.com/autosomal-transfer

There are further details about the transfer program on this page in the FTDNA Learning Centre.


Update
I have received the following e-mail from Family Tree DNA with additional information about the autosomal DNA transfer process.


Dear Project Administrators,
You’ve all been waiting for it, and it’s finally here - transfers for 23andMe© V4 and AncestryDNA™ V2 files!
Here are the details, point by point.
  • Customers can now transfer 23andMe© V4 and AncestryDNA™ V2 files in addition to the 23andMe© V3 and AncestryDNA™ V1 files that Family Tree DNA accepted previously. MyHeritage and Genographic transfers will be supported in the coming weeks.
  • Family Tree DNA still does not accept 23andMe© processed prior to November 2010. A Family Finder test will need to be purchased.
     
  • 23andMe© V3 and AncestryDNA™ V1 now receive a full list of matches and the ability to use the Matrix feature FOR FREE. For only $19, the customer can unlock the Chromosome Browser, myOrigins, and ancientOrigins.


  • 23andMe© V4 and AncestryDNA™ V2 receive all but the most speculative matches (6th to remote cousins), also for free. After transferring, if the customer wants to receive speculative matches, they will have to submit a sample and have a Family Finder run at the reduced price of $59.  
  • Matches should take somewhere between one and 24 hours to appear, depending on the volume of tests in the autosomal pipeline.
  • myOrigins update will be released in the coming weeks. Until then transfers will include only broad populations.
  • Additionally, all previously transferred files that have not been unlocked will receive their matches and have access to the Matrix feature for free as long as the release form is signed. These kits will be also be able to unlock the other Family Finder features for $19. If the transfer was on a kit with another product where the release form has already been signed, then the matches will appear with no further action necessary.
  • The Autosomal Transfer webpage has been enhanced to include a new image and a FAQ section. The FAQ section is displayed towards the bottom of the page.
  • If a customer tries to transfer the same autosomal file a second time, a message will be displayed that the file is a duplicate and will list the kit number of the original kit.
  • The main Autosomal Transfer topic in the Learning Center has been updated. This topic contains the most recent information and now includes all transfer subtopics on the same page. Additional FAQ information will be added to this topic as needed in the future.

Wednesday, 26 October 2016

Family Tree DNA and Assassin's Creed The Movie

Family Tree DNA has teamed up with 20th Century Fox to offer a special DNA testing package which will be promoted with the forthcoming action adventure film Assassin's Creed.

For the duration of the promotion it will be be be possible to purchase a special Assassin’s Creed DNA Testing Bundle for $89 which includes a Family Finder test, a Warrior Gene test and a one-month premium subscription to Findmypast.

There is a also a competition (what they have called a "sweepstakes") to win a trip for two to Las Vegas for an "Assassin’s Creed-themed adventure". The competition appears to be open worldwide but note that the prize only includes domestic flights in the US so if you were one of the lucky winners you would have to pay your own air fare to the US.

The film is released worldwide on 21st December but the tests are available with immediate effect and the competition has already started. Here's the promotion for the Assassin's Creed package.


The Warrior Gene is interesting because it's transmitted on the X-chromosome. At one time Family Tree DNA offered a standalone Warrior Gene test. Jobling et al comment on the Warrior Gene in their article In the blood; the myth and reality of genetic markers of identity (Ethnic and Racial Studies 2016 39(2): 142-161):
The enzyme monoamine oxidase A (MAOA) degrades a subset of neurotransmitters including serotonin, epinephrine, and norepinephrine – molecules that transmit information from one neuron to another. Adjacent to the MAOA gene is a region of DNA that controls how much enzyme is produced, and a common variant of the length of this region (called 3R) leads to reduced production of enzyme compared to other common versions (Sabol, Hu, and Hamer 1998). The gene lies on the X chromosome, so males, who have only one X, show the simplest relationship between the version of the gene they carry and its behavioural consequences. Men carrying the 3R version (the ‘warrior gene’) are more likely to respond aggressively to maltreatment or stress (Caspi et al. 2002). Despite charging almost 100 dollars for the ‘warrior gene’ test, the testing company calls the association between gene variant and behaviour a ‘factoid’, and best used as a ‘cocktail conversation starter’. Nonetheless we might wonder if the results of the test have any influence on the behaviour of people who are tested; the possible influence of the 3R variant was used in 2009 as part of a successful criminal defence in the USA (Brooks-Crozier 2011), and made the difference between thirty-two years’ imprisonment and the death penalty.
See also this excellent article by Adam Rutherford for the New Statesman on Why we can't blame "warrior genes" for violent crimes. (Thanks to Ann Turner for alerting me to this article.)

23andMe and AncestryDNA are already advertising on TV and, as DNA testing goes mainstream, it's important that Family Tree DNA promote their products on mass media to keep up with the competition. So whatever you might think about the Warrior Gene test it's good news that Family Tree DNA are now advertising in cinemas and actively promoting the Family Finder test. This will help to familiarise people with the company name, and perhaps introduce a new demographic to DNA testing who might not otherwise have considered buying a test.

To learn more about the Assassin's Creed package and the competition visit:

https://www.familytreedna.com/assassinscreed

You need to scroll right down to the bottom of the page to find the information about the competition.

Here is the official press release from Family Tree DNA and 20th Century Fox.
Family Tree DNA and 20th Century Fox Team Up for Historical Adventure 
Genetic genealogy pioneers announce exciting partnership with the theatrical release of Assassin’s Creed. 
Houston, Texas — October 25, 2016:

In association with the upcoming theatrical release of the epic adventure film ASSASSIN’S CREED, in theaters December 21, Family Tree DNA is pleased to announce a new partnership with 20th Century Fox and Findmypast, which features the Assassin’s Creed DNA Testing Bundle and Assassin’s Creed Sweepstakes. 
Loosely based on the popular video game franchise of the same name, and starring award-winning actors Michael Fassbender and Marion Cotillard, the movie’s main character Callum Lynch—through a revolutionary technology called the Animus—travels deep into the past to discover that his genetic ancestor, Aguilar, was part of a mysterious secret organization, the Assassin’s, in 15th Century Spain. The action-adventure follows Callum as he relives Aguilar's memories in present day.

As pioneers in the direct-to-consumer DNA testing industry, Family Tree DNA was tapped by 20th Century Fox to be the exclusive testing partner for the film. The company’s premier suite of DNA tests along with the world’s most comprehensive matching database enable users to trace their lineage through time, explore ancestry and connect with relatives across the globe.

Family Tree DNA Director of Product Development, Michael Davila, noted that “The opportunity to partner with 20th Century Fox on the release of Assassin’s Creed is not only exciting but serendipitous. The storyline of Callum Lynch connecting to his ancestral past ties in completely with what our company does in helping people discover their origins and explore family history,” said Davila. 
“We are excited to be partnering with Family Tree DNA,” said Zachary Eller, Senior Vice President, Marketing Partnerships, 20th Century Fox. “They provide a fantastic opportunity to bring the central themes of Assassin’s Creed to a real world application by allowing consumers to actually discover their past.” 
With the purchase of the special limited-time Assassin’s Creed Bundle, customers will be mailed a sample collection kit which, when processed, will provide both Family Tree DNA’s signature Family Finder test and the Warrior Gene DNA test. They will also receive a free one-month premium subscription to Findmypast’s online genealogy service. 
According to Belinda Hanton, Global Head of Partnerships at Findmypast, “We are thrilled to be teaming up with Fox and Family Tree DNA to promote family history research and genetic genealogy. It’s partnerships like this that allow us to speak to completely new audiences and help spread the word that anyone can start exploring their heritage at the click of a mouse. The lives of our ancestors are not only recorded in historical records, but are also written in our DNA and it is now easier than ever before to unlock the incredible stories hidden in our families’ past.” 
Using a simple cheek swab and step-by-step instructions, users return the sample collection test kit by mail, in a provided envelope, directly to Family Tree DNA. Results typically take four to five weeks and are delivered through a private customer dashboard with email notification. Unlike other testing companies, Family Tree DNA results are kept completely confidential and secure privacy settings put users in control of how much information they choose to share.

Family Finder is an autosomal (non-sex) DNA test that finds matches within five generations and includes myOrigins,a powerful mapping tool that provides a detailed geographic and ethnic breakdown of personal genetic ancestry. The Warrior Gene test determines whether a person carries the Monoamine Oxidase A (MAOA) gene variant, dubbed the “Warrior Gene,” which some researchers say may cause certain carriers to engage in more risk-taking behaviors and be able to better assess their chances of success in critical situations. 
Together with the Assassin’s Creed DNA Testing Bundle is the Assassin’s Creed Sweepstakes and a chance to win a Grand Prize trip for two to Las Vegas for an Assassin’s Creed-themed adventure. The experience includes a series of high-octane Assassin’s Creed-inspired activities like a master parkour class, nighttime zip lining and an electrifying sky jump from the tallest tower in the city.

Although no purchase is necessary to enter the contest, purchasing the Assassin’s Creed Bundle earns customers ten additional entries into the Sweepstakes for a greater chance to win a trip to Las Vegas as well as other prizes. Followers will also have the opportunity to earn bonus entries by sharing Sweepstakes social posts on their Facebook and Twitter pages. 
With the exclusive DNA Testing Bundle and Sweepstakes movie tie-in, Assassin’s Creed fans everywhere will be able to jump back in time, embrace their inner warriors and unlock their genetic memories.

“The partnership between Fox’s Assassin’s Creed and Family Tree DNA is a perfect fit,” Davila said. “Test-takers get to find out if they carry the “Warrior Gene” in their DNA, and while they’re at it, will be able to delve into the exciting world of genetic genealogy and discover their own family histories…all through DNA. Everyone has a story to tell…so it’s an absolute win-win scenario.

Tuesday, 24 May 2016

New match thresholds for Family Tree DNA's Family Finder test

As a "trusted blogger" I have been given advanced notice by Family Tree DNA of forthcoming changes to the match thresholds for the Family Finder autosomal DNA test. The changes are to be rolled out very soon once the final quality control checks have been run. An e-mail will be sent out to project administrators in due course. Here are the details I received from Family Tree DNA:
For several years the genetic genealogy community has asked for adjustments to the matching thresholds in the Family Finder autosomal test. After months of research and testing, we will shortly be implementing some exciting changes.

The current matching thresholds – the minimum amount of shared DNA required for two people to show as a match are:

● Minimum longest block of at least 7.69 cM for 99% of testers, 5.5 cM for the other one percent

● Minimum 20 total shared centiMorgans 
Some people believed those thresholds to be too restrictive, and through the years requested changes that would loosen those restrictions.

The following changes will be made to the matching programme.

● No minimum shared centiMorgans, but if the cM total is less than 20, at least one segment must be 9 cM or longer.

● If the longest block of shared DNA is greater than 9 cM, the match will show regardless of total shared cM or the number of matching segments.

The entire existing database will be rerun using the new matching criteria, and all new matches will be calculated with the new thresholds.

Most people will see only minor changes in their matches, mostly in the speculative range. They may lose some matches but gain others.
This is very welcome news. This was a change that many of us had asked for and it's good to know that Family Tree DNA have listened to us.

When setting a cut-off limit it is always difficult to get the balance right between false positive and false negative matches but the previous 20 cM threshold was problematic because all segments right down to 1 cM were included in the total. Family Tree DNA do not currently phase their data before assigning matches (sort the alleles into the maternal and paternal chromosomes) and we know that the vast majority of unphased small segments, particularly under 7 cMs, are false positives.(1) Some people were therefore declared as matches when most of the segments they shared were small pseudosegments, and they were unlikely to share a recent common ancestor. In contrast, some legitimate cousin matches were not showing up because they fell just below the threshold. Under the old system two cousins could potentially share a 15 cM segment but not have enough of the small pseudosegments to make up the 20 cM quota. Anecdotally it has been observed that the 20 cM threshold was a particular problem for people with African ancestry who tend to have fewer of these false coincidental matches on small segments.

Some people were advocating for Family Tree DNA to set the threshold at 7 cMs, but the 9 cM threshold is a sensible compromise. There is still a high false positive rate for unphased 7-9 cM segments, so this will ensure that the reported matches are more likely to be real.

It should also be remembered that, in the vast majority of cases, if you match on a single segment under 10 cMs you will not share a common ancestor within the last ten generations. Even matches of 10 cMs can be very distant.(2) One study found that fewer than 35% of IBD (identical by descent) matches of 10 cMs fall within the last ten generations, and over 30% of segments of this size date back over 20 generations.(3)

I've also noticed in my own data that a lot of the segments in the 7 to 9 cM range seem to fall into large triangulated groups. If these segments are real then this is an indication that they are in what are known as pile up regions. These are regions of the genome where lots of people match because they share the same ethnicity or for some other reason rather than because they share a single recent common ancestor.

Indeed, because of the difficulties in working with unphased segments under 10 cMs many genetic genealogists recommend focusing only on matches who share 10 cMs or more.

I hope to do a comparison of my before and after matches at Family Tree DNA and will be interested to see comparisons from other people, but this is a very welcome and positive change. Thank you Family Tree DNA!

Update
It was not clear from the original announcement but it has now been confirmed that all matches with a total cM count of 20 cMs with a longest segment of 7.69 cMs or more in size will still be reported. Blaine Bettinger has provided a very useful decision tree to clarify the situation in his blog post Family Tree DNA updates matching thresholds. It therefore seems unlikely that many people will lose matches. Note that FTDNA does include all small segments right down to 1 cMs in their match thresholds. Most of these smaller segments, and especially those under 5 cMs are just noise and are best ignored unless you are able to do phasing and very careful chromosome mapping by testing a large number of close family members and known cousins.

Update 25 May 2016
I have received further information about the forthcoming update in an e-mail sent out by Family Tree DNA to all their volunteer group administrators. Here is the relevant section:
We also slightly altered other proprietary portions of the matching algorithm that will, to a small degree, affect block sizes and total shared centiMorgans. These changes should have only marginal effects, if any, on relationships, generally in the distant to remote ranges. 
There’s a separate proprietary formula that is also applied to those with Ashkenazi heritage, but you can, of course, expect to have more new matches than those not of Ashkenazi heritage. 
Please keep in mind this change will not affect close matches, only distant and speculative ones. Some matches will fall off, others will be added. Most people will likely have a net gain of matches. 
Your myOrigins results may change slightly with the rerun, but we have not updated or changed myOrigins yet. We’ll let you know when that happens.

See also

Footnotes
1. See the statistics on false positive matches on the ISOGG Wiki page on identical by descent.
2. See the blog post by Steve Mount on Genetic genealogy and the single segmentOn Genetics, 19 February 2011.
3. See Figure 2 in the paper by Doug Speed and David Balding on Relatedness in the post-genomic era: is is still useful? Nature Reviews Genetics 2015 6: 33-44. 

Saturday, 16 May 2015

Comparing admixture results from AncestryDNA, 23andMe and Family Tree DNA

I have now taken an autosomal DNA cousin-matching test at all three testing companies – 23andMe, AncestryDNA and Family Tree DNA. With this type of test you also get as bonus feature a report of your admixture percentages. I thought it would be a useful exercise to do a comparison of my admixture results from all three companies.

All my known ancestors on all my lines within the last 500 years are from the British Isles. Here is a breakdown on a generation by generation basis:

- All four of my grandparents were born in England. One grandparent was born in Bristol, and my other three grandparents were born in London.

- All eight of my great-grandparents were born in England. Four of my great-grandparents were born in London, two were born in Hampshire, one was born in Bristol and one was born in Gloucestershire.

- I know the birthplaces of 15 of my 16 great-great grandparents and they were all were born in England in the following locations: Berkshire, Bristol (2), Devon, Essex, Gloucestershire, Hampshire, Hertfordshire, London (x 5), Somerset and Wiltshire. My great-great grandparent with an unknown birth location was very likely to have been born in London.

- I know the birthplaces of 24 of my 32 great-great-great grandparents. I have one ggg grandmother who was born in Ireland, and one ggg grandfather who was born in Scotland. My other ggg grandparents were all born in England in the following locations: Bedfordshire, Berkshire (x2), Devon (x2),  Bristol,  Essex, Gloucestershire (x2), Hampshire (x2), Hertfordshire (x3), London (x5), Somerset (x2), Wiltshire. My other eight ggg grandparents are all most likely to have been born in England, probably in Bristol, London and Hampshire.

I am probably fairly typical of someone with ancestry from the south and west of England whose ancestry has been filtered through the melting pot of London.

Here is my Ethnicity Estimate from AncestryDNA. According to the AncestryDNA FAQs (Interpreting my results Q5) the test can "reach back hundreds, maybe even a thousand years, to tell you things that aren't in historical records". In the Ethnicity Estimate White Paper AncestryDNA caution that "Genetic estimates of ethnicity also go back thousands of years, beyond the end of a pedigree paper trail. Regions identified as “populations” in a pedigree may have been very different thousands of years ago, and so may be represented differently in a genetic ethnicity estimate."


Here is the MyOrigins report from Family Tree DNA. The timeframe for the genetic clusters is not given but in the MyOrigins White Paper it is stated that the clusters "span extant modern human genetic variation" but are also "reflective of ancient migrations and admixtures".


23andMe provide the most sophisticated tools. They offer three different Ancestry Composition reports - conservative, standard and speculative. They tell us that these results "reflect where your ancestors lived before the widespread migrations of the past few hundred years".

Here is my conservative estimate:


Here is my standard estimate:


Here is my speculative estimate:


23andMe also provide a chromosome view which shows the breakdown of your admixture across all your different chromosomes. Here is my chromosome view in the speculative mode:

As can be seen, these admixture percentages bear little resemblance to my documented pedigree, and when the companies try to break down Europe into individual countries they come out with quite variable results. It is perhaps only to be expected considering that there is a very limited range of reference populations available. The companies all supplement the publicly available datasets by using samples from their customer databases, but they still only have a very small number of samples from the British Isles. Here is a list of reference samples for Britain and Ireland for each of the three companies.

AncestryDNA reference samples
Great Britain  111
Ireland           138
Source: The AncestryDNA Reference Panel (version 2.0) (available to AncestryDNA customers)

Family Tree DNA MyOrigins reference samples
British      39
Irish         45
Scottish   43

23andMe reference samples
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As can be seen, both Ancestry and Family Tree DNA have very small sample sizes from the British Isles. They have not made any attempt to split the samples into constituent countries. Northern Ireland would be expected to be genetically very similar to Scotland but we don't know if Ancestry's Irish samples are from the north or the south of Ireland or from both countries combined. We don't where in Great Britain their samples were taken from. Family Tree DNA seem to think that Scotland has already separated from Britain and is a country in its own right! In view of this, it is not clear if their British samples also include people of Scottish ancestry or if they now think that Britain only consists of England and Wales. It is also not known if their Irish samples are for people with ancestors from the whole of Ireland or just from the Republic of Ireland.

23andMe have the benefit of a larger dataset but this has not improved the accuracy of their reports, and they have a confusing grasp of geography. They label a cluster as "British and Irish" but describe samples collected from the UK and Ireland. Do they realise that Northern Ireland is part of the United Kingdom? One wonders if customers with ancestors from Northern Ireland described themselves as from Ireland or the UK. It would have made more sense to ask people to define which country within the British Isles their ancestors came from rather than providing two confusing and overlapping options.

In view of these limitations it is therefore not surprising that we often see some bizarre results. For example, it is often the case that Americans come out with much higher percentages of "British" ancestry with these tests than "native" Brits like me. Americans sometimes have surprisingly high percentages of "British" of 80% or more.

The lack of defined reference samples from specific countries within the British Isles also sometimes gives confusing results. I have one project member with seven of his eight great-grandparents born in Wales and one great-grandparent born in Devon. At AncestryDNA he comes out as 64% Irish and 12% Great Britain, 12% Scandinavia and 11% Trace Regions. At Family Tree DNA his ancestry is reported as being 97% from the British Isles and 3% from Finland and Siberia.

There are no doubt problems with the sampling in other countries too which produces similarly misleading results. Joss ar Gall, who writes the Le Gall of Lower Britanny blog, is French and all his ancestry is from Britanny yet, according to his 23andMe test, he is only 19% French. AncestryDNA assigned him with no French DNA at all but found that he was 46% British and 10% Irish. One would expect many similarities between the French and the English but clusters which clearly cross country borders should not be labelled so specifically because people are misled and take the labels too literally.

Admixture tests really need to be used for entertainment purposes only at the present time, and the results should be taken with a very large pinch of salt. However, the tests can sometimes provide useful insights. Generally it is possible to distinguish between populations at the continental level (eg Asian, African and European) provided you're from a population that is not close to a continental border. Admixture from endogamous populations such as Ashkenazi Jews and Finns can also be detected with reasonable confidence. However, it is not possible to distinguish between populations within individual European countries and it may never be possible to do so because our ancestry is so complicated.

Population level comparisons
While admixture results at the individual level are not particularly meaningful there is much more insight to be gained when the results of these tests are compared at the population level.

AncestryDNA have published a few very interesting blog posts with some nice maps comparing the admixture percentages of their British and Irish testers:

- What does our DNA tell us about being Irish by Mike Mulligan, Ancestry blog, 16 March 2015
Exploring our DNA – Europe West by Mike Mulligan, Ancestry blog, 10 April 2015
- AncestryDNA - The Viking in the room by Mike Mulligan, Ancestry blog, 23 June 2015

AncestryDNA also did a similar exercise with their American testers and produced a genetic census of America with a range of maps showing the contribution of the different admixtures to the American population.

Ancestry also provide a useful bar chart which is hidden away in their help menu showing the differences between the various clusters. The chart below shows the differences between European regions. To access the chart click on the question mark in the top right of your screen from your ethnicity estimate page to open up the help and tips menu. Then click on "Why you might have more (or less) from a certain region". There is also a chart which will give you the breakdown for all 26 clusters.


A group of 23andMe scientists published a fascinating paper earlier this year in the American Journal of Human Genetics on The genetic ancestry of African Americans, Latinos, and European Americans across the United States (Bryc, Durand, Macpherson et al 2015).

The future
While these admixture tests will probably never give us all the answers we want, they will no doubt improve over time as better reference samples become available. We are already on the second incarnation of these tests at all three companies and we can expect to see many more improvements in the years to come. I would hope that all three companies will eventually be able to have access to the dataset from the People of the British Isles Project which should give improved estimates for people of British ancestry. It would also help if the reference samples were collected more carefully and with precise countries of origin clearly defined.

This article was updated on 17th May 2015 to include the screenshot of the bar chart from AncestryDNA showing the admixture breakdown within Europe. The article was updated on 18th May to include a mention of AncestryDNA's genetic census of America. The article was updated on 1st January 2017 to include a link to an AncestryDNA blog post on the percentages of Scandinavia DNA found in British and Irish testers.

FURTHER READING
My related blog posts
23andMe
AncestryDNA Ethnicity Estimate
FTDNA MyOrigins
© 2015 Debbie Kennett

Tuesday, 20 January 2015

What is the current size of the consumer genomics market?

The subject of how many people have taken a DNA test is always the source of much speculation, and reliable figures are hard to come by. However, in a report published this week by GenomeWeb Spencer Wells, director of National Geographic's Genographic Project anticipates that "the 3 millionth person" [will] test him or herself during the next few months". In the same article Roberta Estes, who writes the popular DNAeXplained blog, suggests that the three million milestone might already have been achieved. She notes: "23andMe has stated publicly that it has genotyped 800,000 kits, AncestryDNA and the Genographic Project each has genotyped perhaps more than 700,000, and Family Tree DNA has genotyped close to 120,000 people for its Family Finder autosomal DNA offering alone." I thought I would take a look at the available sources for the different companies to see if it might be possible to verify these figures and provide an estimate of the current total.

23andMe
23andMe state in their media fact sheet that they have genotyped more than 800,000 customers.

The 23andMe test is sold in 56 countries of the world. However, I estimate that about 90% of their customer base is in the US. Canada and the UK are currently the only countries where the 23andMe test includes the health and trait reports.

The Genographic Project
The Genographic Project's home page states, as of today's date, that the project has 705,343 participants.

I understood that the Genographic Project kit could be purchased from any country in the world, but from the dropdown menu in their online shop it would appear that the kit is now sold in just 33 countries.

AncestryDNA
AncestryDNA confirmed in August 2014 that they had tested over 500,000 DNA customers. In a presentation given towards the end of last year by Ken Chahine, Ancestry's senior Vice President and General Manager, he stated that AncestryDNA were selling 30,000 to 50,000 DNA kits per month. If we take the middle figure of 40,000 multiplied by six that gives us a figure of 240,000 kits sold since August 2014, bringing the total up to 740,000.

The AncestryDNA test is currently only sold in America, but there are plans to launch the test in the UK, Ireland, Australia and perhaps other countries later this year.

Family Tree DNA
Family Tree DNA provide details only on the number of different types of tests taken and not the total number of customers. According to their website, as of today's date, their stats are as follows:

- 520,257 Y-chromosome DNA records in the database. The Y-DNA database includes 180,005 people who have tested at least 37 Y-STR markers. The FTDNA database also includes several thousand people who have taken the advanced BIG Y test, a comprehensive Y-chromosome sequencing SNP discovery test. FTDNA almost certainly have the largest Y-chromosome DNA database in the world with samples tested at higher resolution than in any other database.

- 190,105 mitochondrial DNA records in the database. The mtDNA database includes 47,849 people who have taken the full mitochondrial sequence (FMS) test. (This test was previously known as the FGS - full genomic sequence test). FTDNA probably have the world's largest database of full mtDNA genomes.

- The number of autosomal Family Finder tests in the FTDNA database has not been publicly disclosed. It is not clear if the 120,000 figure cited by Roberta Estes in the GenomeWeb article mentioned above is an estimate or an actual figure obtained from FTDNA staff, but the number certainly seems to be in line with my own estimates.

FTDNA sell their tests in theory to any of the 200 or so countries of the world. However, they are unable to ship to Iran and Sudan because of customs restrictions.

FTDNA have partnerships with the European company iGENEA and the Middle Eastern company DNA Ancestry & Family Origin. These partnerships have helped to bring in many non-English-speaking customers from Europe and the Middle East, but again many more who will have tested direct with FTDNA.

iGENEA kit numbers are preceded by the letter E. The iGENEA kit numbers in my mtDNA Haplogroup U4 Project go up to kit no. E17977 so it would appear that nearly 20,000 Europeans have tested through iGENEA. Many Europeans will also have tested directly through FTDNA. (It is in fact considerably cheaper to order direct through FTDNA rather than through iGENEA, but iGENEA do have the advantage of a website which is available in French, German, Spanish and Italian.)

The kits from the Middle East are preceded by the letter M. The highest kit with the M prefix that I can find in the large Arab Tribes DNA Project is kit no. 9658 so there are perhaps around 10,000 people who have tested through the FTDNA affiliate in the Middle East.

Family Tree DNA also have partnerships with a number of smaller companies such as DNA Worldwide and Jewish Voice, though these partnerships probably only account for a few thousand kits. For details on the various prefixes see the ISOGG Wiki article on Family Tree DNA kit numbers.

The international diversity of the FTDNA database can be seen in the huge range of geographical DNA projects, which are run by volunteer project administrators from around the world.

Family Tree DNA are the testing partner for the Genographic Project, and all the Geno 2.0 tests are processed in FTDNA's lab in Houston, Texas. Genographic Project participants have the option of transferring their results into the FTDNA database. Genographic Project kit numbers are preceded by the letter N. The highest Genographic Project kit number in the Haplogroup U4 Project is kit number N129937. We therefore know that around 130,000 Genographic Project customers have transferred their results to FTDNA.

Family Tree DNA are the only company who will accept autosomal transfers from other testing companies. They can accept transfers for people who have tested at both AncestryDNA and 23andMe. However, 23andMe transfers can only be accepted if the test was done on the version 3 chip which was sold between November 2011 and November 2013. Kit numbers for the autosomal transfers are prefixed by the letter B. The same prefix is also used for Y-DNA transfers from AncestryDNA and DNA Heritage. AncestryDNA no longer offer Y-STR testing. FTDNA purchased the British company DNA Heritage in April 2011. The highest B kit I can find in my projects is B39616 in the Haplogroup U4 Project, so it would appear that there are getting on for 40,000 third-party transfers in the FTDNA database. Both DNA Heritage and AncestryDNA only ever had quite small Y-DNA databases, and in any case not everyone transferred their Y-DNA results, so I would guess that the majority of the third-party transfers (perhaps in the region of 35,000) are autosomal results from 23andMe and AncestryDNA. It is not clear if the third-party transfers are included in the estimate of the size of the FTDNA Family Finder database or if these transfers are in addition to the autosomal tests processed directly by FTDNA.

It is impossible from these figures to determine precisely how many individuals there are in the Family Tree DNA database because many people who have ordered a Y-DNA test will also have gone on to order a Family Finder test and/or a mitochondrial DNA test and vice versa. The kit numbers probably provide the closest approximation of the number of people in the database. My highest FTDNA kit number is kit number 394825 in the Devon DNA Project. It may well be that the 400,000 milestone has already been passed. If we assume that there are 400,000 FTDNA kits, 130,000 Genographic transfers, 20,000 iGENEA kits, 10,000 kits from FTDNA's Middle Eastern partner, and 5,000 miscellaneous kits, we get a figure of 565,000 which is probably a reasonable estimate of the number of individuals in the FTDNA database.

Other companies
In addition to the big four companies there are a number of other smaller companies such as BritainsDNA, Oxford Ancestors and GeneBase which sell genetic ancestry tests direct to the consumer. A full list of DNA testing companies can be found in the ISOGG Wiki. However, none of these smaller companies disclose the size of their databases, and many of the people who've tested with the smaller companies have retested with one of the big four companies. I hesitate to estimate the number of people tested with these different companies but I do not think the figure can be more than 50,000 and is very likely to be much less than this.

What is the total?
To sum up, the total number of individuals tested at each of the four big companies is as follows;

Genographic Project  705,343
23andMe                    800,000+
Family Tree DNA      565,000 (DK estimate)
AncestryDNA            740,000 (DK estimate)

If we add all these figures together we get a total of 2,810,343. However, this figures makes no allowance for the significant overlap in the four databases as there are many people who have tested at multiple companies. For example, I've had my own DNA tested at 23andMe, Family Tree DNA and AncestryDNA. We can subtract the 130,000 people who have transferred their Genographic results to FTDNA and we can perhaps estimate that about 35,000 people have transferred autosomal DNA results to FTDNA.  That brings the total down to 2,645,343. There is probably more overlap than I've allowed for, but it does seem very likely that there are currently around two and a half million people in the world who have paid for a DNA test with the big four companies. It will be interesting to see what these figures look like this time next year.

© 2015 Debbie Kennett