Family Tree DNA's Latest Updates

Family Tree DNA made many genetic genealogists very happy with their updates last week. I wasn't expecting to see anything new from them for at least two weeks, but they are already releasing another update today. I am extremely encouraged by the wonderful progress that Family Tree DNA is making toward giving its customers exactly what they have been asking for. With these wonderful improvements, they are demonstrating that they really are listening to what we want and need. Thanks again, FTDNA!

These changes are scheduled to go live today.

Rebekah Canada tells us:

Weekly Information Technology/Engineering Update (10 Dec 2013)

Matches Maps Locations Clear Button

Some users have requested the ability to clear their stored map coordinates for their most distant known maternal or paternal ancestors. We have added a Remove Location button to Step 3 of the Update Most Distant Ancestor’s Location wizard.

Family Tree DNA myFTDNA BETA Family Finder – Matrix

Today, we are happy to release our new BETA Family Finder – Matrix page. The Matrix tool can tell you if two or more of your matches match each other. This is most useful when you discover matches with wholly or partly overlapping DNA segments on the Family Finder - Chromosome Browser page. 

Due to privacy concerns, the suggested relationship of your two matches (if related) is not revealed. However, we can tell you whether they are related according to our Family Finder program. To use it, you select up to 10 names from the Match list on the left side of the page and add them to the Selected Matches list on the right side of the page. A grid will populate below the lists. It will indicate whether there is a match (a blue check mark) or there is not a match (an empty white tile).
 

You access the BETA Family Finder – Matrix page through the Family Finder menu in your myFTDNA account.

The page starts out with two list areas: Matches and Selected Matches. You add Matches to the Selected Matches list by clicking on a name and then on the Add button.

Here is a screenshot of the BETA Family Finder – Matches page with a few matches added to the Selected Matches list. 

23andMe Releases a Sample of Their New V4 File: First Look and Analysis

23andMe has released access to a sample file of their new v4 chip. This is a 100% custom chip with hand-selected SNPs. In a departure from the other two companies offering autosomal DNA testing to the genealogy community, they are now using the Illumina iSelect chip as the foundation instead of the Illumina OmniExpress chip. On the new v4 chip, the total number of autosomal DNA and X DNA SNPs has decreased substantially, while the total number of mtDNA SNP and Y-SNPs has increased.

Since I heard about this new chip, I have been concerned about the impact it will have on the genetic genealogy community and, particularly, on the compatibility with 3rd party uploads and tools. If 23andMe customers are unable to take advantage of the extremely beneficial opportunity to upload their data into Family Tree DNA's Family Finder database and to make use of the wonderful tools at GEDmatch, that would be a huge loss for all of us. It would also be a shame if the usefulness of the Y-SNPs and mtDNA SNPs tested by 23andMe is reduced for our community. To try to determine if this will be the case, Dr. Tim Janzen has helped me to analyze the new file overall and Larry Vick has specifically analyzed the Y-SNPs.

The v4 chip currently has just over 602,000 total SNPs versus 967,000 total SNPs on the v3 chip. This chip is not as robust as the chip previously used by 23andMe or the chips used by Family Tree DNA and AncestryDNA for the autosomal and X-SNPs.This is of great concern, but 23andMe has stated that they plan to impute a large number of SNP allele values from our results (see comments at http://blog.23andme.com/news/23andmes-new-custom-chip/), so hopefully Family Tree DNA and citizen scientists will be able to do the same to extract the most utility and compatibility from this platform. I am continually surprised and amazed by the resourcefulness of our community, so I am hopefully optimistic.

This change in platforms was intended to help the company ramp up their processing capacity in conjunction with their massive marketing campaign to acquire one million customers and beyond.  (They can run 24 samples on each v4 chip at once instead of 8 on each of the v3 chips.) Especially in light of 23andMe's recent decision to provide ancestry-related interpretation and raw data exclusively, the v4 chip does not appear to be a beneficial development. In fact, it may result in additional loss of sales. Currently, the genetic genealogy and the DNAAdoption communities generally recommend first testing at 23andMe and then transferring the raw data into FTDNA's Family Finder database in order to be in two databases at a reduced price. If it turns out that FTDNA is unable to continue to accept 23andMe transfers, these recommendations will likely change. Loss of compatibility with Gedmatch would also have a very detrimental effect on the utility for those using the data for genealogical and admixture research.

The following analysis is in depth and intended for those who want the specific details of the changes. Instructions to download the v4 file will follow the analysis.
 
First let's look at the Y-SNPs.

Larry Vick tells us:
I compared my Y-SNP file I downloaded on 14 Aug 2012 to the Y-SNP file I downloaded today to see if my current file has any changes. There weren't any.  I then compared the (v4) file for Greg MENDEL that I downloaded today to a v3 file I downloaded for a friend (CRL) on 21 Mar 2013.

There are 2,329 Y-SNPs in the Greg MENDEL v4 file. CRL had 1,766 Y-SNPs in his v3 file. So the v4 file has 562 more SNPs than CRL's v3 file. Looking at the SNPs, there were 446 in CRL's v3 file that were not in the MENDEL v4 file. There were 1,009 in the MENDEL v4 file that weren't in the CRL v3 file. Of the 446 in the CRL v3 file that weren't in the MENDEL v4 file, 314 were no calls.

Of the 1,009 in the MENDEL v4 file that weren't in CRL's v3 file, 295 were no calls. When I compared the 1,009 in the MENDEL v4 file to my file I downloaded today, 494 were not in my file (although they could have been in past downloads but were removed prior to today's download). I have SNPs from v1, v2, and v3. Of the 515 that were in my file, 99 were no calls.

I compared the 494 that were not in my file to Adriano's file in the Y-Chromosome Comparison Project, and 268 were in his file. All but one of those 268 had i prefixes for the reference sequence number.

I then compared the 226 that weren't in Adriano's file to the ISOGG Y-SNP Compendium by position number (build 37), and 200 were in the ISOGG file. I created a list of those 200 with the first note field. The 26 that weren't in the ISOGG file included the one SNP with an rs number (rs5603911). The MENDEL file had 46 no calls for the 200 SNPs in the ISOGG file. All but one of the 226 that weren't in Adriano's file had i prefix reference sequence numbers.


Now let's look at the overall composition of the new v4 chip as compared to the other platforms.

Tim reviewed the v4 file and compared it to v2, v3, and FF files. The following are some general statistics on which he based his analysis.

atDNA SNPs
v2: 
561,846 atDNA SNPs in 23andMe v2 data in a 2009 download.
515 i atDNA SNPs in 23andMe v2 data in a 2009 download.
556,787 atDNA SNPs in 23andMe v2 data in a fresh download.
758 i atDNA SNPs in 23andMe v2 data in a fresh download.

v3:
930,381 atDNA SNPs in 23andMe v3 data in a fresh download.
7,455 i atDNA SNPs in 23andMe v3 data in a fresh download.

v4:
577,382 atDNA SNPs in 23andMe v4 data.
41,855 i atDNA SNPs in 23andMe v4 data.

Family Finder:
708,092 atDNA SNPs in Family Finder data in general, but a fresh download only had 707,269 SNPs in it.


Y-SNPs
v2:
1880 Y SNPs in 23andMe v2 data in a fresh download. Of these 213 are i SNPs.

v3:
1766 Y SNPs in 23andMe v3 data in a fresh download. Of these 232 are i SNPs.

v4:
2329 Y SNPs in 23andMe v4 data. Of these 526 are i SNPs.


X-SNPs
v2:
13,876 X SNPs in 23andMe v2 data in a 2009 download. Of these 19 are i SNPs.
13,828 X SNPs in 23andMe v2 data in a fresh download. Of these 96 are i SNPs.

v3:
26,007 X SNPs in 23andMe v3 data in a fresh download. Of these 1006 are i SNPs.

v4:
19,487 X SNPs in 23andMe v4 data in a fresh download. Of these 4227 are i SNPs.

Family Finder:
18,022 X SNPs in Family Finder build 37 data in a fresh download.


mtDNA
v2:
2019 mtDNA SNPs in 23andMe v2 data in a fresh download. Of these 1572 are i SNPs.

v3:
2459 mtDNA SNPs in 23andMe v3 data in a fresh download. Of these 2016 are i SNPs.

v4:
3154 mtDNA SNPs in 23andMe v4 data. Of these 2681 are i SNPs.


Here are his comparisons between the various platforms.

atDNA:

• 453,854 atDNA SNPs in 23andMe v4 data are also found in 23andMe v2 data in a 2009 download. Of these SNPs, 419 are i SNPs. 

• 453,357 atDNA SNPs in 23andMe v4 data that are also found in 23andMe v2 data in a fresh download. Of these SNPs, 546 are i SNPs. 

• 509,630 atDNA SNPs in 23andMe v4 data that are also found in 23andMe v3 data in a fresh download. Of these SNPs, 6153 are i SNPs. 

• 304,864 atDNA SNPs in 23andMe v4 data that have rs numbers are also found in Family Finder in a fresh download. 

• I then checked the 41,855 i atDNA SNPs in 23andMe v4 data and checked for matching positions in the Family Finder data. I found that there were 2556 i atDNA SNPs in 23andMe v4 data that had matching positions in the Family Finder data.

• Assuming that all of those matching positions correspond with the same SNP in the Family Finder data, there are a maximum of 307,420 atDNA SNPs in 23andMe v4 data that are also found in Family Finder in a fresh download. 

Y-SNPs:

• 979 Y DNA SNPs in 23andMe v4 data that are also found in 23andMe v2 data in a fresh download. 

• 1320 Y DNA SNPs in 23andMe v4 data that are also found in 23andMe v3 data in a fresh download.

• This means that there are 1009 Y SNPs found on the v4 chip that aren’t found on the v3 chip. 

• There are 563 more Y SNPs in v4 data than in v3 data. 

X-SNPs:

• 11,070 X SNPs in 23andMe v4 data that are also found in 23andMe v2 data in a fresh download. 

• 11,009 X SNPs in 23andMe v4 data that are also found in 23andMe v2 data in a 2009 download. 

• 14,437 X SNPs in 23andMe v4 data that are also found in 23andMe v3 data in a fresh download. 

• 7,513 X DNA SNPs in 23andMe v4 data that are also found in Family Finder in a fresh download.

mtDNA:

• 1698 mtDNA SNPs in 23andMe v4 data that are also found in 23andMe v2 data in a fresh download. 

• 2208 mtDNA SNPs in 23andMe v4 data that are also found in 23andMe v3 data in a fresh download. 

• This means that there are 946 mtDNA SNPs found on the v4 chip that aren’t found on the v3 chip. 

Tim's preliminary conclusions
The fact that there are only 307,420 atDNA SNPs in 23andMe v4 data that are also found in Family Finder is highly concerning. The specificity of matches when comparing v4 data to FF or AncestryDNA data will be significantly reduced in projects such as my Mennonite autosomal project. At DNA SNP coverage for the overlapping SNPs between v4 data compared to FF or AncestryDNA data will only be about 44 SNPs per cM. I don’t know if FTDNA and GEDmatch will be able to allow imports of 23andMe v4 data. The fact that there are about 130,000 more atDNA SNPs in a Family Finder dataset than in v4 and the fact that v4 data won’t be readily uploadable to GEDmatch is forcing me to rethink 23andMe as my primary testing lab for distant relatives.


Third Parties and Download
My sincere hope is that Family Tree DNA and GEDmatch are able to adjust their systems to work with this new data from 23andMe. As soon as I hear anything, I will be sure and report it.

If you are interested in analyzing the file yourself and you have a 23andMe account, these are the directions for downloading the sample v4 file from 23andMe:

Enable the Mendel family in your account here:
https://www.23andme.com/user/edit/examples/

Then select Greg Mendel's raw data file from the drop-down list here:
https://www.23andme.com/you/download/

This file will probably still change slightly as they complete their validation process, but it should be pretty close to what we will start to see for new customers at 23andMe in the coming weeks.

Please let me know what you think. I am especially interested to hear analysis from the citizen scientists and the creators of our community's third party features. 

FTDNA Releases Updates in Response to Requests from Project Administrators

I received an email from Bennett Greenspan, CEO of Family Tree DNA, today with some very welcome news! FTDNA is not wasting any time making good on the promises that they made at their conference last month. Obviously, they really were listening to us! (Take a look at #6...this is a very important update that will make a lot of genetic genealogists happy!)

Today we are releasing some great updates that were requested during our 9th International Conference on Genetic Genealogy.  Here is a quick summary with some screen shots of what to expect.

1. The timeout for myFTDNA has been increased from 30 min to 2 hrs. This will benefit everyone but will especially be appreciated by our Group Admins when they are impersonating into a kit.

2. Changed the word "Triangulation" to "Common Matches" for Family Finder matching. 

3. Instead of using the word "Steps" on the matching pages we will now use "Genetic Distance." This will effect both the Y-DNA and mtDNA matching pages.

4. Fixed the Interactive Tour.  It was getting stuck at the Family Finder section, but will now complete.

 

 5. Updated the Profile Pop up on matching pages with a new design and restored the "About Me" section and badges. This profile is available on all matching pages:  Y-DNA, mtDNA, Family Finder, and Advanced Matching.

 
6. Added the ability for a user to download chromosome browser data for all of their matches. This new option is towards the top right side of the chromosome browser page and will be in Excel format.

These features are already live, so go check them out! I am told that there will be more updates every two weeks, so I'm really looking forward to seeing what they release next (on or about December 18th). Thanks, FTDNA!