Interview with Your Genetic Genealogist - Broadcast to over 50 million Japanese households

They came all the way from Japan to interview a handful of people from Stanford, Illumina, the FDA, the American Society of Genetic Counselors and...you guessed it,  me!  :-)

Earlier this month producers and crew from NHK Japan Broadcasting Corporation came to my home to tape a segment on personal genomics. (NHK is similar to PBS or the BBC.) The story is for a weekly news/documentary program entitled, CLOSE-UP TODAY. The entire program on one Saturday will be dedicated to genetic testing with a focus on DTC genetic testing.  As I understand it, the goal for this segment is to educate the Japanese public on DTC testing. I expect it to be a well rounded show since they were planning on interviewing the FDA, Illumina, physicians at Stanford University, a genetic testing company and genetic counselors. There will be some interviews with Japanese doctors and patients in the program as well. 

DTC genetic testing is still very rare in Japan, but there are companies starting to offer genetic tests to consumers there. They told me that the Japanese people tend to be pessimistic and give up easily when it comes to illness. In Japan, until recently, doctors and family members didn't even tell a person that he/she is terminally ill. Many Japanese people are concerned about getting a genetic test and feel they will be worried about their health all the time and get depressed if they find out they are at higher risk for certain diseases. Apparently, some Japanese physicians are also concerned about how to deal with genetic test results. The producers feel that consumers who take DTC tests need to know how to deal with their results and physicians also need to be trained to work with patients who come to them with test results. They want to encourage the Japanese public to be more positive and proactive in dealing with medical issues. 

The producers intend to show what the DTC genetic testing market is like in the US and demonstrate how Americans can be positive and proactive in dealing with test results, as well as what the experts are saying. They plan on using screenshots from my 23andMe account on air and I walked them through the large amount of health information and resources available from 23andMe. We also discussed some of the actions that I have taken due to my genetic test results.

They were here for a number of hours and we had a very enjoyable afternoon.  I don't know how much of it will make it past the editing room, but we had the opportunity to film a lot of really positive, constructive information. I, of course, could talk about this subject for hours! By the time we were finished, it seemed that all my visitors were interested in testing themselves. In fact, the director even offered to buy one of my unused 23andMe kits!

The show is scheduled to air on March 7th, but that could change depending on foreign affairs at that time. I wish I could ask all of you to watch it, but since I don't think many of my readers are in Japan, it would be in vain.  I have been promised a copy of the show and hope to be able to share it with you all at a later date.

FTDNA hits 5000 "likes" on Facebook and offers a fantastic discount!

This morning the FTDNA page on Facebook reached 5000 "likes" and, as promised, they are offering a one-day coupon for 40% off (for new kits only except Family Finder)). This is the best discount I have ever seen on Family Finder. It is only available for for 24 hours, so order now if you have been wanting to test, but haven't done it yet!

"Congratulations! You have earned a 40% discount any of these tests:

Y-DNA37 (now only $93.40 including shipping if ordered through a project)
mtDNAPlus (now only $99.40 including shipping if ordered through a project)
mtDNAFullSequence 
Y-DNA37+mtDNAPlus
Family Finder (now only $173.40)
Family Finder+mtDNAPlus
FamilyFinder+Y-DNA37
Comprehensive Genome
Warrior Gene
Family Finder add-on to any existing kit (now only $173.40)

The coupon code is 5000FACES. This is only valid for new kits and can't be used on existing kits. Enter the code while ordering at FTDNA. It expires 24 HOURS from now!"

*Update - Kits can even be ordered through projects which already have about a $10 discount (Thanks to BarB A for the info!)

[Disclosure - My company StudioINTV has an existing production agreement with FTDNA that has no bearing on the opinions I express. I also receive a small commission from FTDNA on non-sale orders through my affiliate link, which I use to fund DNA tests. I receive no other compensation in relation to any of the companies or products referenced in my blog.]

FTDNA's Family Finder Gets a New Chip!

Today there was great news for the genetic genealogy world from FTDNA! They have announced that they are converting their autosomal DNA "Family Finder" test to the Illumina platform:

We are changing to the Illumina Omni platform. As part of that change, all Family Tree DNA customers who previously ordered and paid for a Family Finder test will be retested for FREE. The new microarray chip for our Family Finder test is the Illumina OmniExpress. It tests about 710,000 unique autosomal DNA SNPs.

The stated motivation for this change was "better potential for future upgrade options." On top of their customer service, as always, FTDNA has already answered many of the common questions in their new FAQs, so I will just cover the highlights:

1. 710,000 SNPs, which is approximately 200,000 more than the old Affymetrix chip
2. Free upgrade for all existing customers (those who request it will be first)
3. Those who sign up for the conversion by Wednesday, February 16th can expect results within 2 to 3 weeks, while converting the entire existing database is estimated to take 6-8 weeks
4. Existing Family Finder results will continue to be available until everyone has been converted 
5. Still $289, no subscription required
6. All currently in process and future orders will be on this platform
7. Not expected to have a significant change to current matches and/or Population Finder
8. In most cases, a new sample will not be required
9. Instructions to request the upgrade:
  a. Login to your FTDNA account. (https://www.familytreedna.com/login.aspx) If you are a project administrator, you will need to log in using the kit number, not your admin account.
 b. Look for the text box that says “Message From Family Tree DNA! Family Tree DNA announces updates to the Family Finder test! Click here to sign up for a FREE conversion!”
 c. Click on the Click here to sign up for a FREE conversion! link.
 d. Complete the form to sign up.

From what I can tell, this seems to be the same basic Illumina OmniExpress chip that 23andMe is currently using, minus the ~300,000 enhanced and custom SNPs that were added to their version. Since these custom SNPs were likely chosen based on significance for health related interpretations, the ancestry portion should be quite comparable. In fact, the best part of this new development is that this will facilitate the very real potential of cross-company transfers. FTDNA has expressed their intention and desire to accept 23andMe raw data uploads for inclusion in their database, but previously was unable to offer this option due to the incompatibility of the Affymetrix chip versus the Illumina chip (lack of overlapping SNPs). This news should change that and, if the price is right, will result in a greatly increased database for comparisons. It will be interesting to see if 23andMe will also allow for Family Finder raw data transfers into their already large Relative Finder database. It would give their ancestry division a needed boost with an influx of primarily genealogically-minded individuals.

The original Illumina OmniExpress Chip was introduced in January 2010 and enhanced in March. Since the FTDNA version of the chip has close to the original's reported 733,202 SNPs, this is most likely the one that is being used.

Information on this chip (before enhancements) from the press release:

• Premiere Genomic Coverage - Greater than 700,000 strategically selected tagSNPs provide genomic coverage up to 90% for Caucasian and Asian populations as assessed by the International HapMap Project.
• Proven Data Quality - Industry-standard Infinium HD Assay affords greater than 99% average call rates and greater than 99.9% reproducibility.
• Industry Best Throughput - With the iScan System, researchers can process in excess of thousands of samples per week. 

There is a downloadable list of the 733,202 markers on the original Illumina OmniExpress Chip here. As I have noted before, I am not an expert on these chips, so I will wait until some of our more technical friends make the final call on the overlap, but I do anticipate that it will be significant.

This was clearly a good move on the part of FTDNA. I hear that in the two hours after the announcement (starting at 10:30am) the number of people who requested to convert to the new chip was nearly 1,500 and was up to 2,000 by 5 pm.

Things just keep getting better and better for genetic genealogy!


[Disclosure - My company StudioINTV has an existing production agreement with FTDNA that has no bearing on the opinions I express. I receive no other compensation in relation to any of the companies or products referenced in my blog.]

23andMe Relative Finder Update

The latest sale at 23andMe appears to have breathed new life into Relative Finder. This morning I have 30 new predicted relatives in my Relative Finder, my sister has 35 and my niece has 42!  In the seven accounts that I handle each has at least 15 new relatives and most of them have close to 30. Many of the new matches are shared between us, but there are at least 100 unique new individuals. My mother even has three new predicted 3rd cousins! Let's hope these new recruits are interested in genealogy!
(It looks promising so far since I have already received a number of acceptances from my sharing invitations.)

A comparison of my 23andMe mtDNA v3 and v2 results

There are 13 false positive SNPs that are being found in practically everyone's v3 mtDNA results. No doubt, 23andMe will soon remove them as they are aware of the problem. This post will ignore those since they are clearly in error.

As I mentioned yesterday, my reported mtDNA subclade did not changed in my v3 results and is correct - U5b1b2. According to an analysis done by Dr. Ann Turner of my mtDNA data, there are 795 new SNPs in my v3 results, of which 99 are no-calls for me. I had 28 no-calls out of 2133 SNPs in v2 of the chip. 21 of those had calls in v3. The higher rate of no calls on the v3 versus the v2 is because many of the news SNPs are experimental. If it becomes evident that people are getting no-calls for the same SNPs, the list may be pruned by 23andMe to eliminate them.

All SNPs where calls were made in both chips gave identical results.

I have one miscall 16192C, where I have a mutation 16192T. This also occurred in v2 of the chip (and also in my cousin).  According to Dr. Turner, "It is probably due to the fact that it is very close to the poly-C region surrounding 16189. The probes just don't work well in repetitive regions like that. (Side note: 16189C is a very common mutation, so Mother Nature has a bit of a problem there, too!)."

Here is a list of my CRS values:

16184	C
16185	C
16186	C
16187	C
16188	C
16189	T
16190	C
16191	C
16192	C
16193	C

Thank you to Dr. Turner for her generous time and efforts to help all of us to better understand our mtDNA and 23andMe results.

To read more about my mtDNA tests, you can see my post about my Full Mitochondrial Sequence (FMS) test from FTDNA here.

Update on 23andMe's v3 results: Relative Finder comparison and ~30,000 v2 locations missing from v3

This will not be a scientific analysis, but, rather a preliminary summary of what I have found so far in my new 23andMe v3 results. My v3 Relative Finder matches loaded this morning and I have done a quick comparison to my v2 Relative Finder. There are some minor changes, but nothing that appears to be too significant.

(all are predicted)                         v3        vs       v2
3rd Cousins                                          4                     4
4th Cousins                                        38                   40
5th Cousins                                       262                 258
Distant                                                 33                   32
Public Match - 4th Cousins               3                     3
Public Match- 5th Cousins               10                   13

% DNA shared 
mother                                           50.00              50.42
sister                                               53.10              53.69
paternal uncle                               21.10              21.14
maternal aunt                                22.61              22.77
niece                                                24.31              24.49
1st cousin                                        11.45              11.36
1st cousin                                        11.95              11.94
1st cousin                                         8.38                8.37
1st cousin once removed               3.12                3.12
1st cousin twice removed              1.42                1.42
2nd cousin                                        1.15                1.15

Upon a brief initial review, predicted cousins lower than this appear to overwhelmingly share the same percentage as before.

Jim McMillan, who runs the independent "Cousins" matching project, compared my raw v2 data file to my raw v3 data file and this was his conclusion,

"There are at least 30,346 locations that are in v2 that are not included in v3.  So when a v2 is compared to a v3 there are going to be some longer half-identical segments that might not be there when comparing a v2 to a v2."

He also posted on his project thread on the 23andMe Forum:

"I have received v3 results from a contributor who also contributed v2 results. About 30,000 locations that appeared in v2 are missing from v3. Thus, when a v2 data set is compared with a v3 data set, it would be expected that the half-identical segments would be a little longer, and more segments meeting a 5cM and 700 SNP threshold found. All my software tolerates different numbers of SNPs. Where no SNP is found, it is deemed the SNPs would be at least half identical. On first blush, the missing SNPs do not appear to be evenly distributed among chromosomes 1-X.

In Chromosomes 1-x there are 30337 locations missing, and in Y 250, and in MT 172.

I have uploaded to box.net the locations in v2 that are missing in v3. See the details in the zipped spreadsheet at http://www.box.net/shared/b4shehl2qn."

I just received a Twitter message from 23andMe that the v2 SNPs were not removed intentionally. It explained (with some humor), "...some faction always falls out during chip manufacturing process. Biology is messy."

As I mentioned on my blog last night, my Ancestry Painting is still 100% European. However, from a review of the forums, the Ancestry Painting algorithm seems to be much improved for many.

Some customers are seeing improved updates to their haplogroup assignments, however there seems to be a problem with errors in the mtDNA mutations being reported from the new v.3 raw data.  They differ from the FMS results that some of us have received from FTDNA. I will post more information on this as it becomes available.

I am still working on getting details on the new SNPs. Hopefully 23andMe or one of the independent project admins will soon comment on the hundreds of thousands of new SNPs, since that is the most significant change and on what we should be focusing. I hear there is a Spittoon Blog Post on the way. More to come...

Update: 23andMe's New v3 Chip Results Are In

Today there is a lot of excitement in the personal genomics community because 23andMe's eagerly awaited v3 results are finally coming in. The customers receiving their results today are ones who bought their kits near the beginning of the last holiday sale. Making it even more exciting is that, according to 23andMe, they are loading thousands of data sets today in this first round. Apparently, they had a very good response to the last sale. This is very good news for customers who are interested in the ancestry aspects of their genetic scans. Judging from this, over the next month, the number of potential "cousins" should jump substantially from the approximately 60,000 records already in their database.

So far, my health results, Ancestry Painting and U5b1b2 mtDNA haplogroup assignment look identical to my v2 results. I am still waiting for my Relative Finder and Ancestry Finder to load. However, I am hearing that some customers have revised and, apparently, improved Ancestry Paintings as well as updated haplogroup assignments.

Giving a little insight into what changes we can expect, Michelle K from 23andMe posted this in the 23andMe Forums on January 19th:

"The first batch of v3 results will become available by the end of this week. Please note that v2 data will not be overwritten by v3 data, rather the two will be merged into one data file. Here are some changes you can expect to see:

RelFinder and Family Inheritance: The Relative Finder algorithm has been updated. Customers who upgrade to v3 may notice small changes to their percentages DNA shared or segment locations in Family Inheritance. Existing, not-yet-upgraded customers may also see small changes to their results as their relatives upgrade.

Ancestry Painting: The Ancestry Painting algorithm has been updated. Upgrading customers may notice small changes to their percentages. Existing, not-yet-upgraded customers will not be affected.

Haplogroups: Upgraded v3 customers may see a slight change in their haplogroup due to updated haplogroup trees and v3 compatibility. The change, if any, should be very minor -- only affecting resolution and not affecting major group assignments. All other existing customers will have their haplogroups recomputed on the new trees later this year. This means, for example, if a child is analyzed on v3 and their parent is on v2, they may have different haplogroup assignments.
Raw data: Upgraded v3 customers may have data for v2 SNPs they previously had no-calls for, if the SNP is on v3 and it yielded data. A complete list of v3 SNPs is expected to be available in the Mendel example profiles by mid-February."

I will be posting all week with updates about the new v3 results, so stay tuned...