Saturday, 9 November 2013

The new Big Y Test from Family Tree DNA

Family Tree DNA have just announced at their conference the introduction of a new Y-chromosome DNA test to be known as the Big Y. The new test uses next generation sequencing technology which is much more reliable for the Y-chromosome than the chip testing used for the Geno 2.0 test from the Genographic Project and the Chromo 2 test from BritainsDNA. The Big Y is intended as a replacement for the Walk through the Y test which used the slower and much more expensive Sanger sequencing technology.

The Big Y test covers 10 million base pairs. It will provide results for almost 25,000 of the known Y-SNPs. However the exciting part is that this test can also be used for SNP discovery, opening up the tantalising possibility of finding SNPs that will prove to be unique to a particular surname lineage or an individual branch of a family tree.

The introductory price of the new test is $499 (£311). The selling price from 1st December will be $695 (£434). The test currently only seems to be available to existing customers, but it may that the FTDNA home page hasn't yet been updated. There is now a new splash page on the personal pages of male FTDNA customers.
People who have ordered the old Walk through the Y test will receive a voucher giving them an additional $50 off the cost of the new test. The new voucher (coupon) will be available on personal pages from Monday.

No doubt further information will be forthcoming in due course from the people who have attended the conference. It has been possible to pick up quite a bit of the news from the conference tweets (search on Twitter using the hashtag #FTDNA2013).

Details of all the other currently available SNP tests can be found on the ISOGG Y-SNP testing comparison chart. This will now need to be updated to include details of the new Big Y test.

In other news from the conference it would appear that the Genographic Project will be introducing a new Geno test within the next seven to 12 months. It may be that the next Geno test will also use next generation sequencing technology.

Updates
A set of FAQs on the Big Y test are now available on the FTDNA website at: www.familytreedna.com/faq/answers.aspx?id=27

The ISOGG Y-SNP testing comparison chart in the ISOGG Wiki has now been updated to incorporate details of the new Big Y test.

Roberta Estes has advised on her blog that results from the Big Y will be delivered in 10-12 weeks and the results will be accompanied by comparison tools. See her blog post here.

Jennifer Zinck has provided a very nice detailed summary of the first day of the FTDNA conference with further information on the talk on next generation sequencing by David Mittelman, FTDNA's new Chief Scientific Officer, in which the new Big Y test was announced. Click here to read Jennifer's blog post.

CeCe Moore has blogged briefly about the Big Y test. Most importantly she has received confirmation from David Mittelman of  Family Tree DNA that Big Y customers will be able to download their raw data files on request.

See my blog post on The Family Tree DNA Conference 2013 for a compilation of all the blog posts and other coverage from the conference.

Related blog posts
- The Big Y roll out - the SNP tsunami is on its way!
- A confusion of SNPs
- The Y-chromosome interpretation service from YFull.com

34 comments:

Kelly said...

Debbie,
I am following the Twitter feed as well. just wondering if the possibilities of finding New SNPs will make this a viable alternative to the Full Y test.
Kelly

Debbie Kennett said...

There are almost 60 million bases in the full Y chromosome sequence but about half of the Y might never be sequenced because it has lots of impenetrable repetitive regions. The full Y from Full Genomes covers about 27 million bases. The FTDNA test covers about 11 million bases. With the Full Genomes test there's supposed to be one new SNP every 60-90 years. If we extrapolate down from that perhaps we might expect one new SNP every couple of hundred years with the Big Y test as it has less than half the coverage. That would actually work very well for genealogical purposes. However, I'm only guessing and the real test will come when the results start to come through. It's certainly more affordable than the Full Genomes test and I would feel happier having the test done at FTDNA which is an established company with a good infrastructure. I shall be interested to hear what all the haplogroup project admins think.

What I would still like to see is a cheap SNP test so that people can just find out which subclade of R1b they belong to.

Kelly said...

Thanks Debbie.I am seeking feedback from multiple sources and will certainly share whatever I find out. I have been impressed with Full genomes so far aside from their time delays. If they switch to using UCL and/or domestic providers I will be even happier.

Anonymous said...

For $1250 Full Genomes includes 27 million bp coverage, 300 Y-STRs in their test as well as full mtDNA sequence.

So let's do the math:
$495 BigY (10 million bp coverage)
$199 mtDNA full sequence
$395 yDNA 111 STRs
------
$1,095 FTDNA

Full Genomes has the edge IMHO.

I hereby dub the new product the bigWHY?



Vince T. said...

Quoted from the product splash screen: "10 Million base-pair coverage - more than any other Y-DNA test on the market."

Full Genomes Corp. has sequenced 20 to 25 million base pairs per each sample. My own FGC test had reported calls for slightly over 25 million positions. It has been estimated that about 13-15 million of those are viable, belonging to non-recombining regions.

Has FTDNA actually done adequate market research?

Vince T. said...

Anonymous said:
"For $1250 Full Genomes includes 27 million bp coverage, 300 Y-STRs in their test as well as full mtDNA sequence."

That 27 million was misquoted from me, and should have been reported at 25 million.

Jacques Beaugrand said...

and do they give us the result as raw data and in terms of AGTC for each of these 25,000 positions?

Anonymous said...

"Jacques Beaugrand said...
and do they give us the result as raw data and in terms of AGTC for each of these 25,000 positions?"

Who knows?
Where is the list of the 25K SNPs?
Where is the y-2014 tree?

Brian Swann said...

I am with Vince on this. When we get past the hype, it seems to me that Full Genomes is offering getting for double the amount of Y-DNA sequence. And it was not clear where the sequencing was done. In-house at FTDNA or out at Illumina.

Anonymous said...

Other questions to add are how long will it take (64k dollar question!), how long will the analysis take and who has ownership of the SNPs as well as availability of the .bam files. and do we know how many x reads they are doing to compare with the 50x reads at FullG? And does it provide 300-400 STRs too? So more details needed but not that gripped so far.

Brian Swann said...

Look forward to Debbie updating the ISOGG Wiki with the side-by-side comparison chart of Full Y-DNA sequencing - and she will need a new bullet point. Happy to work with you, Debbie.

Ray said...

I believe that many people will opt for the Big Y based on the fact that it has 20 times the coverage of Walk The Y at a more affordable price, but in the end will still feel the need to test the areas not covered in the FTDNA product. The Full Genomes test on the other hand although twice the price seems to offer the ultimate package currently available. I ordered the Full Genomes test in July but my sample is still waiting to be sent to the lab due to delays in testing, which hopfully are now sorted. I also ordered the Big Y from FTDNA today so eventually should be able to make a judgement on which product I consider the best value.

From the impressive FGC results that have been posted so far I suspect that that I will get most satisfaction from the Full Genome product.

Anonymous said...

Does anyone know if FTDNA will use the sample on hand for existing members or if a new kit will be issued?

Anonymous said...

Some more details and questions are answered here... including turn around time and whether existing samples can be used (they can):
http://dna-explained.com/2013/11/10/family-tree-dna-announces-the-big-y/

Mark D said...

Full Genomes uses a lab in China, probably why it may take so long for results. And I, or one, do not trust my DNA sitting around in a Chinese lab.

Anonymous said...

The chinese firm that does the testing for Full Genome is proven and have very good reputation.

Debbie Kennett said...

Unofficially we’ve heard that the coverage will be well above the 50x of the Full Genomes Y test. We don’t yet know what data will be returned to the customer and what sort of analysis will be provided and what tools will be available. A couple of us are updating the Wiki comparison chart as and when we get information so check that page regularly for updates:

http://www.isogg.org/wiki/Y-DNA_SNP_testing_chart

From what I understand FTDNA will be able to use existing samples for the Big Y.

I hope FTDNA will provide some FAQs about the Big Y in due course.

I would also like to see the list of the 25,000 Y-SNPs. It seems that we will have to wait for publication of the long-promised Genographic Paper.

Luckily there are now quite a few people in the genetic genealogy community who have ordered some combination of WTY, Full Genomes, Big Y, Chromo 2 and Geno 2.0. I know of one person who’s ordered all five tests. We should have some good comparative data in due course on Next Generation Sequencing vs. Sanger Sequencing and NGS vs chip genotyping. The comparative tests will enable the citizen scientists to sort out the equivalent names for all the new SNPs that are being discovered.

There are no STRs included in the Big Y test as far as I’m aware. However, the STRs and mtDNA results at Full Genomes are not really so helpful because they have no matching database. FTDNA dominate the Y-STR market and have the world’s largest full mitochondrial sequence database in the world.

George Jones said...

Greg Magoon (an expert chrY Genetic Genealogist and a Contractor of FGC – Full Genomes Corporation) says:
"Regarding the breadth of coverage on chrY: The mapped coverage of the FGC raw data is about 23 million base pairs (mbp). We have estimated the region of reliable mappings in the FGC raw data (corresponding to the high-reliability novel variants) to be 12-16 mbp …”. “Plus, many of the variants classified with lower reliability will likely turn out to be genuine, but further study is needed in those cases.” “As far as I can tell, the region of chrY that is covered by this test is the same as would be obtained through whole genome sequencing, and since FTDNA basically seems to be targeting a smaller subset of chrY, while using similar next-gen sequencing technology (2×100 bp read length Illumina sequencing), their coverage will almost certainly be lower than the FGC test (it will not be higher).” “ If I make some educated guesses about the approach they are using, am expecting that the larger region covered by the FGC option will give roughly 20-60% more reliable SNPs than the FTDNA option.” “But it seems clear that there will be significant regions that are not covered by the new FTDNA offering that are available through the FGC results.”
“Also, in terms of results analysis and interpretation, my sense is that FTDNA will not be offering much here, and may encounter some challenges.” “ The issue of false positives in NGS results is a non-trivial problem, and I wouldn’t be surprised if their analysis has problems in this regard.”” In any case, we have put a lot of resources into making this aspect of FGC;s analysis as solid as possible.”” We also have worked hard to develop a large database of sequence results (from 1000 Genome Project, Personal Genome Project, and elsewhere) to aid in interpreting the results and help place the new variants on the Y-tree.”My understanding from some posts on various forums is that FTDNA is not planning on making the raw read and alignment data available, whereas FGC provides this as an option.”

Based on what Magoon is saying, George Jones notes that some customers may consider this statement on a FTDNA website as somewhat misleading or advertising puffery concerning the new FTDNA “Big Y” test: “10 million base-pair coverage – more than any other Y-DNA test on the market.” Such statements should be investigated by a regulatory government body or consumer affairs group … and IMHO, that also goes for other claims being made in the DTC Genetic Genealogy Testing Marketplace. ISOGG has not the horsepower to do this and censor such companies ... so lets bring in the government if these DTC DNA companies are not going to police themselves.

As others have not on this blog, comparing a regular priced $695 FTDNA Big Y test to a $1000 or so FGC test is not a pure apples to apples comparison as FGC provides far greater greater chrY coverage as Magoon says, 400+ STR reads, mtDNA test, analysis, raw results etc. All these DTC DNA tests without some sound analysis to customers having varying levels of Genetic Genealogy expertise is not a good game plan.

As the Blog author at dna-explained.com notes, neither the Full Genome test not the FTDNA Big Y test is for beginning Genetic Genealogists. We should ask FTDNA Management to fully justify the above noted “Big Y” advertising claim and then report back here our findings. Debbie ... I think you could do that.

Anonymous said...

Someone should ask Full Genomes Corp. if they will
honor FTNDA's BigY $50 coupon towards testing their
full Y test.
;')

Anonymous said...

Guys, this is a highly technical field. Are there any real bio-chemists or genetecists blogging here?

We are diving deep into the woods on a technical field. We need real technicians to answer.

The only thing that is relevant to many of us is to find distant relatives and to assemble our true family tree going back for as long as we can.

FTDNA has thousands and thousands of customers and builds test for the mass market and tries to integrate the results into their family surname and deep clade project system so people can share information and learn more about what they care about.

Coverage of the Y chromosome must obviously be a good thing. Low prices must be a good thing, but we have to ask ourselves what the value is for us. Just because one can scan the ocean of the Y chromosome doesn't mean we are going to find a lot of gold nuggets floating on the ocean. That's why pure coverage is not the holy grail.

Regards,
Mike

Anonymous said...

Another non-technician's comment - BigY offers 60-80% of FGC's viable SNP coverage at a current offer price 40% of FGCs. This seems to be excellent value for money. The significantly lower price important as we need to encourage many people to test in order to place the new SNPs in the phylogenetic tree.

sb10 said...

Good news Debbie. Because the end of year sale started, I ordered a Y-DNA test for my cousin. Also FF. When I did that, there was a coupon for $10 on another order if I uploaded a GEDCOM for my cousin. I did so. Then the website then offered me a Big Y test and I applied the coupon to Big Y. So - if you order a Y-DNA test as a "new" customer, you should also be able to order Big Y.

Debbie Kennett said...

SB, Thank you for letting us know that it is possible for new customers to order the Big Y test once they've ordered another product. The Big Y and the Full Genomes test are really only for advanced users at this time.

Anonymous said...

Dose this require a new swabs? or what ?

Debbie Kennett said...

I understand that FTDNA will be able to use the stored samples so you will not have to do another swab.

Anonymous said...

I did an analysis ydna-67 in a family-historic goal. What is the usefulness of this new analysis ???
Zalmoxis

Debbie Kennett said...

At the moment this is test is really for those people interested in deep ancestry and the scientific discovery process. It doesn't have a direct genealogical application. If you are interested in deep ancestry make sure you join the relevant haplogroup project:

http://www.isogg.org/wiki/Y-DNA_haplogroup_projects.

The project admins will be able to advise you on additional testing.

Peter MacDonald said...

In case anyone is wondering about the Big Y Test release of results today…..it has been very disappointing for pretty much all involved as test results were not delivered as promised today (and a fourth date of "hopeful" release was passed along to customers of the Big Y Test from Nov/Dec 2013..

FTDNA seems very noncommittal in their wording to its customers. Originally Big Y results for many were to be received on 31 Dec 2013. The it was pushed to mid Feb 2014, then to 28 Feb 2014. Now this is the notice that the majority of the Big Y customers received today from FTDNA not through an email but to there account on the FTDNA Website:

“We expect that all samples ordered during the initial sale (last November & December) will be delivered by March 28th. We are processing samples in first come first serve order. If a sample doesn’t pass quality control, we will place it in the next set of results to be processed as long as we have enough DNA sample. If we require an additional sample, we will send a new test kit and place the new sample in the first set to be processed when it is returned.”

The very loose wording at the shows that FTDNA is not guaranteeing delivery of order Big Y test results by 28 March 2014, the they clearly indicate “We expect…”

To find out that the on 28 Feb 2014 that the expected date (which was changed three times to 28 Feb 2014) of 28 Feb 2014 will not be met, however it may are may not be met by 28 March 2014 (even if there are no issues above FTDNA having to process the test) is pretty horrible customer service.

Small-Y said...

Agree with Peter MacDonald. It all taste like a sale trick with "good" results released first, before the real statistics from BigY shows. FTDNA does not answer any questions about how many kits that is actually processed, done and ready. Asking to much questions in their own forum leads to a moderator sending private message and threats to ban you from the forum. Standard FTDNA procedure. When customers is dissatisfied and complain: question them, or threat them. Customer support 101.

Debbie Kennett said...

Peter

Nir Leibovich from Family Tree DNA sent out an e-mail this morning apologising for the delay which you should have received. Here is an extract:

"We are also hearing the frustrations from those who have not yet received their results, and we would like to address the matter publicly in the form of a sincere apology. The entire FTDNA team has been working very hard over the last few months with high determination and many late nights. Launching a new product is always a challenge with many moving parts, some more predictable than others. Unfortunately we ran into some surprises beyond our control when one of our suppliers ran out of certain reagents we needed for running the Big Y product. However we recognize that it is our responsibility and duty to meet our deadlines and keep our customers informed when problems arise."

The full text of the letter can be found here:

http://www.anthrogenica.com/showthread.php?2245-Family-Tree-DNA-Product-Launch-Big-Y/page2

Please also see my recent blog post about the Big Y results:

http://cruwys.blogspot.co.uk/2014/03/the-big-y-roll-out-snp-tsunami-is-on.html

SmallY, I think the e-mail from Nir Leibovich should answer most of your questions. It is not a question of "good results" being released. There is only so much that can be released in one go. This is a trailblazing new product, so we are bound to have a few hiccups along the way. There have been delays with all the new tests in the last year or so (Geno 2.0, Full Genomes, Chromo 2). You just need to be patient.

Small-Y said...

Why does FTDNA anawer the simple question about how many BigY results they have at their hands then? I beleive there are more than a thousand, but only 100 customers have got theirs. Coclusion: the 100 is handpicked in close cooperation with the sale department. The official statement says nothing if they cant be honest about the actual number of BigY test that is already processed. It is so simple to answer but yet they ignore the question and does not comment it, at all. They treat to ban you from their forum instead of being honest to their customers. That tells a whole lot about FTDNA.

Debbie Kennett said...

Small-Y, You are seeing conspiracies where they don't exist. Results are being released on a first come first served basis. The results that have been processed and have gone through quality control have now been released. Other results will be released in stages when they are ready. There was a glitch with the FTDNA website on Friday and I imagine the priority was to get that sorted out first. It is now the weekend so I wouldn't expect to see any more results arriving until next week. The results are what they are. They are very diverse and are not in any way cherry-picked.

Peter MacDonald said...

Hello all,

28 February 2014 has come and gone there isn't much point in duelling in the past. Looking ahead I am still excited to receive my Big Y Test results. Two things that I am waiting an answer from FTDNA are:

1. Does FTDNA currently have enough of the reagent in their current possession to complete the remain of all Big Y Tests?

2. What is the planned scheduled release of each testing group leading up to the expected completion of Big Y Testing.


Hope fully FTDNA will push out this information to its Big Y customers soon. Not receiving notification with updated release test results requires individuals to check in to confirm any changes, resulting in wasted time.

Debbie Kennett said...

Peter

I'm afraid I don't know the answers to your questions. FTDNA are hoping to deliver all the results by 28th March so I assume they have enough reagents to complete the process. You won't need to keep logging in every day because you should receive a notification e-mail to tell you that your results are in. The results are being delivered in batches and I know that more results were released yesterday.

Best wishes

Debbie