Saturday, 1 March 2014

The BIG Y roll out – the SNP tsunami is on its way!

The genetic genealogy community has been eagerly anticipating the arrival of the so-called SNP tsunami for several months and it now seems that the first waves are starting to appear on the horizon. I was one of a select few genetic genealogists and bloggers who was invited to participate late on Thursday afternoon (UK time) in a private webinar led by Dr David Mittelman, Family Tree DNA’s Chief Scientific Officer, in preparation for the rollout of the first results from FTDNA’s next-generation sequencing BIG Y test.1 During the webinar we were given a sneak preview of some sample results from the test and we had the opportunity to ask lots of questions. I don't know what it says about me and my enthusiasm for Y-SNP testing but I seemed to be the one asking most of the questions! I am very excited about the implications of comprehensive Y-chromosome sequencing. These tests will not only allow us to define the exact branching within each haplogroup but will also reach right down into genealogical time and will eventually make it possible to delineate recent branches of the Y-line and identify the common ancestor almost down to the exact generation.

Background
There are almost 60 million base pairs in the Y-chromosome but about half of it is full of repeating complexities which have yet to be deciphered. There are only around 20 million or so bases which are good candidates for sequencing.2, 3 The BIG Y test was designed to provide the most information at the most affordable price. The intention is also to provide information in the most clear and easy-to-use way.

There seems to have been some confusion about how much of the Y-chromosome is sequenced for the BIG Y test so I asked Dr Mittelman for clarification. He advised that the test sequences around 13.5 million bases on the Y-chromosome and provides results for between 11.5 and 12.5 million positions. It is not possible to give a precise figure because NGS results vary from person to person. This is an improvement on the spec that was advertised when the pre-sale was announced in November when a figure of 10 million bases was quoted.

When the BIG Y pre-sale was announced the coverage was advertised as 60x (the number refers to the number of times the Illumina machines read the sequence – the more reads the better). The information on the BIG Y FAQ page has since been updated and the coverage is now being advertised as “55x to 80x average coverage”.

The roll out
The BIG Y tests have been processed in the order in which they have been received, but some people had to supply new DNA samples so their tests will take longer. The first 100 results were released on Thursday 27th February, and there will be a gradual roll out of results running through to the end of March. We had been expecting all the BIG Y results to be released on the same day but it now appears that the anticipated tsunami will be more of a steady trickle of waves  – a slow-motion tsunami4  – rather than one giant flood of data. The following message is now being displayed on the personal pages of people who are awaiting their results:
"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."
My dad is one of the people waiting his results but I did not place the order until the very end of the pre-sale period so his results will probably be amongst the last to be processed. Along with other people who have ordered the BIG Y test I received an e-mail this morning from Nir Leibovich, FTDNA's Chief Business Officer, apologising for the delay. He advised: "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... We hope you will let the wonderful product we produced make up for delays that were needed to refine it! We have updated expected results dates on customer pages and will work around the clock to beat them." [Click here to read the full text of the e-mail.]

How many BIG Y tests have been ordered?
I asked if we could be given an idea of the number of BIG Y tests ordered. Although a precise figure was not revealed we were told that there had been "thousands" of orders and that "FTDNA have more Y than anyone else". I know that large numbers of orders have gone through some of the haplogroup projects. There have been 149 orders in the R1b-U016 Project alone and around 340 orders in the R1b-L21 Project. If you have ordered the BIG Y test do make sure you join the relevant haplogroup project so that the very helpful and knowledgeable volunteer admins can help you to understand your results. There is a list of Y-DNA haplogroup projects in the ISOGG Wiki:

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

What is reported
Screenshots of the user interface and explanations of the various features can be seen on the BIG Y page in the FTDNA Learning Center:

www.familytreedna.com/learn/user-guide/other-test-results/big-y-page

FTDNA have a big internal SNP database with details of 36,562 known SNPs. Customers will be given a list of their results for all the SNPs in the database. They will be told whether they are ancestral or derived for each position, whether or not the SNP is on the tree, the genome reference co-ordinates, their genotype (their DNA letters) and the confidence rating.

There are three confidence levels for the SNP calls. High confidence means that all the reads essentially agree. Medium confidence means that the information looks good but it has to be manually curated. Low confidence indicates noisy data.

NGS coverage varies from person to person but it is expected that results will be provided for between 25,000 to 35,000 known SNPs per person. The amount of overlap with the tests from Full Genomes, Geno 2.0 and Chromo 2 is not yet known, but it is expected that the BIG Y will cover 90% of the SNPs in the Geno 2 and Chromo 2 tests. There are a handful of people in the genetic genealogy community who have tested with all four companies. Some people have also taken the Walk Through the Y test, the previous SNP discovery test from FTDNA which utilised Sanger sequencing. Once the BIG Y results have all been released and compared with the other tests the haplogroup project admins will be able to provide better information on the overlap between all the tests.

Customers will also be given a separate list of novel variants. These are defined as variants which differ from the reference sequence and which are not seen in the FTDNA SNP database. Thankfully the genome reference co-ordinates will be provided which will allow comparisons with SNPs identified in tests from other providers (with the exception of BritainsDNA who have not released the co-ordinates for their new S series SNPs [see my update from 4th March below]). Dr Mittelman does not yet know how many novel SNPs to expect per person. There is currently no function to compare novel variants in the database, but the test is very much a work in progress and he is open to suggestions for new ideas.

Information will not as yet be provided on INDELS (insertions and deletions), but experienced users will be able to extract the information from the raw data.

File formats
Two types of files will be provided: a VCF file and a BED file. These files are not currently available but should be ready for download some time next week.

The VCF (variant call format) file will consist of a list of all the variants identified, tagged by confidence and location. This is essentially a file showing all your differences from the reference sequence. For an explanation of the file format see the paper by Danecek et al (2011).A sample VCF file can be found in the 1000 Genomes Wiki:

www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

The BED file is a text file which will provide a bunch of ranges for all the areas where information is available for which it was possible to make confident calls. This file will cover all the positions that passed quality control. A useful guide to BED files can be found here:

http://genome.ucsc.edu/FAQ/FAQformat.html#format1

Information about the VCF and BED file formats will be added to the BIG Y Learning Center page in due course.

The raw data files in the form of BAM/FASTQ files will also be made available in due course but a decision needs to be made on the best way to provide the data. I imagine that the data will almost certainly be made available in the cloud, perhaps taking advantage of the new Google Genomics service, or another similar application.

Single SNP testing
The value of a DNA test is in the comparison process and the BIG Y test is no exception. It is hoped that large numbers of new SNPs will be discovered, many of which will be in a genealogical time frame. Ideally a paired testing strategy should be adopted with two very distantly related men from the same subclade taking the test. If novel SNPs are found which identify particular family groups then in theory it should be possible to order single SNPs. Single SNPs can be ordered either direct from Family Tree DNA or from Thomas Krahn’s new company YSEQ. The two companies offer a complementary range of SNPs. Single SNPs cost $35 each from YSEQ and $39 each from FTDNA. However, I suspect that if you are able to identify a SNP in the last two hundred years or so that is only likely to be shared by half a dozen men it will not be cost-effective for any company to offer a single SNP test. Much will also depend on the number of new SNPs identified in a given tree. It might well turn out to be more economical for a surname project to club together and pay for BIG Y tests for project members representing branches of the tree that are of particular interest.

There were some misleading reports emanating from the FTDNA group administrators' conference in Houston last November which suggested that FTDNA had an upper limit of 2000 on the number of new SNPs on offer. Dr Mittelman clarifed that there is no limit on the number of new SNPs that can be ordered. There is a limit on the number of SNPs that can be tested at one time on the lab deck and that limit is 2000. FTDNA can in theory calibrate for use as many SNPs as they can order and design but it’s a question of managing the time.

SNP validation
I asked whether it was necessary for SNPs identifed through next-generation sequencing to be validated using Sanger sequencing. Dr Mittelman advised that with high-confidence SNPs the data is very clean and validation is not necessary. Sanger sequencing might be needed for medium- and low-confidence calls where there are flags and not a lot of data. He also advised that next-generation sequencing is being used to validate the SNPs on the new Geno chip.

Poznik et al (2013) (supplementary data) did in fact validate their NGS SNPs using Sanger sequencing and found a concordance rate of 99.92% with just one discordant genotype.2

White paper
Dr Mittelman advised that once all the data has been through quality control FTDNA will then produce a white paper which will provide information on some of the technical details of the test. The paper will cover performance metrics, value proposition, etc, and they also hope to look at mutation rates, something which is of great interest to the genetic genealogy community and a subject of considerable debate and disagreement! The paper should be out in the next four to six weeks or so.

The new Y-tree
BIG Y data is currently being released using the now very out-of-date and somewhat irrelevant 2010 Y-tree. Bennett Greenspan, the Chief Executive Officer of Family Tree DNA, advised in the webinar that they have had teams of people working on the new tree in collaboration with the Genographic Project. The new tree will be fully integrated with Geno 2.0. The tree needs to be ready from both the technical point of view and the graphical interface, and it seems that it is the latter which is proving more problematic. The tree is not dependent on the release of a scientific paper. Bennett advised that it might be ready in the “next several weeks”. When the new tree is finally launched, SNPs from the BIG Y will be automatically mapped on the new tree.

Third-party tools
FTDNA want to encourage people to use third party tools to get more out of their results and to come up with new ways to analyse the data. I have previously written about YFULL, a Russian company which provides a very nice Y-chromosome interpretation service. See my review from November 2013. The service is currently free if you agree to let them have your sequence, but it is expected that they will charge a fee at some point. The Full Genomes Corporation have also indicated that they might be able to analyse BIG Y data though no announcement has yet been made. With the increasing availability of Y-chromosome sequencing data no doubt other tools and analytical services will appear in the future.

Additional questions
After the webinar had finished I realised that there were still some questions that I hadn't asked and David Mittelman kindly provided me with some answers by e-mail.

Q: Are there any plans to provide results for Y-STRs?
A: Big Y does span STRs but that was not the intent of the product. So you can go to the VCF files or the raw data and you will see insertions and deletions at STRs, however, we do not plan to add this to the web page. I would much rather recommend our established and proven STR tests.

Q: Does the BIG Y raw data also include the full mtDNA genome?
A: No, it is comprehensive sequencing of the accessible parts of the Y chromosome. We, as you know, offer full mitochondrial sequencing as a separate product.

Q: Will a list of positive SNP results be posted on the Project SNP pages?
A: Yes, if they are on the tree

Preliminary analysis of BIG Y results
The initial results from the first batch of BIG Y tests were producing an unexpectedly high number of novel variants. Vince Tilroe has analysed some of these results and reports as follows on the U106 mailing list:
It looks like many of the novel variants shared by many Big-Y testees may belong to a particular subclade below R-L20, the haplogroup to which the primary source of the anonymous male donors belongs to, whose sequences were used to build the ChrY reference assembly, and many of those may even be exclusively private to him.  Greg Magoon had filtered them out from the 1KGP and FGC reports, but YFull had assigned "Y" identifiers to some of them.
I've compared novel variants from six Big-Y returns belonging to haplogroup R-L51 and below, and have so far identified 56 "novel variants" shared between at least two of them so far, but individual samples only had between 43 and 48 of those.  This pretty much cuts the typical true novel variant count in half, leaving a count that is more in line to what was expected for this process.  
Charles Moore, the U106 admin, has since received confirmation from another group that many of the novel variants are ancestral shared novel SNPs.

Other SNP tests
Full Genomes Corporation is the only other company which currently offers comprehensive Y-chromosome sequencing. Their test is substantially more expensive than the BIG Y but sequences more of the Y-chromosome. When the BIG Y raw data files become available it will be possible to do a comparison of the two tests. For comparisons of the available SNP tests, including the Geno 2.0 and Chromo 2 chip tests, see the SNP testing comparison chart in the ISOGG Wiki.

What are we going to do with all these SNPs?
I wrote in a previous blog post about the confusion of SNPs generated by the various SNP tests offered by the different testing companies. We now have a situation where four companies/organisations (Family Tree DNA/Genographic Project, Full Genomes, BritainsDNA/ScotlandsDNA and YFull) are maintaining their own proprietary SNP databases. There is a great need for an open access independent database of validated SNPs. ISOGG – the International Society of Genetic Genealogy – are probably in the best position to produce such a database, but they also have responsibility for maintaining the Y-SNP tree. The sheer amount of data generated from the next-generation sequencing tests will represent a significant challenge for the volunteer Y-SNP team. I do wonder if the present tree system is actually sustainable and, if in the long run, it might be better to report results as differences from the reference sequence, as is the practice for mitochondrial DNA. Whatever happens, we will have an interesting year ahead of us.

Are you interested in ordering the BIG Y or another SNP test?
My advice for anyone thinking of ordering SNP testing is to be patient and wait for a few months until all the results from the first batches of BIG Y and Full Genomes tests have been analysed and compared. Once this process has been completed we will have a better picture of the new Y-chromosome landscape and the shape of the tree, and it will then be possible to make an informed choice as to which test to purchase. Dr Mittelman advised that there are no immediate plans for another BIG Y sale. At the moment the priority is to bring down the turnaround time for new orders which is currently 8 to 10 weeks.

If you are interested in being involved make sure you join the relevant haplogroup mailing lists and Facebook groups. If you've tested at Family Tree DNA make sure you join the appropriate haplogroup or subclade project. The mailing lists and groups are usually linked from the haplogroup project websites. There is also a list of mailing lists and Facebook groups in the ISOGG Wiki:

www.isogg.org/wiki/Genetic_genealogy_mailing_lists

Further information
There is a set of BIG Y FAQs in the FTDNA Learning Center:

www.familytreedna.com/learn/y-dna-testing/big-y

The BIG Y page in the Learning Center provides screenshots and descriptions of the user interface:

www.familytreedna.com/learn/user-guide/other-test-results/big-y-page

Elise Friedman presented a webinar on 28th February on the subject of "Getting to know BIG Y Results". A recording of the webinar should eventually be made available in the webinar archive in the Learning Center:

www.familytreedna.com/learn/ftdna/webinars 

Update 2nd March 2014
The recording of the BIG Y webinar is now available online and can be accessed via this link (free registration required):

https://attendee.gotowebinar.com/recording/4739415541486853122

Update 3rd March 2014
I have put the full text of the letter from Nir Leibovich, in which he apologises for the lack of communication about the expected date of release of BIG Y results, online here. Despite expectations to the contrary, it was never FTDNA's intention to deliver all the results on 28th February. That was the date when the results were expected to start rolling out. It also transpires that there is currently no way for FTDNA to change the expected date on customers' personal pages until the expected date has actually passed.

I've received a number of comments about the problem with reagents which contributed to the delay. Dr David Mittelman has contacted me to clarify the issue:
"We sequence the Y using Illumina HiSeq equipment and we ran out of reagents to do this, and for a period in December and January, Illumina had a back order in place so we could not order more. Illumina filled the orders in the second half of January and we continued our work. Back orders happen and since Illumina is the only game in town, we don’t have other vendors to go to, when Illumina runs out. Of course we are now rolling out samples continuously and each week, in batches. Just like we do for all our products and just like Full Genomes and other companies do."
He adds
"In the meantime as more batches complete I am confident people will be thrilled with the data. We were able to deliver better specs than I originally promised and... we will not ship subpar results to anyone. Everyone will get great data."
Update 4th March 2014
Dr Jim Wilson of BritainsDNA/ScotlandsDNA has now released a spreadsheet with details of the genome reference co-ordinates for all the Y-SNPs on the Chromo 2 chip. See the following blog post from CeCe Moore for further details and to download the spreadsheet:

Dr. Jim Wilson and ScotlandsDNA Release Y-SNP Positions for Chromo2

Thomas Krahn has now uploaded the 8000 or so novel markers to Ybrowse. This will allow the genetic genealogy community to cross-check all the new tree branches discovered by Jim Wilson earlier this year. Thomas Krahn has advised that his company YSEQ can design primers for some of the new SNPs as required.

Update 1st April 2014
Although the BIG Y .vcf and .bed files do not include mitochondrial DNA data, it now transpires that mtDNA is included in the BAM files. The mtDNA data can be extracted using third-party tools. For further details see the following blog post from Roberta Estes:

http://dna-explained.com/2014/04/01/mitochondrial-dna-results-from-the-big-y-test

See also Felix Chandrakumar's blog post on the YFull interpretation service which includes a report on the mtDNA data extracted from his BIG Y BAM test:

http://www.fc.id.au/2014/03/yfull-y-chr-sequence-interpretation.html

Footnotes and references
1. For links and resources on next-generation sequencing see the ISOGG Wiki page: www.isogg.org/wiki/Next_generation_sequencing

2. A good description of the Y-chromosome reference sequence is provided by Poznik et al (2013) Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus femalesScience 2013 341; 6145: 562-565:
The Y-chromosome reference sequence is 59.36 Mb, but this includes a 30-Mb stretch of constitutive heterochromatin on the q arm, a 3-Mb centromere, 2.65-Mb and 330-kb telomeric pseudoautosomal regions (PAR) that recombine with the X chromosome, and eight smaller gaps.
This effectively leaves around 22.98 Mb of “assembled reference sequence”. If you can get hold of the Poznik paper it contains a very nice figure (Figure 1. Callability mask for the Y-chromosome) showing the regions of the Y-chromosome in which reliable genotype calls can be made.

On a side note, this paper has come in for a lot of criticism, not the least of which is for the authors' mistaken assumption that mitochondrial Eve and Y-chromosomal Adam should be expected to date back to the same time. For a critique of this paper and some useful related diagrams see the three-part series of articles by Melissa Wilson Ayres: Y and mtDNA are not Adam and Eve: Part 1Y and mtDNA are not Adam and Eve: Part 2 - What it means to be the Most Recent Common Ancestor and Y and mtDNA are not Adam and Eve: Part 3 - Resolving a discrepancy.

3. Further papers of interest are listed on the Y-chromosome page in the ISOGG Wiki: http://www.isogg.org/wiki/Y_chromosome

4.
 The term "slow-motion tsunami" was coined by Charles Moore, the administrator of the R1b-U106 project:  https://groups.yahoo.com/neo/groups/R1b1c_U106-S21/conversations/messages/21323

5.
 Danecek P, Auton A, Abecasis G et al (2011). The variant call format and VCFtoolsBioinformatics 27 (15): 2156-2158.

© 2014 Debbie Kennett

56 comments:

Anonymous said...

Nice report, Debbie ! FTDNA should post it and do themselves a favor ! :-) Colin (USA/Australia)

Anonymous said...

'Ancestral or derived'... is that like inherited or mutated?

Anonymous said...

Nice factual update on a topic in which many are very interested.
-rt_/)

Kelly said...

Debbie,

As always thorough and spot on. I totally agree with your comment "My advice for anyone thinking of ordering SNP testing is to be patient and wait for a few months until all the results from the first batches of BIG Y and Full Genomes tests have been analysed and compared. Once this process has been completed we will have a better picture of the new Y-chromosome landscape and the shape of the tree, and it will then be possible to make an informed choice as to which test to purchase."

Indeed!
Kelly Wheaton

PL said...

Great summarization! Thank you! Do you happen to know why FTDNA is so secret about how many kits actually is processed and complete? if FTDNA have results for 100 kits only or are they sitting on many more results at their hands without releasing the results to their customers? Is the 100 kits currently released to the customers handpicked by Gene by gene to suit the BigY reputation the best FTDNA could accomplish by carefully and strategically pick the ones giving best false positive results? I think it is very strange and dishonest to their customers not telling the truth. There are many who have asked questions like: Have there been only 100 kits processed, or are more results ready but not delivered yet to customers? but the FTDNA responds by ignoring the questions. Not open and honest to their customers in my opinion. I think FTDNA is strategically planning the release of the result by the help of the sales department in an attempt trying to get the kit sold at any cost, not caring about upset customers whose order is constantely delayed. The ones with delayed results is what I believe not interesting enough results to meet the public yet.

Debbie Kennett said...

Thanks Colin. Glad you like the report.

Ancestral SNPs are those for which you test negative. Derived SNPs are the downstream SNPs which are the important ones. If you are derived than you are positive for a SNP which is specific to your clade and is not found in the ancestral population.

Debbie Kennett said...

Dear PL

Did you receive the e-mail from Nir Leibovich that I mentioned in my blog post? FTDNA are not holding back any kits and have not cherry-picked the best ones. They are releasing results as and when they are ready. This is a trailblazing new test. There are bound to be hiccups along the way. It took months for all the problems with Geno 2.0 and Chromo 2 to be sorted out, and there have been delays with the Full Genomes testing too. I can't imagine that FTDNA will want to encourage any new sales until they've processed the existing orders. It's just a question of patience.

Brian Swann said...

Very nice post Debbie. It will be a bit of confusion for much of 2014 I suspect, but gradually the dust will settle and the future trends become clearer. I hope FTDNA will find a little bit of time to look at their sequencing technology especially with regard to the dodgy SNP calls. We may need more data on how all this works for real to assess.

Ponto said...

I first became involved with FTDNA in 2008. I think I have experience with FTDNA.

I just want to say the reagents excuse has been used before by FTDNA.

It is said that liars need good memories.

Personally speaking, I will not have anything more to do with that company.

ISOGG Admin said...

What reagent is it with BigY and what company is the supplier? I need to verify with the company so that FTDNA is not lying, many things points towards FTDNA is not telling the truth.

Debbie Kennett said...

Dear "ISOGG Admin"

Are you the same person as "PL"
and "Ponto"? I do not work for FTDNA. You will need to ask them your question direct. I have no reason to doubt their word.

PL said...

I hsve tried asking FTDNA many questions about this, but no response. I havn't asked about the reagent supplier. I will try that (I have no hope in that we will ever learn what reagent or what supplier it is, because it is all a lie). Perhaps the supplier cares to answer. The problem is, there are no supplier that come short with any reagent. FTDNA already have thousands of results ready from the BigY. They have never denied that, I have claimed it in so many places in so many ways, and they never deny it (like everything else that is incorrect, then they are really fast there and correct faulty information). Not a single word (in defence) when you claim they have alot more results than 100. Why? Why can't they deny it if it isn't the truth? Ask them yourself, and see what their response is.

Debbie Kennett said...

FTDNA have already given you an answer in the form of the letter from Nir Leibovich. There's not really much more that anyone can do if you choose not to believe what you've been told. I am not claiming that FTDNA have a lot more than 100 results. They have received thousands of orders and are only able to process so many at any one time. The roll out has started and will continue.

PL said...

Why doesn't FTDNA deny it then and move on? Instead of private message you and threat to ban you. Instead of putting full moderation on? Instead of just answering: "No, we have only 100 results ready, not a thousand.". That would be a normal respond to the questions, I am not the only one asking, no one is getting an answer. Don't you think an answer on that simple question should be a nice addition to your blog? Can't you ask FTDNA and se if they ignore you too? Or someone else reading here? Ask the questions in their forum, they have subareas for the BigY in their forum where the questions is best suited.

I have paid FTDNA alot of money, if I want to order another BigY I think I, as a customer, deserves to get an answer for my questions instead of threats and total ignorance. Not even a: "I don't know the answer, but I will look into it for you."

Debbie Kennett said...

I don't see that there is a problem. FTDNA have already explained the roll out process. You seem to have misunderstood what they said. With any new test or new technology there are bound to be glitches and it's hard to keep to deadlines. There have been similar problems with the Geno 2.0, Chromo 2 and Full Genomes tests. All forums and mailing lists have their own rules, and reserve the right to put someone on moderation if they violate the rules. It's not for me to comment on your specific situation as I don't know the details and have no interest in getting involved.

Big Fools Day said...

Haha drop the guard Deddie! Jesus, try to be a bit more open minded, are you sure you are not paid by Gene by gene? Dont you agree FTDNA could just answer their customers questions? Dont you agree that their behavior is very odd?

Debbie Kennett said...

Dear BigFoolsDay, Are you PL/Ponto in another guise? It would help if you could reveal your true identity rather than hiding under a bewildering variety of pseudonyms.

I am most definitely not paid by GenebyGene. I can't comment on your problems with the FTDNA Forums as I'm not aware of the full facts, and I have no desire to get involved.

Howard said...

Dear Deddie,

How can you not have any desire to "get involved" with facts about FTDNA BigY after your blogpost? Isn't reporting about all aspects of the Big-Y the purpose with this very interesting and well documented article?

I am not sure why you take FTDNA in defence, it doesn't take much to realise that PL is speaking the truth. I think PL advice to ask FTDNA the question is a very good advice, it will complete your article. Or are you writing an article and a day or two later it is out of your interest? You have no interested at all in knowing what customers wants to know from FTDNA?

I am also waiting for my Big-Y results from FTDNA and as PL describes it interested in the details about the issues and learn more about the causes for the big secrecy.

I have expressed my concern about the lacking customer service from FTDNA, and I have got some answers from their staff, but as soon as I get any close to the subjects of actual number of completed Big-Y results or asks for details about the reagent, then the communication suddenly stops.

Please go on writing articles on subjects that you have no personal interest in. That makes sense.

Debbie Kennett said...

Howard

I've no idea what question PL would like FTDNA to be asked. He's clearly misunderstood what has been written. To clarify matters I've now put the full text of Nir Leibovich's e-mail online, as it occurred to me that PL might not have seen the full letter.

I've received clarification from David Mittelman with regards to the reagents. I've added an update at the end of my blog post.

I'm happy to follow up on questions relating to the BIG Y but I do not wish to get involved in personal spats on FTDNA Forums which have nothing to do with me.

PL said...

"You seem to have misunderstood what they said.".

Okay let us pretend I have misunderstod FTDNA when they ignore my questions about Big whY then. Their blank answer is read wrong by me. Luckily YOU havn't misunderstood them, right? then YOU can answer my question, am I correct? Here is my 3 main questions:

How many BigY is actually processed and FTDNA have the results for? Is it only 100 or is it more like 1000?

What reagent did they ran out of?

What company is their supplier of that reagent?

One additional question I havn't got any response from FTDNA on: When (what date) did they notice that the reagent stock was not going to last for more than 100 kits?

Since you havn't misunderstod FTDNA, like me, then you must have the answers for me. Thank you in advance for the answer to the questions that FTDNA refuse to give me. Or are you suggesting that I misunderstand FTDNA's forum moderator when she threats to ban me, and when they put full moderation on in their forum? I mean, that is quite difficult to misunderstand. Total ignorance and lack of any resonds or answers is also difficult to misunderstand. I am not sure why you are suggesting I am misunderstanding an empty answer?

Well, I look forward for the answers, perhaps you have a magical way of reading between the lines of Dr David Mittelman message, but then I am sorry I lack that ability.

Debbie Kennett said...

My understanding is that FTDNA are releasing results in batches as they are processed, as I've already explained in my blog post. They are not sitting on 1000 unreleased results. Dr Mittelman has already answered your questions about the Illumina reagent. I don't know the technical details as to which reagent is used but I'm sure Illumina can help you though I fail to see why you think it's such a big issue.

PL said...

Okay, thank you. That didn't answer any of my question but atleast you tried. Onto another topic, there have been such a fuzz about FTDNA staff being so busy and they work and work around the clock, their customers cry a tear for their heroes working so hard, so hard. You who have such insight: what the hell are they doing month after month in their lab with their BigY orders around the clock working their asses off when they obly had reagent to process 100 kits? That does not makes sense. Please explain

Debbie Kennett said...

The BIG Y test is still in beta-testing. I don't know all the ins and outs of the work involved but there must be a huge amount of work involved. There were probably lots of test runs. It takes days to runs the samples through the Illumina machines anyway. The results then all have to go through quality control, they have to be collated and uploaded to the website. The Full Genomes results were months behind schedule. Even the chip tests from Geno 2.0 and BritainsDNA were several months behind. This is new technology. It takes time to get it right.

Ponto said...

I am not PL. My internet identity is Ponto.

If you want to believe the same old same old, the reagents supplier thing, okay. I don't. I have heard the boy cry wolf too many times already.

A fool and their money are soon parted, Ms Kennett, and I intend to stop being fooled yet again by them.

Kelly said...

As far as reagent goes i believe Full Genomes Corp. had similar issues with supplies via Illumina so perhaps it might be better to investigate what Illumina is up to?

Howard said...

Why should we investigate Illumina? I am not a Illumina customer, are you?

Debbie Kennett said...

The commenters on this blog post seem to have a strange preoccupation with reagents. If they want to learn more then no doubt Illumina will help them to understand how the process works.

PL said...

Debbie, please stop trying to be funny. I know for sure what reagents is needed in the process. It would be very interesting to know what reagent they ran short of. Unluckily FTDNA is trying their best not to let us know, that is kind of strange don't you agree? ;)

Debbie Kennett said...

I really don't understand why you need to know these details.

PL said...

Debbie, read my first comment again. I have proposed that FTDNA eventually is not telling their customers the truth. When FTDNA is not releasing the details, that is like fuel on that fire. The truth is in the details.

Debbie Kennett said...

As I said before, I think you are seeing conspiracies where they don't exist.

Peter MacDonald said...

I am a Big Y Test customer who has not yet received his test results. I have asked the questions below on the FTDNA Forum but have not seen any reply, as well I am waiting for the Customer Service Desk to provide answered for the following two questions:

1. Does FTDNA have the materials (including the reagent that caused the delay) in its possession required to complete all Big Y Tests by 28 March 2014?

2. To my understanding there has only been a general date of 28 March 2014, in which FTDNA expects all Big Y Tests to be completed. Will FTDNA be sending out a more detailed list of when tests will be processed?

PL said...

Debbie, what are you claiming to be a conspiracy theory? FTDNA not answering questions is a fact, FTDNA threating to ban you when you ask for details in their forum is a fact, FTDNA not updating their customers is a fact and so on. Everything is easily verifiable, I am not sure if you dont, or dont want to understand. It seems like the latter is the truth

Gail Riddell said...

What is it with people who love to shoot the "messenger"? Debbie is a volunteer (who spends untold hours for no recompense - like so many of us) who adores genetic genealogy and what it can do, and in my opinion, she is merely passing on the information she knows. THANK her, not quibble with her over something for which she has no control over!

If your beef is with FTDNA, then sit on their "doorstep", please and let us know of the findings of which you learn. After all, we all know when we are the first to try out anything totally new, there are bound to be "teething"problems!

PL said...

I am not shooting the messanger. I am not questioning her, she is questioning me (for a reason I can't figure out?) Read the comments again. I am sure every customer knows what I am talking about and I think Debbies article (and comments here) is biased. I have no clue as to why Deddie pretends she have no clue what I am talking about. From where I come from the normal behaviour is to take customers threated bad by companies in defence, perhaps that is not the normal behaviour where Deddie lives. Of course I question her when she for no reason question everything I write, but shooting the messenger is an exaggeration in my opinion. It would be more fair if Deddie just accepted that there are issues with FTDNA and the BigY sale, instead of living in denial. If one wants to live in denial, that is okay, but please stop question people (like me) who sees the truth and dare to speak about it in the public. If you live in denial, do it silent.

Debbie Kennett said...

PL, FTDNA are answering questions but you do not believe the answers. That is what I mean by your conspiracy theories. As I've said before it is not my place to get involved with your personal problems on the FTDNA Forums.

PL said...

Debbie, FTDNA might be answering questions, but not my questions. I can assure you it is not a theory, it is a fact, FTDNA does not answer the questions. I established a mail conversation communication with David Mittelman yesterday and asked him my questions. I got two e-mails from him but no answers for my simple questions. He put energy in writing other irrelevant things instead. I am not surprised. Is that a conspiracy theory also? I can forward the emails to you if you dont beleive me :)

Debbie Kennett said...

PL, I have not got time to get drawn into a prolonged debate, and this will be my last response on the subject. As far as I'm concerned all the questions that I've asked have been answered to my satisfaction. It would be much better if you would just let FTDNA get on with the task of rolling out the BIG Y results rather than wasting their time asking the same questions over and over again that they've already answered.

PL said...

Funny that you moderated Howards comment away, that was one of the best statements here, summarizing the situation. I mean, that moderation style is kind of like imitating the moderation taking place on FTDNA forum, the posts that make best sense is moderated away, welcome to the brave new world

PL said...

Well, as a conclusion we can say that you claim I fabricate information or trust in conspiracy theories and when I offer you fact (which is also very easy verified) you are not interested? I think that is the perfect description of someone living in denial. Look the word up: denial

Debbie Kennett said...

PL, "Howard", "Big Fools Day", and "ISOGG Admin" appear to be one and the same person posting under different pseudonyms. If you wish to comment on this blog please post in your own name.

Peter MacDonald said...

Hello everyone,

Just wanted to comment on my 5 March 2014 post, I have had some questions asked regarding it, which has made me realize that I did clearly articulate the situation. I had been waiting for a response to some questions I posed on the FTDNA Forum a few days prior, however I had contacted the FTDNA Customer Service email just prior to adding comments to this Blog.

On a positive note the FTDNA Customer Service representative responded to my email in a very timely manner, in which it was confirmed that FTDNA does indeed have all the materials (including reagents) in their possession required to test the remainder of the Big Y customers. As well, FTDNA are expecting to be releasing a more detailed timeline for the remaining Big Y Test results releases shortly.

Debbie Kennett said...

Thank you Peter for the update from FTDNA.

James K said...

Waiting on Big Y. Email from helpdesk claimed the Feb 28 delay was a last minute event yet the Feb 27 webinar shows they knew the Dec tests were not going to be ready for the Feb 28. Think we deserve honesty from FTDNA. Saw the apology letter where he downplays the long history of delays because the company likes to shoot for unrealistic target dates.

PNG said...

Debbie, I can't see how saying that SNPs you don't have are "ancestral" makes any sense. If you are negative for a SNP, it didn't occur in your ancestry. Your sequence at that point is the ancestral sequence, but calling a negative result an "ancestral SNP" seems like a recipe for confusion.

Debbie Kennett said...

PNG, I didn't come up with the terminology and we're stuck with what we have, even though it is very confusing. The ancestral state is the original state before any mutations occur. We say that someone is "positive" for a mutation which defines a new branch. If you're negative it means you have the ancestral state (ie, no mutation, hence the negative status).

PNG said...

Debbie, I had an exchange with Charles Moore the other day in which he said (in essence) that "ancestral SNPs" are SNPs that you do have but they occurred upstream, before the clade defining SNP of your group, e.g. if you are U106 any SNP on the line leading to U106, like M269, is an ancestral SNP. You said an ancestral SNP is one that you don't have. You two are using the term "ancestral SNP" in contradictory ways. I've been reading genetics papers for decades - I was a biochemist. Geneticists talk about ancestral sequence or derived sequence. I realize genetic genealogy is its own culture with its own language, and I can figure out what is meant, but it seems like it would help the newbies if terms were used in a consistent way.

Debbie Kennett said...

PNG

I've written to FTDNA to see if they can update their FAQs and provide a proper explanation for ancestral vs derived. In the meantime I found these links which I hope might be of help:

http://www.isogg.org/course/glossary.htm

http://www.familytreedna.com/learn/faq-items/ancestral-state/

http://www.familytreedna.com/learn/faq-items/derived-state/

Peter MacDonald said...

I have received my Big Y Results and am very glad I signed up for the test. Prior to taking the Big Y, I knew that I was L1065. Results have immediately taken me 4 SNPs downstream of L1065. On top of this I have the Big Y has me positive with a high confidence for an additional 82 Novel (variant) SNPs. Once these novel/variant SNPs are compared with the results of others (which may take some time) much will be learned about my paternal linage.

Although the Big Y had a rocky start this time around (remained of Big Y test results are scheduled to be completed prior to 28 March 2014) I am extremely satisfied with the product that FTDNA has created.

Once all the novel/variant SNPs are sorted out, I believe that the Big Y will be the most beneficial genetic genealogy test on the market. From my personal experience with both my currently known results and the expected follow-on information that is expected, I highly recommend this product to anyone interested in their paternal ancestry. Well worth the investment.

Debbie Kennett said...

Peter, Thanks for your feedback. I'm still waiting for my dad's results. I think your investment will continue to grow over time. As with all DNA testing the value is in the comparison process and the more people who take the BIG Y/Full Genomes tests the more we will learn.

Doug Morrison said...

Debbie,

You are right, that the more people who test then the more we as a group will learn. I belong to the L21+, M222+ project, but that project is loaded with speculation as to what group(s) of people it could represent and there are a number of dedicated and enthusiastic genetic volunteers who are trying to make sense of it. And so I took the Big Y test to help support their efforts (and I received those test results just the other day).

Best,

Doug

Debbie Kennett said...

Doug, Good luck with your Big Y test. It's going to take a while to interpret all these results and do the comparisons with the tests from all the other companies. There have already been lots of downstream M222 SNPs appearing on the Chromo 2 chip. It will be interesting to see how many of these can be replicated in the Big Y and how many new SNPs will be discovered. M222 really needs these SNPs because people can have large numbers of matches with the STRs.

Doug Morrison said...

Debbie, yes, what with all of the new SNP testing standards now in use, including the variations in their labeling, the Internet rumor is that 2014 is going to be an unsettled, "shake-down" year. But all of that will eventually get settled.

Jeepguy2014 said...

My cousin took the Big Y test to supplement is Y-DNA he did years ago. He got the results back but has no clue what all this data means and what to do with it.

What the heck does all this mean?


CTS11985+, CTS12478+, CTS2664+, CTS3063+, CTS3358+, CTS3575+, CTS3654+, CTS4716+, CTS4244+, F1209+, F3692+, F719+, F82+, L104+, L11+, L132+, L138+, L141+, L15+, L150+, L151+, L16+, L407+, L468+, L470+, L482+, L483+, L498+, L500+, L502+, L506+, L51+, L52+, L585+, L747+, L752+, L754+, L761+, L768+, L773+, L779+, L82+, L23+, L265+, L278+, L350+, L389+, M168+, M173+, M207+, M213+, M235+, M269+, M294+, M299+, M306+, M343+, M365+, M74+, M89+, M9+, M94+, P108+, P128+, P131+, P132+, P133+, P134+, P135+, P136+, P138+, P139+, P14+, P140+, P141+, P143+, P145+, P146+, P148+, P149+, P151+, P157+, P158+, P159+, P160+, P161+, P163+, P166+, P187+, P207+, P224+, P225+, P226+, P228+, P229+, P230+, P231+, P232+, P233+, P234+, P235+, P236+, P237+, P238+, P239+, P242+, P243+, P244+, P245+, P280+, P281+, P282+, P283+, P284+, P285+, P286+, P294+, P295+, P297+, P305+, P310+, P311+, P312+, P316+, PF2591+, PF2608+, PF2611+, PF2615+, PF2747+, PF2748+, PF2749+, PF2770+, PF3561+, PF5869+, PF5871+, PF5882+, PF5886+, PF5888+, PF5953+, PF5956+, PF5957+, PF5964+, PF5965+, PF5982+, PF6246+, PF6249+, PF6250+, PF6263+, PF6270+, PF6271+, PF6272+, PF6409+, PF6425+, PF6430+, PF6432+, PF6434+, PF6438+, PF6463+, PF6494+, PF6495+, PF6498+, PF6500+, PF6506+, PF6507+, PF6509+, PF6524+, PK1+, SRY10831+, SRY2627+, P69+, P9+, P97+, PAGES00026+, PAGES00081+, PAGES00083+, V221+, V241+, V250+, Z177+, Z195+, Z199+, M415+, M42+, M45+, M526+, Z204+, F313+, Z269+, CTS10893-, F3198-, Z205-, Z207-, Z264-, Z266-, M65-, Z202-, Z203-, PF1023-, PF2462-, U152-, P66-, M37-, M222-, M228-, L4-, L96-, M126-, M153-, M160-, L163-, L165-, L193-, L196-, L20-, L21-, L226-, L144-, F1287-, F2536-, CTS4299-, CTS5284-, CTS606-, CTS7416-, CTS8234-, CTS9454-, CTS4015-

Jeepguy2014 said...

I did the Y-DNA 67 marker but now I am glad I didn't do the Big Y. That was pretty pricey just to get a bunch of numbers that don't mean anything to most novice users. We were expecting it to give you matches like the Y-DNA does.

Debbie Kennett said...

Jeepguy

The Big Y test is only for experienced users. A single Big Y test on its own is not going to be of any help for genealogical purposes at the present time. The Big Y test is a SNP discovery test to identify new subclades. The discovery process involves people sharing their results within haplogroup projects in order to identify new shared downstream SNPs.

The list is a list of all the SNPs (markers) for which your cousin is positive. He is in the Z195 subclade which is a branch of the big P312 subclade. He should join the P312 and subclades project:

https://www.familytreedna.com/public/atlantic-r1b1c/ 

The Big Y results might explain the longhand name you said he'd been given in a comment elsewhere. The database seems to be in the process of being recalculated so you might find that the names will change in the next day or so. Either way, the haplogroup project admins should be able to help you.