The $1000 Genome? – Not Exactly

HiSeqXTen

You may have seen the headlines and the announcement this week by Illumina, manufacturer of gene sequencing equipment, that the $1000 genome is finally here.  Hallelujah –  jump for joy – right?  Sign me up – where can I order???

Well, not so fast.

It’s a great headline – and depending on how you figure the math – it’s not entirely untrue, but it’s a real struggle to get there.  Some marketing maven did some real spreadsheet magic!  What is that old saying, “lies, damned lies and statistics”?  Maybe that’s a little harsh, but it’s not too far off.

So, is the $1000 genome here or not?  Well, kindof.  It depends on how you count, and who you are.  You see, it’s a math thing.

It’s kind of like a mortgage.  How much did your house cost?  Let’s say $100,000 – that was the price on the “for sale” sign.  But by the time you get the mortgage paid off, 30 years later, the cost of that house is way more than $100,000, probably more than $250,000 and if you add in the cost of taxes, closing costs and maintenance, even more.  This will only depress you, so don’t think about, especially when you sell your house for $150,000 and declare that you “made” $50,000.  But I digress…

So, let’s translate this to the $1000 genome.

Dr. David Mittleman, Chief Scientific Officer for Gene by Gene, Ltd., parent company of Family Tree DNA, was at the conference this week where the Illumina announcement was made. I asked him several questions about this new technology and if it was ready for prime time yet.

His first comment shed some light on costs.

“The HiSeqX Ten system is actually a ten-pack of new HiSeq instruments, each costing 1 million dollars. So you have to spend $10 million on equipment before you can even get started.”

Ouch.  I guess I won’t be buying one anytime soon!

To begin with, without the cost of the kits or processing or staff or software or installation or financing or support contracts or profit, a company would have to sell 10,000 kits at $1000 to even bring the cost of the equipment to $1000 per kit.

So, how did Illumina figure the cost of the $1000 genome?  The $1000 is broken down as $800 on reagents, $135 on equipment depreciation over 4 years, and $65 on staff/overheads.

This means that to obtain that $1000 per genome price, you have to run the equipment at full capacity, 24X7, 18,000 kits per year, for 4 full years.  And that still doesn’t include everything.  You also need service contracts, installation, additional labor, etc.  You can read more about the math and cost of ownership here.

And sure enough, when I asked David about who has purchased one so far, there are two buyers and both are institutions.  This is an extremely high end product, not something for the DTC consumer marketspace.

Now this isn’t to say this announcement is a bad thing – it’s not – it’s just not exactly what the headlines suggest.  It’s the $1000 genome for those with deep pockets who can purchase a $10,000,000 piece of gear and then run 18,000 samples, for 4 years, plus expenses.  But yes, it does technically break down to $1000 per test as long as you hit all of those milestones and ignore the rest of the expenses.  If you can afford $10 million and have the staff to run it, you probably don’t care about the cost of installation, labor and support contracts.  They are just necessary incidentals – like gas for my lawn mower!

In spite of the fancy math, it’s truly amazing how far we’ve come when you consider that a single full genome sequence still cost about 3 million in 2007, and in November 2012 Gene by Gene was the first to offer full sequencing commercially and offered it to their customers for an introductory price of $5495.  Of course, with no analysis tools and few testers, I can’t imagine what one would do with those results.  This has changed somewhat today.  The full genome with some analysis is available today to consumers for $7595, but the question of what is available that is genealogically useful to do with these results still remains, and will, until many more people test and meaningful comparisons are available.

The Illumina announcement also raises the issue of software investment to do something useful with the massive amount of data this new equipment will generate…also nontrivial, and that software does not exist yet today.

There are other issues to be addressed as well, like open access libraries.  Will they exist?  If so, where?  Who cares for them?  How are they funded?  Who will have access?  Will this data be made available in open access libraries, assuming they exist?

Illumina has reported that entire countries have approached them asking for their population to be sequenced, which also begs questions of privacy, security and how exactly to anonymize the samples without them becoming useless to research.  This high tech watershed announcement may spur as many questions as answers, but these issues need to be resolved in the academic environment before they trickle down to the consumer marketspace.

This is not to minimize the science and technology that has propelled us to this breakthrough.  It is a wonderful scientific and technological advancement because it will allow governments or large institutes to do huge population-wide studies.  This is something we desperately need.  Think for a minute if our Population Finder ethnicity results were based on tens of thousands of samples instead of selected hundreds.

For genetic genealogists, we are poised to benefit in the future, probably the more distant than the near future.  The $1000 genome for consumers not only isn’t here, it’s not even within sniffing distance.  So put your checkbooks away or better yet, buy a Big Y or a Family Finder test for a cousin, something that will benefit you in the short term.

This next step in the world of genetic discovery is exciting for research institutes, but it’s not yet ready for consumer prime time.  We will be the beneficiaries, but not the direct consumers….yet…unless you want to move to one of those countries who wants their entire population sequenced.  Our turn will come.  Maybe the next time we see an announcement for the $1000 genome it will be calculated in normal home-owning-human terms.

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2013’s Dynamic Dozen – Top Genetic Genealogy Happenings

dna 8 ball

Last year I wrote a column at the end of the year titled  “2012 Top 10 Genetic Genealogy Happenings.”  It’s amazing the changes in this industry in just one year.  It certainly makes me wonder what the landscape a year from now will look like.

I’ve done the same thing this year, except we have a dozen.  I couldn’t whittle it down to 10, partly because there has been so much more going on and so much change – or in the case of Ancestry, who is noteworthy because they had so little positive movement.

If I were to characterize this year of genetic genealogy, I would call it The Year of the SNP, because that applies to both Y DNA and autosomal.  Maybe I’d call it The Legal SNP, because it is also the year of law, court decisions, lawsuits and FDA intervention.  To say it has been interesting is like calling the Eiffel Tower an oversized coat hanger.

I’ll say one thing…it has kept those of us who work and play in this industry hopping busy!  I guarantee you, the words “I’m bored” have come out of the mouth of no one in this industry this past year.

I’ve put these events in what I consider to be relatively accurate order.  We could debate all day about whether the SNP Tsunami or the 23andMe mess is more important or relevant – and there would be lots of arguing points and counterpoints…see…I told you lawyers were involved….but in reality, we don’t know yet, and in the end….it doesn’t matter what order they are in on the list:)

Y Chromosome SNP Tsunami Begins

The SNP tsumani began as a ripple a few years ago with the introduction at Family Tree DNA of the Walk the Y program in 2007.  This was an intensively manual process of SNP discovery, but it was effective.

By the time that the Geno 2.0 chip was introduced in 2012, 12,000+ SNPs would be included on that chip, including many that were always presumed to be equivalent and not regularly tested.  However, the Nat Geo chip tested them and indeed, the Y tree became massively shuffled.  The resolution to this tree shuffling hasn’t yet come out in the wash.  Family Tree DNA can’t really update their Y tree until a publication comes out with the new tree defined.  That publication has been discussed and anticipated for some time now, but it has yet to materialize.  In the mean time, the volunteers who maintain the ISOGG tree are swamped, to say the least.

Another similar test is the Chromo2 introduced this year by Britain’s DNA which scans 15,000 SNPs, many of them S SNPs not on the tree nor academically published, adding to the difficulty of figuring out where they fit on the Y tree.  While there are some very happy campers with their Chromo2 results, there is also a great deal of sloppy science, reporting and interpretation of “facts” through this company.  Kind of like Jekyll and Hyde.  See the Sloppy Science section.

But Walk the Y, Chromo2 and Geno 2.0, are only the tip of the iceburg.  The new “full Y” sequencing tests brought into the marketspace quietly in early 2013 by Full Genomes and then with a bang by Family Tree DNA with the their Big Y in November promise to revolutionize what we know about the Y chromosome by discovering thousands of previously unknown SNPs.  This will in effect swamp the Y tree whose branches we thought were already pretty robust, with thousands and thousands of leaves.

In essence, the promise of the “fully” sequenced Y is that what we might term personal or family SNPs will make SNP testing as useful as STR testing and give us yet another genealogy tool with which to separate various lines of one genetic family and to ratchet down on the time that the most common recent ancestor lived.

http://dna-explained.com/2013/03/31/new-y-dna-haplogroup-naming-convention/

http://dna-explained.com/2013/11/10/family-tree-dna-announces-the-big-y/

http://dna-explained.com/2013/11/16/what-about-the-big-y/

http://www.yourgeneticgenealogist.com/2013/11/first-look-at-full-genomes-y-sequencing.html

http://cruwys.blogspot.com/2013/12/a-first-look-at-britainsdna-chromo-2-y.html

http://cruwys.blogspot.com/2013/11/yseqnet-new-company-offering-single-snp.html

http://cruwys.blogspot.com/2013/11/the-y-chromosome-sequence.html

http://cruwys.blogspot.com/2013/11/a-confusion-of-snps.html

http://cruwys.blogspot.com/2013/11/a-simplified-y-tree-and-common-standard.html

23andMe Comes Unraveled

The story of 23andMe began as the consummate American dotcom fairy tale, but sadly, has deteriorated into a saga with all of the components of a soap opera.  A wealthy wife starts what could be viewed as an upscale hobby business, followed by a messy divorce and a mystery run-in with the powerful overlording evil-step-mother FDA.  One of the founders of 23andMe is/was married to the founder of Google, so funding, at least initially wasn’t an issue, giving 23andMe the opportunity to make an unprecedented contribution in the genetic, health care and genetic genealogy world.

Another way of looking at this is that 23andMe is the epitome of the American Dream business, a startup, with altruism and good health, both thrown in for good measure, well intentioned, but poorly managed.  And as customers, be it for health or genealogy or both, we all bought into the altruistic “feel good” culture of helping find cures for dread diseases, like Parkinson’s, Alzheimer’s and cancer by contributing our DNA and responding to surveys.

The genetic genealogy community’s love affair with 23andMe began in 2009 when 23andMe started focusing on genealogy reporting for their tests, meaning cousin matches.  We, as a community, suddenly woke up and started ordering these tests in droves.  A few months later, Family Tree DNA also began offering this type of testing as well.  The defining difference being that 23andMe’s primary focus has always been on health and medical information with Family Tree DNA focused on genetic genealogy.  To 23andMe, the genetic genealogy community was an afterthought and genetic genealogy was just another marketing avenue to obtain more people for their health research data base.  For us, that wasn’t necessarily a bad thing.

For awhile, this love affair went along swimmingly, but then, in 2012, 23andMe obtained a patent for Parkinson’s Disease.  That act caused a lot of people to begin to question the corporate focus of 23andMe in the larger quagmire of the ethics of patenting genes as a whole.  Judy Russell, the Legal Genealogist, discussed this here.  It’s difficult to defend 23andMe’s Parkinson’s patent while flaying alive Myriad for their BRCA patent.  Was 23andMe really as altruistic as they would have us believe?

Personally, this event made me very nervous, but I withheld judgment.  But clearly, that was not the purpose for which I thought my DNA, and others, was being used.

But then came the Designer Baby patent in 2013.  This made me decidedly uncomfortable.  Yes, I know, some people said this really can’t be done, today, while others said that it’s being done anyway in some aspects…but the fact that this has been the corporate focus of 23andMe with their research, using our data, bothered me a great deal.  I have absolutely no issue with using this information to assure or select for healthy offspring – but I have a personal issue with technology to enable parents who would select a “beauty child,” one with blonde hair and blue eyes and who has the correct muscles to be a star athlete, or cheerleader, or whatever their vision of their as-yet-unconceived “perfect” child would be.  And clearly, based on 23andMe’s own patent submission, that is the focus of their patent.

Upon the issuance of the patent, 23andMe then said they have no intention of using it.  They did not say they won’t sell it.  This also makes absolutely no business sense, to focus valuable corporate resources on something you have no intention of using?  So either they weren’t being truthful, they lack effective management or they’ve changed their mind, but didn’t state such.

What came next, in late 2013 certainly points towards a lack of responsible management.

23andMe had been working with the FDA for approval the health and medical aspect of their product (which they were already providing to consumers prior to the November 22nd cease and desist order) for several years.  The FDA wants assurances that what 23andMe is telling consumers is accurate.  Based on the letter issued to 23andMe on November 22nd, and subsequent commentary, it appears that both entities were jointly working towards that common goal…until earlier this year when 23andMe mysteriously “somehow forgot” about the FDA, the information they owed them, their submissions, etc.  They also forgot their phone number and their e-mail addresses apparently as well, because the FDA said they had heard nothing from them in 6 months, which backdates to May of 2013.

It may be relevant that 23andMe added the executive position of President and filled it in June of 2013, and there was a lot of corporate housecleaning that went on at that time.  However, regardless of who got housecleaned, the responsibility for working with the FDA falls squarely on the shoulders of the founders, owners and executives of the company.  Period.  No excuses.  Something that critically important should be on the agenda of every executive management meeting.   Why?  In terms of corporate risk, this was obviously a very high risk item, perhaps the highest risk item, because the FDA can literally shut their doors and destroy them.  There is little they can do to control or affect the FDA situation, except to work with the FDA, meet deadlines and engender goodwill and a spirit of cooperation.  The risk of not doing that is exactly what happened.

It’s unknown at this time if 23andMe is really that corporately arrogant to think they could simply ignore the FDA, or blatantly corporately negligent or maybe simply corporately stupid, but they surely betrayed the trust and confidence of their customers by failing to meet their commitments with and to the FDA, or even communicate with them.  I mean, really, what were they thinking?

There has been an outpouring of sympathy for 23andme and negative backlash towards the FDA for their letter forcing 23andMe to stop selling their offending medical product, meaning the health portion of their testing.  However, in reality, the FDA was only meting out the consequences that 23andMe asked for.  My teenage kids knew this would happen.  If you do what you’re not supposed to….X, Y and Z will, or won’t, happen.  It’s called accountability.  Just ask my son about his prom….he remembers vividly.  Now why my kids, or 23andMe, would push an authority figure to that point, knowing full well the consequences, utterly mystifies me.  It did when my son was a teenager and it does with 23andMe as well.

Some people think that the FDA is trying to stand between consumers and their health information.  I don’t think so, at least not in this case.  Why I think that is because the FDA left the raw data files alone and they left the genetic genealogy aspect alone.  The FDA knows full well you can download your raw data and for $5 process it at a third party site, obtaining health related genetic information.  The difference is that Promethease is not interpreting any data for you, only providing information.

There is some good news in this and that is that from a genetic genealogy perspective, we seem to be safe, at least for now, from government interference with the testing that has been so productive for genetic genealogy.  The FDA had the perfect opportunity to squish us like a bug (thanks to the opening provided by 23andMe,) and they didn’t.

The really frustrating aspect of this is that 23andMe was a company who, with their deep pockets in Silicon Valley and other investors, could actually afford to wage a fight with the FDA, if need be.  The other companies who received the original 2010 FDA letter all went elsewhere and focused on something else.  But 23andMe didn’t, they decided to fight the fight, and we all supported their decision.  But they let us all down.  The fight they are fighting now is not the battle we anticipated, but one brought upon themselves by their own negligence.  This battle didn’t have to happen, and it may impair them financially to such a degree that if they need to fight the big fight, they won’t be able to.

Right now, 23andMe is selling their kits, but only as an ancestry product as they work through whatever process they are working through with the FDA.  Unfortunately, 23andMe is currently having some difficulties where the majority of matches are disappearing from some testers records.  In other cases, segments that previously matched are disappearing.  One would think, with their only revenue stream for now being the genetic genealogy marketspace that they would be wearing kid gloves and being extremely careful, but apparently not.  They might even consider making some of the changes and enhancements we’ve requested for so long that have fallen on deaf ears.

One thing is for sure, it will be extremely interesting to see where 23andMe is this time next year.  The soap opera continues.

I hope for the sake of all of the health consumers, both current and (potentially) future, that this dotcom fairy tale has a happy ending.

Also, see the Autosomal DNA Comes of Age section.

http://dna-explained.com/2013/10/05/23andme-patents-technology-for-designer-babies/

http://www.thegeneticgenealogist.com/2013/10/07/a-new-patent-for-23andme-creates-controversy/

http://dna-explained.com/2013/11/13/genomics-law-review-discusses-designing-children/

http://www.thegeneticgenealogist.com/2013/06/11/andy-page-fills-new-president-position-at-23andme/

http://dna-explained.com/2013/11/25/fda-orders-23andme-to-discontinue-testing/

http://dna-explained.com/2013/11/26/now-what-23andme-and-the-fda/

http://dna-explained.com/2013/12/06/23andme-suspends-health-related-genetic-tests/

http://www.legalgenealogist.com/blog/2013/11/26/fooling-with-fda/

Supreme Court Decision – Genes Can’t Be Patented – Followed by Lawsuits

In a landmark decision, the Supreme Court determined that genes cannot be patented.  Myriad Genetics held patents on two BRCA genes that predisposed people to cancer.  The cost for the tests through Myriad was about $3000.  Six hours after the Supreme Court decision, Gene By Gene announced that same test for $995.  Other firms followed suit, and all were subsequently sued by Myriad for patent infringement.  I was shocked by this, but as one of my lawyer friends clearly pointed out, you can sue anyone for anything.  Making it stick is yet another matter.  Many firms settle to avoid long and very expensive legal battles.  Clearly, this issue is not yet resolved, although one would think a Supreme Court decision would be pretty definitive.  It potentially won’t be settled for a long time.

http://dna-explained.com/2013/06/13/supreme-court-decision-genes-cant-be-patented/

http://www.legalgenealogist.com/blog/2013/06/14/our-dna-cant-be-patented/

http://dna-explained.com/2013/09/07/message-from-bennett-greenspan-free-my-genes/

http://www.thegeneticgenealogist.com/2013/06/13/new-press-release-from-dnatraits-regarding-the-supreme-courts-holding-in-myriad/

http://www.legalgenealogist.com/blog/2013/08/18/testing-firms-land-counterpunch/

http://www.legalgenealogist.com/blog/2013/07/11/myriad-sues-genetic-testing-firms/

Gene By Gene Steps Up, Ramps Up and Produces

As 23andMe comes unraveled and Ancestry languishes in its mediocrity, Gene by Gene, the parent company of Family Tree DNA has stepped up to the plate, committed to do “whatever it takes,” ramped up the staff both through hiring and acquisitions, and is producing results.  This is, indeed, a breath of fresh air for genetic genealogists, as well as a welcome relief.

http://dna-explained.com/2013/08/07/gene-by-gene-acquires-arpeggi/

http://dna-explained.com/2013/12/05/family-tree-dna-listens-and-acts/

http://dna-explained.com/2013/12/10/family-tree-dnas-family-finder-match-matrix-released/

http://www.haplogroup.org/ftdna-family-finder-matches-get-new-look/

http://www.haplogroup.org/ftdna-family-finder-new-look-2/

http://www.haplogroup.org/ftdna-family-finder-matches-new-look-3/

Autosomal DNA Comes of Age

Autosomal DNA testing and analysis has simply exploded this past year.  More and more people are testing, in part, because Ancestry.com has a captive audience in their subscription data base and more than a quarter million of those subscribers have purchased autosomal DNA tests.  That’s a good thing, in general, but there are some negative aspects relative to Ancestry, which are in the Ancestry section.

Another boon to autosomal testing was the 23andMe push to obtain a million records.  Of course, the operative word here is “was” but that may revive when the FDA issue is resolved.  One of the down sides to the 23andMe data base, aside from the fact that it’s not genealogist friendly, is that so many people, about 90%, don’t communicate.  They aren’t interested in genealogy.

A third factor is that Family Tree DNA has provided transfer ability for files from both 23andMe and Ancestry into their data base.

Fourth is the site, GedMatch, at www.gedmatch.com which provides additional matching and admixture tools and the ability to match below thresholds set by the testing companies.  This is sometimes critically important, especially when comparing to known cousins who just don’t happen to match at the higher thresholds, for example.  Unfortunately, not enough people know about GedMatch, or are willing to download their files.  Also unfortunate is that GedMatch has struggled for the past few months to keep up with the demand placed on their site and resources.

A great deal of time this year has been spent by those of us in the education aspect of genetic genealogy, in whatever our capacity, teaching about how to utilize autosomal results. It’s not necessarily straightforward.  For example, I wrote a 9 part series titled “The Autosomal Me” which detailed how to utilize chromosome mapping for finding minority ethnic admixture, which was, in my case, both Native and African American.

As the year ends, we have Family Tree DNA, 23andMe and Ancestry who offer the autosomal test which includes the relative-matching aspect.  Fortunately, we also have third party tools like www.GedMatch.com and www.DNAGedcom.com, without which we would be significantly hamstrung.  In the case of DNAGedcom, we would be unable to perform chromosome segment matching and triangulation with 23andMe data without Rob Warthen’s invaluable tool.

http://dna-explained.com/2013/06/21/triangulation-for-autosomal-dna/

http://dna-explained.com/2013/07/13/combining-tools-autosomal-plus-y-dna-mtdna-and-the-x-chromosome/

http://dna-explained.com/2013/07/26/family-tree-dna-levels-the-playing-field-sort-of/

http://dna-explained.com/2013/08/03/kitty-coopers-chromsome-mapping-tool-released/

http://dna-explained.com/2013/09/29/why-dont-i-match-my-cousin/

http://dna-explained.com/2013/10/03/family-tree-dna-updates-family-finder-and-adds-triangulation/

http://dna-explained.com/2013/10/21/why-are-my-predicted-cousin-relationships-wrong/

http://dna-explained.com/2013/12/05/family-tree-dna-listens-and-acts/

http://dna-explained.com/2013/12/09/chromosome-mapping-aka-ancestor-mapping/

http://dna-explained.com/2013/12/10/family-tree-dnas-family-finder-match-matrix-released/

http://dna-explained.com/2013/12/15/one-chromosome-two-sides-no-zipper-icw-and-the-matrix/

http://dna-explained.com/2013/06/02/the-autosomal-me-summary-and-pdf-file/

DNAGedcom – Indispensable Third Party Tool

While this tool, www.dnagedcom.com, falls into the Autosomal grouping, I have separated it out for individual mention because without this tool, the progress made this year in autosomal DNA ancestor and chromosomal mapping would have been impossible.  Family Tree DNA has always provided segment matching boundaries through their chromosome browser tool, but until recently, you could only download 5 matches at a time.  This is no longer the case, but for most of the year, Rob’s tool saved us massive amounts of time.

23andMe does not provide those chromosome boundaries, but utilizing Rob’s tool, you can obtain each of your matches in one download, and then you can obtain the list of who your matches match that is also on your match list by requesting each of those files separately.  Multiple steps?  Yes, but it’s the only way to obtain this information, and chromosome mapping without the segment data is impossible

A special hats off to Rob.  Please remember that Rob’s site is free, meaning it’s donation based.  So, please donate if you use the tool.

http://www.yourgeneticgenealogist.com/2013/01/brought-to-you-by-adoptiondna.html

I covered www.Gedmatch.com in the “Best of 2012” list, but they have struggled this year, beginning when Ancestry announced that raw data file downloads were available.  GedMatch consists of two individuals, volunteers, who are still struggling to keep up with the required processing and the tools.  They too are donation based, so don’t forget about them if you utilize their tools.

Ancestry – How Great Thou Aren’t

Ancestry is only on this list because of what they haven’t done.  When they initially introduced their autosomal product, they didn’t have any search capability, they didn’t have a chromosome browser and they didn’t have raw data file download capability, all of which their competitors had upon first release.  All they did have was a list of your matches, with their trees listed, with shakey leaves if you shared a common ancestor on your tree.  The implication, was, and is, of course, that if you have a DNA match and a shakey leaf, that IS your link, your genetic link, to each other.  Unfortunately, that is NOT the case, as CeCe Moore documented in her blog from Rootstech (starting just below the pictures) as an illustration of WHY we so desperately need a chromosome browser tool.

In a nutshell, Ancestry showed the wrong shakey leaf as the DNA connection – as proven by the fact that both of CeCe’s parents have tested at Ancestry and the shakey leaf person doesn’t match the requisite parent.  And there wasn’t just one, not two, but three instances of this.  What this means is, of course, that the DNA match and the shakey leaf match are entirely independent of each other.  In fact, you could have several common ancestors, but the DNA at any particular location comes only from one on either Mom or Dad’s side – any maybe not even the shakey leaf person.

So what Ancestry customers are receiving is a list of people they match and possible links, but most of them have no idea that this is the case, and blissfully believe they have found their genetic connection.  They have found a genealogical cousin, and it MIGHT be the genetic connection.  But then again, they could have found that cousin simply by searching for the same ancestor in Ancestry’s data base.  No DNA needed.

Ancestry has added a search feature, allowed raw data file downloads (thank you) and they have updated their ethnicity predictions.  The ethnicity predictions are certainly different, dramatically different, but equally as unrealistic.  See the Ethnicity Makeovers section for more on this.  The search function helps, but what we really need is the chromosome browser, which they have steadfastly avoided promising.  Instead, they have said that they will give us “something better,” but nothing has materialized.

I want to take this opportunity, to say, as loudly as possible, that TRUST ME IS NOT ACCEPTABLE in any way, shape or form when it comes to genetic matching.  I’m not sure what Ancestry has in mind by the way of “better,” but it if it’s anything like the mediocrity with which their existing DNA products have been rolled out, neither I nor any other serious genetic genealogist will be interested, satisfied or placated.

Regardless, it’s been nearly 2 years now.  Ancestry has the funds to do development.  They are not a small company.  This is obviously not a priority because they don’t need to develop this feature.  Why is this?  Because they can continue to sell tests and to give shakey leaves to customers, most of whom don’t understand the subtle “untruth” inherent in that leaf match – so are quite blissfully happy.

In years past, I worked in the computer industry when IBM was the Big Dog against whom everyone else competed.  I’m reminded of an old joke.  The IBM sales rep got married, and on his wedding night, he sat on the edge of the bed all night long regaling his bride in glorious detail with stories about just how good it was going to be….

You can sign a petition asking Ancestry to provide a chromosome browser here, and you can submit your request directly to Ancestry as well, although to date, this has not been effective.

The most frustrating aspect of this situation is that Ancestry, with their plethora of trees, savvy marketing and captive audience testers really was positioned to “do it right,” and hasn’t, at least not yet.  They seem to be more interested in selling kits and providing shakey leaves that are misleading in terms of what they mean than providing true tools.  One wonders if they are afraid that their customers will be “less happy” when they discover the truth and not developing a chromosome browser is a way to keep their customers blissfully in the dark.

http://dna-explained.com/2013/03/21/downloading-ancestrys-autosomal-dna-raw-data-file/

http://dna-explained.com/2013/03/24/ancestry-needs-another-push-chromosome-browser/

http://dna-explained.com/2013/10/17/ancestrys-updated-v2-ethnicity-summary/

http://www.thegeneticgenealogist.com/2013/06/21/new-search-features-at-ancestrydna-and-a-sneak-peek-at-new-ethnicity-estimates/

http://www.yourgeneticgenealogist.com/2013/03/ancestrydna-raw-data-and-rootstech.html

http://www.legalgenealogist.com/blog/2013/09/15/dna-disappointment/

http://www.legalgenealogist.com/blog/2013/09/13/ancestrydna-begins-rollout-of-update/

Ancient DNA

This has been a huge year for advances in sequencing ancient DNA, something once thought unachievable.  We have learned a great deal, and there are many more skeletal remains just begging to be sequenced.  One absolutely fascinating find is that all people not African (and some who are African through backmigration) carry Neanderthal and Denisovan DNA.  Just this week, evidence of yet another archaic hominid line has been found in Neanderthal DNA and on Christmas Day, yet another article stating that type 2 Diabetes found in Native Americans has roots in their Neanderthal ancestors. Wow!

Closer to home, by several thousand years is the suggestion that haplogroup R did not exist in Europe after the ice age, and only later, replaced most of the population which, for males, appears to have been primarily haplogroup G.  It will be very interesting as the data bases of fully sequenced skeletons are built and compared.  The history of our ancestors is held in those precious bones.

http://dna-explained.com/2013/01/10/decoding-and-rethinking-neanderthals/

http://dna-explained.com/2013/07/04/ancient-dna-analysis-from-canada/

http://dna-explained.com/2013/07/10/5500-year-old-grandmother-found-using-dna/

http://dna-explained.com/2013/10/25/ancestor-of-native-americans-in-asia-was-30-western-eurasian/

http://dna-explained.com/2013/11/12/2013-family-tree-dna-conference-day-2/

http://dna-explained.com/2013/11/22/native-american-gene-flow-europe-asia-and-the-americas/

http://dna-explained.com/2013/12/05/400000-year-old-dna-from-spain-sequenced/

http://www.thegeneticgenealogist.com/2013/10/16/identifying-otzi-the-icemans-relatives/

http://cruwys.blogspot.com/2013/12/recordings-of-royal-societys-ancient.html

http://cruwys.blogspot.com/2013/02/richard-iii-king-is-found.html

http://dna-explained.com/2013/12/22/sequencing-of-neanderthal-toe-bone-reveals-unknown-hominin-line/

http://dna-explained.com/2013/12/26/native-americans-neanderthal-and-denisova-admixture/

http://dienekes.blogspot.com/2013/12/ancient-dna-what-2013-has-brought.html

Sloppy Science and Sensationalist Reporting

Unfortunately, as DNA becomes more mainstream, it becomes a target for both sloppy science or intentional misinterpretation, and possibly both.  Unfortunately, without academic publication, we can’t see results or have the sense of security that comes from the peer review process, so we don’t know if the science and conclusions stand up to muster.

The race to the buck in some instances is the catalyst for this. In other cases, and not in the links below, some people intentionally skew interpretations and results in order to either fulfill their own belief agenda or to sell “products and services” that invariably report specific findings.

It’s equally as unfortunate that much of these misconstrued and sensationalized results are coming from a testing company that goes by the names of BritainsDNA, ScotlandsDNA, IrelandsDNA and YorkshiresDNA. It certainly does nothing for their credibility in the eyes of people who are familiar with the topics at hand, but it does garner a lot of press and probably sells a lot of kits to the unwary.

I hope they publish their findings so we can remove the “sloppy science” aspect of this.  Sensationalist reporting, while irritating, can be dealt with if the science is sound.  However, until the results are published in a peer-reviewed academic journal, we have no way of knowing.

Thankfully, Debbie Kennett has been keeping her thumb on this situation, occurring primarily in the British Isles.

http://dna-explained.com/2013/08/24/you-might-be-a-pict-if/

http://cruwys.blogspot.com/2013/12/the-british-genetic-muddle-by-alistair.html

http://cruwys.blogspot.com/2013/12/setting-record-straight-about-sara.html

http://cruwys.blogspot.com/2013/09/private-eye-on-britainsdna.html

http://cruwys.blogspot.com/2013/07/private-eye-on-prince-williams-indian.html

http://cruwys.blogspot.com/2013/06/britainsdna-times-and-prince-william.html

http://cruwys.blogspot.com/2013/03/sense-about-genealogical-dna-testing.html

http://cruwys.blogspot.com/2013/03/sense-about-genetic-ancestry-testing.html

Citizen Science is Coming of Age

Citizen science has been slowing coming of age over the past few years.  By this, I mean when citizen scientists work as part of a team on a significant discovery or paper.  Bill Hurst comes to mind with his work with Dr. Doron Behar on his paper, A Copernican Reassessment of the Human Mitochondrial DNA from its Root or what know as the RSRS model.  As the years have progressed, more and more discoveries have been made or assisted by citizen scientists, sometimes through our projects and other times through individual research.  JOGG, the Journal of Genetic Genealogy, which is currently on hiatus waiting for Dr. Turi King, the new editor, to become available, was a great avenue for peer reviewed publication.  Recently, research projects have been set up by citizen scientists, sometimes crowd-funded, for specific areas of research.  This is a very new aspect to scientific research, and one not before utilized.

The first paper below includes the Family Tree DNA Lab, Thomas and Astrid Krahn, then with Family Tree DNA and Bonnie Schrack, genetic genealogist and citizen scientist, along with Dr. Michael Hammer from the University of Arizona and others.

http://dna-explained.com/2013/03/26/family-tree-dna-research-center-facilitates-discovery-of-ancient-root-to-y-tree/

http://dna-explained.com/2013/04/10/diy-dna-analysis-genomeweb-and-citizen-scientist-2-0/

http://dna-explained.com/2013/06/27/big-news-probable-native-american-haplogroup-breakthrough/

http://dna-explained.com/2013/07/22/citizen-science-strikes-again-this-time-in-cameroon/

http://dna-explained.com/2013/11/30/native-american-haplogroups-q-c-and-the-big-y-test/

http://www.yourgeneticgenealogist.com/2013/03/citizen-science-helps-to-rewrite-y.html

Ethnicity Makeovers – Still Not Soup

Unfortunately, ethnicity percentages, as provided by the major testing companies still disappoint more than thrill, at least for those who have either tested at more than one lab or who pretty well know their ethnicity via an extensive pedigree chart.

Ancestry.com is by far the worse example, swinging like a pendulum from one extreme to the other.  But I have to hand it to them, their marketing is amazing.  When I signed in, about to discover that my results had literally almost reversed, I was greeted with the banner “a new you.”  Yea, a new me, based on Ancestry’s erroneous interpretation.  And by reversed, I’m serious.  I went from 80% British Isles to 6% and then from 0% Western Europe to 79%. So now, I have an old wrong one and a new wrong one – and indeed they are very different.  Of course, neither one is correct…..but those are just pesky details…

23andMe updated their ethnicity product this year as well, and fine tuned it yet another time.  My results at 23andMe are relatively accurate.  I saw very little change, but others saw more.  Some were pleased, some not.

The bottom line is that ethnicity tools are not well understood by consumers in terms of the timeframe that is being revealed, and it’s not consistent between vendors, nor are the results.  In some cases, they are flat out wrong, as with Ancestry, and can be proven.  This does not engender a great deal of confidence.  I only view these results as “interesting” or utilize them in very specific situations and then only using the individual admixture tools at www.Gedmatch.com on individual chromosome segments.

As Judy Russell says, “it’s not soup yet.”  That doesn’t mean it’s not interesting though, so long as you understand the difference between interesting and gospel.

http://dna-explained.com/2013/08/05/autosomal-dna-ancient-ancestors-ethnicity-and-the-dandelion/

http://dna-explained.com/2013/10/04/ethnicity-results-true-or-not/

http://www.legalgenealogist.com/blog/2013/09/15/dna-disappointment/

http://cruwys.blogspot.com/2013/09/my-updated-ethnicity-results-from.html?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+Cruwysnews+%28Cruwys+news%29

http://dna-explained.com/2013/10/17/ancestrys-updated-v2-ethnicity-summary/

http://dna-explained.com/2013/10/19/determining-ethnicity-percentages/

http://www.thegeneticgenealogist.com/2013/09/12/ancestrydna-launches-new-ethnicity-estimate/

http://cruwys.blogspot.com/2013/12/a-first-look-at-chromo-2-all-my.html

Genetic Genealogy Education Goes Mainstream

With the explosion of genetic genealogy testing, as one might expect, the demand for education, and in particular, basic education has exploded as well.

I’ve written a 101 series, Kelly Wheaton wrote a series of lessons and CeCe Moore did as well.  Recently Family Tree DNA has also sponsored a series of free Webinars.  I know that at least one book is in process and very near publication, hopefully right after the first of the year.  We saw several conferences this year that provided a focus on Genetic Genealogy and I know several are planned for 2014.  Genetic genealogy is going mainstream!!!  Let’s hope that 2014 is equally as successful and that all these folks asking for training and education become avid genetic genealogists.

http://dna-explained.com/2013/08/10/ngs-series-on-dna-basics-all-4-parts/

https://sites.google.com/site/wheatonsurname/home

http://www.yourgeneticgenealogist.com/2012/08/getting-started-in-dna-testing-for.html

http://dna-explained.com/2013/12/17/free-webinars-from-family-tree-dna/

http://www.thegeneticgenealogist.com/2013/06/09/the-first-dna-day-at-the-southern-california-genealogy-society-jamboree/

http://www.yourgeneticgenealogist.com/2013/06/the-first-ever-independent-genetic.html

http://cruwys.blogspot.com/2013/10/genetic-genealogy-comes-to-ireland.html

http://cruwys.blogspot.com/2013/03/wdytya-live-day-3-part-2-new-ancient.html

http://cruwys.blogspot.com/2013/03/who-do-you-think-you-are-live-day-3.html

http://cruwys.blogspot.com/2013/03/who-do-you-think-you-are-live-2013-days.html

http://genealem-geneticgenealogy.blogspot.com/2013/03/the-surnames-handbook-guide-to-family.html

http://www.isogg.org/wiki/Beginners%27_guides_to_genetic_genealogy

A Thank You in Closing

I want to close by taking a minute to thank the thousands of volunteers who make such a difference.  All of the project administrators at Family Tree DNA are volunteers, and according to their website, there are 7829 projects, all of which have at least one administrator, and many have multiple administrators.  In addition, everyone who answers questions on a list or board or on Facebook is a volunteer.  Many donate their time to coordinate events, groups, or moderate online facilities.  Many speak at events or for groups.  Many more write articles for publications from blogs to family newsletters.  Additionally, there are countless websites today that include DNA results…all created and run by volunteers, not the least of which is the ISOGG site with the invaluable ISOGG wiki.  Without our volunteer army, there would be no genetic genealogy community.  Thank you, one and all.

2013 has been a banner year, and 2014 holds a great deal of promise, even without any surprises.  And if there is one thing this industry is well known for….it’s surprises.  I can’t wait to see what 2014 has in store for us!!!  All I can say is hold on tight….

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Sequencing of Neanderthal Toe Bone Reveals Unknown Hominin Line

This week, in the journal Nature, scientists reported on the full sequencing of a Neanderthal toe bone found in the Denisova Cave in the Altai Mountains, the location where the Denisovan skeleton found in 2008 and sequenced earlier this year was also found.

The abstract of the paper, which is behind a paywall, says:

We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

The abstract also includes this graphic from the paper

Neanderthal 12-22-2013 cropped

This sequence is significant because of a number of unique findings.

  1. The skeleton showed physical traits of both Neanderthals and modern humans and is thought to be about 50,000 years old.
  2. Genetic sequencing revealed that this bone belonged to a Neanderthal woman, not a Denisovan, although other Denisovan remains, including one previously sequenced, have been found in this cave.
  3. The closest genetic relative is found in the Mezmaiskaya Cave in the Caucasus Mountains, some 2000+ miles distant.  Admittedly, we don’t have a lot of sequenced remains for comparison.
  4. Sequencing revealed a heretofore unknown genetic line of archaic humans.  This person obtained from between 2.7 to 5.8 percent of their genome from this unknown line. That percentage is equal to someplace between a great-great-great-grandparent and a great-great-great-great-great-grandparent, assuming only one ancestor was involved.  If this unknown human lineage was admixed into the population in multiple individuals, then the trace amounts could be passed around forever, just like the Neanderthal and Denisovan lineages are in Europeans today.
  5. This unknown line could be homo erectus.
  6. There is no evidence that this unknown human lineage interbred with either modern humans or Neanderthals.  I would presume this means that this unknown line then bred with the Denisovan group which did not manifest itself in contemporary humans.
  7. This individual was inbred with their parents being closely related, possibly half-siblings or an uncle and niece, or an aunt and nephew or a grandfather and granddaughter or grandmother and grandson.  Inbreeding was also common among the woman’s recent ancestors.  Another article headline this week pronounced that “Neanderthals Liked Incest” which I found to be offensive.  Incest is a highly negatively charged cultural word.  In the not so recent past, the practice of inbreeding was perfectly acceptable in European royalty.  Furthermore, we have no idea how these people felt about inbreeding, hence the word “liked” is misleading.  It could well be that they lived in a small nuclear family group and there were no other choices for partners.  There could also be other cultural and selection factors at play here of which we are unaware.  For example, perhaps males were more protective of mothers and children to whom they were related than ones where they had no family or group ties – increasing the likelihood of survival of offspring of women to whom the males were related.
  8. At least half of a percent of the Denisovan genome came from Neanderthals, but none of the Denisovan genome has yet been detected in Neanderthals.  If this holds, it would imply that our ancestors either bred with Neanderthals and Denisovans separately, or with Denisovans who carried Neanderthal DNA.  Given that most Europeans carry more Neanderthal DNA than Denisovan, the second scenario alone is unlikely.  It’s also possible that we simply haven’t found Neanderthal’s who did carry Denisovan DNA.
  9. More than 31,000 differences were found between modern humans and Neanderthals and Denisovans, many having to do with brain development.

Dienekes discussed this research in his blog as well.  Note his “family tree.”

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

 

Neuroarchaeologists Uncover Iberian Origin of Unusual Alzheimer’s Gene Mutation

Alzheimers in IberiaNeuroarchaeologists, a term I haven’t heard before, but one we’ll likely hear into the future.  Genetics, neurology, genealogy, population genetics….they are all becoming intermixed today solving puzzles that are so complex that just a few years ago, there would have been no prayer of solving them at all.

Take early onset Alzheimers, for example.  Keep in mind that this type of Alzheimer’s is only one of several, and much about this disease remains unknown, but for this particular kind of Alzheimer’s disease, this breakthrough is monumental, as is the fact that they can trace it to the Iberian peninsula in the 16th century.

The history of our ancestors truly is in our genes.

This research was performed at the University of California at Santa Barbara and published this month in Alzheimer’s and Dementia, the Journal of the Alzheimer’s Association.  Unfortunately, the academic article is behind a paywall.

Researchers tested more than 100 family members who have the disease.  While many predictably showed onset signs of the disease as expected about age 45, some appeared to be protected by as much as a decade.  The question was what was protecting these people and does that protective mechanism have relevance for the rest of the people afflicted by Alzheimer’s disease.  The answer isn’t yet evident, and research continues, but the process they used to identify this mutation is fascinating.

The team worked with historians and genealogists and using records as old as 1540, managed to track this family, along with their mutation, to a single individual from the Iberian peninsula about the time that Spanish Conquistadors were colonizing Columbia in the early 1500s.

They may call this new field neuroarchaeology, but I think it’s more neurogenealogy, unless they’re excavating graves someplace.  But I bet they think neuroarchaeology just sounds more scientific.  So, want to get assistance with your genealogy….having a dread disease, or being a politician….either one will help immensely.

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

400,000 Year Old DNA from Spain Sequenced

Atapuerca Cave Remains

Talk about record shattering.  400,000 year old DNA has now been sequenced, and that quite handily breaks the previous 100,000 year old record.  The only problem is that these ancient and archaic people weren’t staying where they were supposed to.  Well, that’s “supposed to” according to the story we thought we knew.  Obviously, we didn’t know, and ancient DNA is only beginning to tell the story, which isn’t at all like we thought it would be.

Before now, Neanderthals were thought to have settled in the west, meaning Europe primarily, and Denisovans in the East, in Siberia.  This is due to where bones have been found and the DNA sequenced from just a few.  However, this new find from a cave in Atapuerca, Spain changes all of that.  These people were not closely related to Neanderthal, who were later found in Germany, but instead are related to the Denisovans, their remains found some 4000 miles east, per mitochondrial DNA, meaning their direct matrilineal line.  However, even though they are related, they are distantly related.

Yesterday the mitochondrial sequence appeared on GenBank, after the release of the paper.  According to Ian Logan, this new sequence has just over 500 mutations, about half of which can be matched with Denisovan and the other half are unique.  So while the Denisovan and this new sequence do share a maternal ancestor, they are many, many generations distant.  Of course, that would be expected, because they are about 350,000 years apart too in terms of time, or a meager 14,000 generations.

What does this mean?  The scientists don’t know for sure.  Perhaps these Atapuerca Cave people were the ancestors of Denisovans and Neanderthals.  Perhaps the Denisovan mitochondrial DNA “washed out” over generations in the Neanderthal or maybe not enough Neanderthal remains have been located and sequenced.  Neither Neanderthal nor Denisovan mitochondrial DNA has been found in any living humans or relatively contemporary burials, meaning not outside of Neanderthals and Denisovans.  In short, we need more skeletons and more DNA to reveal more information about our ancient ancestors.  It opens the possibility that modern humans are but a small sprig on the larger and quite ancient Denisovan/Neanderthal Eurasian tree.  We don’t know where modern humans fit in all of this, but according to autosomal genetic results, everyone with either European or Asian heritage carries some of them in all of us, just not the mitochondrial line.  We are just beginning this journey of discovery.

For more, access the Science article, Dienekes Anthrolpology Blog and John Hawks blog.  The academic article in Nature, A mitochondrial genome sequence of a hominin from Sima de los Huesos, by Meyer et all is behind a paywall.

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Watson, Crick and Spotted Dick

dna 1953

In September, 2013, my husband, Jim, and I visited the British Isles.  This trip was planned around various aspects of genealogy and family history – all of which pertain to and were enabled by DNA.  I’m going to be sharing portions with you over the next several weeks.  These stories will all include DNA, but I’m also going to share other photos with you.  The culture, so different from ours, is critically important to understanding our ancestors and these areas are simply beautiful.  I’d like to share the entire experience, not just the DNA piece.  So I’m inviting you along on my day in London.  Come on….we’ll have fun!

I didn’t plan my trip to England with Watson and Crick’s DNA model in mind – that part just kind of evolved, a positive mutation, so to speak.

Jim and I traveled with a family group that indeed did make this trip as a result of DNA – but that is another story for another article, several, in fact.  In any case, we weren’t really in charge of where we were staying in London – the tour company took care of fanthat – supposedly.  That is a long and sorry saga which I’ll spare you.  Let’s just say we weren’t staying at the hotel where we were SUPPOSED to have reservations and the one where we were staying didn’t have air conditioning.  It was “broken.”  It should have been an aha moment when they handed me a fan when we checked in.  At least they did that much.  It was very hot.

Suffice it to say, we were close to Hyde Park and Kensington Gardens in London.  The idea was that we could take a walk in the park if we wanted to.  Flowers often grace every nook and cranny in Europe and the thought of walking and viewing was quite enticing to me.  Here is a rose garden in front of a private home near Hyde Park. Just lovely.

London rose garden

The London subway is a bit overwhelming, but it really a good transportation system once you get used to it.  You can get places far more quickly by subway than by car on the surface streets.

london subway

Still, you stand a high probability of getting lost, at least initially, and it’s pretty intimidating.  So we opted to walk when we could.  Plus, you get to see a lot more of the area that way.  After all, it’s not always the destination.  Sometimes, it’s about the journey.

Before we left for London, I searched for the location of the double helix model created by Watson and Crick in 1953 when they discovered DNA.  I found that it is in the British Science Museum.

After arrival in London, looking at the map, I discovered that the Science Museum was just on the other side of Hyde Park.  I asked and was told that it’s about a 10 minute walk.  Have I mentioned never to believe a British person about distances???  It must be genetic – they seem to have a distance judgment impairment gene!

Jim and I set out to walk to the Museum because it seemed like a much better option than three different subway transfers.  And after all, it was only 10 minutes away and only drizzling.

Me hyde park

We cut across the park and enjoyed the walk and found the museums, further away than we thought, of course.  We discovered we were walking on the Princess Diana Memorial walkway, and only after we got home and looked at the photo did I realize that Kensington Palace is behind me.

British parks and gardens are really quite remarkable.  There are a lot of them and they have beautiful statues and flowers. This statue is of Prince Albert.

prince albert

Half an hour or 45 minutes later, we arrived at the Science Museum.  It’s quite large, and we asked where the DNA exhibit was located, received directions, and off we went.  We were pleased to see that they had an entire exhibit area devoted not to DNA but to what makes people unique.  Of course DNA had a prominent position in that exhibit.

dna book

The “books of genes” shown above and below is actually the top back of a seat in the museum exhibit.

dna seat

But we were unable to find the Watson/Crick model.  We asked a second time and the guard told us that it was downstairs “by the autos.”  We had just come through that area and we didn’t quite believe it would be there, but since it wasn’t where we were, we went to look.  Sure enough, in with the 1950s cars and the earliest computers, in a display case but not near anything else similar, we found the double helix model with only a small display description.  In fact, we had walked right past it earlier and didn’t notice it because where it is located and how it is displayed is so nondescript.

dna sign

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The helix model itself is kind of difficult to see because it’s small and kind of thin and in the middle of a case with glass on all sides.  Jim is trying to get a good picture, but that is almost impossible between its position and the glass and lighting.

Crick Watson Jim

The model is constructed using clamps.

Crick Watson closeup

It’s actually difficult to see because the aluminum templates, shown below (wiki photo) are on a flat plane so they are being photographed sideways.

DNA model leaves

I was thrilled to see the model, but saddened that it has been relegated to the section of “vintage cars” when it was the discovery that fueled many of the life-changing medical discoveries of the past few years and nearly everything in the exhibit we had just seen about what makes people unique.  If not DNA, then what?

The Crick/Watson double helix model should be the crown jewel of these types of exhibits, not relegated to a place in the footnotes of the 1950s.

The model itself is elegant in that its simplicity belies the complexity of DNA.  Yet, that complexity is comprised of simplest of elements combined in the simplest of manners.  It’s hard to believe sometimes that we are looking at the recipe for reproduction, for all of life itself.

Here are Crick and Watson with the model.

crick watson with model

Of course, we walked back to our hotel, but we took a bit of a different route, past both sets of palace gates (below) and up some side streets.

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Glory be, we also found a Starbucks!!  We discovered a beautiful old church on Kensington High Street and slipped into the courtyard which is also the cemetery.

church high kensington

It’s hard to believe that just a few feet away on the other side of the fence the London traffic and hustle and bustle are in full force.

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This courtyard is a tiny haven of tranquility. Of course, I had to look at the stones to see if there were any familiar names.  After all, some of my ancestors were here – however, they weren’t wealthy enough to have stones in churchyards.

Some things have no equivalent here.

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Humps, in case you are wondering, are speed bumps.  The even more interesting sign was the one that had a picture of two humps, side by side, on the same sign.

We passed this lovely pub that is just so quintessentially English and so beautiful.  Surely looks inviting doesn’t it.  Want to have an ale???

OLYMPUS DIGITAL CAMERA

That evening, we met up with my cousins from New Zealand (more about that later) in The Swan Pub, a very quaint and very English old coaching pub across from Hyde Park, and had an English dinner of what else, fish and chips.

But that wasn’t the end of the adventures.  Nosiree….there was what we term as  “adventure eating” left to be done.  There was Spotted Dick on the dessert menu.  Yes, we did, we had to order that and try some.  Here’s Jim getting ready to try Spotted Dick.  Looks kind of apprehensive doesn’t he.  I must admit, it was very, very good.

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I hope you’ve enjoyed coming along with me on my day in London visiting Watson, Crick and Spotted Dick.

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Native American Gene Flow – Europe?, Asia and the Americas

Pre-release information from the paper, “Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans” which included results and analysis of DNA sequencing of 24,000 year old skeletal remains of a 4 year old Siberian boy caused quite a stir.  Unfortunately, it was also misconstrued and incorrectly extrapolated in some articles.  Some people misunderstood, either unintentionally or intentionally, and suggested that people with haplogroups U and R are Native American.  That is not what either the prerelease or the paper itself says.  Not only is that information and interpretation incorrect, the paper itself with the detailed information wasn’t published until November 20th, in Nature.

The paper is currently behind a paywall, so I’m going to discuss parts of it here, along with some additional information from other sources.  To help with geography, the following google map shows the following locations: A=the Altai Republic, in Russia, B=Mal’ta, the location of the 24,000 year old skeletal remains and C=Lake Baikal, the region from where the Native American population originated in Asia.

native flow map

Nature did publish an article preview.  That information is in bold, italics and I will be commenting in nonbold, nonitalics.

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians1, 2, 3, there is no consensus with regard to which specific Old World populations they are closest to4, 5, 6, 7, 8. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia9, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date.

Within the paper, the authors also compare the MA-1 sequence to that of another 40,000 year old individual from Tianyuan Cave, China whose genome has been partially sequenced.  This Chinese individual has been shown to be ancestral to both modern-day Asians and Native Americans.  This comparison was particularly useful, because it showed that MA-1 is not closely related to the Tianyuan Cave individual, and is more closely related to Native Americans.  This means that MA-1’s line and Tianyuan Cave’s line had not yet met and admixed into the population that would become the Native Americans.  That occurred sometime later than 24,000 years ago and probably before crossing Beringia into North America sometime between about 18,000 and 20,000 years ago.

The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers10, 11, 12, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages5.

The paper goes on to say that MA-1 is a member of mitochondrial (maternal) haplogroup U, very near the base of that haplogroup, but without affiliation to any known subclade, implying either that the subclade is rare or extinct in modern populations.  In other words, this particular line of haplogroup U has NOT been found in any population, anyplace.  According to the landmark paper,  “A ‘‘Copernican’’ Reassessment of the Human Mitochondrial DNA Tree from its Root,” by Behar et al, 2012, haplogroup U itself was born about 46,500 years ago (plus or minus 3.200 years) and today has 9 major subclades (plus haplogroup K) and about 300 branching clades from those 9 subclades, excluding haplogroup K.

The map below, from the supplemental material included with the paper shows the distribution of haplogroup U, the black dots showing locations of haplogroup U comparison DNA.

Native flow Hap U map

In a recent paper, “Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity” by Brandt et al (including the National Geographic Consortium) released in October 2013, the authors report that in the 198 ancient DNA samples collected from 25 German sites and compared to almost 68,000 current results, all of the ancient Hunter-Gatherer cultural results were haplogroup U, U4, U5 and U8.  No other haplogroups were represented.  In addition, those haplogroups disappeared from the region entirely with the advent of farming, shown on the chart below.

Native flow Brandt map

So, if someone who carries haplogroup U wants to say that they are distantly related to MA-1 who lived 24,000 years ago who was also related to their common ancestor who lived sometime prior to that, between 24,000 and 50,000 years ago, probably someplace between the Middle East where U was born, Mal’ta, Siberia and Western Europe, they would be correct.  They are also distantly related to every other person in the world who carries haplogroup U, and many much more closely that MA-1 whose mitochondrial DNA line is either rare as chicken’s teeth (i.e. never found) or has gone extinct.

Let me be very clear about this, there is no evidence, none, that mitochondrial haplogroup U is found in the Native American population today that is NOT a result of post-contact admixture.  In other words, in the burials that have been DNA tested, there is not one example in either North or South America of a burial carrying mitochondrial haplogroup U, or for that matter, male Y haplogroup R.  Native American haplogroups found in the Americas remain subsets of mitochondrial haplogroups A, B, C, D and X and Y DNA haplogroups C and Q.  Mitochondrial haplogroup M has potentially been found in one Canadian burial.  No other haplogroups have been found.  Until pre-contact remains are found with base haplogroups other than the ones listed above, no one can ethically claim that other haplogroups are of Native American origin.  Finding any haplogroup in a contemporary Native population does not mean that it was originally Native, or that it should be counted as such.  Admixture and adoption have been commonplace since Europeans first set foot on the soil of the Americas. 

Now let’s talk about the Y DNA of MA-1.

The authors state that MA-1’s results are found very near the base of haplogroup R.  They note that the sister lineage of haplogroup R, haplogroup Q, is the most common haplogroup in Native Americans and that the closest Eurasian Q results to Native Americans come from the Altai region.

The testing of the MA-1 Y chromosome was much more extensive than the typical STR genealogy tests taken by consumers today.  MA-1’s Y chromosome was sequenced at 5.8 million base pairs at a coverage of 1.5X.

The resulting haplotree is shown below, again from the supplementary material.

Native flow R tree

 native flow r tree text

The current haplogroup distribution range for haplogroup R is shown below, again with comparison points as black dots.

Native flow R map

The current distribution range for Eurasian haplogroup Q is shown on the map below.  Haplogroup Q is the most common haplogroup in Native Americans.

Native flow Q map

Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians2, 13.

Kennewick Man is probably the most famous of the skeletal remains that don’t neatly fit into their preconceived box.  Kennewick man was discovered on the bank of the Columbia River in Kennewick, Washington in 1996 and is believed to be from 7300 to 7600 years old.  His anatomical features were quite different from today’s Native Americans and his relationship to ancient people is unknown.  An initial evaluation and a 2010 reevaluation of Kennewick Man let to the conclusion by Doug Owsley, a forensic anthropologist, that Kennewick Man most closely resembles the Ainu people of Japan who themselves are a bit of an enigma, appearing much more Caucasoid than Asian.  Unfortunately, DNA sequencing of Kennewick Man originally was ussuccessful and now, due to ongoing legal issues, more technologically advanced DNA testing has not been allowed.  Nova sponsored a facial reconstruction of Kennewick Man which you can see here.

Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago14, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

In addition to the sequencing they set forth above, the authors compared the phenotype information obtainable from MA-1 to the Tyrolean Iceman, typically called Otzi.  You can see Otzi’s facial reconstruction along with more information here.  This is particularly interesting in light of the pigmentation change from darker skin in Africa to lighter skin in Eurasia, and the question of when this appearance change occurred.  MA-1 shows a genetic affinity with the contemporary people of northern Europe, the population today with the highest frequency of light pigmentation phenotypes.  The authors compared the DNA of MA-1 with a set of 124 SNPs identified in 2001 by Cerquira as informative on skin, hair and eye pigmentation color, although they also caution that this method has limited prediction accuracy.  Given that, they say that MA-1 had dark hair, skin and eyes, but they were not able to sequence the full set of SNPs.  MA-1 also had the SNP value associated with a high risk of male pattern baldness, a trait seldom found in Native American people and was not lactose tolerant, a trait found in western Eurasians.  MA-1 also does not carry the mutation associated with hair thickness and shovel shaped incisors in Asians.

The chart below from the supplemental material shows the comparison with MA-1 and the Tyrolean Iceman.

Native flow Otzi table

The Tarim Mummies, found in the Tarim Basin in present-day Xinjiang, China are another example of remains that seem out of place.  The earliest Tarim mummies, found at Qäwrighul and dated to 1800 BCE, are of a Europoid physical type whose closest affiliation is to the Bronze Age populations of southern Siberia, Kazakhstan, Central Asia, and the Lower Volga.

The cemetery at Yanbulaq contained 29 mummies which date from 1100–500 BCE, 21 of which are Mongoloid—the earliest Mongoloid mummies found in the Tarim Basin—and eight of which are of the same Europoid physical type found at Qäwrighul.

Notable mummies are the tall, red-haired “Chärchän man” or the “Ur-David” (1000 BCE); his son (1000 BCE), a small 1-year-old baby with brown hair protruding from under a red and blue felt cap, with two stones positioned over its eyes; the “Hami Mummy” (c. 1400–800 BCE), a “red-headed beauty” found in Qizilchoqa; and the “Witches of Subeshi” (4th or 3rd century BCE), who wore 2-foot-long (0.61 m) black felt conical hats with a flat brim. Also found at Subeshi was a man with traces of a surgical operation on his neck; the incision is sewn up with sutures made of horsehair.

Their costumes, and especially textiles, may indicate a common origin with Indo-European neolithic clothing techniques or a common low-level textile technology. Chärchän man wore a red twill tunic and tartan leggings. Textile expert Elizabeth Wayland Barber, who examined the tartan-style cloth, discusses similarities between it and fragments recovered from salt mines associated with the Hallstatt culture.

DNA testing revealed that the maternal lineages were predominantly East Eurasian haplogroup C with smaller numbers of H and K, while the paternal lines were all R1a1a. The geographic location of where this admixing took place is unknown, although south Siberia is likely.  You can view some photographs of the mummies here.

In closing, the authors of the MA-1 paper state that the study has four important implications.

First, we find evidence that contemporary Native Americans and western Eurasians shareancestry through gene flow from a Siberian Upper  Palaeolithic population into First Americans.

Second, our findings may provide an explanation for the presence of mtDNA haplogroup X in Native Americans, which is related to western Eurasians but not found in east Asian populations.

Third, such an easterly presence in Asia of a population related to contemporary western Eurasians provides a possibility that non-east Asian cranial characteristics of the First Americans derived from the Old World via migration through Beringia, rather than by a trans-Atlantic voyage from Iberia as proposed by the Solutrean hypothesis.

Fourth, the presence of an ancient western Eurasian genomic signature in the Baikal area before and after the LGM suggests that parts of south-central Siberia were occupied by humans throughout the coldest stages of the last ice age.

The times, they are a changin’.

Dr. Michael Hammer’s presentation at the 9th Annual International Conference on Genetic Genealogy may shed some light on all of this seeming confusing and somewhat conflicting information.

The graphic below shows the Y haplogroup base tree as documented by van Oven.

Native flow basic Y

You can see, in the lower right corner, that Y haplogroup K (not to be confused with mtDNA haplogroup K discussed in conjunction with mtDNA haplogroup U) was the parent of haplogroup P which is the parent of both haplogroups Q and R.

It has always been believed that haplogroup R made its way into Europe before the arrival of Neolithic farmers about 10,000 years ago.  However, that conclusion has been called into question, also by the use of Ancient DNA results.  You can view additional information about Hammer’s presentation here, but in a nutshell, he said that there is no early evidence in burials, at all, for haplogroup R being in Europe at an early age.  In about 40 burials from several location, haplogroup R has never been found.  If it were present, especially in the numbers expected given that it represents more than half of the haplogroups of the men of Europe today, it should be represented in these burials, but it is not.  Hammer concludes that evidence supports a recent spread of haplogroup R into Europe about 5000 years ago.  Where was haplogroup R before spreading into Europe?  In Asia.

Native flow hammer dist

It appears that haplogroup K diversified in Southeast Asian, giving birth to haplogroups P, Q and R. Dr. Hammer said that this new information, combined with new cluster information and newly discovered SNP information over the past two years requires that haplogroup K be significantly revised.  Between the revision of haplogroup K, the parent of both haplogroup R, previously believed to be European, and haplogroup Q, known to be Asian, European and Native, we may be in for a paradigm shift in terms of what we know about ancient migrations and who is whom.  This path for haplogroup R into Europe really shouldn’t be surprising.  It’s the exact same distribution as haplogroup Q, except haplogroup Q is much less frequently found in Europe than haplogroup R.

What Can We Say About MA-1?

In essence, we can’t label MA-1 as paternally European because of Y haplogroup R which now looks to have had an Asian genesis and was not known to have been in Europe 24,000 years ago, only arriving about 5,000 years ago.  We can’t label haplogroup R as Native American, because it has never been found in a pre-Columbian New World burial.

We can say that mitochondrial haplogroup U is found in Europe in Hunter-Gatherer groups six thousand years ago (R  was not) but we really don’t know if haplogroup U was in Europe 24,000 years ago.  We cannot label haplogroup U as Native because it has never been found in a pre-Columbian New World burial.

We can determine that MA-1 did have ancestors who eventually became European due to autosomal analysis, but we don’t know that those people lived in what is now Europe 24,000 years ago.  So the migration might have been into Europe, not out of Europe.  MA-1, his ancestors and descendants, may have lived in Asia and subsequently settled in Europe or lived someplace inbetween.  We can determine that MA-1’s line of people eventually admixed with people from East Asia, probably in Siberia, and became today’s First People of North and South America.

We can say that MA-1 appears to have been about 30% what is today Western Eurasian and that he is closely related to modern day Native Americans, but not eastern Asians.  The authors estimate that between 14% and 38% of Native American ancestry comes from MA-1’s ancient population.

Whoever thought we could learn so much from a 4 year old?

For anyone seriously interested in Native American population genetics, “Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans” is a must read.

It’s been a great month for ancient DNA.  Additional recent articles which pertain to this topic include:

http://www.nytimes.com/2013/11/21/science/two-surprises-in-dna-of-boy-found-buried-in-siberia.html?src=me&ref=general&_r=0

http://www.sciencedaily.com/releases/2013/11/131120143631.htm

http://dienekes.blogspot.com/2013/11/ancient-dna-from-upper-paleolithic-lake.html

http://blogs.discovermagazine.com/gnxp/2013/11/long-first-age-mankind/#.Uo0eOcSkrIU

http://cruwys.blogspot.com/2013/11/day-1-at-royal-societys-2013-ancient.html

http://cruwys.blogspot.co.uk/2013/11/day-2-at-royal-societys-2013-ancient.html

http://www.sciencedaily.com/releases/2013/11/131118081251.htm

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I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

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Rosalind Franklin Gets a Google Doodle For Her 93rd Birthday

Rosalind_FranklinRosalind Franklin’s 93rd birthday is today.  Don’t know who she is?  Well, you’re not alone.  She is the unsung hero of DNA discovery.

Franklin is best known for her work on the X-ray diffraction images of DNA which led to the discovery of the DNA double helix. Her data, according to Francis Crick, were “the data we actually used” to formulate Crick and Watson’s 1953 hypothesis regarding the structure of DNA. Franklin’s images of X-ray diffraction confirming the helical structure of DNA were shown to Watson without her approval or knowledge. This image and her accurate interpretation of the data provided valuable insight into the DNA structure, but Franklin’s scientific contributions to the discovery of the double helix are often overlooked.

She may have been overlooked elsewhere, and particularly in terms of the Nobel prize awarded to Crick and Watson, but she has not been forgotten and was honored today by Google in a doodle!

rosalind franklin google doodle

http://en.wikipedia.org/wiki/Rosalind_Franklin

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I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

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James Watson on DNA

James Watson is most likely the most famous living scientist.  Everyone knows that he, along with Francis Crick discovered the DNA molecule back in 1953, 60 years ago.  In 1962, those two along with Maurice Wilkins were awarded the Nobel prize for their discovery.

As we remember scientists and their discoveries, I think we often miss the human element of the process.  How they feel and felt at the time, what they think and thought, the softer side of science.

Watson Crick 1953

This photos shows Francis Crick and James Watson together in 1953 at Cambridge, from the Collection of the Cold Springs Harbor Lab Archives.

CNN interviewed Watson recently, and you can read the article and see the video here.

I found some of his quotes to be very interesting.

“All you can say is that you were very lucky. You were born at the right time and your parents gave you books when you were young.”

I’m all for that.  I was and am an avid reader and I instilled that in both of my children as well.

Watson equates his passion for DNA and genetic research to his ancestor’s passion for the Gold Rush.  I can empathize with that – once the DNA bug bites you, it’s lifelong and unrelenting!  Passion fuels discovery of any type.  Watson discovered a very different kind of gold – the elixir of all humanity.

Of the day they discovered DNA, he says, “We went to lunch.  We had to tell people we’d done something important, but they didn’t know what we were saying.”  That’s certainly not the case today.  “Done something important” is an incredible understatement – perhaps the strongest understatement I’ve ever seen.

He said he felt queasy when they told everyone within hearing distance that they had found the secret of life.  Well, making the discovery of the millennium will do that to you!

I understand how he felt though.  I get the same look he must have received when I explain to my family how excited that I am that we’ve found a new haplogroup.  Thank heavens for our genetic genealogy community today.

Watson’s reaction to the Eureka moment of discovery, “All we could say when we got it: It’s so beautiful.”

watson crick dna model

DNA model built by Crick and Watson in 1953 is on display in the National Science Museum of London.  You can read the amazingly short paper published in Nature here or an annotated version here.

dna diagram from paperAt right is the diagram of DNA from the 1953 paper.  Its elegance, simplicity and symmetry is stunningly beautiful.

For those interested, Nature compiled what they consider to be the 5 classic DNA papers of which the Watson/Crick paper is one, of course.

Interestingly, Watson says he doesn’t want to die before he sees cancer cured and feels it could happen.  I certainly hope so.  Whenever this does happen, you know that genetics will certainly play a prominent role in the cure.  Discoveries in medicine as well as in other genetics fields like molecular biology, evolutionary genetics, population genetics and genetic genealogy continue to be made every day – all stemming from this monumental discovery in 1953.

Watson says of himself, “I wanted to understand the world about me better.  I wanted to do something important with my life.”  Do you think he succeeded?

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

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