Gene by Gene Announces Landmark DNA DTC Full Genome Sequence

Gene by Gene, the parent company of Family Tree DNA, formally announced it’s direct to consumer (DTC) offering of full sequence human genome testing.

Testing will be performed in their state of the art research center, shown above, in Houston, Texas.  You can read more about Gene by Gene and their 4 divisions, DNA DTC, Family Tree DNA, DNA Traits and DNA Findings at www.genebygene.com.

Family Tree DNA was established 12 years ago to service the Genetic Genealogy market space, which didn’t yet exist at that time.  Family Tree DNA was an innovator in that field, and has brought the same innovative and entrepreneurial spirit to their other companies established since.

This new offering, the first of it’s kind, reaches out to researchers and others in need of “research only” next generation full genomic sequencing.

“Given the explosive demand for accurate, timely, and large-scale next
generation sequencing, we’re pleased to make our Genomics Research Center
available to investigators exploring the cutting edge of research to pioneer and
enhance treatment of disease, enhance quality of life, break new ground in
genealogical inquiry and otherwise advance the science of genomics,” Gene By
Gene President Bennett Greenspan said. “The launch of DNA DTC is the perfect
complement to our other divisions, through which we make genetic testing
advances every day in the fields of ancestry, health and relationship testing.”

Using the Illumina platform, DNA DTC will offer both full genomic sequence and full exome testing, adding these two items to their menu of over 200 types of DNA tests performed.  Gene by Gene’s lab has already processed more than 5 million discrete DNA tests for more than 700,000 individual clients.  Their institutional clients include the National Geographic Society’s Genographic project and other clients such as France’s Institut Pasteur, Israel’s Rabin Medical Center and the University of Utah.

By bringing full genomic sequencing to the public, they have broken the sound barrier in personal genetics, the veritable X-factor.  The full humane genome was first sequenced in 2003 at a cost of about 3 billion dollars.

A full genome sequence still cost about 3 million in 2007, but DNA DTC is offering it today for an amazing $5495.

While consumers will be able to order the full genome (or exome) test, if they want, it comes with no tools, as it is focused at the research community who would be expected to have their own analytical tools.  However, genetic genealogists being who and what they are, I don’t expect the research market will outweigh the consumer market for long, especially when the price threshold reaches about $1000.  For years the “$1000 genome” has been bantered about, and I expect with the next generation of technology, we may see it sooner than later.  The fact that it has dropped from 3 million to $5495 in 5 years is astounding.

Aside from DNA DTC and Family Tree DNA, the other two  Gene by Gene divisions are DNA Traits (www.dnatraits.com)  which provides CLIA Regulated Diagnostic tests for genetic diseases and DNA Findings (www.dnafindings.com)  which provides AABB certified paternity and relationship testing.

You can read the entire press release here:                    http://www.marketwatch.com/story/gene-by-gene-launches-dna-dtc-2012-11-29

Way to go Max and Bennett and everyone at Gene by Gene!  Congratulations!

So, who is going to be the first in the genetic genealogy community to order this test???

Averages, TIP Calculator and One Size Fits All

Averages.  We all know what that means, conceptually.  You add a group of numbers together and divide by the total of the numbers you added together.  For example, 9 number locations that have a value of 10 each totals 90.  If you divide 90 by the number of number locations, 9, you get 10 as the average.  Of course, that’s a very simple example, but the concept applies no matter how many number locations or how big or small the numbers.

Often, we don’t grasp a good working knowledge of how to apply that math concept as it relates to our DNA results.

What I’m referring to here is the TIP calculator provided by Family Tree DNA, but this concept applies equally as well to any TMRCA (Time to Most Recent Common Ancestor) calculation, regardless of who is calculating it.  The underpinnings, are, by necessity, the same.

At Family Tree DNA, the TIP calculator, the little orange button above, is available to you to compare Y-line results to matches and it will give you a rough idea of how long ago you can expect to have a common ancestor.

One of the most common questions I receive reads something like this:

“The TIP calculator says that we should be related at 99% within 12 generations, but my genealogy shows that it should be 8 generations.  What is wrong?”

Or something like this:  “The TIP calculator says we are related, but I have no idea how to interpret any of these numbers.”

The answer is that nothing is wrong and these are ranges of possibilities, based on average mutation rates of individual markers.  Having said that, we know absolutely that mutations are random events.  You can see this demonstrated in the Estes project where Abraham Estes (born 1647) who had 12 sons produced one line who has several people with no mutations as compared to Abraham, and another descendant whose line from another son has 8 mutations in the same  timeframe.  Now it’s obvious that both of these are on the outer bands of the spectrum, and the average is 4, which really is not reflective of either of these lines, but is dead center accurate for two of Abraham’s other sons’ lines.

Recently, I was working with the Nemaha Half-Breed Allottee, a list of names of mixed European/Native American individuals who received individual land allotments in 1860 in Nebraska from the government as a result of an 1830 treaty.  When analyzing the 365 people who had European names, I realized that this is the perfect example of averages and how they do, and don’t, work.  So let’s visit the Nemaha for a minute.

There are 122 different surnames represented, and the average then is that 2.99 people should carry each surname.  365 divided by 122=2.99.  So let’s say 3 people, as it’s very close.

In reality, here’s how the surname distribution breaks down.

Number of People Carrying Surname Number of Surnames
1 54
2 18
3 10
4 12
5 8
6 6
7 4
8 3
9 2
10 0
11 1
12 0
13 0
14 0
15 1
16 0
17 0
18 1

You can see that only 10 surnames actually have 3 people who carry them, for a total of 30 people, or about 12%.  For the remainder, 90 surnames have fewer than 3 people, for a total of 25%, and 63% of the surnames have more than 3 people who carry that surname.

Stated a little differently, this average is accurate for 12% of the people, and inaccurate for 88%. It is close for many.  About 23% fall directly on either side, meaning 2 people or 4 people carry that surname.

So what is the message here?  Averaging tools, TIP included, do the best with what they have, which includes results at both ends of the spectrum.  In this case, it includes the 54 surnames with only one person each, and the 3 surnames who each have over 10 people each, 11, 15 and 18, totaling 44 people.  If these people were trying to make sense of these averages, 3 people per surname, these numbers would be totally irrelevant to them.

So the lesson here is to use these tools as a guideline, and nothing more. You could be in the middle and these tools could apply to your family exactly, or you could be in the family who has 18 people carrying one surname instead of the “average” of 3.

This reminds me very much of the ‘one size fits all” nightshirt that got passed around for some years at home when I was a kid.  “One size fits all” really meant “fits no one” and translated into “no one was happy.”  Of course, if you don’t understand the meaning of “one size fits all” and averages, you might be happy and think you have an answer that you don’t.

Free DNA Intro Webinars

Sometimes last minute opportunities are the best!  Thanks to the APG, the Association of Professional Genealogists (www.apgen.org), these two webinars are free for everyone.  But act quickly – because the first one is today (Tuesday), November 27th at 9 this evening.  Think of it as a spontaneous date.  Yes, I know more notice would have been nice, but our original session was canceled by the storm and until today, I didn’t realize it was free to nonmembers as well.  So you’re all invited!!!

Session 1: 

DNA Explained: An Intro to DNA for Genealogists
Tuesday, 27 November 2012 — 9:00 p.m. Eastern Standard Time
Presented by Roberta Estes

Join us to learn how DNA can be used for genealogical research. You’ll learn about how DNA testing works for both males and females, including an introduction to Y-DNA, mtDNA, and autosomal DNA. We’ll make science understandable, and by the end of this lecture, you’ll be putting together your own genealogical DNA test plan. Have a pedigree chart handy for quick reference.

Reserve your Webinar seat now at:
https://www1.gotomeeting.com/register/659356625

Session 2:

Yikes, My DNA Results are Back! Now What???
Thursday, 29 November 2012 — 9:00 p.m. Eastern Standard Time
Presented by Roberta Estes

Have results but aren’t sure what to do with them? This webinar will walk you through how to interpret your results and get the most out them. This presentation covers both Y-line and mitochondrial DNA. Autosomal DNA results will also be discussed in a future webinar.

Reserve your Webinar seat now at:
https://www1.gotomeeting.com/register/317067593

Bigfoot is Real???

If a new paper yet to be published and currently undergoing peer review is valid, it appears that Bigfoot, also known as Sasquatch, is indeed, real and a hominid mix, meaning that Sasquatch is a human relative that arose approximately 15,000 years ago as a hybrid cross of modern Homo sapiens with an unknown primate species.

Following five years of research, a team of scientists has sequenced several Sasquatch genomes.  Results show that Bigfoot is a mixture between a human female, about 15,000 years ago, and a male, a previously unknown hominin related to Homo sapiens and other primate species.  Wow.  What a discovery!

This begs several questions.  Is all of the mitochondrial DNA the same, inferring a single maternal ancestor?  They have sequenced 20 different mitochondrial samples.  Given that the mitochondrial DNA is reportedly identical to that of modern humans, we can presume, one would think, that the mitochondrial DNA is Native American, so a member of haplogroup A, B, C, D or X.  Hopefully the forthcoming paper will be more specific.

The scientists fully sequenced three Bigfoot nuclear DNA samples and the results are stunning.  The male is not a contemporary human and they have eliminated both Neanderthal and Denisovian males as possible founders.

Dr. Melba Ketchum, one of the paper’s authors, states that, “The male progenitor that contributed the unknown sequence to this hybrid is unique as its DNA is more distantly removed from humans than other recently discovered hominins like the Denisovan individual. Sasquatch nuclear DNA is incredibly novel and not at all what we had expected. While it has human nuclear DNA within its genome, there are also distinctly non-human, non-archaic hominin, and non-ape sequences. We describe it as a mosaic of human and novel non-human sequence. Further study is needed and is ongoing to better characterize and understand Sasquatch nuclear DNA. Genetically, the Sasquatch are a human hybrid with unambiguously modern human maternal ancestry.”

There are subtle and not so subtle messages buried here as well.  Obviously, for the team to acquire 20 samples to process, there has to be a population of these creatures living in North America.  Of course, everyone has heard of Sasquatch and seen photos and videos, but until this, nothing has been terribly convincing.  There has been no smoking gun.  If this research is valid and passes peer review, it not only confirms that Sasquatch is real, it vindicates many of the people who have had “sightings” over the years.  It becomes the smoking gun.  But as with much science, it raises more  questions than it answers.

For example, are there any non-admixed Sasquatch progenitors left, meaning the males that founded the Sasquatch line with the human female?  How would we tell the difference?  This of course implies that some sort of pre-hominid species existed on this continent before Native Americans arrived from Asia and had existed separate from hominids for a long time.  Is there other evidence of this creature in North America?

Where were these samples collected?  Are the Sasquatch samples studied from across North America or from one region only?  Are all of the Sasquatch related to each other, and how closely?  In other words, were there multiple founder events?  Was the Y-line DNA sequenced and what does it tell us? Were there multiple male founders or did the Sasquatch line arise from a “one time” event?  Do any of the Native tribes in these regions have oral history regarding either Sasquatch or interbreeding with Sasquatch type creatures?

Are there “Sasquatch” in other parts of the world as well?  The Yeti or Abominal Snowman of Nepal seems to be similar, and a scalp purportedly exists from that creature.  If DNA samples outside of North American have been sequenced, are they related to the North American Sasquatch or did they arise separately, assuming they too exist?

And finally, do these creatures have “rights” and are they the same “rights” as humans?  Given that they carry human mitochondrial DNA, and many Native tribes are maternally based, would they be considered “Native American?”  How do we, as humans, deal with this?  Are we learning that humanity is really a continuum?

Indeed, I look forward to seeing this published paper and I hope it is legitimate and not pseudo-science of some sort.  The mere fact that the scientiests have opted for academic publication versus a book or TV documentary certainly alludes to the fact that it is legitimate research.  You can read more about this announcment at these links.  I’ll let you know when the paper becomes available.

http://www.seattlepi.com/business/press-releases/article/Bigfoot-DNA-Sequenced-In-Upcoming-Genetics-Study-4063604.php

http://www.prweb.com/releases/prweb2012/11/prweb10166775.htm

Facebook Link

We’re on Facebook now at www.facebook.com/DNAexplain.

I’m hopeful that reaching out through Facebook will attract some new people to genealogy.

You can also visit the Native Heritage Project Facebook page at www.facebook.com/NativeHeritageProject.

Facebook requires 25 “likes” before they will issue a direct link, so thank to everyone who “liked” these pages.

Thanksgiving, Spilling the Beans and Reaching Out

Everyone in the US and Canada celebrates the holiday of Thanksgiving, although on different dates.  Traditionally, as all children learn in grade school, in the US this holiday celebrates the Pilgrims being helped by the Indians to survive and a feast they jointly held in Plymouth, Massachusetts in 1621.  There is a lot of debate about that event, whether it happened or not, but I think it’s actually irrelevant.  More important is what Thanksgiving has morphed into, what it is today.

It’s a family day, often more so than Christmas, especially in the northern climates.  In my family, and many others, at Thanksgiving you see more extended family than at Christmas, where Christmas is more immediate family.  In the North, travel has become difficult or iffy at best by the end of December, but the end of November generally is still safe.  Now that I’ve said that of course we’ll have a blizzard.

Thanksgiving is the time when my Aunt Verma inadvertently spilled the beans on the “skeleton in the closet” at the dinner table.  You could have heard a pin drop.  Well, before the gasps.

Thanksgiving is the time to ask about those ancestors or family members, even if you think you know the answer.  Because, you may not.  Often, it’s for lack of asking the question or introducing the subject that you don’t learn those stories.

Probably the number one regret of genealogists is that they never reached out when they could.

Today, reaching out isn’t just across the dinner table or while doing dishes, a favorite time to pick the brains of your relatives, it’s about reaching out using new technology.

If you could make contact with someone who has photos of your great-grandmother, wouldn’t you want to do that?  How about someone who has a copy of the family Bible owned by your Revolutionary War ancestor?  Maybe a tin type and journal of your Civil War ancestor.  Who has those today?  Maybe you don’t even know they exist.

If they aren’t in your family, it will take a new form of reaching out to find them.  I’ve celebrated Thanksgiving this week by reaching out to the younger generation.  I don’t mean to stereotype, but let’s face it, you’ll never meet these people on Rootsweb. Where do you find them?  Facebook, that’s where.  Want to find out what pictures their grandma has in the attic?  Well, you have to make contact with them so they will ask their grandma, or tell their grandma to check out your Facebook page.  And yes, more and more, grandma is using Facebook.

Now stop groaning.  I can hear you from here!  I know, I groaned too.  But I did it anyway.  We need to interest young people.  They can DNA test and someday, maybe one  of them will be who you pass the proverbial family torch to.  If you’re like me, it’s not one of your kids, no matter how badly you want it to be. I think I burned them out in courthouses at the copy machine when they were kids.  My bad.

This is not difficult.  If you are not on Facebook, summon up your courage and go to www.facebook.com and sign up.  If you are already on Facebook, skip down 2 or 3 paragraphs to the section on setting up pages and groups.

If you’re really uncertain, you can google about how to get started using Facebook, but it’s actually really easy and intuitive.  You want to be on Facebook because your kids and grandkids are there and you’re going to lose touch with them and how they communicate if you don’t join.  Just do it.

Once you join, just type names into the top bar to look for your friends and family, where it says “search for people, places and things.”  Then send them a friend request.  You’ll see the “Friend” button, just click on it.  This isn’t difficult, you just need to get used to it.  Here are the results when I searched for Jim.

Once you are a friend, you will see what they put on their timeline and their status posts.  These include photos and such.  I see new photos of my grandkids just about every day.  Your news feed aggregates all of the people and projects that you are following.

Of course, you’ll want to post something, eventually, yourself.  The best way to get a conversation started is to ask questions, just like at Thanksgiving.

On Facebook, you do that by typing something in the field that says “What’s on  your mind?”  Facebook is one big informal conversation.

After you get at least a little comfortable with Facebook and your News Feed, you’ll want to set up either a project group or a page.

Here’s what I did.  And by the way, I am not “comfortable” with Facebook but I just did this anyway.  The only way to get comfortable is to work with the software.

I set up two pages and I’m going to set up project groups.  My new pages are ”DNAexplain” and “Native Heritage Project.”  You will have to type those names (minus the quotes) in the search bar at the top of the page at Facebook to find them.  That’s how Facebook works.  Then you click on the image and then click on “like” to connect yourself to them.  So please, do me a favor and “like” both of them.  Facebook requires 25 likes for a new group or page to be recognized as legitimate.

Pages are public.  They are generally for entities, meaning businesses and organizations.  You might want to put a family association there.  ISOGG (International Society of Genetic Genealogists) is there, for example, as is the Lost Colony Research Group.  Everything posted on these pages is available for everyone to see.

Groups can be set up to be entirely public, private or secret, meaning by invitation only.   Facebook has a help page that discusses these differences.  Groups are generally for more personal discussions.  For example, you might choose to form a “by invitation only” intimate family group.  You might choose to set up a Page to advertise your family association and to attract people who are interested in addition to a group for more private discussions.  Remember, the whole point of this exercise it to reach out, so the more public your presence, the better chance you’ll have of attracting interested people.  Be aware however, that these pages are not text searchable and do not have archives like Yahoo Groups or Rootsweb.  But then again, this is for reaching out, not archiving.

To create a page, which is what I recommend for surname projects, scroll all the way down to the bottom of your Facebook page and click where it says, “create a page.”  From there on, Facebook guides you.

To create a group, on the left hand banner, Facebook will show you any groups you are a member of, and at the bottom of the list, it says “create groups.”  Click there and again, Facebook guides you through the rest.

Here is my commitment.  If a Facebook page or group does not exist for each one of my DNA surname or other pet projects, I’ll create one by year end.   Yes, this year, 2012.  There is nothing like the present moment.  I’m reaching out to the next generation.  After all, the old folks are gone now, so I need new information targets:)  Who knows what I’ll find, but if I don’t reach out and try, I’ll find absolutely nothing!  I want more family information to be thankful for by next Thanksgiving!!!  I want to honor those who have gone before by preserving the information about their life.  That is what heritage is.

How about you?  How can you reach out and what do you hope to find?

Otzi Was A Brown Eyed, Left Handed Farmer


Otzi, the mummified man found in 1991 in the Italian alps has provided a huge amount of information to science for one man, especially one who has been dead for more than 5300 years.  Otzi was killed by an arrow to the back, probably bleeding to death, although maybe not right away.  Based on blood analysis, he may have had companions with him who were also injured.

He was an old man at the time, 45.  Most didn’t survive that long.  Surrounding the mummy was his quiver, copper ax, interpreted as a status symbol, knife and other belongings, which were nearly missed when the body was recovered.  He was dressed in hides from multiple species of animals, sported a bear-skin hat and a woven grass cloak.  He had eaten unleavened bread, fruit and deer meat only a couple of hours before his death.  He had also taken herbal medicine suggesting that perhaps his meal didn’t set too well with him.  He had tattoos which may have been related to a healing ritual since they were on or near body parts which showed wear, knees and ankles, which were probably painful to him.  Hair on his clothes tells us he herded cows, sheep and goats.  He was diminutive compared to today’s people at 5’3″ and 110 pounds.

If you think about it, Europe didn’t have a large population then.  Otzi may be an ancestor of many of us. But then again, maybe not, because genetic analysis tells us that he may have suffered from reduced fertility.  But we could easily still be related in some way, as the population was fairly small and the large population of Europe grew from the founders.  Otzi and his family clearly were founders of the European population.

When Otzi was first discovered, the National Geographic Society did a facial reconstruction of Otzi, depicting him as a robust, healthy relatively young-looking man.  More recent cranial imaging capabilities combined with genetic analysis and other fields of research have shown us that indeed, he wasn’t quite so healthy.  Robust Otzi is shown below.  Perhaps this resembled a younger Otzi.

Otzi, at his death, looked like the more recent reconstruction at the top of this blog.

Most recently, last week, at the American Society of Human Genetics meeting, scientists reported that Otzi was a farmer.  While this may not sound remarkable, it is, just the fact that they can determine this, and what his DNA and other similar DNA reveals about migration and settlement patterns.  It turns out that Otzi most closely resembles people from Sardinia, a large island off the west coast of Italy, not the hunter gatherers in the Alps where he was found.

Isotope analysis of his teeth tell us that Otzi did not grow up in the Alps where he died (red balloon), but south about 50 km near the village of Feldthurns (blue balloon).  But he didn’t grow up in Sardinia (yellow balloon), so that connection is further back in time.

In addition, his DNA also resembled the DNA of the farmers of Bulgaria and Sweden, but again, not the hunter-gatherer population.  Not only does this tell us that Otzi was a farmer, but it tells us how and where the farming population settled, and who they were.

http://www.huffingtonpost.com/2012/11/09/otzi-the-icemans-genes-central-europe_n_2099809.html

More interesting info here:

http://www.livescience.com/24666-otzi-iceman-mummy-life-death.html

Otzi, it appears, was left handed, was probably lactose intolerant and had Lyme disease, making him the earliest known case.  He was also more closely related to Neanderthals than Europeans today.  Today’s Europeans uniformly carry roughly between 2% and 4% Neanderthal ancestry.

Otzi’s mitochondrial DNA line may well be extinct.  If not extinct, then no others have yet been discovered.  He is a subgroup of the K1 lineage, named K1o (that is O for Otzi, not a zero.) His Y-line DNA is haplogroup G2a2b.

http://en.wikipedia.org/wiki/%C3%96tzi

National Geographic has funded significant research on Otzi and has provided additional information and reconstruction photos here:

http://news.nationalgeographic.com/news/2011/02/pictures/110225-otzi-iceman-new-face-science-mummy-oetzi/#/iceman-oetzi-otzi-reconstructed-new_32525_600x450.jpg