Digging Up Dad, Exhumation and Forensic Testing Alternatives

Dad in suit

I didn’t do it.  I really didn’t.  Ok, I wanted to, but I didn’t.

Yes, I seriously considered exhuming my father.  Ok, now that you’ve stopped gasping, let me tell you about the story, and what I did instead, and how successful it was, and wasn’t.

My father, William Sterling Estes, died in a car accident in 1963.  That means he’s been dead now for 50 years, half a century.  Depending on the source, he had between 2 and several children.  His obituary names me as his daughter, then inadvertently mixed up my mother, his x-wife’s name with that of his sister.  So my mother is listed as my father’s sister in his obit and his sister isn’t listed at all.  Neither is his other daughter, my half-sister.  For any of you who follow my family story, you already know it’s bizarre, so this unfortunate error should come as no surprise and would only provide Jeff Foxworthy with fodder for his “you might be….if” series.

But, as you’ll see, that obituary is part of the problem and so is the fact that he has been dead 50 years now.  That’s 50 years for his DNA to degrade.

My father was, well, ahem, somewhat of a playboy.  I keep finding children, and rumors of children, scattered about as I kept researching.  I keep waiting for a solid half-sibling match to some poor unsuspecting person on one of these autosomal tests too.  It hasn’t happened yet, but I’m just sure that one day it will.

And I haven’t published my blog article on Ilo yet, but suffice it to say that if you know of an Ilo (or maybe Flo?) who had a male child about 1920 in or near Battle Creek, Michigan and was briefly “married” to William Sterling Estes who was serving at Camp Custer at the time….I need to talk to you.

Now you’d think with all of these alleged children, there would be a male child to test, but the only male child I knew of back when DNA testing began was the male child of Ilo who I have never been able to identify, let alone locate.  I hadn’t found my “brother” Dave yet at that time, but as it turned out, Dave’s DNA did not match the Estes line anyway, so that would have been a red herring.

My Estes line out of Claiborne County Tennessee, for all of the males in earlier generations, dwindled to only a few, then to none in my generation.  The best I could do was a descendant of a male 3 or 4 generations upstream in my tree, and where there are paternity questions in more recent generations, a descendant from up the tree isn’t helpful, or wasn’t before autosomal testing.

Ah yes, that paternity question.  You see, it wasn’t definite.  A descendant tested the Y chromosome, and he was off just enough markers to be considered a problematic match.  But, it was enough to introduce doubt.  And doubt is a horrible nag for a companion – especially for the family genealogist who has spent the past three and a half decades working on this “doubtful” family.  In other words, OMG!!!  This was the genealogical equivalent of a panic attack.  And what could I do?  There was no one else to test.

On the chart below, the green line is the Estes ancestral line, as we know it today, proven by both genetics and genealogy.  The purple is the anonymous participant that tested and had the questionable match to the green ancestral Estes line.  The yellow group was then “suspect” because of the questionable match.  When I found David, supposedly my father’s son, and he tested, matching neither the purple participant nor the Estes ancestral line, it nearly put me over the edge.  My cousin, Buster agreed to test, which confirmed the ancestral Estes line back to Lazarus, which left the yellow still in the questionable realm.  There were no living males to test in the yellow line.

Digging up dad 1

So, I considered exhuming Dad.  That possible paternity issue had shaken me, pretty much to the bone, and I desperately wanted to know.  Was I barking up the wrong tree?  Was my Dad not my Dad, but David’s Dad?  David and I clearly were not genetic half-siblings, suggested at that time by CODIS testing, but proven eventually by 23andMe testing.  Was my Dad not the child of his father, William George?  Was his father maybe not the child of his father, Lazarus?  Why did my grandfather not look like the other Estes men?  We knew that John R. Estes matched the ancestral Estes line, but we had no one else to test below John R. on the tree.

Below, my great-great-grandfather, John Y. Estes, at left, my great-grandfather, Lazarus, center and my grandfather, William George, at right.

Digging up dad 2

Why did my son look so much like my father?  Was I just seeing things that weren’t there?  Below, my father as a teen in his military uniform and my son about the same age.

digging up dad 3

Without a male to test the Estes Y-line DNA, how would I ever know?

One day, a package arrived in the mail.  My step-mother had died some years ago, and her daughter had found a group of letters in her mother’s belongings that she felt I should have.  Among those letters were letters from my grandfather to my father.

Letters?  Envelopes?  Stamps?  Saliva?  DNA?  JACKPOT!!!  WOOHOOOO!!!!!!!

At the time my grandfather mailed those letters to my father, in the 1960s, my grandfather was living alone, so he should have licked the envelope and the stamp himself.

I called Bennett Greenspan at Family Tree DNA.  He referred me to a private lab that “does things like this,” called Trace Genetics.  Before you start googling, the company was subsequently sold and has now been defunct for years.  However, at that time they were doing custom processing of private forensic samples.

Yes, anything like that is considered forensic.  Anything you have to extract DNA from before you can have it processed in a regular lab is forensic work.

So, I got an estimate, took out a loan, and told them to go ahead.  You think I’m kidding, but I’m not.  The cost was in the $2000 range FOR EACH ATTEMPT.  So, we tried the envelope first.  No DNA.  Then we tried the stamp.  We got DNA, but it was female, so we knew it was contaminant DNA.  Think of how many people handle an envelope in the processing and delivery of mail, not to mention all the people who had handled it since.  Then we tried a second envelope.  No dice.

I was beyond frustrated and so were the two wonderfully patient scientists I was working with at Trace Genetics.  We all desperately wanted DNA.  In all fairness, they told me very clearly up front that there was a less than 50% chance of obtaining  ANY DNA, let alone usable DNA, let alone Y-line DNA.  Yes, the odds were very much stacked against me, and I knew it.

Y-line DNA is the least obtainable.  Most forensic work is done using mitochondrial DNA.  That’s because in each cell there is a total of 1 Y chromosome and there are thousands of mitochondria.  So the chances of recovering mitochondria are much greater than a Y chromosome.

Still, I had to try.  If you’re thinking of the word obsessed, I certainly wouldn’t argue with you.

Then I remembered, I had my father’s VFW hat.  I had it stored away in an old train case with other memorabilia from my childhood.  That was the one and only thing of my father’s I ever had – that hat.  I still remember him wearing it and I remember going to the VFW hall with him.  They had a slot machine and sometimes he used to let me pull the arm on the machine.  That was great fun.

I asked my friendly scientist at Trace Genetics what to do with the hat.  He suggested that I look for hairs in the interior of the hat, under the hatband, and then he told me how to extract the hair without touching it myself using sterile gloves.  I did so, put the hair in a Kleenex, put the Kleenex in an envelope and overnighted it to Trace Genetics.  This hair had the all-important follicle attached, the only part of the hair that will provide DNA.

I was positive, just positive, that this time was the jackpot.  But it wasn’t, and neither was the next hair.

Are you adding up the numbers in your mind?  Well, I assure you, I was adding them up.  And it wasn’t the money that bothered me, but the lack of results.  I was devastated.

Dad tombstone

So, I considered exhumation.  I looked into it, and I discovered a couple of things that were very important and were likely show-stoppers.

  1. In order to exhume someone, you have to petition the court and give a reason.  Then, you have to obtain the written, notarized, permission from every single descendant.  Yes, I said EVERY SINGLE DESCENDANT.  If even one disagrees, or refuses, it’s done, a deal-killer, dead.
  2. The cost of said exhumation is about $20,000 including all expenses, like attorney fees, backhoe, medical examiner, etc..

Choke, sputter, cough….clutching chest….

I happened to know someone who actually did exhume their ancestor, not for DNA testing, but because the cemetery was going to wind up at the bottom of a lake.  And yes, the entire process did cost in the neighborhood of 20K, a price-tag they did not anticipate in advance nor expect.

I had my doubts that any court would approve an exhumation for obtaining DNA for genealogy, but they might approve it to move the grave to Tennessee where my father’s family was buried.  Dad was (and is) buried alone in Indiana.

OLYMPUS DIGITAL CAMERA

But to move him, the cost of the exhumation would increase exponentially.  Moving a body which is considered medical waste is not inexpensive.  By way of comparison, to bring my sister home from Arizona to Michigan for burial was in the neighborhood of 10K.  And that would have been in addition to the 20K for exhumation.

For a minute, I thought about my brother, Dave, the long haul truck driver and I wondered if he had any room in that truck between pallets of yogurt.  But I got a grip on myself before asking him. I had visions of Dave putting Dad back in the sleeper cab…but I digress.

Ok, now we were talking the price of a car or a small house…a vacation home maybe or a trip around the world.  And it wasn’t 2K at a time, but an all or nothing proposition.

Not only did I not have the 20K or 30K, I couldn’t justify borrowing it, so I decided to leave sleeping Dad’s lie, so to speak.

I also decided that really, while I desperately did want to know about the paternity issue and its resolution, that I’m an Estes no matter what.  It’s my maiden name, it’s my name now that I’m married (I married a Kvochick, need I say more) and it will be my name on my tombstone.  So, I’m an Estes no matter whether I descended from them genetically or not.

I intentionally have not addressed any moral or ethical issues about exhumation.  Some feel the dead should be left alone, undisturbed.  However, there is precedent… the Catholic church regularly exhumes their saints to see if the body is well preserved.  I didn’t know what to think, truthfully, along those lines, and before I could have and would have actually made that decision, I would have had to think long and hard about it.  Would I have been there for the exhumation?  Could I have stayed away?  Would I have wanted to see my father like that?  All questions I would have had to answer, but did not have to, because the other issues precluded exhumation.

The first issue I would have encountered was who, exactly, were his descendants, and how, exactly, legally, was that determined?  I mean, does the court go by the obituary?  If so, my mother was his sister.  But I had a real half-sister.  Was she included?  No place did it say that she was his descendant.  He didn’t have a will.  And what about the children we knew about but couldn’t find?  Would that preclude the exhumation?  Or should we just stay quiet about them?  No, too many ethical issues and thorny problems, and that is BEFORE you get to the money issue.

I’m glad I didn’t slog through that mess, because before long, autosomal testing came about – not CODIS testing – which was inconclusive at best – but wide spectrum testing using hundreds of thousands of DNA positions, today’s 23andMe and Family Tree DNA’s Family Finder tests.

I have several Estes cousins who aren’t direct male lines but who who are fairly close genetically and I’m not related to any of them through any other genealogical lines.  If I matched them, it would be proof positive that I indeed was a blood descendant of the Estes line.  I wasn’t happy testing just one or two, so I tested 5 or 6 of my cousins from different children of my great and great-great-grandfather – and yes, I did indeed match all of them.

What a relief!  I didn’t have to dig up Dad or spend the equivalent of a couple years of college education.

But for those who are indeed as desperate as I was, let me tell you the following.

  1. There are very few labs that will do this kind of processing.  It is very unpopular as you basically have to shut the entire lab, sanitize it, and run no other tests until you are done.  You can see a forensic lab clean room in Ripan Malhi’s lab at the University of Illinois.
  2. Best case, with a relatively recent sample, meaning one from someone who died recently, you have about a 50% chance of useable DNA retrieval.  That’s BEST CASE.
  3. Skin is good.  The best is an electric razor contents.  Do NOT touch them.  Put the entire razor with contents into a plastic bag and DO NOT seal it.  Keep it in a temperature stable environment.  No attic or basement.   Sometimes hairbrushes have skin flakes in with the hair.
  4. Hearing aids are good.  Again, do not touch, etc.  Blood is good.  Spit is good.  A Kleenex is wonderful, providing you are sure it is their Kleenex.  If your mother was like my mother, check her bathrobe pockets.
  5. Older things like hair, sweat, envelopes etc. are not so good.  The older the sample, the less likely you’ll be able to retrieve DNA.  It degrades with time and these aren’t particularly good to begin with.
  6. Digging up a grave without doing all of the paperwork is illegal, and the legalities vary by locality – so consult an attorney and get the check book ready.  I just thought I should mention that little illegal detail, just in case.  I know genealogists are innovative and sometimes desperate people.

Having said all of that, don’t go throwing anything away.  There is new technology on the horizon that will only need one cell of DNA – so I’m told.  Seeing how far we’ve come in the past decade, I don’t doubt that someday this will be true, and someday may be closer than you think.  And no, I do not know how far away that horizon is.

So, store your DNA item safely.  Label it.  Do not seal it in plastic.  Do not store it in the attic (heat) or basement (cold, humidity) but someplace fairly temperature regulated.

One time when working with an archaeological specimen, we were told to freeze the sample.  Well, we did, in a plastic cool-whip container with water.  However, the electricity went out while the person whose freezer the specimen was stored in was out of town.  Their friend went to their house and did them the very big favor of disposing of everything in the fridge and freezer before they came home.   Needless to say, we were just sick.  So, don’t freeze it either.  Besides that, freezing in a frost-free refrigerator (that by definition defrosts itself regularly) is not the same as freezing a specimen in a laboratory temperature controlled stable environment.

So, what’s the upshot of this?

  • Forensic genetics is expensive
  • Exhumations are extremely expensive and fraught with all kinds of legal and technical landmines
  • There are very few labs, if any, that will process private forensic samples
  • When DNA is retrieved from a forensic specimen, it may be contaminant, not the DNA of the person you think it belongs to
  • When DNA is retrieved from a forensic specimen, you still have to pay for the DNA testing, in addition – and it may not work
  • When DNA is retrieved from a forensic specimen, if it does amplify, it will most likely be mitochondrial DNA
  • Using today’s combined genetic genealogy tests, there is almost always a way around the lack of a particular DNA donor, making exhumation and or forensic testing unnecessary

And if you’re considering grabbing a shovel, an urge which I well understand, I’ll leave you with the advice of an ethicist that Family Tree DNA invited to speak at their annual conference a few years ago, “Don’t do anything in the dark of night that you wouldn’t do in the middle of the day.”  Put another way, don’t do anything you wouldn’t be comfortable seeing in the headlines, because if you get caught, that’s where you’ll be:)

But then again, those headlines would certainly be something interesting for future generations of genealogists to dig up about you!

Announcing the Native American Haplogroup C DNA Project

Sitting Bull

Marie Rundquist and I would like to announce the formation of the Native American Haplogroup C project, titled Y-DNA Haplogroup C-P39 Project.

Native American males who descend from direct paternal ancestors who crossed the Bering land bridge from Asia some 10,000+ years ago fall into one of two haplogroups, or genetic clans.  One is haplogroup Q and the other is haplogroup C.

Since both haplogroup Q and haplogroup C are found among Asians, not everyone with these haplogroups in the Americas are Native Americans – only certain subgroups identified by specific mutations that occurred shortly before, during or shortly after the migration process.

In order to group Native American descendants together to better study these haplogroups and to coordinate their genealogies, we have created a haplogroup C project just for people who are Native American descendants.

Native Americans who carry haplogroup C are indeed quite rare and are identified by a special mutation, a SNP marker, known as P39, within haplogroup C.  This haplogroup subgroup is also known by the name C3b.

We would like to invite all men who are haplogroup C and carry mutation P39, or anyone who is haplogroup C and has a family history of paternal line Native ancestry to join the project.

You may recognize the names of the administrators.  If not, let me introduce them.

Marie Rundquist’s Amerindian Ancestry out of Acadia Project has rewritten the history of the Native American’s who married into the Acadian families in Canada beginning in the 1600s and before the Acadian deportation and scattering in 1755.  I wrote about the extremely interesting Acadian Germain Doucet family who, it turns out, is haplogroup C3b.  In addition, Marie, an Acadian and Native descendant herself, is an author.  Her book, Finding Anne Marie details another discovery of a Native American ancestor in an Acadian family.

I too am a Native American descendant from several different genealogical lines, including, ironically, the Acadian Doucet line.  I have been involved with Native American genetic genealogy since dinosaurs roamed the earth.  Ok, not quite that long, but since this science was taking its first tentative steps, about 12 years now.  I manage and co-manage several DNA projects that involve or are dedicated to Native American heritage.  I, along with others, was a partner in the revolutionary 2010 Native American SNP discovery.

Genetic advances and discoveries relevant to Native history and genealogy are regularly covered on my blog, www.dna-explained.com.  It’s searchable, just enter the word “Native” into the search box.  In addition, I maintain a historical focus on the Native people through the Native Names project which is focused on extracting the earliest names of Native people found in colonial documents.  To date, they number over 30,000 individuals and over 8,000 surnames.  Adventures in this project and a wide range of Native history are discussed on my blog, www.nativeheritageproject.com.

Both administrators come to you with years of genealogy and genetic experience.  We welcome project members as well as questions anyone might have.  We’re excited to be threads in the tapestry of unfolding history and hope you will join us.

http://www.familytreedna.com/public/ydna_C-P39/default.aspx

DNA Day

Did you know that today is DNA Day?  Did you know that there was such a thing as DNA Day?  It’s a holiday.  Did you take the day off work today?  What?  You didn’t know??

Well, you’re not alone if you didn’t know all of this, and you’re not THAT far behind either.  DNA Day was created by Congressional Resolution in 2003 – a date to commemorate two very important events – the 50th anniversary of the publication of the paper in Nature in which the discovery of DNA was announced by James Watson, Francis Crick, Maurice Wilkins, Rosalind Franklin and the celebration in 2003 of the complete sequencing of the Human Genome. DNA cake                       To find out more about this great cake, click here.

dna day 1

The double helix model built by Crick and Watson on display at the Science Museum in London.

Here’s what the 2003 Congressional Resolution said:

Whereas April 25, 2003, will mark the 50th anniversary of the description of the double-helix structure of DNA by James D. Watson and Francis H.C. Crick, considered by many to be one of the most significant scientific discoveries of the 20th Century;

Whereas, in April 2003, the International Human Genome Sequencing Consortium will place the essentially completed sequence of the human genome in public databases, and thereby complete all of the original goals of the Human Genome Project;

Whereas, in April 2003, the National Human Genome Research Institute of the National Institutes of Health in the Department of Health and Human Services will unveil a new plan for the future of genomics research;

Whereas, April 2003 marks 50 years of DNA discovery during which scientists in the United States and many other countries, fueled by curiosity and armed with ingenuity, have unraveled the mysteries of human heredity and deciphered the genetic code linking one generation to the next;

Whereas, an understanding of DNA and the human genome has already fueled remarkable scientific, medical, and economic advances; and

Whereas, an understanding of DNA and the human genome hold great promise to improve the health and well being of all Americans: Now, therefore, be it

Resolved by the Senate (the House of Representatives concurring), That the Congress-

(1) designates April 2003 as `Human Genome Month’ in order to recognize and celebrate the 50th anniversary of the outstanding accomplishment of describing the structure of DNA, the essential completion of the sequence of the human genome, and the development of a plan for the future of genomics;

(2) designates April 25, 2003, as ‘DNA Day’ in celebration of the 50th anniversary of the publication of the description of the structure of DNA on April 25, 1953; and

(3) recommends that schools, museums, cultural organizations, and other educational institutions across the nation recognize Human Genome Month and DNA Day and carry out appropriate activities centered on human genomics, using information and materials provided through the National Human Genome Research Institute and through other entities.

Passed the Senate February 27, 2003.

http://www.genome.gov/11008128

The resolution only declared a one-time celebration, not an annual holiday.  DNA Day celebrations have been organized by the National Human Genome Research Institute (NHGRI) starting in 2010.  April 25th has been since declared “International DNA Day” and “World DNA Day” by several organizations.

To visit the DNA Day webpage, click here.

dna dayMaybe more important to genetic genealogists is that Family Tree DNA almost always has a sale today and true to form, they are this year as well.  The sale, extended from this past weekend, ends tonight.

But for planning purposes, now that you know, plan to celebrate this important holiday next year by taking the day off work and doing something interesting like:

  • Swab a friend
  • Swab a cousin
  • Swab your spouse to see if you two are related and/or if s/he has the warrior gene
  • Swab your dog to see what kind of mutt s/he is
  • Swab your parents/grandparents
  • Swab any older generation person in your family
  • Upgrade a genealogy cousin’s DNA test (with their permission of course)
  • Be a DNA ambassador and visit a school or genealogy organization to speak about personal genetics
  • Take yourself on a date to a science museum

Happy DNA Day!!!

A Buck By Any Other Name

buck

A Buck by any other name might be Hogan, Logan or Williams.  I think we have a case of surname schizophrenia.  We have four surnames involving 3 people.

Do you sometimes wonder why you or one of your relatives matches a whole group of people by a different surname, and none by the surname you expected them to match?

This 1888 Indian Census page for the Seneca on the Allegany Reservation in New York just might give you a clue as to why you’re not matching whom you think you should be matching..

Not matching who you expect to match is sometimes called a Nonpaternal Event (NPE) or I prefer the term undocumented adoption.  But this case doesn’t seem to be undocumented at all…it’s well documented….it’s just that we can’t understand it.

So let’s say this is your family and the husband, I presume is Augustus Buck.  So far, that looks normal.  But this is where normal ends.

Your name is Acsah.  If you’re married to Augustus Buck, your name would be Acsah Buck.  This is how all of the other families are recorded, so you would be too.  Except you have this little note that says either (Logan was) or Hogan was).  Is that a maiden name?  No one else’s maiden or other names are listed.  Is Acsah maybe not the wife of Augustus and the mother of Alfred noted below?  If that is the case, then why are they listed as Buck now?

And Alfred has his own set of problems.  He is noted as Alfred Buck, age 2. One would assume the child of Acsah and Augustus Buck, judging from the rest of the entries.  But Alfred had this note that says (was Williams.)  What does that mean?  It’s certainly not his maiden name.

Does that mean that Alfred isn’t a Buck at all?  Is Alfred even the son of Acsah?  Is Alfred really a Williams.  Was Acsah married to a Williams before Augustus?  That would seem to be pushing it given that she is only 18 and Alfred was born when she was 16.  Did she have time to be married earlier?

So, if Alfred’s descendants were to DNA test, would they match a Buck, a Williams, a Hogan or a Logan?  Or maybe none of the above if Acsah had Alfred before she married Augustus by someone not listed on the “was” list.  Maternal naming was a very common Native American occurrence and what is today considered to be illegitimacy was not viewed through the lens of colonial or Victorian America.

And just think, if you are Alfred’s great-grandson and you took the Yline DNA paternal line test, expecting to match a Buck, and you were instead matching a Williams, Hogan or Logan, and if you never saw this census page, you would have no clue as to potentially why.  Of course, if you aren’t matching a Buck or a Logan, Hogan or Williams, then all bets are off.  But at least, there is a clue here that something is not like the rest of the families recorded in the census.  It’s something to work with.

Of course, this makes me wonder how many more census entries warrant notes and of course never received them.  And of course, a legend to interpret the note would be nice too:)

Gene by Gene Signs Agreement with MD Anderson Cancer Center

It’s really nice to know that the labs owned by Gene by Gene, which includes the lab that processes the Family Tree DNA tests, are so highly regarded.  The MD Anderson Cancer Center is THE cancer treatment center, very highly regarded, ranked as the #1 cancer treatment center in the US and one the first three comprehensive cancer treatment centers, focusing on academics, research and treatment.  Congratulations to Gene by Gene.  Gene by Gene and MD Anderson will make a great team!  The press release is follows:

Gene By Gene Signs Agreement with MD Anderson Cancer Center

Will provide clinical phase instruction, training and supervision for students as part of agreement

 HOUSTON — Apr. 23, 2013 – Gene By Gene, Ltd., the Houston-based genomics and genetics testing company, announced that it has signed an agreement with the University of Texas MD Anderson Cancer Center to become one of its affiliated clinical laboratories.

Under the agreement, scientists at Gene By Gene’s Genomic Research Center will provide the clinical phase instruction, training and supervision required for students in the Molecular Genetic Technology Program, one of eight undergraduate programs offered through MD Anderson’s School of Health Professions.

“We’re delighted to partner with Gene By Gene, with its long and pioneering history in the field of genomics,” said Program Director, Peter Hu, Ph.D., with the School of Health Professions.  “Gene By Gene’s sequencing, next-generation sequencing and microarray laboratory will provide the top level of experience and training that we want all our molecular students to attain.”

Gene By Gene’s Genomic Research Center is a CLIA registered lab which has processed more than 5 million discrete DNA tests from more than 700,000 individuals and organizations globally.  It is now one of only 36 laboratories in the United States, including the Yale University School of Medicine and the Baylor College of Medicine, to achieve this prestigious affiliation.

“We’re very proud to be able to share our laboratory and expertise with MD Anderson’s School of Health Professions,” said Gene By Gene President Bennett Greenspan.  “It’s an honor to be among the select few companies and institutions that are invited to affiliate with this prestigious institution.  In addition, this is a wonderful opportunity for Gene By Gene to continue investing in the next generation of leaders in genomic and genetic science, and we’re thrilled to welcome the first students to our Genomics Research Center this May.”

About Gene By Gene, Ltd.

Founded in 2000, Gene By Gene, Ltd. provides reliable DNA testing to a wide range of consumer and institutional customers through its four divisions focusing on ancestry, health, research and paternity.  Gene By Gene provides DNA tests through its Family Tree DNA division, which pioneered the concept of direct-to-consumer testing in the field of genetic genealogy more than a decade ago.  Gene by Gene is CLIA registered and through its clinical-health division DNA Traits offers regulated diagnostic tests.  DNA DTC is the Research Use Only (RUO) division serving both direct-to-consumer and institutional clients worldwide.  Gene By Gene offers AABB certified relationship tests through its paternity testing division, DNA Findings.  The privately held company is headquartered in Houston, which is also home to its state-of-the-art Genomics Research Center.

DNA Survives Bomb Blasts

Bomb1

In a surprising development, Discovery News reports that DNA can survive bomb blasts, and may indeed provide much needed links to who assembled that bomb.

Bomb 2

Dr. David Foran is performing ground breaking, and ground shaking, research into the remnants of such bombs, proving that the DNA obtained, as minute as it is, is readily identifiable to the person who handled the bomb, of course, assumed to be the builder and perpetrator.

Bomb 3

http://news.discovery.com/tech/videos/tech-dna-survives-bomb-blast.htm

Work on forensic genetics is being done at the Forensic Biology Department at Michigan State University.

Some of their cases, including that of the Boston Strangler, can be seen here.

You can take a look at their DNA labs and equipment here.

I never imagined with the heat and force of a bomb blast that DNA evidence would be able to be recovered.  I’m glad to know that genetics may well play a role in bringing these types of criminals to justice.

DNA Day Sale at Family Tree DNA

ftdna sale 4-2013

Beginning today and ending Monday night, April 22nd, at midnight, Family Tree DNA will be having an extensive DNA Day Sale.  Of note, both mitochondrial Full Sequence and Family Finder upgrades will be included, which seldom happens.  Family Tree DNA is taking this opportunity as well to announce technology upgrades in their sequenceing equipment.

If you have been considering either, this is a great sale and a good time to order these tests.  Family Tree DNA’s announcement to project administrators today is provided below.

SPECIAL DNA DAY REDUCED PRICING
We are pleased to announce our 2013 DNA DAY Promotion.While the special pricing features all the major tests, we’re   placing particular emphasis on the Full Mitochondrial Sequence and Family   Finder. We’ll offer Y-DNA upgrades during a Father’s Day sale and will give   you those details at that time.By carefully choosing the sale options and limiting the length   of the sale, we will be better able to focus our resources on processing the   tests efficiently and avoiding delays in delivering results.

We are proud to announce we have successfully moved our mtDNA   Full Sequencing line from Sanger DNA sequencing to what is called Next   Generation Sequencing (NGS). This gives us much greater capacity to process   tests, to reduce costs without sacrificing quality, and to ensure shorter   turnaround times.

We must run the entire sequence every time we process an mtDNA   full sequence test, even for upgrades. However, in recognition of your prior   investment- and National DNA Day – we’re offering our lowest price ever for   the FMS and upgrades.

Rather than the 8-10 weeks first generation sequencing   required, we expect results to be completed within 5-6 weeks. This does   depend on the number of orders received though. If their DNA is already at   our lab, those who order first may expect even shorter turnaround times.

For a limited time we will be selling the FMS for $189 and   whether you’ve tested HVR1 or HVR1+2, you’ll be able to upgrade to the Full   Sequence for just $129!

In addition, we are also lowering the Family Finder to $169 for   this sale!

Here is the list of all tests under the promotion:

Full MtDNA Sequence…. $189
Upgrades to FMS….$129
Y-DNA37 (new and add-on)…. $119
Y-DNA67 (new and add-on)…. $199
Y-DNA37 + Full MtDNA Sequence…. $308
Y-DNA12 + FF…. $218
Y-DNA37 + FF…. $288
Y-DNA67 + FF…. $368
Family Finder…. $169
Family Finder + Full MtDNA Sequence…. $358
SuperDNA….$388 (Y-67 + FMS)
Comprehensive DNA…. $557 (Y-67 + FMS + FF)

The sale will begin tonight, April 18th, at 6PM CDT and will   conclude at 11:59PM CDT on Monday April 22nd. All orders must be placed and   paid for by the end of the sale to receive the promotional price.

There will be no need for a coupon – all prices will be   automatically adjusted on the website.

THANK YOU FOR YOUR   CONTINUED SUPPORT
Bennett Greenspan
President
Family Tree DNA

Swabbing the (Recently) Deceased

Ezekiel EstesMeet Ezekiel Estes, son of Susanna Estes and ?  Ezekiel was born in 1814 in Halifax County, Virginia, and died in 1885, not terribly long after the camera was invented.  That is clearly when this photo was taken, at his death.

His great-grandchildren didn’t know that his father was ?  The family rumor had always been that Susanna, his mother, was apparently married to an Estes cousin, which explained why her surname as a “widow” was the same as her maiden name.  However, a lot of courthouse records research, reading of old depositions that still exist and DNA testing of a descendant proved that indeed, Ezekiel’s father was not an Estes man.

How many of you have a photo like this, or maybe one even better, with the casket showing?  Believe it or not, people made postcards of these kinds of photos.  In the early 1900s, there were photos of children who had died that were dressed and posed with the parents, as if they were still alive.  Can’t make it to the funeral, don’t worry…you get a picture.

But back then, once someone was dead, they were, well, dead forever… gone, except for that one photo.  Today, that’s not quite the case, because one can preserve DNA and part of that person will live forever through the information their DNA provides.  I mean, if we had Ezekiel’s actual DNA, we might be able to figure out who his father was.

So, what do you do if you meant to have Aunt Gladys swab at the family reunion this summer, but she had the bad judgment to pass away at Memorial Day?  Don’t just throw up your hands and show up at the funeral empty handed.  The funeral director is your friend.  They do a fine job of cheek swabbing.

Call Family Tree DNA (on the phone, not e-mail), tell the customer service representative the situation and ask for a kit to be overnighted to either the funeral director or a family member who can be counted on to take it to the funeral director the same day.  The funeral director will swab the cheek of the dearly departed and you will indeed still have the DNA information that Aunt Gladys meant to give you at the reunion.  Indeed, it’s a wonderful last gift and legacy for her to leave for you and the rest of her family and descendants.

Yes, and I know the next question that’s coming.  What about digging up the dead or testing things left behind?  Well, you’ll have to wait for a future article to discuss that in detail.  It’s much easier and infinitely less expensive to get a swab kit to the funeral director, let’s put it that way.  Plus, you’re pretty much guaranteed to get DNA from a cheek swab and attempting to retrieve DNA from personal items later is less than 50% successful, best case, and sometimes much less.  So, enlist the help of the funeral director, call Family Tree DNA or keep a swab kit handy at home at all times!

DIY DNA Analysis, GenomeWeb and Citizen Scientist 2.0

You just never know who you’re talking to on the internet.  Justine Petrone and I had exchanged e-mails about genetic genealogy in the past.  Earlier this week, I received an different type of e-mail from Justin, as the editor of GenomeWeb’s BioArray News which covers the microarray and biochip sector of the genomics market.  Justin, it turns out, has been writing about SNPs for a long time!

diy dnaJustin’s personal genetic genealogy adventures had inspired him and he was in the process of writing an article about what he termed DIY array data analysis – “downloading your raw data and playing around with it with a variety of online calculators.”  He said he found it intriguing that “thousands of people with limited scientific backgrounds are becoming amateur bioinformaticians and swapping SNP data with one another.”  Kind of the techo version of swapping spit, pardon the pun.

I have to tell you, this intrigues me too – not just because it’s happening, but because it’s happening on such a huge scale and that it’s being productive in ways we couldn’t even imagine just a few years ago.  For an example, take a look at my recent (and still in process) series titled, “The Autosomal Me” (Part 1 is at the bottom).”  Part 8 was published this week, Part 9 is still to come.

Yesterday, Justin’s article was published, “Customers of Ancestry Testing Services Turning to DIY Analysis Tools to Reanalyze Raw Array Data.”  Unfortunately, the full article is available for subscribers only, and a trial subscription is $95 for 3 months.  Remember, this is a professional journal for scientists – not for hobbyists, so while it’s steep for our end of the world, it’s normal in the professional arena.

Update note – Justin has generously offered to provide a complimentary copy of the article to those in the genetic genealogy community.  To request the article, contact Justin at jpetrone@genomeweb.com.

So let’s take a look, in general, at what Justin had to say.

Justin did a great job, I think, of portraying this new DIY phenomenon fairly.  He interviewed the heavy hitters in this field: representatives from Ancestry.com and 23andMe, Spencer Wells from National Geographic’s Genographic project, Bennett Greenspan from Family Tree DNA, Dienekes Pontikos, author of Dienekes’ Anthropology World, Dr. Doug McDonald, author of some of the earliest BGA software, Razib Khan, author of Discover Magazine’s Gene Expression blog, and me.

Of course, Justin couldn’t discuss this topic without talking about GedMatch, which has become the default toolbox for DIY autosomal DNA analysis, with the exception of Doug McDonald who performs complimentary biogeographical analysis.  Doug’s tools are not available at GedMatch.

The good news is that every one of the people that Justin interviewed was positive about the DIY phenomenon.  Of course, there were caveats about not taking every tool at face value, about actually analyzing not just accepting, and about security and privacy – but overall, these folks all agreed that individual analysis is not just a good thing, but full of potential.

I particularly like the quote by Dienekes.  He said that these tools are good for science “because of the plurality of eyes” which means that interesting patterns may emerge “that might be missed in more narrowly-focused research.”  Not only is this true, but the sheer magnitude of participation and data provides such good fodder for discovery – not just by the new wave of citizen scientists, but for academics who want to collaborate and focus on particular topics too.

In my discussions with Justin this week, I remembered that what I’ll call the Citizen Science Revolution was really spurred in 2005 by Leo Little, now deceased, in whose honor Thomas Krahn named the L SNPs discovered at the Family Tree DNA lab.  Leo must be getting a good chuckle about now.   See what you started Leo?

In December of 2010, I was personally involved with another citizen scientist discovery which marked a major milestone in haplogroup Q, delineating the European Q from the Native American version.  This discovery involved Lenny Trujillo, the participant who happened to be my client and Rebekah Canada, one of the administrators of the haplogroup Q project, plus Thomas Krahn at the Family Tree DNA lab.

And of course, we all know about the most recent discovery of the root of the Y tree, A00 involving Bonnie Schrack, a citizen scientist,  Michael Hammer from the University of Arizona and again, Thomas Krahn at the Family Tree DNA lab.

There have been more, many more, but these are three of the most memorable contributions to the genetics field by citizen scientists.  The message here is that anyone who chooses to ignore the citizen science trend, this flash mob of genetics, does so at their own peril.  It’s encouraging to see that this trend is being embraced, albeit slowly, by the larger genetics community.

We have been fortunate that the first wave of citizen scientists in genetic genealogy were often doctors or scientists in other venues who brought with them their understanding and computational skills to apply this new, and often most personal, arena.  With DIY tools available, the second wave has started now.  We’re educating the newcomers, helping them though blogs, education from the testing companies and through project administrators, ISOGG and ISOGG’s wiki, a variety of webinars sponsored by various groups, conferences and online lists and forums to understand their results.  In turn, as new initiates become educated in this emerging field, they bring with them their unique skill sets, background, genealogy and perspectives, and lo and behold, we have the new emerging model, Citizen Scientist 2.0!

The Autosomal Me – Extracting Data Segments and Clustering

This is Part 8 of a multi-part series, “The Autosomal Me.”

Part 1 was “The Autosomal Me – Unraveling Minority Admixture” and Part 2 was “The Autosomal Me – The Ancestors Speak.”  Part 1 discussed the technique we are going to use to unravel minority ancestry, and why it works.  Part two gave an example of the power of fragmented chromosomal mapping and the beauty of the results.

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets.  Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.  In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

In Part 6, “The Autosomal Me – DNA Analysis – Splitting Up” we began the analysis part of the data we’ve been gathering.   We looked at how to determine whether minority admixture on specific chromosomes came from which parent.

Part 7, “The Autosomal Me – Start, Stop, Go – Identifying Native Chromosomal Segments”, took a deeper dive and focused on the two chromosomes with proven Native heritage and began by comparing those chromosome segments using the 4 GedMatch admixture tools.

In this segment, Part 8, we’ll be extracting all of the Native and Blended Asian segments on all 22 chromosomes, but I’ll only be using chromosomes 1 and 2 for illustration purposes.  We will then be clustering the resulting data to look for trends.  If you’re following along and using this methodology, you’ll be extracting the Native segment start and stop locations from all 22 chromosomes.

I apologize in advance for the length of this article, but there was just no good place to break it into pieces.

So, let’s get started.  As a reminder, we are using the admixture tools at www.gedmatch.com.

I experimented with several types of extractions to see which ones best reflected the results found by both 23andMe and Dr. McDonald and confirmed by the start and stop segments in the highly Native segments of chromosomes 1 and 2 in Part 7 of this series.  We verified that all 4 tools accurately reflected and corroborated the segments listed as Native, so now we’re going to apply that same methodology to the rest of our chromosomal data.

Initially, I tried to use the information from chromosomes 1 and 2 to extract the Native chromosomes using only the “best” tool, but when I looked at all 4 tools, I quickly realized that there was no single “best” choice.  A couple of crucial points came to light.

  • Some of the geographic colors are almost impossible to tell apart.
  • None of the tools are universally best.
  • When looking at all 4 tools, generally a “best 3 out of 4” approach allowed for one of the tools to be wrong, to perhaps reference a slightly different data base that called the segment differently or for the colors to be indistinguishable.  In other words, if three called a segment Native and one did not, it’s Native and conversely, if less than 3 call it Native, in this comparison, it’s not.

Unfortunately, this created an awful lot of work.  This is probably the best example of where automation tools could and would make a huge difference in this process.

I did two separate extracts.  The first one is what I refer to as the “Strong Native” extract and the second is the “Blended Asian.”  In part, I did these separately as a check and balance to be sure that my first extraction was accurate.

In the first extract, I selected only one category, the one best fitted to “Native American” for each tool.  I used the following categories for each admixture tool:

  • MDLP – Amerind
  • Eurogenes – North Amerindian
  • Dodecad – NE Asian
  • Harrappaworld – American

I completed this process for every chromosome, but I’m only showing the first two chromosomes in this article.

By way of example, using the first tool, MDLP, North Amerind looks black, but is actually very dark grey.  It is, fortunately, distinctive.

On the chromosome painting below, my results for the first part of chromosome 1 are shown in the first band, and mother’s for the same segment are shown as the second band.  The bottom band represents common segments and the black is non-matching segments, meaning those I obtained from my father.  Sometimes this third band can help you determine what you are really seeing in terms of colors and blending, but it’s not always useful.  In this case, trying to spot a small amount of dark gray against black is almost impossible, so not terribly helpful.  But if you were looking for red, that would be another story.  As you move through this process, remember, it’s not exact and utilizing best 3 of 4 will help you recover from any major errors.

You can see that my grey segments show up from about 12-13 and then again at about 14.5.  Sometimes it’s difficult to know how to count something.  For example, my Native at 14.5 – it’s actually more like 14.25 -14.5, but I chose not to divide further than half mb segments.  As long as you are consistent in whatever methodology you select, it will work out.

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Please note that when reading these charts, that the small hash mark is the indicator for the measure.  In other words, the small hash mark above 10M means that is the 10M location.  It’s obvious here, but on some charts, the hash mark and the location legend look to be 1-off.  Again, as long as you’re consistent, it really doesn’t matter.

Mother’s Native segments are more pronounced and obvious.  They range from about 8-14.  Using the actual tools, you would record this and then continue scrolling to the right until you reach the end of the chromosome.  On chromosomes 1 and 2, I found the strong Native segments for the four admixture tools, as shown below.

The boxed numbers show the areas that were found “in common” between 23andMe, Dr. McDonald and the admixture tools, as determined in Part 7 of this series.  Highlighted segments show segments where at least 3 of 4 admixture tools reported Native heritage.  As you can see, there were clearly additional Native segments not reported by 23andme and Dr. McDonald.

Strong Native Chromosomal Detail Table

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Because we have both my and mother’s results, we can infer my father’s contribution.  Clearly, some of his will wind up being some amount of “noise” and some IBS segments, but not all, by any means, and this is the only way to get a “read” on Dad.  This is one form of phasing data.  Phasing refers to various methodologies of figuring out which DNA comes from what source, meaning which parental line.

While the strongest Native segments are the ones individually most likely to indicate Native American ancestry, that really isn’t the whole story.  I discovered that many of these Native segments are actually embedded in other segments that are indicative of Native heritage too.  In other words, it’s not a line in the sand, yes or no, but more of a sliding scale.

On the chromosome painting below, this one using Eurogenes, with my results shown above and mother’s below, you can see two excellent examples.  Regions relevant to Native ancestry include:

  • Red – South Asian
  • Brown – Southwest Asian
  • Yellow – North Amerindian and      Arctic
  • Putty – Siberian
  • Emerald – East Asian

You can see that while mine is almost universally yellow, or Native, with a little Siberian (putty) mixed in for good measure between 169-170, a hint of East Asian (emerald) plus a little Asian (red), mother’s isn’t.  In fact, hers is a mixture of Native American and South Asian (red), with more red than yellow,  Siberian (putty) and a large segment of East Asian (emerald green).

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While her yellow Native segments alone would be staggered across this entire segment in 7 different pieces, when taken together as a whole, the “blended Asian” segment reaches entirely across the screen with the exception of 1 mb between 161.5-162.5, roughly.

The following Blended Asian Chromosomal Detail Table shows all of the blended Asian segments using all four of the admixture tools for chromosomes 1 and 2.

It’s clear that these regions are not solely “Native American” but reach back in time genetically into Asia, particularly Northeast Asia.

Again, the boxed numbers show the “in common” segments between all tools and the yellow highlighted segments are common between at least three of the four admixture tools.

Please note that there were some issues distinguishing colors, as follows:

  • For the MDLP comparison, Mesoamerican and Paleo Siberian are both putty colored and indistinguishable on the chart.  Also, the apple green for Arctic Amerind is very similar to the Austronesian.
  • When using Dodecad, Southeast Asian (light green) and South Asian (apple green) are nearly impossible to distinguish from each other on the graphs.
  • When using HarappaWorld, the apple green for Siberian was very similar to the light forest green for Papua New Guinea and was very difficult to distinguish.  The South Asian putty appears often with the other Native markers, and I considered including this group, but it too was difficult to distinguish from other regions so in the end, I opted not to include this category.
  • If you are colorblind – get help as this is impossible otherwise.

Blended Asian Chromosomal Detail Table

On the blended Asian Chromosome Detail Table, I added yellow highlighting where the same segments show in other Asian geographies that showed in the Strong Native table.  In each column, the Strong Native category is the last one at the bottom of the list.

The blue highlighting shows other common segments found that were not included in the Strong Native segments.  For a Strong Native yellow segment to be highlighted, it had to be present in 3 of 4 tools, or 75%.  In the Blended Asian group, there are a total of 15 categories between the 4 admixture tools, so for a segment to be shaded blue, it must be found in at least 8 of the categories, so just over half.  There are many segments that are found in several categories across the tools.  For example, segment 192-193 on chromosome 1 is found five times.  This isn’t to say you should discount this segment, only that it isn’t one of the strongest, most universal.  Surprisingly, there really weren’t too many that were close to the cutoff.  Several, but not a majority, were in the 4 or 5 range, only one was at 7.

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Clustering

The third step in data extraction is to look at all of the data together.  In this step, we are removing the geographic boundaries of Siberian, N. Amerindian, etc. and combining all of our data.  I have only combined the data within columns, not between columns, so we can get a feel for which tool or tools performed best or maybe not so well.  Each chromosome in each column has its data ordered numerically, and yes, this is a manual cut and paste process.  Sorry.  I warned you, this is an very manually intensive process.

After I put each column in numerical order, I arranged them so that the numbers were approximately in a line, or a row, with each other.  For example, in the first group below, you can clearly see that the first cluster of results is found using all 4 tools.  When looked at individually, only the blue results were noted as common (at least 8 of 15 for blue), but when viewed as a cluster, you can see between the tools that the cluster itself runs from about 7.5, with a small break from 8-9, and then to about 14.5.  As you would expect the beginning and end points of the cluster trail off and are not uniform between tools, but the main part of the cluster is found in all the tools.  This introduces the question of how to measure a cluster.  In this case, there is a clean break using all tools between 8 and 9, but that is only 1 mb, rather difficult to measure accurately.  You could record this as two distinct clusters but since it’s very closely adjacent the rest of the cluster, I’m inclined to include this as one large cluster and use the starting and ending segments for the cluster as a whole, in other words, the cluster runs from 7.5 through 14.5.  The alternate, or more conservative methodology would be to use the “in common” numbers, but in this case, that would be only 10-11.5 and I think you would miss a great deal of useful data.  So, for clusters, I’m recording the full extent of the cluster.  In some cases, you may need to exercise a judgment call.

Let’s look at the second group of numbers, beginning with 18.5 in Harrappaworld.  This grouping runs though about 28.  Eurogenes found some blended Asian between 27-28.5 as well in two of the geographies, but over all, of the 15 tools, we don’t see much.  This could be a result of a number of things.  I could have had problems with the colors, there may be only a very small amount and it may be categorized as something else with the other tools.  I would not consider this a cluster, and using our best 3 or 4 methodology eliminates this cluster from consideration.  This also holds true for 43-43.5.

However, the next cluster, from 55.5 to 58 is found in the Strong Native comparison, indicated by the yellow highlighting and is found using all 4 tools.  This is definitely a cluster.

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I’ve synthesized the cluster information into a list.  From the clusters above, I’ve created a list that I will be using in the next segment for data input into my spreadsheet of matches.  The blended segments below that include Strong Native segments are shown with yellow.

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Using the GedMatch admixture applications, we’ve isolated the strongest Native and the Blended Asian segments and clusters in preparation for identifying specific Native family lines within our group of matches.

This process shows that, for the most part, the Strong Native segments picked up the strongest signals, about half of the segments that will be useful in determining Native admixture, although it does miss some.

When we use the clustering technique to view our results across all the admixture tools, we see a somewhat different picture emerge, adding several Blended Asian clusters.

In Part 9 of this series, we will use the highlighted Strong Native segments and the Blended Asian clusters, both of which suggest Native chromosomal “hotspots” to begin our comparison to our genetic matches for genealogical relevance.  In other words, using this information, we will determine which genealogical lines carry Native ancestry.

Part 9 may be somewhat delayed.  The good news is that Family Tree DNA is finishing work on their Build 36 to Build 37 conversion.  The bad news is that it fell right in the middle of writing this series.  When they finish Build 37, I’ll finish Part 9 of this series.  In the mean time, you can be extracting your minority segments using the tools and techniques that we have covered in Parts 1-8.