Friday, September 6, 2013

Where is Genetic Genealogy Going? Who is Driving the Agenda?


Several indicators suggest the genetic genealogy marketplace is in a state of flux. So what else is new?

What impact will the departure of Thomas and Astrid Krahn from FTDNA have on the company’s commitment to further explore the Y-chromosome? This is a particularly interesting question at a time when FullGenomes is on the verge of having actual customer results from its pricey first round of tests of the full Y-chromosome.
    
After the dust clears from the separation of Anne Wojcicki from Sergey Brin, it appears likely that 23andMe will not be seriously affected. Even though it is Anne’s company, it has been Sergey’s billions and Parkinson’s gene that have been the driving forces behind this company’s growth.
    
DNA testing has not been incorporated into any of the first seven segments of Who Do You Think You Are? Ancestry is a principal sponsor and the company's databases are prominently featured in most episodes. If it is Ancestry’s business plan to grow the DNA side of its business, this is a strange way to go about it.

Not to be left on the sidelines, Geno 2.0 apparently is fine tuning its marketing focus. Emphasis on the sale of its public participation kits will be concentrated in the English speaking world which in general is already to most tested part of the world.

Regional commercial ventures are springing up in various parts of the UK.

All of this makes it clear that our agenda is being set by commercial entities. That’s not bad. We would be nowhere without the framework they have created. Most of us do not want it to be set by various world governments which may be the primary alternative to the free enterprise system.


Where do you want our community to go in the next decade? Probably the next six months is a more reasonable time frame for a business plan in this marketplace. Or is it? How can we as consumers, both individually and collectively, best communicate our ideas – dare I say dreams – as to where we want genetic genealogy to move next? Does ISOGG have an opportunity for a more proactive role? Are there other venues for this discussion?

Sunday, September 1, 2013

Solving A Mystery With Women's DNA


Many still believe that only male DNA is useful for genealogical purposes. They need to wake up and smell DNA developments of the last 3 years. I recently helped a woman unravel an old mystery in her family using her autosomal and mitochondrial DNA test results. I will call her "Allyson" to protect the guilty dead and the living innocents. Here are some of the facts:

  • The adopted daughter of Allyson’s great aunt was thought to be a family member;
  • This adoptee was born in the 1920s;
  • The adoptee’s daughter, who I will call "Bertha", is alive and has taken a mitochondrial DNA test and a Family Finder autosomal DNA test at FTDNA.


Speculation within the family included:

  • This adoptee was the result of an illicit coupling of Allyson’s grandmother and her ex-husband long after their divorce;
  • This adoptee was the result of a teenage fling of Allyson’s mother.
  •  Allyson also has taken both a mitochondrial DNA test and a Family Finder autosomal DNA test at FTDNA.


The Mitochondrial DNA results:

Mitochondrial DNA is more definitive in ruling out potential relationships than in proving them. Their results could have ruled out Allyson’s mother and grandmother as potential mothers for Bertha’s mother. However, Allyson and Bertha are exact matches over all 16,569 locations on their mitochondrial DNA. They are the only exact matches for each other currently in the database. This means that the two share a direct maternal line (umbilical cord) ancestress probably within genealogical time. FTDNA says that such a match has a 50% probability of a common direct umbilical cord line ancestress within 5 generations and a 95% probability of a common direct umbilical cord ancestress within 22 generations. In this case the results do not prove how close the common ancestress actually lived, but they do add some credibility to the belief that this was an adoption within the family. Based on this result some hypotheses were formulated.

Research Hypotheses: 

#1. Bertha’s mom was the biological daughter of Allyson’s maternal grandmother and grandfather; 

#2. Bertha’s mom was the biological daughter of Allyson’s maternal grandmother and some unknown male – at least unknown to us; 

#3. Bertha’s mom was the biological daughter of Allyson’s mom and some unknown male.

No hypothesis was defined to include Allyson’s mom AND dad being the biological parents as existing letters clearly document that they did not meet until a few years after the birth of Bertha’s mother. On the other hand it can be documented that Allyson’s maternal grandmother and grandfather remained in contact long after their divorce.

Dick Eastman has famously blogged that there is no such thing as a ½ cousin. He quoted the venerable Black’s Law Dictionary to support his assertion. Well Dick, we would never be able to solve some of our genealogical mysteries unless we are able to split some cousins and other relatives in this manner.

If we want support for hypothesis # 1 above, we would need to find evidence that Allyson and Bertha could be 1st cousins. To support hypothesis # 2 above, we would need to find evidence that Allyson and Bertha could be ½ first cousins. If hypothesis # 3 above is correct Allyson would have a ½ aunt relationship with Bertha. In these three cases Allyson and Bertha would be expected to share either about 12.5% (1st cousins), about 6.25% (½ first cousins) or 12.5% (½ aunt). These percentages can be derived from the chart on the ISOGG Wiki: 

Cousin tree (with genetic kinship)


Relation with Adoptee’s Daughter “Bertha”
Maternal Grandmother is mother of Adoptee
Allyson’s Mother is mother
Maternal Grandfather is Father
Hypothesis #1
Maternal Grandfather is not Father
Hypothesis #2
Allyson’s father is not Father of Adoptee
Hypothesis #3
“Allyson”
1st cousin—12.5%
Half 1st cousin—6.25%
Half Aunt—12.5%
Male Cousin
1st cousin—12.5%
Half 1st cousin—6.25%
Half 1st cousin-once removed—3.125%
Female Cousin #1
1st cousin—12.5%
Half 1st cousin—6.25%
Half 1st cousin-once removed—3.125%
Female Cousin #2
1st cousin—12.5%
Half 1st cousin—6.25%
Half 1st cousin-once removed—3.125%

 Expected % of Shared Autosomal DNA 
for each Hypothesis

Oops! Using the autosomal data at hand we would not be able to distinguish between hypotheses 1 and 3. The expected amount of shared DNA would be the same in both cases. Fortunately there are three living 1st cousins of Allyson who might be willing to test. Two are female and one is male. In this case their sex would not matter because we have already established the maternal haplogroup of the adoptee. All we would need is their autosomal matches with Allyson and Bertha. These cousins would not add to our ability to distinguish between options #1 and #2 because their amounts of DNA shared with Bertha should mirror those of Allyson in both cases. Both Allyson and each of the 3 cousins should be shown to be 1st cousins with Bertha in #1 and ½ first cousins in # 2. So no increase in diagnostic ability is gained by collecting DNA from the 3 additional cousins.

But wait! We do not need them to help distinguish between #1 and #2. We might need their test results to differentiate between #1 and #3. Great! While Allyson would be a ½ aunt (sharing about 12.5%) in #3, the other 3 cousins would only be ½ 1st cousins (sharing about 3.125%) a significant difference. So it looks like it may be possible to collect enough information to solve this mystery.

The Solution:

Actually, it turned out to be quite a bit simpler than all that. As we saw much earlier in this saga, FTDNA predicted that Allyson and Bertha were 1st to 2nd cousins. For our purposes that is quite an extensive range. If they share matching segments that would be expected of 1st cousins, they would also share the amount Bertha would expect to share with a ½ aunt. But that is not the amount they share. They only share about ½ that amount. In this case it would have been easier to determine this if Allyson and Bertha had tested at 23andMe rather than FTDNA since the former reports matches in terms of % of match. FTDNA reports it in terms of centiMorgans (cMs) and SNPs matched. Although there may be handy conversion tables to translate these into % of match, Dr D had difficulty finding one. But he did find this one posted by Lindsay in her blog Confessions of a Cryokid:

According to Matt Dexter, on the FTDNA Forum, here is a breakdown of sum shared DNA ranges for various relationships:
  • Parent/child: 3539-3748 centimorgans (cMs)
  • 1st cousins: 548-1034 cMs
  • 1st cousins once removed: 248-638 cMs
  • 2nd cousins: 101-378 cMs

Although this table turned out to be very useful, it was compiled over 2 years ago. In autosomal DNA testing time that was almost light years ago. We now have tens of of thousands of more results that should have expanded our databases. Dr D would expect a currently compiled breakdown to show more overlap between the categories. 

Once the table in Lindsay's blog post was found, it showed that the 428.42 cMs shared between Allyson and Bertha were well within the expected range that would be expected for a 1st cousin-once removed relationship.

But 1st cousin-once removed is not one of the expected outcomes in the hypothesis table above. Or is it? Isn't it the equivalent of a ½ first cousin? I think we have a winner! The hypothesis that best meets the autosomal results is #2. The most likely biological parents of Bertha's mom are Allyson's maternal grandmother and an unknown male. Allyson's maternal grandfather seems to be ruled out as the biological father of Bertha's mother. Although testing additional cousins might lead to greater certainty, that does not appear to be necessary to identify the most likely candidate to be Bertha's grandmother. 

Saturday, August 31, 2013

Dr D Will Be Busy This Fall



Dr D will be busy this fall and may further neglect his blog posts. This next week he begins teaching a weekly genealogy seminar within our continuing care retirement center here in Nashville. The first 6 sessions will be the Readers Digest condensed version of his 2011 Crash Course in Genealogy.



In subsequent weeks we will tour Europe looking for the footprints of ancestors.

Beginning September 4th
at 2:30 PM in the Assembly Room

The first 6 sessions will be updates of the series presented in Spring 2012 on US Genealogy Research:

·       Seminar 1. Genealogy Overview
– September 4th

·       Seminar 2. Free search sites on the Internet featuring Google & FamilySearch
– September 11th

·       Seminar 3. 20th Century US Research
      [Thinking backward]
 – September 18th

·       Seminar 4. 19th Century US Research
– September 25th

·       Seminar 5. Colonial Research
– October 2nd

·       Seminar 6. Adding DNA Testing to your researcher’s toolkit
– October 9th


Going to Europe:  European research will be frustrating unless you have already discovered the town and/or parish of your ancestors’ origin, but you are welcome to go along for the ride.

·       Seminar 7. England & Wales – October 16th

·       Seminar 8. Scotland and Ireland – October 23rd

·       Seminar 9. Scandinavia -- October 30th

·       Seminar 10. Germany – November 6th

Additional sessions may include Eastern Europe, France and the Netherlands, and advanced topics on DNA testing for genealogy

In addition, Dr D will be on the other side of the lectern as a student at the Osher Lifelong Learning Institute (OLLI) at Vanderbilt University taking the course Science Behind the Medicine and Medical Advances.

Retirement is not for sissies!

Monday, August 12, 2013

The Genetic Gods Were Smiling


Last week the genetic gods must have been smiling on bloggers -- at least a couple of us. Judy Russell reported in her The Legal Genealogist blog that she had discovered her first "known relationship" through 23andMe

At about the same time I experienced my easiest "known relationship" find there. In this case it was not a match with me but a match between my daughter-in-law and a male predicted to be a:
2nd Cousin 3.57% shared, 12 segments
As you may know a match of this size is consistent with a second cousin match but it is also consistent with a first cousin -- twice removed. 

Those of you bucking for an “A” in genetics this semester may have already noticed one important thing about the matches shown below that made this genealogy mystery much easier to solve:


There is a significant match on chromosome X. Why is that significant some of you may ask? If you were paying attention above, I told you that the unknown potential second cousin was male. That means he inherited his entire X chromosome from his mother. Therefore, his match with my daughter-in-law must be on his mother's side of his family tree. This cuts in half the number of branches of his tree we had to consider.

It did not reduce the amount of my daughter-in-law's tree we had to examine. She had inherited one X chromosome from her mother; but she had also inherited one from her father as well. So I sent a list of her 8 great-grandparents to the wife of her match who was the family genealogist. The wife responded, "It's Homer and Hilda". Mystery solved!

His mother and the mother of my daughter-in-law are 1st cousins. I've had a few other successes at 23andMe but none this easy to achieve.

Thursday, August 8, 2013

Henrietta Lacks Revisited


When I first blogged about Henrietta Lacks a couple of years ago, I titled the blog "Right to Own Our Own Bodies". I'm on the road in Salt Lake City attending the Federation of Eastern European Family History Societies conference so this update post will be briefer than normal. However, this morning's news certainly warrants attention.

Several news outlets including The Guardian and Associated Press Francis S Collins, Director of the National Institutes of Health announced yesterday that an agreement had been reached with family members after six decades:

"Under the agreement, two family members will sit on a six-member committee that will regulate access to the genetic code.
"The main issue was the privacy concern and what information in the future might be revealed," David Lacks Jr., grandson of Henrietta Lacks, said at a news conference.
Jeri Lacks Whye, a granddaughter who lives in Baltimore, said: "In the past, the Lacks family has been left in the dark" about research stemming from HeLa cells. Now, "we are excited to be part of the important HeLa science to come."

Behind the scenes negotiations have been underway since March to reach this landmark arrangement. This follows on the heels of the Supreme Court decision in the Myriad Genomics case earlier this summer.

Finally some humanity is being used to guide this exploding new technology!

Friday, August 2, 2013

Are Your Genes Still Free?


It gets murkier and murkier. The day after the Supreme Court ruled that natural human genes could not be patented, Gene by Gene [and perhaps Ambry Genetics] started offering BRCA1 and BRCA2 testing for $999. Myriad Genomics had been offering it for  about $4,000. Great news for womankind. But now Myriad has sued.

“If [Ambry and Gene by Gene] are proved wrong, and I think they will be, it will be at the expense of women who want to be tested,” Gold said. “It’s legal, but not ethical.” For Professor Gold's comment in context read the full story in Wednesday's The Daily Pennsylvanian.


Dr. D agrees with Ambry Genetics' claim that our genes should be free to express their vital information:



Although that expression cannot be free (as in no cost); it should not be restricted from most women because of artificially high pricing. 

I at least partly agree with Professor Gold. I am not a patent lawyer. I am also not a geneticist. Therefore, I do not claim to understand all the legal and biological intricacies of this current law suit. I don't have an opinion as to whether of not patent law gives Myriad a legal leg to stand on. However, I strongly believe that Myriad's position is not ethical. Not many women can draw on the financial resources Angelina Jolie could draw on when she had to make a potentially life or death decision. However, they still need access to the most relevant information their body can give them before they make that decision.


Disclosure: I am an unpaid volunteer manager for two surname DNA projects hosted at Family Tree DNA (FTDNA). FTDNA is a subsidiary of Gene by Gene. FTDNA is one of four genetic genealogy labs through which I have tested my own DNA. I have no financial interest in any of these companies.

Monday, July 29, 2013

Stanford Medical School Teaches Genomics


Stanford University School of Medicine is researching the most effective methods to teach fundamental genomics. It turns out that one activity that boosts mastery of course content by 31% is something many of you have done already. It was to test their own genome and use the results in the course. This result was published June 23rd week in an article entitled "Evidence That Personal Genome Testing Enhances Student Learning in a Course on Genomics and Personalized Medicine". The abstract said in part:


An emerging debate in academic medical centers is not about the need for providing trainees with fundamental education on genomics, but rather the most effective educational models that should be deployed. 
We hypothesized that use of personal genome testing in the classroom would enhance the learning experience of students.
Undergoing personal genome testing and using personal genotype data in the classroom enhanced students' self-reported and assessed knowledge of genomics, and did not appear to cause significant anxiety.

Just three years ago it was reported in Inside Stanford Medicine that:


The question of whether to offer personal genotyping to students has undergone a yearlong, vigorous debate by a medical school task force.... Although not all task force members favored such a class, a majority recommended its adoption. School officials agreed. 

This is a positive step forward in bringing the future physicians into the age of personalized genomic medicine.

The question of whether to offer personal genotyping to students has undergone a yearlong, vigorous debate by a medical school task force, with course organizers addressing concerns that were raised by members of the group. - See more at: http://med.stanford.edu/ism/2010/june/genotype.html#sthash.fVAKPxLz.dpuf

I
The question of whether to offer personal genotyping to students has undergone a yearlong, vigorous debate by a medical school task force, with course organizers addressing concerns that were raised by members of the group. Although not all task force members favored such a class, a majority recommended its adoption. School officials agreed that the course should be offered, given the numerous safeguards built into the curriculum by the organizers. - See more at: http://med.stanford.edu/ism/2010/june/genotype.html#sthash.fVAKPxLz.dpuf
The question of whether to offer personal genotyping to students has undergone a yearlong, vigorous debate by a medical school task force, with course organizers addressing concerns that were raised by members of the group. Although not all task force members favored such a class, a majority recommended its adoption. School officials agreed that the course should be offered, given the numerous safeguards built into the curriculum by the organizers. - See more at: http://med.stanford.edu/ism/2010/june/genotype.html#sthash.fVAKPxLz.dpuf
The question of whether to offer personal genotyping to students has undergone a yearlong, vigorous debate by a medical school task force, with course organizers addressing concerns that were raised by members of the group. Although not all task force members favored such a class, a majority recommended its adoption. School officials agreed that the course should be offered, given the numerous safeguards built into the curriculum by the organizers. - See more at: http://med.stanford.edu/ism/2010/june/genotype.html#sthash.fVAKPxLz.dpuf

Sunday, July 28, 2013

Walk of Death a Good Read




Walk of Death by Mike Tabor is billed as a forensic novel and it is every bit that. Mike has been since 1983 the Chief Forensic Odontologist for the State of Tennessee Office of the Medical Examiner. In his day job, he is a dentist. Mike’s father lives in our continuing care retirement center here in Nashville. According to the publisher’s blurb:

In the spring of 1997, two rural Tennessee addicts find themselves under investigation for dealing crystal meth. Together, they concoct an ill-conceived plan to outrun the law, letting nothing stand in their way. Murder, insurance fraud and switched identities are only the beginning of a cat and mouse mystery that leaves an unidentified murder victim in their wake.
As the case goes unsolved, Dr. Chris Walsh, Chief Forensics Odontologist of the Tennessee Medical Examiners office sets his sights on identifying the nameless victim and solving the gruesome crime.
Fact and fiction collide in this intricate and chilling story by first time author Dr. Mike Tabor. Culled from real case history, Tabor leads the reader on a journey that takes them from the world famous Body Farm in Knoxville, TN to the site of World Trade Center terror attacks and the identification of nearly 1000 victims.
Intrigue, drama and edge-of-your-seat suspense help make Walk of Death an exciting and frightening read that rivals some of the best crime dramas ever published.

The author says the book is about 75% fact and 25% fiction and the story is largely autobiographical. One element of the fiction part is that the names of the characters have been changed to protect the _____. Only the dogs were allowed to keep their real names. This combination works to create a gripping true crime forensic docudrama which has rich character development of both the good guys and the bad. 
    
I’m sure most of the regular readers of this blog will enjoy the book. When fingerprint identification fails because of the condition of the corpse, dental records usually fill the breach if they can be located. Teeth can provide up to 5 to the 32nd power combinations for identification. That is a very big number. But what happens when dental identification also fails? I won’t say more because I don’t want to give the ending away -- except that you may want a hankie handy for the conclusion. 

Wednesday, July 24, 2013

Genealogy Shows


I hope you watched the first episode of Who Do Your Think You Are? last night on The Learning Channel. It featured Kelly Clarkson. Seven episodes will follow this summer. If you can’t get The Learning Channel or missed this episode for other reasons, you soon should be able to view it online. However, last night's episode does not seem to be working correctly yet. It was just loaded and only plays for a minute or two. I don't know if the site is overloaded or there is some other problem. In the meantime you can enter the sweepstakes to win a Trip to the Motherland.by answering a question based on that first episode. If you saw it what do you think about that episode?

Next week Christina Applegate will be the featured celebrity. 

Soon after WDYTYA completes its eight week run in September, genealogy junkies will be treated to the latest import from Europe -- this time from Ireland. Genealogy Roadshow will kick off a four week run on Public Television on September 23rd at 9:00 PM (8:00 Central). While WDYTYA traces its pedigree back to England and BBC, Genealogy Roadshow is patterned after the RTE show now beginning its second season which features the genealogical quests of ordinary people. 

Henry Lewis Gates is working on a new series as well; but I have yet to see a release schedule for it. Hopefully we will get to watch it in 2014.

Thursday, July 18, 2013

Kelly Clarkson Leads Off Who Do You Think You Are?


It's time to mark your calendar and/or set your DVR to watch the first episode of the new season of Who Do You Think You Are? This season 8 episodes will air on the The Learning Channel. Kelly Clarkson will be featured in episode 1. The producers are aiming for a younger audience in their choice of subjects. It will be interesting to see how much content can be included in the new half-hour format. Episode 1 will air Tuesday, July 23 at 9 PM (8 PM Central).


This season's full lineup of celebrities is listed below:


If you should miss an episode, after they air they can be watched online.

If you want to see non-celebrities featured in a show like this, watch for "Genealogy Roadshow" coming in September on Public Television.