This article is probably less polished than my normal articles. I’d like to get this information out and to you sooner rather than later, and I’m still on the road the rest of this week with little time to write. So you’re getting a spruced up version of my notes. There are some articles here I’d like to write about more indepth later, after I’m back at home and have recovered a bit.
Max Blankfield and Bennett Greenspan, founders, opened the conference on the first day as they always do. Max began with a bit of a story.
13 years ago Bennett started on a quest….
Indeed he did, and later, Bennett will be relating his own story of that journey.
Someone mentioned to Max that this must be a tough time in this industry. Max thought about this and said, really, not. Competition validates what you are doing.
For competition it’s just a business opportunity – it was not and is not approached with the passion and commitment that Family Tree DNA has and has always had.
He said this has been their best year ever and great things in the pipeline.
One of the big moves is that Arpeggi merged into Family Tree DNA.
10th Anniversary Pioneer Awards
Quite unexpectedly, Max noted and thanked the early adopters and pioneers, some of which who are gone now but remain with us in spirit.
Max and Bennett recognized the administrators who have been with Family Tree DNA for more than 10 years. The list included about 20 or so early adopters. They provided plaques for us and many of us took a photo with Max as the plaques were handed out.
I am always impressed by the personal humility and gratitude of Max and Bennett, both, to their administrators. A good part of their success is attributed, I’m sure, to their personal commitment not only to this industry, but to the individual people involved. When Max noted the admins who were leaders and are no longer with us, he could barely speak. There were a lot of teary eyes in the room, because they were friends to all of us and we all have good memories.
Thank you, Max and Bennett.
The second day, we took a group photo of all of the recipients along with Max and Bennett.
With that, it was Bennett’s turn for a few remarks.
Bennett says that having their own lab provides a wonderful environment and allows them to benchmark and respond to an ever changing business environment.
Today, they are a College of American Pathologists certified lab and tomorrow, we will find out more about what is coming. Tomorrow, David Mittleman will speak about next generation sequencing.
The handout booklet includes the information that Family Tree DNA now includes over 656,898 records in more than 8,700 group projects. These projects are all managed by volunteer administrators, which in and of itself, is a rather daunting number and amount of volunteer crowd-sourcing.
Session 1 – Amy McGuire, PhD, JD – Am I My Brother’s Keeper?
Dr. McGuire went to college for a very long time. Her list of degrees would take a page or so. She is the Director of the Center for Medical Ethics and Health Policy at Baylor College of Medicine.
Thirteen years ago, Amy’s husband was sitting next to Bennett’s wife on an airplane and she gave him a business card. Then two months ago, Amy wound up sitting next to Max on another airplane. It’s a very small world.
I will tell you that Amy said that her job is asking the difficult questions, not providing the answers. You’ll see from what follows that she is quite good at that.
How is genetic genealogy different from clinical genetics in terms of ethics and privacy? How responsible are we to other family members who share our DNA?
What obligations do we have to relatives in all areas of genetics – both clinical, direct to consumer that related to medical information and then for genetic genealogy.
She referenced the article below, which I blogged about here. There was unfortunately, a lot of fallout in the media.
Identifying Personal Genomes by Surname Inference – Science magazine in January 2013. I blogged about this at the time.
She spoke a bit about the history of this issue.
In 2004, a paper was published that stated that it took only 30 to 80 specifically selected SNPS to identify a person.
2008 – Can you identify an individual from pooled or aggregated or DNA? This is relevant to situations like 911 where the DNA of multiple individuals has been mixed together. Can you identify individuals from that brew?
2005 – 15 year old boy identifies his biological father who was a sperm donor. Is this a good thing or a bad thing? Some feel that it’s unethical and an invasion of the privacy of the father. But others feel that if the donor is concerned about that, they shouldn’t be selling their sperm.
Today, for children conceived from sperm donors, there are now websites available to identify half-siblings.
The movement today is towards making sure that people are informed that their anonymity may not be able to be preserved. DNA is the ultimate identifier.
Genetic Privacy – individual perspectives vary widely. Some individuals are quite concerned and some are not the least bit concerned.
Some of the concern is based in the eugenics movement stemming from the forced sterilization (against their will) of more than 60,000 Americans beginning in 1907. These people were considered to be of no value or injurious to the general population – meaning those institutionalized for mental illness or in prison.
1927 – Buck vs Bell – The Supreme court upheld forced sterilization of a woman who was the third generation institutionalized female for retardation. “Three generations of imbeciles is enough.” I must say, the question this leaves me with is how institutionalized retarded women got pregnant in what was supposed to be a “protected” environment.
Hitler, of course, followed and we all know about the Holocaust.
I will also note here that in my experience, concern is not rooted in Eugenics, but she deals more with medical testing and I deal with genetic genealogy.
The issues of privacy and informed consent have become more important because the technology has improved dramatically and the prices have fallen exponentially.
In 2012, the Nonopore OSB Sequencer was introduced that can sequence an entire genome for about $1000.
Originally, DNA data was provided in open access data bases and was anonymized by removing names. The data base from which the 2013 individuals were identified removed names, but included other identifying information including ages and where the individuals lived. Therefore, using Y-STRs, you could identify these families just like an adoptee utilizes data bases like Y-Search to find their biological father.
Today, research data bases have moved to controlled access, meaning other researchers must apply to have access so that their motivations and purposes can be evaluated.
In a recent medical study, a group of people in a research study were informed and educated about the utility of public data bases and why they are needed versus the tradeoffs, and then they were given a release form providing various options. 53% wanted their info in public domain, 33 in restricted access data bases and 13% wanted no data release. She notes that these were highly motivated people enrolled in a clinical study. Other groups such as Native Americans are much more skeptical.
People who did not release their data were concerned with uncertainly of what might occur in the future.
People want to be respected as a research participant. Most people said they would participate if they were simply asked. So often it’s less about the data and more about how they are treated.
I would concur with Dr. McGuire on this. I know several people who refused to participate in a research study because their results would not be returned to them personally. All they wanted was information and to be treated respectfully.
What the new genetic privacy issues are really all about is whether or not you are releasing data not just about yourself, but about your family as well. What rights or issues do the other family members have relative to your DNA?
Jim Watson, one of the discoverers of DNA, wanted to release his data publicly…except for his inherited Alzheimer’s status. It was redacted, but, you can infer the “answer” from surrounding (flanking regions) DNA. He has two children. How does this affect his children? Should his children sign a consent and release before their father’s genome is published, since part of it is their sequence as well? The academic community was concerned and did not publish this information. Jim Watson published his own.
There is no concrete policy about this within the academic community.
Dr McGuire then referenced the book, “The Immortal Life of Henrietta Lacks”. Henrietta Lacks was a poor African-American woman with ovarian cancer. At that time, in the 1950s, her cancer was considered “waste” and no release was needed as waste could be utilized for research. She was never informed or released anything, but then they were following the protocols of the time. From her cell line, the HeLa cell line, the first immortal cell line was created which ultimately generated a great deal of revenue for research institutes. The family however, remained impoverished. The genome was eventually fully sequenced and published. Henrietta Lacks granddaughter said that this was private family information and should never have been published without permission, even though all of the institutions followed all of the protocols in place.
So, aside from the original ethics issues stemming from the 1950s – who is relevant family? And how does or should this affect policy?
How does this affect genetic genealogy? Should the rules be different for genetic genealogy, assuming there are (will be) standard policies in place for medical genetics? Should you have to talk to family members before anyone DNA tests? Is genetic information different than other types of information?
Should biological relatives be consulted before someone participates in a medical research study as opposed to genetic genealogy? How about when the original tester dies? Who has what rights and interests? What about the unborn? What about when people need DNA sequencing due to cancer or another immediate and severe health condition which have hereditary components. Whose rights trump whose?
Today, the data protections are primarily via data base access restrictions.
Dr. Mcguire feels the way to protect people is through laws like GINA (Genomic Information Nondiscrimination Act) which protects people from discrimination, but does not reach to all industries like life insurance.
Is this different than people posting photos of family members or other private information without permission on public sites?
While much of Dr. McGuire’s focus in on medical testing and ethics, the topic surely is applicable to genetic genealogy as well and will eventually spill over. However, I shudder to think that someone would have to get permission from their relatives before they can have a Y-line DNA test. Yes, there is information that becomes available from these tests, including haplogroup information which has the potential to make people uncomfortable if they expected a different ethnicity than what they receive or an undocumented adoption is involved. However, doesn’t the DNA carrier have the right to know, and does their right to know what is in their body override the concerns about relatives who should (but might not) share the same haplogroup and paternal line information?
And as one person submitted as a question at the end of the session, isn’t that cat already out of the bag?
Session 2 – Dr. Miguel Vilar – Geno 2.0 Update and 2014 Tree
Dr. Vilar is the Science manager for the National Geographic’s Genographic Project.
“The greatest book written is inside of us.”
Miguel is a molecular anthropologist and science writer at the University of Pennsylvania. He has a special interest in Puerto Rico which has 60% Native mitochondrial DNA – the highest percentage of Native American DNA of any Caribbean Island.
The Genographic project has 3 parts, the indigenous population testing, the Legacy project which provides grants back to the indigenous community and the public participation portion which is the part where we purchase kits and test.
Below, Dr. Vilars discussed the Legacy portion of the project.
The indigenous population aspect focuses both on modern indigenous and ancient DNA as well. This information, cumulatively, is used to reconstruct human population migratory routes.
These include 72,000 samples collected 2005-2012 in 12 research centers on 6 continents. Many of these are working with indigenous samples, including Africa and Australia.
42 academic manuscripts and >80 conference presentations have come forth from the project. More are in the pipeline.
Most recently, a Science paper was published about the spread of mtDNA throughout Europe across the past 5000 years. More than 360 ancient samples were collected across several different time periods. There seems to be a divide in the record about 7000 years ago when several disappear and some of the more well known haplogroups today appear on the scene.
Nat Geo has funded 7 new scientific grants since the Geno 2.0 portion began for autosomal including locations in Australia, Puerto Rico and others.
Public participants – Geno 1.0 went over 500,000 participants, Geno 2.0 has over 80,000 participants to date.
Dr. Vilar mentioned that between 2008 and today, the Y tree has grown exponentially. That’s for sure. “We are reshaping the tree in an enormous way.” What was once believed to very homogenous, but in reality, as it drills down to the tips, it’s very heterogenous – a great deal of diversity.
As anyone who works with this information on a daily basis knows, that is probably the understatement of the year. The Geno 2.0 project, the Walk the Y along with various other private labs are discovering new SNPs more rapidly than they can be placed on the Y tree. Unfortunately, this has led to multiple trees, none of which are either “official” or “up to date.” This isn’t meant as a criticism, but more a testimony of just how fast this part of the field is emerging. I’m hopeful that we will see a tree in 2014, even if it is an interim tree. In fact, Dr. Vilars referred to the 2014 tree.
Next week, the Nat Geo team goes to Ireland and will be looking for the first migrants and settlers in Ireland – both for Y DNA and mitochondrial DNA. Dr. Vilars says “something happened” about 4000 years ago that changed the frequency of the various haplogroups found in the population. This “something” is not well understood today but he feels it may be a cultural movement of some sort and is still being studied.
Nat Geo is also focused on haplogroup Q in regions from the Arctic to South America. Q-M3 has also been found in the Caribbean for the first time, marking a migration up the chain of islands from Mexico and South America within the past 5,000 years. Papers are coming within the next year about this.
They anticipate that interest will double within the next year. They expect that based on recent discoveries, the 2015 Y tree will be much larger yet. Dr. Michael Hammer will speak tomorrow on the Y tree.
Nat Geo will introduce a “new chip by next year.” The new Ireland data should be available on the National Geographic website within a couple of weeks.
They are also in the process up updating the website with new heat maps and stories.
Session 3 – Matt Dexter – Autosomal Analyses
Matt is a surname administrator, an adoptee and has a BS in Computer Science. Matt is a relatively new admin, as these things go, beginning his adoptive search in 2008.
Matt found out as a child that he was adopted through a family arrangement. He contacted his birth mother as an adult. She told him who his father was who subsequently took a paternity test which disclosed that the man believed to be his biological father, was not. Unfortunately, his ‘father’ had been very excited to be contacted by Matt, and then, of course, was very disappointed to discover that Matt was not his biological child.
Matt asked his mother about this, and she indicated that yes, “there was another guy, but I told him that the other guy was your father.’ With that, Matt began the search for his biological father.
In order to narrow the candidates, his mother agreed to test, so by process of elimination, Matt now knows which side of his family his autosomal results are from.
Matt covers how autosomal DNA works.
This search has led Matt to an interest in how DNA is passed in general, and specifically from grandparents to grandchildren.
One advantage he has is that he has five children whose DNA he can then compare to his wife and three of their grandparents, inferring of course, the 4th grandparent by process of elimination. While his children’s DNA doesn’t help him identify his father, it did give him a lot of data to work with to learn about how to use and interpret autosomal DNA. Here, Matt is discussing his children’s inheritance.
Session 4 – Jeffrey Mark Paul – Differences in Autosomal DNA Characteristics between Jewish and Non-Jewish Populations and Implications for the Family Finder Test
Dr.Jeffrey Paul, who has a doctorate in Public Health from John Hopkins, noticed that his and his wife’s Family Finder results were quite different, and he wanted to know why. Why did he, Jewish, have so many more?
There are 84 participants in the Jewish project that he used for the autosomal comparison.
What factors make Ashkenazi Jews endogamous. The Ashkenazi represent 80%of world’sJewish population.
Arranged marriages based on family backgrounds. Rabbinical lineages are highly esteemed and they became very inbred with cousins marrying cousins for generations.
Cultural and legal restrictions restrict Jewish movements and who they could marry.
Overprediction, meaning people being listed as being cousins more closely than they are, is one of the problems resulting from the endogamous population issue. Some labs “correct” for this issue, but the actual accuracy of the correction is unknown.
Jeffrey compared his FTDNA Family Finder test with the expected results for known relatives and he finds the results linear – meaning that the results line up with the expected match percentages for unrelated relatives. This means that FTDNA’s Jewish “correction” seems to be working quite well. Of course, they do have a great family group with which to calibrate their product. Bennett’s family is Jewish.
Jeffrey has downloaded the results of group participants into MSAccess and generates queries to test the hypothesis that Jewish participants have more matches than a non-Jewish control group.
The Jewish group had approximately a total of 7% total non-Ashkenazi Jewish in their Population Finder results, meaning European and Middle Eastern Jewish. The non-Jewish group had almost exactly the opposite results.
- Jewish people have from 1500-2100 matches.
- Interfaith 700-1100 (Jewish and non)
- NonJewish 60-616
Jewish people match almost 33% of the other Jewish people in the project. Jewish people match both Jewish and Interfaith families. NonJewish families match NonJewish and interfaith matches.
Jeffrey mentioned that many people have Jewish ancestry that they are unaware of.
This session was quite interesting. This study while conducted on the Jewish population, still applies to other endogamous populations that are heavily intermarried. One of the differences between Jewish populations and other groups, such as Amish, Brethren, Mennonite and Native American groups is that there are many Jewish populations that are still unmixed, where most of these other groups are currently intermixed, although of course there are some exceptions. Furthermore, the Jewish community has been endogamous longer than some of the other groups. Between both of those factors, length of endogamy and current mixture level, the Jewish population is probably much more highly admixed than any other group that could be readily studied.
Due to this constant redistribution of Jewish DNA within the same population, many Jewish people have a very high percentage of distant cousin relationships.
For non-Jewish people, if you are finding match number is the endogamous range, and a very high number of distant cousins, proportionally, you might want to consider the possibility that some of your ancestors descend from an endogamous population.
Unfortunately, the photo of Dr. Paul was unuseable. I knew I should have taken my “real camera.”
Session 5 – Finding Your Indian Prince(ss) Without Having to Kiss Too Many Frogs
This was my session, and I’ll write about it later.
Someone did get a photo, which I’ve lifted from Jennifer Zinck’s great blog (thank you Jennifer), Ancestor Central. In fact, you can see her writeup for Day 1 here and she is probably writing Day 2’s article as I type this, so watch for it too.
Session 6 – Roundtable – Y-SNPs, hosted by Roberta Estes, Rebekah Canada and Marie Rundquist
At the end of the day, after the breakout sessions, roundtable discussions were held. There were several topics. Rebekah Canada, Marie Rundquist and I together “hostessed” the Y DNA and SNP discussion group, which was quite well attended. We had a wide range of expertise in the group and answered many questions. One really good aspect of these types of arrangements is that they are really set up for the participants to interact as well. In our group, for example, we got the question about what is a public versus a private SNP, and Terry Barton who was attending the session answered the question by telling about his “private” Barton SNPs which are no longer considered private because they have now been found in three other surname individuals/groups. This means they are listed on the “tree.” So sometimes public and private can simply be a matter of timing and discovery.
Here’s Bennett leading another roundtable discussion.
Session 7 – Dr. David Mittleman
Dr. Mittleman has a PhD in genetics, is a professor as well as an entrepreneur. He was one of the partners in Arpeggi and came along to Gene by Gene with the acquisition. He seems to be the perfect mixture of techie geek, scientist and businessman.
He began his session by talking a bit about the history of DNA sequencing, next generation sequencing and a discussion about the expectation of privacy and how that has changed in the past few years with Google which was launched in 2006 and Facebook in 2010.
David also discussed how the prices have dropped exponentially in the past few years based on the increase in the sophistication of technology. Today, Y SNPs individually cost $39 to test, but for $199 at Nat Geo you can test 12,000 Y SNPs.
The WTY test, now discontinued tsted about 300,000 SNPs on the Y. It cost between $950 (if you were willing to make your results public) and $1500 (if the results were private,)
Today, the Y chromosome can be sequenced on the Illumina chip which is the same chip that Nat Geo used and that the autosomal testing uses as well. Family Tree DNA announced their new Big Y product that will sequence 10 million positions and 25,000 known SNPs for an introductory sale price of $495 for existing customers. This is not a test that a new customer would ever order. The test will normally cost $695.
Candid Shots
Tech row in the back of the room – Elliott Greenspan at left seated at the table.
ISOGG Reception
The ISOGG reception is one of my favorite parts of the conference because everyone comes together, can sit in groups and chat, and the “arrival” adrenaline has worn off a bit. We tend to strategize, share success stories, help each other with sticky problems and otherwise have a great time. We all bring food or drink and sometimes pitch in to rent the room. We also spill out into the hallways where our impromptu “meetings” generally happen. And we do terribly, terribly geeky things like passing our iPhones around with our chromosome painting for everyone to see. Do we know how to party or what???
Here’s Linda Magellan working hard during the reception. I think she’s ordering the Big Y actually. We had several orders placed by admins during the conference.
We stayed up way too late visiting and the ISOGG meeting starts at 8 AM tomorrow!
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