The Genetic Genealogist

A news release announces the completion of a DNA collection project by SMGF (Sorenson Molecular Genealogy Foundation) in Mongolia. The goal of the project is to study the descendants of ancient nomads from the Eurasian steppes. The collection was performed in conjunction with the National University of Mongolia and represents “the most comprehensive [DNA collection project] in the history of Mongolia, incorporating all of the country’s geographic regions and major ethnic populations.” In total, more than 3,000 DNA samples and pedigree charts were obtained from 24 different ethnic groups.

According to the news release, the “global fascination with Mongolian icons such as Genghis Khan and Attila the Hun” played a role in promoting the project:

“For many centuries, Mongolians have held an ongoing fascination in genealogy, spurred in part by reverence for ancestors and for oral traditions – with some family and clan names stretching back as far as the 10th Century (AD). Under Genghis Khan’s rule in the 13th Century, Mongols invaded Eurasian territory, then ruled there for more than two centuries. In the 20th century the then-USSR gained political control of Mongolia and its leaders systematically worked to eradicate Mongolian national identity – especially the Khan connection – executing or imprisoning an estimated 100,000 Mongols between 1922 and 1940. In recent years, however, there has been a renaissance of Mongolian national identity, accompanied by a widespread search for Mongolian genetic roots – which the SMGF-NUM partnership will continue to foster.”

Some other goals of the project:

• To study the unique genetic characteristics of indigenous and mixed populations in Mongolia;
• To document and preserve oral histories;
• To add the new historic and genetic data to SMGF’s publicly-available Sorenson Database; and
• To promote family history record-keeping and increase the availability of genealogical record-keeping in Mongolia

Information from the study will be published in “books, journals, and other publications” and will be available on the SMGF website, which is touted as “the world’s leading online repository of correlated genetic and family history information for people throughout the world, which currently contains in excess of five million records from more than 170 countries.”

As I mentioned back in June,  Ancestry.com has teamed up with Sorenson Genomics to offer DNA testing.  Today I received the following notification announcing the beta launch of dnaancestry.com.  A Y-DNA test with 33 markers will be $149, while a Y-DNA test with 46 markers will be $199 (if you look at the sample results page, you’ll see a list of the 46 markers tested).  An mtDNA test will be $179, although the exact testing parameters for the mtDNA test are unclear at this point (the website only states that HVR1 and HVR2 will be sequenced).

Introducing DNA Ancestry
We want you to be one of the first to know we’re adding a powerful new dimension to genealogical research by integrating the world’s largest online collection of historical records and family trees with DNA testing. Currently in beta, DNA Ancestry is another way we’re helping people expand their family trees and connect with family across distance and time.

We created DNA Ancestry to help users:

• Validate existing research.
• Break through genealogical dead ends.
• Discover and connect with genetic cousins.
• Collaborate and expand their family trees.
• Learn about ancient origins.
• Review, decipher and save test results safely and conveniently online.

As the DNA Ancestry database grows, we will continue to compare your results with the results from new users and notify you by email when we find potential matches.

How does it work?

1. Purchase a DNA test kit. Your kit will include three collection swabs, an envelope for recording your information and a postmarked return envelope.
2. Swab the inside of your mouth. Follow the instructions provided, rubbing each swab inside both of your cheeks.
3. Mail your kit to our labs. We’ll begin analyzing your DNA sample as soon as we receive it. Results are typically available within 2-3 weeks after the lab receives them.
4. View your results online.
   • Your personal DNA profile
   • A map displaying the location of participants matching your DNA
   • A table comparing your DNA profile with matching profiles
   • A chart showing the range of generations in which you and another participant may share a common ancestor.
   • Safe, secure, and anonymous, e-mail connections with potential genetic cousins
   • A haplogroup prediction, map and migration history

What tests are available?
DNA Ancestry currently offers the following genealogical tests:

PATERNAL LINEAGE TEST
Y chromosome 33 marker test $149
Y chromosome 46 marker test $199

• These tests provide an indicator of the direct paternal line and can be compared to others’ results to find matches signifying relationships
• Only males can be tested, though females may have a male relative in their paternal line tested by proxy
• Includes a paternal haplogroup prediction, which indicates the direct paternal line’s ancient ancestry

MATERNAL LINEAGE TEST
mtDNA test $179

• This test includes a maternal haplogroup prediction, which indicates the direct maternal line’s ancient ancestry
• Both males and females can be tested

What’s next for DNA Ancestry?
Very soon you’ll be able to add your DNA test results to your online family tree. This will make it even easier to connect to the 3 million other Ancestry.com member trees on the site and tap into thousands of hours of completed genealogical research.

Surname Projects
Our initial beta launch of DNA Ancestry Version 1.0 will not include DNA surname projects support. We are taking the input we have received from Project Coordinators surveys, as well as other outside information, and are using it to build DNA Projects in a way that will be better for all of our members. Until then, we encourage project coordinators to continue to build projects and monitor results through the Relative Genetics site with their Relative Genetics login. The project data and members will transfer over to DNA Ancestry with our DNA Ancestry Version 1.1 launch, which is planned for the end of the year.

Already had your DNA tested?
DNA Ancestry has a function that will let users add their test results to the DNA Ancestry database and allow them to connect with others who share their DNA.

Learn more about DNA Ancestry at DNA.Ancestry.com.

Yesterday we saw that many funeral directors offer DNA retrieval and storage as one of their services. Today, we’ll look into the WHY of DNA storage, and bring up some of the ethical questions it raises.

Why store DNA from the recently deceased?

Undoubtedly, someone who has never heard of DNA retrieval and storage will probably ask WHY we should store a dead relative’s DNA.

The reason most commonly quoted is that the DNA can be used in the future to identify inherited traits such as genetic disorders and other phenotypic characteristics. In 2006, the New England Historic Genealogical Society published an article by Edwin M. Knights, M.D. entitled “DNA Banking for Medical Information.” In the article, Dr. Knights gives a number of reasons for banking DNA from both living and deceased individuals, many of which he gleaned from the Human Genetic Society of Australasia. He states:

• “To allow for molecular diagnosis and characterization of the mutation should this become available in the future, DNA needs to be stored from affected individuals. If none of the affected individuals in the family are available, it may be appropriate to store DNA from a fetus after termination of a pregnancy at risk, or from a stillbirth or neonatal death at risk for the disorder, especially in the case of X-linked recessive conditions.

The National Society of Genetic Counselors, on the other hand, has stated that there are only two occasions when DNA banking is appropriate (the Society has a brochure available here (pdf)).

1. When current technology has failed to find a genetic cause for what appears to be an inherited disease in a family, or

2. When genetic testing is not feasible or available to an affected individual, but may be available in the future.

From a medical standpoint, it is unclear how useful stored DNA might be. According to Eric Juengst, an associate professor of biomedical ethics in MetroHealth Medical Center in Cleveland, until recently testing multiple generations for a hereditary disease like Huntington’s chorea was not unusual. But scientific advances have allowed the same information to be gathered by testing just one individual. “The way that genetic tests are being sold to the public as prevention tools are no more powerful than the tools we use today like cholesterol tests,” Juengst said. “This is a very minimal service.”

Do we really need our parents’ DNA for information? As far as we know, almost everything we need to know about our propensity for genetic disease is contained in our own genome. For me, the reason I would save my ancestor’s DNA is to learn about their genealogy, not about any predisposition I might have towards disease.

“The DNA samples also could be used to determine paternity, which might reveal a few unexpected and unwanted surprises, Juengst said.“You might find out your dad really wasn’t your father,” he said. “Maybe that secret was supposed to go to the grave. We’re supposed to respect the dead and we need to respect their genetic secrets as well.”

If I save my great-grandmother’s DNA and analyze it for genealogical information, am I showing disrespect?

Ethical Questions Associated with DNA Banking:

Banking DNA from the deceased raises many ethical dilemmas and forces us to ask difficult questions. The American Society of Human Genetics (ASHG) has issued a “DNA Banking and Analysis” statement that offers a number of interesting questions surrounding DNA Banking:

1. Who Owns the DNA in a Bank?

2. Under What Circumstances, if Any, Should the DNA Diagnostic Laboratory Release Results or Deposited DNA to Anyone Other than the Patient?

3. Should DNA Banks and/or DNA Diagnostic Laboratories Be Certified?

A recent article available at New England Ancestors, “DNA Banking for Medical Information”, suggests the obvious, that DNA should be stored today for tests that will only be available tomorrow. The article also lists some of the most important questions facing companies that offer DNA banking and consumers that plan to partake of these services:

1. Why is the DNA being banked?

2. Who owns the banked DNA?

3. Who controls the bank, and how secure is it?

Although both of the above studies were about DNA banking in general, the questions also apply to DNA retrieval from the dead.

I also wonder whether offering DNA retrieval and storage to someone who is grieving is unethical. In a way, the service is offering the bereaved the ability to retain a piece of the deceased and to store that piece for an indefinite period of time. Someone who is grieving might jump at this chance to prolong their ability to hold onto the deceased. On the other hand, perhaps it might help the healing process.

The most important concern about DNA retrieval from the deceased is the question of consent. Unless the deceased was asked before death, retrieval is without consent. Currently, however, you can obtain and analyze anyone’s DNA without consent, so perhaps this isn’t as radical as it seems. As a recent article in the New York Times discussed, some people have gone to great lengths to obtain a distant relative’s DNA against their wishes. In most cases, at least the DNA retrieval from the dead won’t be against their written or vocal wishes. But it will still be taken without consent.

In conclusion, I’m not completely against DNA retrieval and storage, especially when consent is given. Who knows what that DNA might be good for in the future. My analysis is just meant to look at some of the potential problems with DNA storage, and to foster thought and conversation. Our genomes are able to hold many secrets. Only recently have we had the technology to reveal these secrets. What are your thoughts?

The field of genomics is exploding. Every day, the mysteries of our genome are revealed and we learn more and more about the power of DNA. Soon, with affordable whole-genome sequencing, we will be able to analyze our own personal genome for clues about our ancestry, our propensity for disease, and insight into our body and our personality. In fact, this is already well underway.

Undoubtedly, each of us will be faced with a decision in our lifetime – do we want to learn the secrets of our genome, or do we want to live without that knowledge, as all of our ancestors have done for millions of years. This decision is a personal one, and at this point I don’t think there’s any right or wrong answer.

But what about those who are unable to make that decision? For example, an infant is unable to give consent for genetic testing, but many states in the US routinely test newborns for genetic disorders. Today and tomorrow we will be examining another group of individuals who are not able to consent to genetic testing – the recently deceased.

DNA Banking

There are number of companies in the US and throughout the world that offer DNA retrieval from recently deceased individuals. Kauber-Miller Funeral Home in Pataskala, Ohio has been using DNA Connections to offer storage service to bereaved families. In a 2004 interview, Mr. Miller stated that the service has been popular:

“About 30 percent of the families take advantage of it,” he said. “It seems to be a generational thing, with younger people more in favor of it.”

In 2004, the cost was $295 before embalming and $459 after embalming. Before embalming, a blood sample is dried on specially coated cards and stored inside a vault at DNA Connections’ headquarters. After embalming, a skin sample must be taken to retrieve the DNA.

Perhaps surprisingly, the ability to store a deceased person’s DNA has been around for more than ten years. In 1998, an article in the Huntington’s Disease Lighthouse newsletter described a DNA storage service from Cincinnati-based DNA Analysis, Inc. For $350, the company would take hair, blood, and cheek swab samples for long-term storage. The family would also receive a “genetic fingerprint”, although it is unclear exactly what that phrase means.

The ability to store DNA from both the living and the recently deceased is increasing every day. The City of San Bruno in California recently posted online instructions for banking the DNA of children in your own freezer. Although the instructions were provided to assist in finding or identifying lost relatives, it could be used for anyone. Even retailers have entered the market, offering a home DNA storage kit for only $29.99.

In 2006, the New England Historic Genealogical Society published an article by Edwin M. Knights, M.D. entitled “DNA Banking for Medical Information.” In the article, Dr. Knights makes the following comment:

“For an increasing number of disorders there is urgent need to store DNA from elderly members of the family or affected persons whose life expectancy is reduced. We would go much further, as we feel strongly that DNA information is becoming so important that DNA should be banked from every elderly adult who has had children. This is particularly true because so many are now choosing cremation rather than traditional methods of burial, in which case DNA evidence is lost forever. It is becoming increasingly important for descendants to know what DNA they have inherited in order to modify or prevent subsequent serious medical conditions in future generations. Of course DNA also provides a priceless resource for genealogical pedigree studies. This objective can be achieved easily if we enlist the cooperation of funeral directors.”

DNA Storage in Other Countries:

Storage of a deceased person’s DNA is also being offered in the UK. According to Avi Lasarow, founder and director of DNA Bioscience Today, “in the UK the cremation rate is 73%, and the public need to be aware that there is a real need to store this vital piece of medical information.”

Interestingly, Mr. Lasarow also suggested that Funeral Homes might be liable for NOT offering DNA storage. “Given the importance of DNA preservation and knowing that upon cremation and most likely embalming that there will be no possibility of getting samples, we are beginning to wonder if there is an implied responsibility among funeral directors to make families aware of this service,” Lasarow said.

So it appears that DNA storage is being offered by funeral directors and retailers around the world. But it raises a few important questions – how necessary or useful is a dead person’s DNA, and is the retrieval of DNA from someone who has not given consent ethical? We’ll look into this tomorrow.

Companies that Offer DNA Retrieval and/or Banking:

1. DNA Safe Storage

2. DNA Connections

3. DNA Analysis

4. Genetic Identity

5. GeneSaver

6. PRO-DNA

7. DNA Diagnostics Center

8. DNA Products

9. Heritage DNA

10. DNA Genetic Connections

11. Legacy Biogenetics

12. Beta Genetics

13. Affiliated Genetics

14. GeneTree

15. GeneLink

16. DNA Bioscience

For More Information:

• Genethics.ca
• NEJM
• National Society of Genetic Counselors

Dogs, just like humans, have interesting genealogical histories. And a new DNA test unveiled by DNAPrint Genomics will help you examine your dog’s genetic past. The test is aimed at uncovering the relative percentages of four ancient ancestral breeds in a modern dog – wolf-like, herders, hunters, and mastiff. The test, which will retail for $99, examines 204 canine Ancestry Informative Markers (AIMs) in the dog genome. For more information, go to www.doggiednaprint.com (not working as of 08/18).

“The test will contain a consent form, mouth swabs, swab envelope, as well as a return envelope. Simply fill out the consent form, follow the step-by-step cheek swab instructions and send the completed consent forms and test swabs in the enclosed return envelope. Within six to nine weeks, participants will receive the results of their dog’s DNA test. These will include raw genetic data, a graphic depiction of the animal’s DNA plus information on how to interpret the results of this DNA test.”

The test also represents a new venture by DNAPrint – a DNA database. Pet owners will be allowed to compare their dog’s score to DNAPrint’s database of purebred and mixed breeds to allow accurate breed identification. I think this is a great move, because one of the most interesting aspects of DNA testing is the ability to compare the results to a database, or to another person.

So I guess my only question is, how do you get a dog to fill out and sign a consent form?

HT: Hsien at EyeonDNA.

One of the steps in analyzing the results of a Y-DNA test is to search through Y-DNA databases to look for potential matches. These matches, depending on how well they match, might be relatives, either close or distant (in recent genealogical terms – we’re all distantly related, of course).

One of those databases is YHRD (Y-STR haplotype reference database). The project has two main goals:

1. The generation of reliable Y-STR haplotype frequency estimates for minimal and extended Y-STR haplotypes to be used in the quantitative assessment of matches in forensic and genealogical casework, and;
2. The assessment of male population stratification among world-wide populations as far as reflected by Y-STR haplotype frequency distributions

According to the YHRD website:

“To this end, a growing number of diagnostic and research laboratories have joined in a collaborative effort to collect population data and to create a sufficiently large reference database. All institutions contributing in this project, participated in an obligate quality control exercise.
“This database is interactive and allows the user the search for Y-STR haplotypes in various formats and within specified metapopulations. Related information i.e. STR characteristics, mutations, population genetic analyses etc. is documented.”

The YHRD database is contantly being updated, and on August 10th, Release 22 was added:

“Release 22 is out with 52,655 haplotypes in 464 populations. 50,867 haplotypes of these are completely typed for 9 (Minimal haplotype) and 23,981 for 11 loci (Extended or SWGDAM haplotype). Twenty populations were added or updated today: two Amerindian tribal populations from the Formosa province in Argentina (Pilaga, Toba), one from Venezuela (Caracas), two from provinces in Colombia (Boyaca, Cundinamarca), three from Siberian nomad populations (Western and Central Evens, Iengra Evenks), one from Belarus (Pinsk), three from Ukraine (Kiev, Lviv, Lugansk), three populations from Capetown in South Africa, three from Ravenna, Rimini and Val Marecchia in Italy, one from Hungary, one from Peru and one from Oran in Algeria. We would like to thank the following colleagues for submissions and updates: Daniel Corach and his group (Buenos Aires, Argentina), Brigitte Pakendorf and her group (Leipzig, Germany), Neal Leat and his group (Capetown, South Africa), Susi Pelotti and her group (Bologna, Italy), Pamzsav Horolma and her group (Budapest, Hungary), Ignacio Briceno Balcazar and his group (Bogota, Colombia), Lisbeth Borjas and Tatiana Pardo (Venezuela), Sergey Kravchenko and his group (Kiev, Ukraine), Gian Carlo Iannacone and his group (Lima, Peru) and Carlo Robino and his group in Torino, Italy. Please refer to the section YHRD contributors to get more information.”

HT: Dienekes’ Anthropology Blog

I recently came across a review article by Henry T. Greely, a Professor of Law, Professor (by courtesy) of Genetics, and Director of the Center for Law and Bioethics at Stanford. The article is entitled “The Uneasy Ethical and Legal Underpinnings of Large-Scale Genomic Biobanks (pdf)” and was recently published in the Annual Review of Genomics and Human Genetics.

According to Mr. Greely, the identity of participants in large-scale genomic biobanks cannot effectively protected. A biobank is defined as a database of genotypic and phenotypic data. Using genetic information, physical information, or a combination of the two, people can identify an individual in such a large database:

“Someone really interested could get a DNA sample from me – from a licked stamp, a drinking glass, or some tissue – and have it genotyped for a few hundred dollars, but few will have to go to the genomic data; the phenotypic and demographic data will often be sufficient.”

“Eliminating name, mailing address, and social security number does not eliminate identifiers; it just eliminates the easiest identifiers, making the search somewhat more difficult and expensive.”

Unfortunately, it is impossible to remove all the data one could use to identify biobank participants. As Mr. Greely opines, “[t]he more the data is removed or obscured, the more scientific value is lost; the more data is kept, the less real the anonymity.”

So what is the answer? First, consent forms must reveal the fact that while biobanks will attempt to provide anonymity, they simply will not be able to guarantee it. They must also reveal that they cannot inform subjects of all the risks and benefits because many future research topics haven’t even been suggested as of yet. Second, biobanks must prevent participants from being upset by unexpected uses of their materials, either through a thorough consent form, or through general communication with research subjects (such as a mailing list or online community). Third, researchers have a moral (and perhaps legal) duty to inform participants of potentially harmful information uncovered by research. This raises a whole host of questions, including how significant the correlation between a gene and a disease must be to require a participant’s knowledge, how long the biobank should monitor the participant’s genetic information, and whether the biobank should be responsible for genetic counseling.

Mr. Greely raises a number of interesting questions that will have to be answered by governments and companies around the world as the need for biobanks increases and the relative ease of biobank creation decreases.

On June 28, the University of Chicago’s Newberry Library presented a panel discussion entitled “Genetic Genealogy and the Ancestries of African Americans” with Rick Kittles. In addition to being an associate professor of medicine at the University, Mr. Kittles is also the science director of AfricanAncestry.com.

The panel also included Christopher Rabb, a genealogist. The two discussed the difficulties facing African Americans who are interested in discovering their roots. After exhausting paper records, Mr. Rabb used DNA testing to learn more about his paternal and maternal lineages.

Despite the successes of genetic genealogy, “[b]oth Rabb and Kittles recognized that genetic testing for ancestry complicates the history and social reality of race in the United States,” noting that 30% of African Americans descend from Europeans.

Then the articles states the following:

Genetic genealogy has its detractors. In a heated question-and-answer session, panel moderator and genealogist Tony Burroughs grilled Kittles on African Ancestry’s accuracy. Using a proprietary database of 30,000 genetic samples from Africa, the company’s work has never been published, reproduced, or otherwise independently verified. Furthermore, because the tests use the DNA of current population groups, the “ancestry tests” in effect tell only the location of “cousins” in Africa, not necessarily where African Americans’ ancestors were located 400 years ago.

“The audience was largely unconcerned by Burroughs’s objections, responding with murmurs, sighs, and rolled eyes. After the program, glowing smiles and firm handshakes bombarded the man whose work promises history and identity for millions.”

I don’t think I would classify Tony Burroughs as a “detractor” of genetic genealogy. He’s just a big fan of good science. Like Mr. Burroughs, I too am wary of any database that isn’t public, or available for peer review, such as the AfricanAncestry.com database. Here’s a comment by Mr. Burroughs in a previous interview:

“DNA is going to be very important and it’s on the cutting edge,” said professional genealogist Tony Burroughs, who teaches at Chicago State University. “But it’s not a panacea. You’re not going to discover your entire family tree from a little spit on a cotton swab.”

Eventually, a video of this panel discussion will be available online.

Megan Smolenyak picked up on a small but very interesting detail in the story – the fact that 60 minutes was filming the presentation. It seems that they might be planning a piece on genetic genealogy. Megan also discussed some of the reasons that Burroughs questions AfricanAncestry.com’s database.

Two weeks ago, EyeonDNA posted about genetic genealogy testing in the Czech Republic by two companies, Genomac and Forensic DNA Service. A recent article in the Prague Post details the animosity over ethical concerns which exists between these two competitors.

A few days later, Ludvik Urban responded to the article via Rootsweb, and EyeonDNA shared Mr. Urban’s response with her readers. Today, you can read Genomac’s response (from one of the founders, Dr. Marek Minarik) to Mr. Urban’s concerns about the company.

Whew! Luckily, both sides were able to share their side of the story – it makes for some interesting reading!

With Friday’s release of a paper in PLoS Genetics, the Genographic Project also released a spreadsheet with the results of over 16,000 mtDNA tests, including HVS-I and SNP results (available here). In addition to sequencing the HVS-I region of mtDNA samples the Project is now testing 22 SNPs. These SNPs were chosen based upon a number of factors, which are discussed in the paper.

“Twenty one SNPs and the 9-bp deletion make up the total of 22 biallelic sites. For simplicity, we will refer to all biallelic sites as SNPs. The number of SNPs tested was gradually increased from ten at inception of the project to the 22 currently used. The ten initial SNPs were 3594, 4580, 5178, 7028, 10400, 10873, 11467, 11719, 12705, and 14766 (numbers refer to the nucleotide position in the mitochondrial genome). The panel was augmented to a total of 20 coding-region SNPs by including the following additional ten SNPs: 4248, 6371, 8994, 10034, 10238, 10550, 12612, 13263, 13368, and 13928. The panel was further augmented by the addition of SNP 2758, to a total of 21 coding-region SNPs and finally by including the 9-bp deletion at position 8280 to a total of 22 coding-region SNPs (Figure 4). Two further changes were made: positions 8994 and 13928 used in some early work were respectively replaced with their phylogenetic equivalents 1243 and 3970. Therefore, the current panel includes the following SNPs, with their respective gene locations shown in brackets [33]: 2758 (16S), 3594 (ND1), 4248 (M), 4580 (ND2), 5178 (ND2), 6371 (COI), 7028 (COI), 8280 (9-bp deletion) (NC7), 8994 (ATPase6), 10034 (G), 10238 (ND3), 10400 (R), 10550 (NDRL), 10873 (ND4), 11467 (ND4), 11719 (ND4), 12612 (ND5), 12705 (ND5), 13263 (ND5), 13368 (ND5), 13928 (ND5), and 14766 (Cytb).”

The early mtDNA samples were not tested for all SNPs, so your results may not be included in this particular spreadsheet. If you log into the Project with your Project ID #, then click on “See Your DNA Results” overlayed on the map, you will see a circle for SNPs. Click there and you’ll be able to see which of the SNPs you tested positive for.

If you download the spreadsheet and are able to identify your mtDNA based upon the HVS-I results, you can get your results for each of the SNPs tested above. For instance, I was able to identify my contribution because it is so unique. Then I was able to look at all the SNP results for my DNA. Of course I can’t be 100% sure that the sample is mine, but I’m about 99% sure.

I didn’t get these results emailed or mailed to me because I originally tested with FTDNA and agreed to add my results to the Project. For those readers that tested with the Project originally, did you get a table with the SNP results included in your HVS-I results?