The Genetic Genealogist

Last week the genetic genealogy community lost one of its treasured members, Leo W. Little.

Leo’s passing was announced on the GENEALOGY-DNA mailing list on Sunday evening. Since then, many members of that mailing list, the ISOGG Yahoo Group, and the DNA- ANTHROGENEALOGY Yahoo Group have expressed their sympathy to Leo’s family and expressed their admiration for his work and contributions to the field of genetic genealogy.

Leo was the administrator of at least two DNA Projects, including the null439 DNA Project, and the Little DNA Project. The null439 group was begun by Leo after he helped characterize the “Little SNP” in 2002, a SNP that is also called “L1″ or “S26″. In 2005 Leo posted an email to the GENEALOGY-DNA that explained the discovery of the SNP, which defines the R1b1b2a1c Haplogroup in the new 2008 ISOGG Y-DNA Haplogroup Tree (previously known as R1b1c9a). The L1 SNP causes the primers used by Family Tree DNA to analyze Y-STR repeats at DYS439 to fail to anneal, and thus no result is recorded for that locus (i.e., it is “null”). The result is recorded as a default 12 with a blue asterisk. Here is Leo’s description from the null439 page:

“SNPs are passed down from father to son, and all males with a null439 SNP descend from a common ancestor who lived within the last 5000 years. Most null439 males with known origins have roots in England or Germany. The null439 SNP is also called “L1” or “S26“. L1/S26 is carried by about a half of one percent of R1b males. All males with L1/S26 also have the SNP “S21” (also known as “U106“) which defines the R1b1b2g subgroup (formerly R1b1c9).”

The null439 Project currently has at least 83 members, including myself. In June 2006 my Y-DNA analysis revealed that I have the L1 SNP and thus had no result at DYS439. When I joined the null439 project at FTDNA, Leo promptly emailed me and welcomed me to the group.

Other Contributions

But the S26 SNP and the null429 group are just a few of Leo’s contributions to the field. Other work includes his incredibly useful “Eclectic Genetic Genealogy Information” page, or a number of articles at the Little DNA Project (including this one entitled “Tracing the Borders Littles through DNA Testing“). Indeed, a search of the GENEALOGY-DNA archives reveals at least 150 messages posted by Leo’s email address (lwlittle@yahoo.com), and a search of his name reveals many more messages in which he was mentioned. Leo was a consultant for the Sorenson Molecular Genealogy Foundation, a member of the following organizations: the Association of Professional Genealogists, the International Society of Genetic Genealogy, and the Austin Genealogical Society. In July 2005, Leo’s work was highlighted in an article from Time magazine entitled “Can DNA Reveal Your Roots?“:

“One of the less controversial aspects of genetic genealogy is its ability to help people fill in gaps in their family tree. Leo Little, a retired engineer in Austin, Texas, had used historical records to trace his lineage back to his great-great-grandfather Thomas Little, who was born in Alabama in 1816. Then, he says, “I hit a brick wall. I knew my Littles were from the South, but there were a lot of Littles from the South, and it was impossible to sort out.” After he took a DNA test from Family Tree DNA, he began leading one of the company’s 1,900 surname projects, in this case checking test results on Littles. As a result, he has identified three distant cousins. By pooling their family records, the cousins have been able to trace their roots all the way back to 1680.”

Since Leo’s passing was so unexpected, the family is still dealing with the shock. On Monday, Terry Barton posted to the ISOGG Yahoo Group that the family had been contacted, and that Mrs. Little had requested that there be “no phone calls, no emails, no cards, no contact of any kind.” She did mention the possibility of a memorial fund in the future. Additionally, Mrs. Little indicated that she would try to respond to Leo’s emails at some point.

If you would like to leave a comment below, I will compile them and send them in letter to Mrs. Little when she is ready to receive mail. In addition, this post will be available indefinitely as a memorial to Leo Little. Thank you to Katherine Hope Borges for her assistance in completing this post.

UPDATE From Katherine (May 27 2008):

Leo was heavily involved in his church history project and donations may be made in his name to (with thanks to Derrell and Terry for sharing this info):

Highland Park Baptist Church
5206 Balcones Drive
Austin TX 78731

In DNA Fund, we will have fund designated for a “Leo Little Memorial Scholarship”, but since the 501(c)(3) is not yet in effect, contributions are not tax-deductible. However, contributions may be sent to DNA Fund’s General Fund at Family Tree DNA and will be designated for null research.

The Quantified Self has a follow-up to last week’s post about the reproducibility of SNP testing by 23andMe and deCODEme using Illumina SNP chips (see the Quantified Self’s post and my post). In that post, it was revealed that two comparisons of the 560,000 overlapping SNP results from the two different companies had revealed differences of just 23 locations for one individual and 35 for another.

Soon after last week’s post, one of these individuals – Ann Turner – contacted The Quantified Self with new information that 4 of the SNPs on her list of 35 disagreeing results are also on the other person’s list of 23 disagreeing results (Antonio Oliveira). From Ann’s email to The Quantified Self:

Four of those (rs11149566, rs4458717, rs4660646, and rs754499) were also found in Antonio’s list. That’s more than you would expect by chance.

Interesting results, and as Kelly at TGS points out, “This is why sharing results is so valuable and a key to great quantified self understanding.” For anyone who might be interested in doing further comparison, here is Oliveira’s list (also available here):

rs4660646, rs4458717,rs754499, rs11149566, rs1934496, rs10933181, rs9881405, rs1064205, rs312330, rs11100437, rs2955195, rs7033246, rs1536928, rs10793963, rs10894749, rs3921012, rs510978, rs12296276, rs4965862, rs2290505, rs12960185, rs4814138, rs6615048

And here is Turner’s list (also available here):

rs4660646, rs4458717,rs754499, rs11149566, rs10435795, rs1045363, rs10743414, rs10945383, rs11179382, rs11707159, rs11915402, rs1209171, rs1221986, rs12907462, rs1303912, rs13422439, rs161381, rs17328647, rs1961196, rs1966357, rs2016461, rs2064034, rs2290516, rs2853981, rs3952469, rs4336661, rs4423481, rs4572718, rs6531490, rs6942478, rs7102702, rs7812884, rs845217, rs9332128, rs9476380

For everyone not familiar with SNPs, or Single Nucleotide Polymorphisms, see this brief introduction at Wikipedia, including the helpful diagram, or read the SNP Page at SNPedia (which links to a helpful YouTube video).

Many people do not realize that the genetics of the future will rely heavily on the work done by previous, current, and future generations of genealogists. Researchers hoping to uncover links between a disease and a particular gene or mutation often recruit entire families or use compiled genealogical databases for information. Just a few of the recent examples of researchers benefiting from the work of genealogists include:

1. Genizon BioSciences will examine genetic diseases using DNA from descendants of the Quebec Founder Population;
2. A mutation believed to increase the risk of colon cancer was traced to a single family in the early 1600′s;
3. A recent study pinpointing the mutation responsible for blue eyes used data from the Copenhagen Family Bank, and;
4. Numerous studies published by deCODE, a company that uses an exclusive database of Icelandic genealogy (80% of all Icelandic people who have ever lived can be traced on family trees).

In honor of the contributions that genealogists have and will make to scientist’s understanding of the genetic basis of disease, and in honor of the many unique and well-written genealogy blogs, I created The Genealogists, a Feedburner network (subscribe via RSS here). The network, which helps unite genealogy bloggers and introduce new blogs to readers, currently has 18 members:

Please feel free to stop by each of these wonderful blogs, or to ensure that you don’t miss any of the latest genealogy news simply subscribe to The Genealogist feed.

I received an email from Denis Savard of the E3b Project, asking me to post the following for my readers. For the non-genetic genealogists, E3b is a Y-DNA Haplogroup (info here). The E3b Project was also ISOGG’s “DNA Project Website-of-the-Week” 14 Nov 2007.

Here’s the announcement:

Dear Readers,

The worldwide E3b Project proudly announces a new milestone: reaching the 700 member mark.

Since its launch this past June, the E3b project’s website (http://www.haplozone.net/e3b/project) has been steadily growing and is gradually being transformed into a dynamic place of learning, collaboration and research for all things related to E3b.

Here are some of the new developments from the last couple of months:

+ The new V-Series SNP tests have proven very popular among our E-M78 subclade participants and we have been very successful in further dissecting the E3b1a subclade into several distinct and finer branches. So far, about 70% of M78+ participants have also tested V13

+ (E3b1a2), which is the most prevalent European E3b subclade, and among these a single downstream M224+ (E3b1a2b) was also found. Of the remaining members that have requested the V Series test, 17.7% came back as V22+ (E3b1a3), and 11.4% came back as V12+ (E3b1a1). These and other statistics are periodically updated at the following page: http://www.haplozone.net/e3b/project/page/5

+ This last week the fall edition of the Journal of Genetic Genealogy has published the much anticipated research paper by E3b project’s collaborator Steven Bird, “Y-Haplogroup E3b-V13 as a Possible Indicator of Settlement in Roman Britain by Soldiers of Balkan Origin”. You can find and read this interesting document at this link: http://www.jogg.info/32/bird.pdf

+ Our database has recently been updated to include Elise Friedman’s extended haplotype cluster analysis, an in-house system which enables us to classify E3b haplotypes into well defined clusters based on allele similarities, which normally tend to correlate with biogeographical backgrounds. This focused analysis on individual haplotypes nicely complements the software based output from commonly used software applications that we use to create cladograms and neighbor joining diagrams, etc. Please go to the following page: http://www.haplozone.net/e3b/project/cluster

+ Another important trend in the last few months has been the inclusion of more collaborators who have volunteered to promote the project, to provide guidance to new members and take part in a collaborative effort to spread the new scientific discoveries and findings related to the origin, diffusion and phylogeny of this ancestral haplogroup.

+ Next comes our forum, the Double~Helix community (http://community.haplozone.net/), which has also proven itself as an ideal place for new E3b participants to inquire about their results or exchange their observations. Besides reading the opinions of regular participants, the team at hand will try to point out possible relationships of distinct haplotypes, predict a downstream mutation and identify a specific sub-cluster if enough markers are provided or maybe recommend specific additional testing.

If that wasn’t enough, Dr. Dirk Schweitzer is now preparing a basic guide to E3b, including subclade descriptions, geographic distributions, etc., since most online E3b reference pages currently available elsewhere are already outdated. A public link to this information will be announced here when available.

In sum, there are many exciting new things happening as we speak.

All that has been previously mentioned plus the inclusion of new haplotype data from relevant genetics population studies that enable members to match their haplotypes against a growing dataset is providing all members with new insight about their distant origins and helping us all to understand the bigger DNA picture.

Finally, we wish to thank all the Geographic and Surname Project administrators that responded to our recent request to invite their E3b participants to our haplogroup project. The response has been phenomenal and we’re sure your Project members will thank you for it. Here’s our FTDNA link: http://www.familytreedna.com/public/e3b

Best Wishes To All From The Team At The E3b Project.

Forty advanced placement science students at Soldan International High School in St. Louis have submitted their DNA for testing with the National Geographic Society’s Genographic project. An article in the St. Louis-Post Dispatch highlights some of the statements made by the students and faculty:

“Many times students don’t see the relevance of what they’re learning,” said Assistant Principal Alice Manus, the Soldan project coordinator. “What they’re learning here will have all sorts of relevance because, really, we’re looking into their lives.”

One student, named John, had more reason to be excited about this test than most – his father died when he was only 13. “I never knew him that well,” said the Soldan sophomore. “Maybe this will tell me more about who he was and where he came from.”

I think this is a great way to introduce students to issues associated with genomic sequencing including the science, the societal impact, and the ethical issues. I do wonder, however, how the class afforded the testing. Sometimes companies will offer reduced rate packages to encourage testing. I would hate to think that this sort of project would only be available to affluent communities that can afford the price of the test (even the $99 test at the Genographic project).

Discovering Biology in a Digital World blogged about this yesterday. One of that post’s concerns was how a teacher would deal with potential non-paternal events revealed by the testing. This is definitely a valid concern, although it would be rare since non-paternal events are most often uncovered through comparative genetic genealogy.

I was especially shocked to read the comments at Discovering Biology in a Digital World. A comment left by a Christopher stated that he “had no idea that National Geographic had this Project – or that its actually open to the public as well.” Christoper, don’t you know that there’s an entire blog devoted to genetic genealogy?

On the heels of last week’s announcement that Sorenson Molecular Genealogy Foundation (SMGF) will be collecting DNA samples in Mongolia comes new information that the company will be conducting a similar project in Panama.

According to the announcement, SMGF has partnered with the Gorgas Memorial Institute (Instituto Conmemorativo Gorgas de Estudios de la Salud Panama) and will attempt to collect 1,500 to 2,000 DNA samples with pedigree charts. The project will gather DNA from each of Panama’s nine provinces and three territories and will include individuals from all major ethnic groups, and from both urban and rural areas:

“We are honored to join with Gorgas Memorial Institute, Panama‘s primary institute for health and population studies, to study this country’s diverse, multi-faceted populations,” said Dr. Scott Woodward, executive director of the Sorenson Molecular Genealogy Foundation. “Panama is a fascinating melting pot, its genetic and cultural mix having been influenced by a broad array of Native American populations, Africans from the slave trade, and Europeans and Asians from multiple eras.”

Panama, of course, has always been a land bottleneck, forcing all southward human migrations through a 60-mile-wide corridor. As a result, the country has “been heavily trafficked by various Native American populations emigrating north and south, Africans from the slave trade, Spanish conquistadores and other European explorers and settlers, and various Asian populations working on the Panama Canal and other projects.”

Interestingly, the project will also analyze ancient bone samples that were recently discovered in Panama Viejo. Panamanian project leaders are hoping that this will help bolster Panama’s national identity:

“ ‘Knowing the genetic composition of the people that lived in Panama more than 1000 years ago may give us proof that permanent human settlement has been present here for a long time and that this country is not only a bridge for people to walk by,’ said Motta. Knowing the genetic mix of our people will also teach us that we are not simply made of whites, blacks, American Indians and Asians, but that we are a rich and beautiful mixture of all of these races.’”

SMGF has a map that displays all the areas in the world in which the project has performed DNA collection projects.

Dr. Wilmot James, head of the African Genome Project and honorary professor of human genetics at the University of Cape Town, is heading a DNA collection project in South Africa. Dr. James is joined by his colleague Himla Soodyall, a scientist at the National Health Laboratory Service and an associate professor in the Division of Human Genetics at the University of Witwatersrand. On September 9^th, James and Soodyall collected swab samples from a number of Capetonians.

The African Genome Project is supported by the South African genealogy website Ancestry24.com (although I was not able to find any information there). One of the goals of the project is to create a public genetic database to examine “how the country became populated over thousands of years” by filling in the gap in current DNA databases.

According to Dr. James:

“No one group can lay claim to South Africa. Everyone is a settler, and we will show how people came here in waves of migration.”

The results are due out in early 2008.

23andMe has been the subject of much discussion in the biotech and personalized medicine circles of the blogosphere (See here, here, here, here, here, here, here, and here for plenty of information/speculation/discussion).

In August, 23andMe announced (“23andMe and Illumina Forge Consumer Genomics Goliath”) that they have partnered together to offer “consumer genotyping” – more about that in a minute. Illumina produces “SNP chips”, chips that can test a genome for thousands of SNPs (single nucleotide polymorphisms) at a time. For example, the company has one chip that tests one million SNPs for as little as $600, and another chip that tests 550,000 SNPs (the HumanHap550) for only $300-$450. Interestingly, Illumina is also able to custom build chips to add specific SNPs if the customer so desires. Additionally, as the announcement touted, Illumina is also exploring the world of inexpensive whole-genome sequencing, suggesting that this partnership with 23andMe could transition from cheap SNP testing to cheap whole-genome sequencing at some point in the future.

Despite all the conversation and information, the company’s products and services have never been explicitly stated. Although the website states the following, the general public has not known how that would translate into a tangible product or service:

“Our goal is to connect you to the 23 paired volumes of your own genetic blueprint (plus your mitochondrial DNA), bringing you personal insight into ancestry, genealogy, and inherited traits. By connecting you to others, we can also help put your genome into the larger context of human commonality and diversity.”

Yesterday, however, we got a much clearer picture thanks to the Illumina, Inc. Analyst Day in New York City (thanks to Matthew Herper for a great write-up at “Google’s Genetic Start-Up,”). At this meeting, Jay Flatley, chief executive of Illumina, revealed some tantalizing hints about 23andMe’s upcoming launch. Here is a brief outline of the product that has resulted from the partnership between 23andMe and Illumina:

1. Send in a DNA sample (either spit or cheek swab).

2. The DNA is sent to Illumina to for “consumer genotyping”. This means that Illumina uses one of its SNP chips to screen DNA for the presence or absence of certain SNPs, or single nucleotide changes in the DNA sequence.

3. Illumina reports the SNP variations to 23andMe.

4. 23andMe “make[s] that information available through a password-protected Web site” which customers can access to see their personal SNPs.

5. 23andMe will (ultimately) provide information about the meaning or medical/genealogical implication of each individual SNP.

For those of us who are interested in genetic genealogy, It appears that 23andMe’s product might be directed more toward genetic genealogy than medical application:

“Initially, Flatley said, the company will be more focused on ancestry – questions like which parent one got more traits from – than medicine. Many researchers say most genetic discoveries are so far only of limited medical utility.”

Flatley has already scanned his genome and accessed 23andMe’s interface. Additionally, he offered the service free to everyone at the meeting who was willing to sign up (lucky bastards).

You can see the webcast of Jay Flatley’s presentation at Illumina’s website. There hasn’t been much written about this revelation as of today, but I found mention at GigaOM, Genome Technology Online, and Megan’s Roots World.

So what does this partnership between 23andMe and Illumina really mean for someone interested in genetic genealogy? Well, I’m glad you asked. Although some of our personal SNPs are spontaneous, many of them came from either our mother or our father. Genetic genealogists have long taken advantage of SNP inheritance to identify our Y-DNA or mtDNA haplogroup, for example. SNP testing can potentially be one of the most interesting and most lucrative offerings in genetic genealogy, although the field is still in its infancy. Current SNP testing for genetic genealogy, known as “autosomal testing”, involves making conclusions based on a few hundred SNPs and don’t allow something I call “SNP tracking”, the ability to compare SNPs between individuals. 23andMe, potentially, will offer a service that tests million(s) of SNPs, each of which can be individually analyzed and compared.

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.