The Genetic Genealogist

The Virginia Commonwealth University Life Science Center has released the results of the VCU Life Sciences Survey and I thought I’d share some of the interesting results.

The most surprising result of the survey is that 80% of surveyed adults favor making genetic testing “easily available to all who want it,” similar to values in 2001 and 2004.  Don’t tell this to the New York and California Departments of Health!

The Benefits Outweigh the Risks

54% of adults believe that the benefits of genetic testing outweigh the risks, while 25% believe that the risks outweigh the benefits.  It’s interesting to see the education breakdown of this question.  44% of people with a high school degree or less believe that benefits outweigh risks, compared to 67% of people with a college degree or more.  And 29% of people with a high school degree or less believe that risks outweigh benefits, compared to 20% of those with a college degree or more.

Nature vs. Nurture

So which is stronger – our genetic inheritance or our lifestyle/environment?  57% of respondents believe that “our environment and living practices” are “a more important influence on people’s behavior, while 27% believe that it is “the genes we inherit.”  The respondents were also asked how scientists would respond to the same question.  They believed that 42% of scientific experts would say that our genes are a more important influence and 39% would say that our environment and living practices are more influential.

Further Information

See the following links for more coverage of the study: VCU News Center; GenomeWeb News (free reg. required); ScienceDaily.

Last week I had the opportunity to attend a lecture by Spencer Wells, director of the Genographic Project from National Geographic and IBM.

The talk was a Syracuse Symposium event, and the first big event ever to be held in Syracuse University’s new $110 million Life Sciences Center.  I thought it was fitting that the first event to celebrate the future of the new life sciences building was a lecture that examined the collective genetic journey of mankind.

Dr. Wells began by giving the audience a very brief introduction about DNA and genetic genealogy.  He included a great quote that “The question of origin is actually a question about genealogy.”  For those that are not familiar with the Genographic Project, it was launched in 2005 and includes three primary missions:

1. Global DNA sampling from indigenous and traditional cultures which retain a geographic link with their current location;
2. Public participation; and
3. The legacy fund, which is funded by the public participation aspect of the project and aims to “empower indigenous and traditional peoples by supporting locally-led efforts.”

Dr. Wells is a great speaker and the hour-long lecture went by extremely quickly.  Some of the more interesting information he shared is not readily available on the Genographic Project’s website:

• According to current projections, the project is about halfway finished and is predicted to end in 2011.
• So far, 41,000 samples have been collected from indigenous populations, and 270,000 kits have been purchased by public participants in 130 countries (currently at about 800 kits ordered per week!).
• The indigenous DNA samples are stored for future analysis – this will undoubtedly be an irreplaceable asset as indigenous populations continue to decline (although it does raise issues of informed consent; do indigenous people really understand the information?).
• Eventually, the Genographic Project’s database will be searchable.

Valuable Research

He also highlighted the previous papers that resulted in party from the Genographic Project, including:

• The Genographic Project Public Participation Mitochondrial DNA Database
• The Dawn of Human Matrilineal Diversity
• Y-Chromosomal Diversity in Lebanon Is Structured by Recent Historical Events
• Identifying Genetic Traces of Historical Expansions: Phoenician Footprints in the Mediterranean

A new paper, soon to be released, will examine the genetic ancestry of the Toubou people indigenous to northern Chad in Saharan Africa.  The Toubou people have a rich and interesting history, but their actual genetic roots are unclear.  According to Sougoui, a Toubou:

“The Genographic Project is a great opportunity for us, the Toubou, because we are a people who are extremely interested in our origins… According to Toubou legend, we are a people who came from different places. This is a question that we continually talk about. We are anxiously waiting for the results of this study to answer this question for us. It is important for us as Toubou to know where we came from, how we got separated from other peoples, and how we actually fit into the world God created.”

Dr. Wells showed a short clip of a new documentary that is being made about the Genographic Project.  In the clip, we were shown the challenges of collecting DNA from the Toubou; looks like it will be another very interesting documentary.  See more about the Toubou project here and here.

The Q&A Session

During the Q&A session, someone asked what regions are missing from the database.  Perhaps unsurprisingly, the answer was the Americas and Australia.  Apparently the Project has had a very difficult time getting permission to take samples from these populations.

Many of the questions reflected the fact that many people are confused about the inheritance of Y-DNA and mtDNA.  Half the them were about whether a child or a sibling would have the same or different Y-DNA or mtDNA.

Conclusion

Dr. Wells is a great lecturer, and I highly recommend watching him speak if you are ever able to do so.  I learned a great deal about the Genographic Project, and I look forward to the information that will continue to be released from this valuable endeavor.

The Personal Genome Project (PGP) was established to analyze and publicly share the genomes and personal information of up to 100,000 volunteers in order to advance understanding of “genetic and environmental contributions to human traits and to improve our ability to diagnose, treat, and prevent illness.”  In the first phase of the PGP, ten volunteers (the “First 10″ – see information about the First 10 here on my blog and at the PGP website) have had their DNA analyzed and have given their personal information.

Last month, George Church, the PGP’s principal investigator, reported that the project expected to publish data about the First 10 on its website in mid- to late October.  Church might have meant genotype (i.e. sequencing) information, since some information about phenotype, health history, and medication has already been posted on the PGP website.  There is information about each of the 10 participants, although there is currently no active link to their genetic information:

1. George Church
2. John Halamka
3. Esther Dyson
4. Misha Angrist
5. Kirk M. Maxey
6. Stan Lapidus
7. Keith Batchelder
8. Steven Pinker
9. Rosalynn Gill
10. James Sherley

Note that the First 10 are listed as “Participant #1″, “#2″, etc.  I debated about whether or not to attempt to identify them based on sex, ancestry, and date of birth, but since it was so simple to do that I decided to assign a name to the Participant number (I’m pretty sure I got them all right, depending on the quality of the source information I was able to find online).  Indeed, the PGP has clearly stated over and over that anonymity cannot be guaranteed for participants.  Additionally, I’ve always felt that one of the goals of the first phase of the PGP was to educate people about the effects of making your genomic sequencing information and health information freely available online.  Some would argue that the effects are completely or mostly dangerous, while others would argue that the effects are completely or mostly benign.  The PGP might help examine some of these questions.

There’s more information about the PGP in a recent Wired article.  HT: twitter from Jason Bobe of The Personal Genome.

The American Society of Human Genetics is having its 58th Annual Meeting in November.  As I was looking through the meeting abstracts, I noticed that there were a number of abstracts that dealt with topics related to genetic genealogy.  I thought some of you would be interested in getting an advance look at genetic genealogy research that will be publicly released and published over the next year or two.  Although I didn’t include the whole abstracts for most of them, I did include a link for further investigation.  (Note: I got this idea from Dienekes’ Anthropology Blog).

Interestingly, the first five abstracts all include researchers from the Sorenson Molecular Genealogy Foundation, showing how much the Foundation is providing to the genetic genealogy community.

Also very interesting is the final abstract which argues that genetic genealogy, in combination with large-scale genomic analyses, will result in reduced privacy.

“By contributing samples and information to repositories specializing in genetic genealogy, individuals make important contributions to our collective knowledge, but they do so at the risk of revealing personal information shared by unwitting relatives.”

Allocation of YSTR Microvariant Alleles to Y-Chromosome Binary Haplogroups. A. L. Pollock, K. Ritchie, P. A. Underhill, A. A. Lin, S. R. Woodward, U. A. Perego, N. M. Myres

“To identify YSTR microvariant alleles potentially useful for elucidating further phylogenetic substructure within binary haplogroups, we have assessed the haplogroup affiliation of microvariant alleles found at informative frequencies in public YSTR databases for the following YSTR loci: DYS385, DYS392, DYS441, DYS446, DYS447, DYS449 and DYS464. We report haplogroup affiliations for each variant allele and geographic origins of representative samples.” Read more here…

L1c2a, the (African) Haplogroup With The Longest Mitochondrial Genome! K. Ritchie, U. A. Perego, A. Achilli, N. Angerhofer, N. M. Myres, A. Torroni, S. R. Woodward

“During a recent survey of the nearly 58000 mtDNA control region haplotypes currently present in the publicly accessible Sorenson Molecular Genealogy Foundation database, we observed a small number of mtDNAs (n=16) characterized by the presence of unusually long insertions of up to 200 bases. A small subset of these particularly long mtDNA haplotypes shared an identical insertion of 15 bases.” Read more here…

The mitochondrial DNA landscape of modern Mexico. A. Achilli, U. A. Perego, J. E. Gomez-Palmieri, R. M. Cerda-Flores, K. H. Ritchie, A. Pollock, N. Angerhofer, A. Escobar-Mesa, A. Torroni, N. M. Myres, S. R. Woodward, Sorenson Molecular Genealogy Foundation, SLC, Utah (USA)

“Analysis of the mitochondrial DNA (mtDNA) control region sequences, including HVS-I, HVS-II and HVS-III, from more than 2,000 subjects revealed an overwhelming Native American legacy in the modern Mexican population, with ~90% of mtDNAs belonging to the four major pan-American haplogroups A2, B2, C1 and D1. This finding supports a European contribution to the Mexican gene pool primarily by male settlers and confirms the effectiveness of employing the uniparentally-transmitted mtDNA as a tool to reconstruct a country’s history.” Read more here…

The origin of Native Americans from a mitochondrial DNA viewpoint. U. A. Perego, A. Achilli, L. Milani, M. Lari, M. Pala, A. Olivieri, B. Hooshiar Kashani, J. E. Gomez-Palmieri, N. Angerhofer, A. Pollock, K. H. Ritchie, N. M. Myres, S. R. Woodward, D. Caramelli, A. Torroni

“Our comprehensive overview of the four pan-American branches of the mtDNA tree suggests a scenario with a human entry and spread into the Americas from Beringia about 20,000 years ago, and preliminary data raise the possibility that the uncommon five Native American haplogroups might have marked additional migratory events from Asia or Beringia. Overall, through a combined analysis of modern and ancient Native American mtDNA, we are making an effort for reconstructing the complex pre-Columbian history at both macro- and micro-geographic levels.” Read more here…

Mitochondrial DNA footprints in modern Mongolia. S. R. Woodward, A. Achilli, U. A. Perego, J. E. Gomez-Palmieri, D. Tumen, E. Myagmar, D. Bayarlhagva, K. H. Ritchie, A. Pollock, N. Angerhofer, A. Torroni, N. M. Myres, Sorenson Molecular Genealogy Foundation, SLC, UT (USA)

“In 2007, through a well-planned collection effort, researchers at the Sorenson Molecular Genealogy Foundation and the National University of Mongolia were able to gather over 3,000 DNA samples, informed consents, and genealogical data throughout the country of Mongolia, including samples from 21 distinct tribal or ethnic populations. All the samples were sequenced for the three hypervariable segments of the mitochondrial DNA (mtDNA) control region to assess the genetic composition of modern Mongolia.” Read more here…

Early Siberian Maternal Lineages in the Tubalar of Northeastern Altai Inferred from High-Resolution Mitochondrial DNA Analysis. R. Sukernik, I. Mazunin, E. Starikovskaya, N. Volodko, N. Eltsov

“We showed that the core of the Tubalar genetic makeup proved to be a mixture of “west” (H8, U4b, U5a1, and X2e) and “east” Eurasian (A and B1) haplogroups derived from macrohaplogroup N, and Siberian derivatives of the macrohaplogroup M identifiable by subhaplogroup-specific mutations. For example, among the 36 Tubalar mtDNA samples that belong to haplogroup D, 10 (28%) harbored diagnostic markers of the subhaplogroup D3a2a shared with the Chukchi and Eskimos. This finding verified at the complete sequence level we attributed to ancient link between early Siberians, who underwent pronounced differentiation in the Altai-Sayan region, and some of the Eskimo tribes.” Read more here…

Population Structure in Mongolia from a Mitochondrial DNA Perspective. L. Pipes, A. A. Pai, D. Labuda, T. G. Schurr

“To clarify the complex population history of Mongolia, we analyzed variation in the mtDNAs of 190 individuals from several Mongolian ethnic groups, including the Uriankhai, Zakhchin, Derbet, Khoton and Khalkha. We screened all samples for phylogenetically informative coding region SNPs and sequenced HVSI to assess control region variation in them. Our data suggest that the mtDNA diversity present in our population is consistent with the general pattern of variation observed in East Asia, with the most frequent haplogroups being C, D and G. Haplogroup variation in Mongolian ethnic groups reveals considerable maternal diversity with a predominance of basal M types. Interestingly, the Mongolians also possessed West Eurasian haplogroups, such as H, J and K, which are not commonly observed in East Asia, even at low frequencies. Read more here…

Genetic History of human populations of East African inferred from mtDNA and Y chromosome analyses. J. Hirbo, S. Omar, M. Ibrahim, S. Tishkoff

“Our results indicate that East African populations have some of the most ancestral Y chromosome and mtDNA lineages in Africa, suggesting that they may have been an ancient source of dispersion throughout Africa. Additionally, we find evidence for ancient geneflow between East Africa and the Middle East. We also ascertained the effect of the Bantu-expansion and signature of recent migration of Cushitic-speaking groups originating from Ethiopia on peopling of East Africa.” Read more here…

Analysis of mtDNA and Y-chromosome haplogroups in Mexican Mestizos and Amerindian groups. I. Silva-Zolezzi, B. Z. Gonzalez-Sobrino, J. K. Estrada-Gil, A. Contreras, J. C. Fernandez, E. Hernandez-Lemus, L. Sebastian, F. Morales, R. Goya, C. Serrano, G. Jimenez-Sanchez

“For this we included genotypic data from 163 mt SNPs and 123 Y chromosome SNPs present in the Illumina Human1M chip of 450 individuals, 300 mestizos from six states located in different regions: Northern, Central and Southern; and 150 individuals from different Amerindian groups (Tepehuanes, Zapotecos and Mayas). With this information, we are measuring genetic diversity using Fst and AMOVA analysis. Admixture analysis includes average and individual ancestral contribution estimates using autosomal SNPs. Initial results show that in our Mestizo sample, 88% of the mt haplogroups are Amerindian (A, B, C or D), and the rest includes European and African lineages. We have identified differences in proportions of each haplogroup in both Mestizos and Amerindians.” Read more here…

Using mtDNA and Y-chromosome for estimating group ancestry: Implications for case-control studies. K. Stefflova, M. Dulik, A. Pai, A. Walker, T. Schurr, T. Rebbeck

“We examined the possible role of mtDNA and the non-recombining portion of the Y-chr. (NRY) as ancestry informative markers (AIMs) for admixed groups (self-identified African Americans (AA) or European Americans (EA)) collected as part of a prostate cancer case-control study. We deeply typed both mtDNA (HVS-I, II, 36 coding SNPs) and the NRY (37 SNPs) in a group of 226 AA cases and controls and compared this group to 206 EA cases and controls, and 49 Senegalese…We found a sex biased admixture for AA where 13.2% of mtDNAs and 34.5% of NRYs were of non-African origin. We also found a small amount of admixture in EA (~3% mtDNA, 1.5% NRY).” Read more here…

New tool (mtPHYL) proposed for phylogenetic analysis of human complete mitochondrial genomes. N. Eltsov, N. Volodko, E. Starikovskaya, R. Sukernik
“The algorithm which we created was implemented in the mtPHYL. This program reconstructs the phylogenetic trees and calculates the respective ages for the clusters within the tree. It can be used to glean a bulk of entire mitochondrial sequences from GenBank database instantly. In addition, it automatically categorizes the mutations and identifies affected genes along with their conservation indices and amino acid replacements. Our software may be easily modified to analyze any non-recombining DNA regions. mtPHYL is available from authors upon request (eltsovnp@bionet.nsc.ru) and at www.bionet.nsc.ru/labs/mtgenome/programs.html.” Read more here…

Y chromosome microsatellite haplotypes in the Hutterite founders. M. Caliskan, I. Pichler, C. Platzer, P. P. Pramstaller, C. Ober

“The current population of >12,000 Schmiedeleut Hutterites are descendants of 38 male founders who were born between 1700 and 1830 in Europe. Only 12 of these founders, each with a unique surname, have living male descendants related through male-only lineages. DNA samples were available in our laboratory for 75 male descendants of 11 of the 12 founders, accounting for 673 independent paternal meioses. We genotyped 9 microsatellite loci, which included a mean of 6.8 (range 2-23) males per lineage to evaluate potential relationships between the founders. Fourteen different haplotypes were identified, with an average of 3.5 (range 1-8) pairwise differences between haplotypes. All descendants within each of 9 lineages had identical Y haplotypes. Descendents of two of these lineages, 2 and 10, had the same haplotype despite different surnames, suggesting possible relatedness between the founders of these two lineages.” Read more here…

Genetic variation in tribes of Eastern and North-Eastern India: inference from distribution of Y-chromosomal polymorphisms. M. Borkar, F. Ahmed, F. Khan, S. Agrawal
“Objectives: To investigate the paternal population history of total 607 individuals from nine populations of Eastern and North-Eastern tribes from India. Methods: 34 binary markers and 17 short-tandem-repeat loci from the non-recombining part of the human Y chromosome were analyzed by RFLP, Sequencing and Genescanning. Results: The tribal populations were characterized by a diverse set of 15 haplogroups. A single haplogroup (O-M175) accounts for ~70% of North-East Indian Y chromosomes.” Read more here…

Inferential Genotyping in Mormon Founders and Utah pedigrees. J. Gitschier
One concern in human genetics research is maintaining the privacy of individuals who contribute samples for investigation. While this concern is raised typically in the context of private medical information, I would argue that a signficant contributor to loss of privacy may lie with genealogical investigations, as much information is freely available online through a variety of websites, thus facilitating the discovery of genetic relationships. During sabbatical in the laboratory of Chris Tyler-Smith (Wellcome Trust Sanger Center), I genotyped the Y chromosome of HapMap samples with 16 short tandem repeat (STR) markers as well as lineage specific markers to determine whether the Y chromosome genetic information in this sample was consonant with the purported ancestry of the subjects. As one of the HapMap populations (CEU) is comprised of Utah pedigrees of European descent, I then queried whether the contributors of these samples might be descendents of Joseph Smith and Brigham Young, two founders of the Latter-day Saints. Remarkably, through iterative use of two online archives, FamilySearch and Sorenson Molecular Genetic Foundation, I was able to infer the Y chromosome STR haplotypes of these two founders. Although none of the CEU contributors appeared to be direct descendents of the two men, based on haplotype analysis, I was able to make predictions for the surnames of the CEU participants by the same process. For more than half of the unrelated CEU samples (16/30), at least one exact match was revealed and for 13 of these, a single surname was associated. For the remaining 14 samples, a match was nearly perfect, with only one or two of the microsatellite markers varying, typically by only one repeat unit, as might be expected through microsatellite instability within a pedigree. By contributing samples and information to repositories specializing in genetic genealogy, individuals make important contributions to our collective knowledge, but they do so at the risk of revealing personal information shared by unwitting relatives. This problem will be exacerbated as genome-wide markers and sequences, which may bear physical, health and behavioral information, emerge and are employed in genealogical research.

On December 30th, 2007, I blogged the following:

“[A]ffordable whole-genome sequencing is getting closer and closer every day (my prediction – which is based solely on my own educated guess – is that I will be able to sequence my entire genome for $1,000 or less by the end of 2009).”

It was pretty bold at the time, and I’ve since wondered if I was too optimistic, but now comes news that at least one other person agrees with my prediction.  Harvard professor and genetics researcher George Church – also principal investigator for the Personal Genome Project (PGP) – stated at two conferences, one last week and one this week, that by mid-October of 2008, 36-fold coverage of the human genome will be available for $5,000.  Church went on to say that the $1,000 human genome will be available by the end of 2009.

For more information about Church’s statements, see “PGP to Publish Initial Data Sets Next Month As Church Predicts $1,000 Genome in 2009” (registration required) at In Sequence, and a blog post by John Moore of Chilmark Research who attended a “Personal Genomics” session at this year’s EmTech (where Church reiterated the $5,000 and $1,000 hallmarks) .

The Personal Genome Project

At the same Yale University symposium where he discussed the crashing price of sequencing, Church announced that the PGP plans to publish data gathered from the “First 10″ (see here and here for the identities and backgrounds of the First 10) on October 21st at the PGP website.  These 10 volunteers will meet on October 20th to review their data and give permission to proceed.

Also, according to the In Sequence article, Church has indicated that “approximately 5,000 volunteers are currently ‘queued up at the entrance exam stage’” for the next round of the PGP.

Welcome to the September 14, 2008 edition of Gene Genie!  Bloggers have begun to pick up posting with the end of summer, and it seems like everyday there’s a bunch of new interesting posts about the human genome.

96well at Reportergene presents “Trends in development of reporter genes.”  Reportergene is also looking for bloggers/reporters to join the blog’s community and help create the “main repository of news and tools for reportergenomists.”  See here for more information.

fightingfatigue presents » Have Japanese Researchers Found Diagnostic Tool for ME/CFS? posted at Fighting Fatigue.  According to a study discussed in the article, there might now be a test able to diagnose Chronic Fatigue Syndrome.

Genomes by the Handful

Human genomes are being sequenced by the handful these days.  Knome has recently delivered their first sequenced genomes to customers on 8gb USB drives placed in engraved boxes.  Additionally, news came last week that the first Arab genome had been sequenced.  As Mailund on the Internet asks, is this news anymore?

What good are all these genomes if the non-scientist citizen doesn’t understand anything about genetics?  Andrew at Think Gene discusses a lesson created by Dana Waring and colleagues at the Personal Genetics Education Project in “Personal Genetics Education Project: Lesson 1”

Lower Prices

On September 8th, 23andMe announced a reduction in the price of their DNA analysis from $999 to $399.  The news was discussed on Dienekes’ Anthropology Blog, Eye on DNA, bbgm, ScienceRoll, and at Geneforum.  It even led Attila to buy a kit.  The price drop also prompted a great discussion among some of the members of the DNA Network.  First, see “Cheap personal genomics: the death-knell for the industry?” at Genetic Future.  Andrew at Think Gene writes “23andMe Is DTC Genomics and Nobody Should Be Surprised” and “Why the “Database Sale Story” is Silly.”  This in turn is mentioned by Steve the Gene Sherpa at “A lot to chew and then spit!“  See also my “Follow-Up to 23andMe’s Price Drop.”

The Marriage Gene?

Mary Meets Dolly discusses “The marriage gene“, in which an article in the Baltimore Sun writes that “men who lack a particular variant of a gene that influences brain activity are more likely to be devoted, loving husbands and more likely to be involved with women who praise them as emotionally close and available.”  Rebecca Taylor mentions that genes are rarely the sole influencing factor in anyone’s behavior.

As a bit of housekeeping, if you aren’t already subscribed to the DNA Network, be sure to note that Daniel’s Genetic Future has moved to Scienceblogs.  Update your RSS feed!

Dinosaur Beer

Last but not least, news about ancient yeast.  Although this isn’t related to human genetics, I did my graduate research on yeast and thought I would indulge a little here.  Aminopop mentions that a new brewing company, Fossil Fuels, is making beer with revived 25-million year-old yeast.  Apparently, “the ancient yeast provides the wheat beer with a distinctively ‘clove-y’ taste and a ‘weird spiciness at the finish.’”

So ends the 37th edition of Gene Genie.  Edition 38 will be hosted in a few weeks.  You can submit your blog article for the next edition at the carnival submission form. Past posts and future hosts can be found on the blog carnival index page, or at the official Gene Genie blog!

Yesterday I wrote about 23andMe’s decision to lower their price to $399 (down from $999) while adding more genealogically-relevant SNPs and partnering with Ancestry.com.  Although I don’t have any further information about the new SNPs, I’ve seen a couple of interesting articles about the price drop around the blogosphere.

Aaron Rowe at Wired science writes “Human Genetics is Now a Viable Hobby.”  He notes that the new price is “well within the reach of cash-strapped grad students, frugal genealogy buffs and other not-so-early adopters.”  The comment thread is an interesting read as well.

“Cheap as chips”

Daniel MacArthur of Genetic Future writes “Cheap as chips: 23andMe slashes the price of personal genomics” at his new scienceblogs location.  Daniel also notes that the updated product “will certainly be popular with genetic genealogists” because of the addition of Y-DNA and mtDNA SNPs, and agrees with my hypothesis that other companies will follow suit and lower their prices.  Daniel also mentions the Personalized Medicine Collaborative (PMC) at the Coriell Institute for Medical Research, which is offering free personal genome scans to 10,000 individuals this year.

The Death of DTC Genetics?

Andrew Yates at Think Gene has suggested that free testing by the PMC will kill Direct-to-Consumer (DTC) genetics.  However, as Ann Turner commented on his post, the PMC does not return raw data, only interpretation of items they consider “medically actionable.”  This is the exact reason why PMC will not kill all DTC testing.  I think Andrew fails to appreciate that this is not a new world of genetic testing; genetic genealogists have been doing this for over 8 years now, and all we care about is the raw data.  The more raw data, the better.  Thus, history suggest that at least to the early adopters, raw data is vital.  Andrew answers Ann’s concerns by saying:

“So? I don’t get back the raw data of any other medical tests I take. If you just want a SNP sample of your genome because it’s cool, go buy a 23andMe or deCODEme test. That’s like getting an x-ray because you “want to see what your bones look like.” OK, some people may want to do this… and hey, I bought a 23andMe test for this reason… but most people aren’t choosing their x-ray test provider based on whether they get to keep their x-rays. “

But genetic genealogists (and undoubtedly many others) DO chose their testing provider based on the results they receive.  Sure, we like to know which haplogroup we fit into, but ultimately the most useful aspect of genetic genealogy is the comparison of Y-STR numbers (i.e. the raw data).  And genetic genealogy is an enormous market that has yet to be completely tapped.

(The other problem with Andrew’s assertion is that interpretation of genetic information (unlike a broken bone in an x-ray) varies; a SNP might mean one thing to company A based on study X, while it means another to company B based on study Y.  And this is, of course, an unavoidable result of the current stage of genomic science.  But why should I rely on just one source to interpret my genetic data?  Why can’t I interpret it myself or allow another entity to interpret it?  This is why entities such as SNPedia have recently been created.  After all, to use an analogy, aren’t you supposed to get a second opinion from a different doctor?)

And last but certainly not least, David P. Hamilton at bnet writes “23andMe’s Price Cut: The End of Commerical Personal Genomics?“  David suggests that 23andMe’s price cut is “an attempt to jump-start the data collection in order to kick the real money engine [data mining a large database of genotype/phenotype information created by 23andMe] into gear.”  However, he notes that this is a problem because it is difficult to extract phenotypic information from users, and because scientists can now afford to do their own large-scale genomic studies as the result of lowering prices (and free tests via the PMC).

See the new article at Seed Magazine “Inheriting Confucius,” which discusses efforts to generate a family tree containing the 2 million+ descendants of Confucius.

Kong De-Yong, a 77th(!) generation descendant of Confucius, has been compiling the tree for the last 10 years.  Although the Committee is accepting submissions from women and other previously excluded groups, it is not accepting DNA contributions.  According to the article, this “hints at the limits of Chinese engagement with the age of genomics, and demonstrates how high cultural stakes can constrain science.”  Unfortunately, as the author of the article suggests, many people might be afraid of the results of such DNA testing: “Given the potential implications of genetic knowledge for long-presumed members of the [Confucius] family, they think it better not to know.”

However, there is of course no need for the Committee’s participation in order to learn more about Confucius’ DNA or Confucuis’ descendants (although it would be nice, of course).  A Confucius DNA Project has already been initiated by the Beijing Institute of Genomics, and Confucius descendants can submit a sample for analysis for the price of $125.

Thomas Goetz has written another terrific article about genetic testing and the Personal Genome Project.  This article, entitled “The Gene Collector,” appears in Wired Magazine.  The article provides some new information about the PGP, including some of the incredibly detailed phenotype information that will be collected from the next 100,000 volunteers in the project.

The article also reveals the tenth and final participant of the “First 10″, the original 10 volunteers in the PGP.  I wrote about the first nine volunteers in the PGP almost exactly one year ago and noted that the tenth participant had not yet released his or her name.  The Wired article, however, mentions a number of participants including George Church, Esther Dyson, Rosalynn Gill, John Halamka, and Steven Pinker.  Indeed, a check of the PGP website confirms that Steven Pinker is the last PGP volunteer to be identified.

From the PGP-10 website:

“Steven Pinker, Ph.D. is the Johnstone Family Professor of Psychology at Harvard University, and has also taught at Stanford and MIT. His research on visual cognition and the psychology of language has won prizes from the National Academy of Sciences, the Royal Institution of Great Britain, and the American Psychological Association. He has also received five honorary doctorates, several teaching awards, and numerous prizes for his books The Language Instinct, How the Mind Works, and The Blank Slate. He serves on the Usage Panel of the American Heritage Dictionary and many editorial boards, and often writes for Time, The New York Times, The New Republic, and other publications. He has been named Humanist of the Year, and is listed in Foreign Policy and Prospect magazine’s “The World’s Top 100 Public Intellectuals” and in Time magazine’s “The 100 Most Influential People in the World Today.” His latest book is The Stuff of Thought: Language as a Window into Human Nature, published by Penguin books in the fall of 2007.”

There is more information at Dr. Pinker’s Harvard website and at Wikipedia.

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.