The Genetic Genealogist

I once told someone that in addition to learning about their ancient origins (such as Y-DNA and mtDNA haplogroups), many genetic genealogists would ideally like to match every portion of their DNA with the contributing ancestor.  Although this might seem to be beyond the reach of current genetic ancestry testing, it has actually already begun.  The family compare function of 23andMe, for example, is already being used by genetic genealogists for just this purpose; people who have matching DNA segments can compare ancestry and attempt to identify the ancestor who might have contributed the DNA.

For obvious reasons, medical geneticists have for many years been using genealogy to trace founder mutations in populations.  For example, in 2008 scientists traced a colon cancer gene in the United States to a Mr. and Mrs. George Fry who arrived in the New World around 1630 (see A Single Colon Cancer Gene Traced to 1630).

Tracing A Heart Disease Gene in South Africa

Now, scientists in South Africa recently announced that they had traced a gene responsible for a hereditary heart disease called familial heart block (PFHB) to a Portuguese immigrant who arrived in South Africa in 1696.

From the article:

“The rogue gene was found in three branches of an Afrikaans familial group that can trace its ancestry back to one Portuguese individual who landed on the shores of the Cape at the end of the 17th century.

Prof Andries Brink, former dean of Stellenbosch University’s faculty of Health Services, first described the disease in 1977 and published a paper at the time in the South African Medical Journal. The paper, titled Progressive familial heart block – two types, was co-authored by genealogy specialist Marie Torrington.

It was Torrington who discovered that the disease was brought into South Africa by the Portuguese immigrant who arrived in South Africa in 1696. He subsequently married a woman of Dutch descent, and genetics has carried PFHB down all the generations since then. No matter where in the country they live, every South African suffering from PFHB today is descended from that couple.”

The Journal of Clinical Investigation article is here.

As part of her doctoral research, Sudeepa Abeysinghe is asking people who have purchased genomic tests to complete the “User Experiences of Direct-to-Consumer Genomic Testing Survey”.  According to Sudeepa, the survey focuses on the consumer experience and is completely independent of any testing company.

Although I’m late on reporting this (it was already covered by GenomeWeb, for example), I thought I would mention it in case anyone has missed the previous coverage and might be interested in completing the survey.

This is an opportunity for genetic genealogists to share their experiences and voice their thoughts regarding DTC genomic testing.

An article in the United Arab Emirate newspaper The National (wikipedia) does a terrific job of highlighting recent research from Family Tree DNA.  The story – “DNA could illuminate Islam’s lineage” – discusses research that has attempted to elucidate the Y-DNA signature of Mohammed.  Although Mohammed did not have a son, he had a daughter who married her paternal second cousin, thus passing to Mohammed’s grandchildren the same Y-DNA.  From the article:

“For almost 1,600 years, the title Sharif, Sayyed, or Habib has been bestowed on Muslims who have been able to trace their roots back to the Prophet Mohammed through intricate family trees, oral histories and genealogical records. But now an American DNA lab says it may have identified the DNA signature of descendants of the Prophet Mohammed, and perhaps the prospect of a direct, more accurate means of confirming or identifying such a connection.”

The caveat, as the story briefly mentions by the phrase “if their oral tradition is accurate”, is that no one has an authenticated DNA sample directly from Mohammed.  If there were, this type of research would not be needed.  Instead, the conclusion that it might be Mohammed’s Y-DNA is based on testing individuals who are likely to be descended from Mohammed and looking for a common Y-DNA signature.  Until a DNA sample from Mohammed is obtained (likely an impossibility), the conclusion will not be 100% proven, which means that any information about this conclusion should also contain info about this caveat.  Of course, as all genealogists know, almost none of our conclusions about ancestry/descendancy are 100% proven, especially when they are based at least in part on oral and paper records.

Sharifs DNA Project at FTDNA

There is a public Sharifs DNA Project at Family Tree DNA, which contains the following information:

“Sharif’s are people who claim to be descendant from the Prophet Muhammad, Peace on him, through the two sons of his daughter Fatima Ezzahra, which are Hassan and Hussein. The descendants of Hassan and Hussein sons of Ali Ibn Abi Taleb spread all over the world and particularly in the muslim world from Indonesia to Moroco. There are actually hundreds of thousand of people who are claiming to be be Sharifs. Some of them have a lot of genealogy documents heritated from fathers to sons and which contain many data about the genealogy trees.”

Perhaps the deduced Y-DNA signature is there?

Twitter

I first announced this story early this morning via twitter.  If you are a twitter user and would like to follow me, just click below:

Image by Aaron Logan

Roughly 6 million years ago, the Hominini subtribe of the Hominidae family tree (the so-called “great apes”) diverged into two known branches, with one branch (genus Pan ) resulting in modern-day Chimpanzees and Bonobos, and the other branch (genus Homo) resulting in modern-day humans.

Since there has only been 6 million years of divergent evolution, Chimpanzees/Bonobos and Humans share a great deal of DNA sequence in common (although estimates vary widely and typically depend on what, exactly, is being considered in the comparison).

The Close Cousins DNA Project

On May 31, 2008, the Close Cousins DNA Project was launched by Bill Davenport as a result of a discussion on the Genealogy-DNA mailing list regarding the relatedness of human and chimpanzee Y-DNA.  From the launching post:

Three days ago, John Marsh sprung on us the idea of testing a chimpanzee on FTDNA’s standard 67 Y-DNA STR markers. To quote John: “Chimpanzee and Bonobo are sufficiently different to each other, and to humans, to make differences between their Y-DNA markers potentially interesting, and give insights into how mutations of Y STRs have wandered along over very long time periods. The common ancestor of humans and Chimps is about 100 times longer than the common ancestor of all human male lines”  Today, I am announcing the formation of the Chimpanzee Y-DNA Project. In FTDNA’s database it will be a Y-Haplogroup project and the official name is Close_Cousins. The original goal is for fun and curiosity since we don’t really know what we’ll get. But hopefully we make some interesting discoveries that may prove useful and encourage further research.

Goals of the Close Cousins Project

One of the goals of the Project is to obtain a DNA sample from a chimpanzee and a bonobo (preferably a cheek swab) and have it analyzed at 67 STR markers by Family Tree DNA.  Although the project has graciously received funds from a number of donors (see here for a list of these scientifically curious and kind donors) that will enable the purchase of a regular 67-marker test from FTDNA, there will almost certainly be extra analysis required due to 6 million years of sequence divergence.  However, Bennett Greenspan of FTDNA has kindly offered to cover the costs associated with extra processing.

Why compare the human Y-STR markers with the chimpanzee markers?  Aside from merely satisfying intellectual curiosity, this project could reveal interesting information about the mutation rates of some markers, among other information.

A Request for Help

Last December, I became a co-administrator of the Close Cousins Project with Bill Davenport.  As such, I am requesting your help in advancing this project.  Our biggest current hurdle is identifying a source of chimpanzee and bonobo Y-DNA.  Do you have any insightful ideas to share about how to obtain the necessary DNA?  Do you have an acquaintance who might have [legal] access to chimpanzees and/or bonobos?  Know someone who owns a chimpanzee and/or bonobo? We would appreciate any helpful suggestions or connections in our pursuit of this project.

A Postscript

Lastly, as a law student I am cognizant of the fact that collection of DNA from a non-human primate – even using a painless mouth swab – might trigger some state and/or federal regulations.  I am working to ensure that the project satisfies these regulations when collecting DNA from primates.

Image via CrunchBase

DAVIDE at the European Genetics and Anthropology Blog recently posted two interviews (here and here) with customers of 23andMe’s large-scale genome scanning service, one from Finland and one from the U.S.

It’s very interesting to see the responses of these anonymous individuals, particularly since they are from different countries.

For example, both were asked why they decided to purchase the 23andMe test – “Was it to test your ancestry or genetic health risk factors?”  Interestingly, for both individuals ancestry was the motivating factor behind testing.  More support for my conclusion that these companies should strongly promote the ancestral aspects of their products.

Other Questions

Here are a few examples of other questions in the interviews:

Q: How would you rate the accuracy of the scan against what you know about your origins?

Q: Has the information about your ancestry changed how you now identify ethnically or look at certain cultures or world regions? For example, do you now show more interest in Asia knowing that you have some East Asian admixture?

Q: Were you in any way disappointed with the results? For example, were you let down by where you ended up on the genetic maps or who your closest individual matches were?

Q: Looking back, was the experience worth the $399? Will you recommend the test to your family and friends?

If you are thinking about testing at a genome scanning company, be sure to read these interviews to get a feel for the process.

HT: Daniel MacArthur at Genetic Future.

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.