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Andrew Pollack at the New York Times wrote an article published today entitled “Dawn of Low-Price Mapping Could Broaden DNA Uses.”  The article is about a start-up company called Complete Genomics which will begin sequencing customer’s genomes for $5,000 starting in the second quarter of 2009.  From the article:

“Complete Genomics will not begin its service until the second quarter of next year. By then, the cost of competing technologies will no doubt have fallen further. Just last week, Applied Biosystems, a leading manufacturer, said it expected that its newest machine would allow a human genome to be sequenced for $10,000, although that includes only the cost of consumable materials, not labor or the machinery.”

The article next mentions Knome, which is still offering complete genomes for $350,000.  I expect that price to drop dramatically within the next few months.  Indeed, as the article points out:

“Complete Genomics will not offer a service to consumers. But it will provide sequencing for consumer-oriented companies like Knome.  Knome is already exploring farming out its sequencing to Complete Genomics. “We anticipate we’d be able to significantly drop our price,” said Jorge C. Conde, the chief executive of Knome, which is based in Cambridge, Mass.”

Interestingly, the company says that they are still making money at $5,000, and hopes to sequence a million genomes by 2013:

“Mr. Reid [the chief executive] said Complete Genomics hoped to perform 1,000 human genome sequences next year and 20,000 in 2010, with a goal of completing a million by 2013. That assumes the company can raise the money and find partners to build 10 sequencing centers at a cost of $50 million each. It also assumes there will be enough demand.”

Will there be enough demand?  What effect will this have on the cost of sequencing by other companies?  What effect will this have on the field of genetic genealogy?

Yesterday, RootsTelevision.com celebrated its two-year birthday.  RootsTelevision was created by Megan Smolenyak Smolenyak and Marcy Brown in 2006, and currently contains programs in 25 different channels!  You can read more about the site and about its creation at Megan’s Roots World.

You might remember that a few weeks ago I was interviewed by Dick Eastman for RootsTelevision.com, which was a terrific experience.  And don’t forget, you can stay up-to-date on RootsTelevision.com’s DNA Channel right here at The Genetic Genealogist!

Last week, Randy Seaver of Genea-Musings posed a genetic genealogy question on his blog.  I posted a possible solution in the comments there, but I am asked this question regularly and thought I would discuss it here.

At a recent meeting that Randy attended, a woman in the audience asked the speaker:

“I don’t know who my father is. He and my mother had relations in Naples, Italy back in the 1950’s and I was born. I have no siblings. My mother did not tell me his name and there is no father’s name on my birth certificate. Can DNA research help me?”

This particular situation is exceptionally challenging.  If the child had been a boy, he would have his father’s Y-DNA and a decent chance at identifying his father’s surname (and thus could perhaps further elucidate his actual identity with the combination of DNA research and traditional genealogical research).  If the unknown parent had been the mother, the daughter would possess the unknown parent’s mtDNA and a remote but possible chance of finding an mtDNA match and using traditional genealogical techniques to identify the mother.

The Question

Given this situation, Randy asked:

“Are there any other opportunities based on the whole genome of this woman, comparing the genome of her mother (assuming a sample is available), and determining the parts of her DNA she inherited from her father, then finding a match somehow with genomes of persons in Italy? That’s a big order, but it might be possible at some time in the future. Perhaps there are sperm bank or criminal blood samples from the time period in Naples that could be compared. Is that too far-fetched? Even for 20 years from now?”

My response

I agree that AS OF TODAY, there is little to no hope that the woman will discover the identity of her father.  However, people almost always believe that this mystery will never be resolved because there is no Y-DNA or mtDNA solution.  Of course, as we all know, the child inherited 50% of her genome from her father. It is my hypothesis that somewhere in that DNA is a clue to her father’s ancestry which can ultimately be used to identify her father.

How will autosomal (non-sex chromosome) DNA reveal her father’s identity?  As genomic sequencing becomes cheaper and cheaper, it will be possible to sequence an entire genome relatively cheap (first under $1,000, then eventually under $100).  With this technology, genealogical and medical organizations will use vast autosomal DNA and family chart databases to trace genes and mutations through genealogies.  SMGF, for example, is already collecting both DNA and family charts, and is set to release the Sorenson Autosomal Database in the near future.

Additionally, earlier this year a deadly mutation that leads to colon cancer was traced to an English couple that emigrated to the United States in 1630, almost 400 years ago.  Although not everyone with this mutation is descended from this couple, many are; thus, if you have the mutation, it is very possible that you are descended from this couple and this would provide a clue to your ancestry that could be explored with traditional genealogical research.  With cheap sequencing scientists and genealogists will be able to trace unimportant ‘quiet’ mutations through time and genealogies, just as scientists have already done with health-related mutations.

So how will all this help the woman identify her father?  Someday in the very near future she will be able to query her genome against a database of genomes and ancestries.  Just as a deadly colon cancer mutation can be linked to a certain family, it is likely that the woman has one or more random mutations in her genome that are linked to certain families.  Using traditional genealogical research (to rule out inheritance of those mutations through her mother, for example) and genetic technology, she might be able to use that knowledge to identify possible sources of half her DNA.

Caveats

The scenario I posit requires two things which are not currently available:

1. Cheap and widely-available genomic sequencing; and
2. One or more databases compiling autosomal DNA and genealogies which can be queried.

Ethical Concerns

For most people, being able to identify your own ancestors based on your own DNA poses few if any ethical dilemmas.  However, what if your neighbor or your stalker or even law enforcement wants to use a sample of your DNA to identify your ancestors?  Additionally, what if your living ancestor doesn’t wish to be identified?  Does the ancestor have that right, or is possible identification through genetic genealogy just one of the consequences of parenting a child anonymously or simply having sex with another person?

If you are considering going to Auckland in January for the Australian Federation of Family History Organisations 12th Congress then let me remind you that the early-bird registration closes on the 30th September. If you were not considering going then let me try to change your mind!

This is a marvellous opportunity to hear speakers from around the world and to learn more about how to find your ancestors and discover more about their lives. The opportunity to mingle with other researchers is also a huge, often overlooked, benefit. People who think the way we do! People who don’t think it’s odd to include cemeteries in the sights of a town, and who understand how exciting each new discovery is.

Dick Eastman, the technology guru; Paul Allen, co-founder of Ancestry.com and now the CEO of FamilyLink; Elaine Collins, Commercial Director of FindMyPast; John Grenham, the Irish research guru; Michael Gandy, editor of the Society of Genealogists’ journal and a very entertaining speaker; Megan Smolenyak, an expert on DNA research; Cora Num, website guru; these are a few of the famous international speakers that will be lecturing and running workshops over the four days of the conference.

Topics cover research in Australia, England, Ireland, New Zealand, Scotland, technology, DNA, and specific how-to sessions such as preserving documents and heirlooms and writing your family history. Many sessions run concurrently so that you can always find something of interest for every session, and some lectures are repeated at other times so you can sort out clashes in the programme with other lectures you want to see. Hands-on workshops are available in many of these subject areas as well.

Accommodation is available at the College where the conference will be run, or alternatives can be found in nearby motels.

These Congresses are only run every three years. The last one was in Darwin in 2006 and I can’t tell you how much I enjoyed it; it could have gone on for another four days and I would have been happy! The next one will be in Adelaide in 2012, which seems a long way away at the moment.

Here is the message from the Convenor, Richard Hollier:

REMINDER

For those of you who have not yet registered for the AFFHO 2009 Congress this email is to remind you that the earlybird registration closes on 30 September 2008.

Still undecided?

Look at the benefits:

• Around 15 speakers from outside Australasia
• Four consecutive lecture streams
• Plus parallel workshop stream with up to 4 additional options
• Networking with fellow genealogists from throughout the world
• On site accommodation in gorgeous surroundings
• Range of social events and tours
• Registration cost lower than previous AFFHO congresses and comparable to NZSG when compared on a daily cost
• Convenient online registration

Go online http://www.affhocongress2009.org and register now

Don’t miss this highlight on the 2009 genealogical calendar!!

Any questions or issues please email me or one of the congress committee. Contact details are on the website.

Regards

Richard

Richard Hollier
Conference Convenor
c/- 24 Gretel Place
Hillcrest, North Shore City 0627
New Zealand
Phone: +64 9 4190521
Email: convenor@affhocongress2009.org

I personally will be taking advantage of the opportunity to do some research on my long-neglected New Zealand ancestors and I am going over a week early. Perhaps I’ll see some of you there!

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.

I’ve been meaning to write about recent two papers, one in Current Biology and one in Nature, that attempt to identify and characterize a relationship between genetic sequence or SNP and geography.  Amazingly, both papers found a very strong correlation between genetics and geography.

From a news article regarding the paper in Nature (note that I haven’t verified that the paper supports the statement; HT: Yann Klimentidis’ Weblog):

"The map was so accurate that when Novembre’s team placed a geopolitical map over their genetic "map", half of the genomes landed within 310 kilometres of their country of origin, while 90% fell within 700 km."

Although there are some caveats, for example in one of the papers all of an individual’s grandparents had to have similar geographic origins in order for the method to identify ancestry, these types of studies will continue to discover and refine the methods and findings.  As Kambiz stated at Anthropology.net, "With higher resolution GeneChips, ideally full genomes, and larger samples, we’ll be able see much more accurate genetic-geographic separations of populations."

There has been much discussion of these papers in the blogosphere, including at the Spittoon (here and here), john hawks weblog, and Dienekes’ Anthropology Blog (here and here), just to name a few.

There is also a short but very interesting video associated with the Nature paper (HT: ScienceRoll - you were right Berci!).  From the video:

“If your ancestors came through Ellis Island you probably know their ethnicity but might have only a vague idea of exactly where they’re from. Now this amazing genetic map of Europe shows it is possible to pinpoint a person’s geographic origins to within a couple hundred miles with a simple DNA sample.”

On September 5th at the 2008 Federation of Genealogical Societies Conference in Philadelphia, Pennsylvania, I was interviewed by Dick Eastman.  In the interview we discuss my blog, DNA testing in general, and my free ebook, “I Have the Results of My Genetic Genealogy Test, Now What?” (which is available for download in the sidebar of the blog).

If the player doesn’t appear in the post, the interview is available here (http://rootstelevision.com/players/player_conferences.php?bctid=1811559654).  It was a pleasure to meet and talk with Dick, and I hope you enjoy the interview.

Journalist Maggie Greenhouse writes an entertaining article about genetic genealogy entitled “Who Do You Think You Are? Company Can Help Trace Genetic Ancestry” (Houston Chronicle, Sept. 19, 2008) .  Much of the article is about Oxford Ancestors (OA), a genetic genealogy company based in England, but the article also mentions some companies in the United States:

“Houston is also home to Family Tree DNA, a company that offers the same services as Oxford Ancestors. Last year, Harvard professor Henry Louis Gates joined forces with Family Tree DNA to help African Americans looking for answers about their past. AfricanDNA, the company Gates launched in November 2007, offers both genetic testing and genealogical tracing services for African Americans.”

Interestingly, the article mentions that OA databases have DNA from approximately 30,000 people.  By the way, I also noticed that the OA website has been completely redesigned.  It was a much needed update and looks good

I’ve recently been contacted by the people responsible for a new family tree website called It’s Our Tree. It’s free and just requires you to enter your name and email address. I’ve just registered and now it wants me to enter my parents and grandparent and so on, and to invite my relatives to join as well.

There are more and more of these sites around; some are free and some are not. Ancestry lets you create your family tree for free and let’s you know whether it has any “hints” for these people: either trees with the same people in them or databases which may have them. You can’t see the hints, though, unless you have a subscription.

GenesReunited is a similar kind of thing. I don’t know if you can start from scratch without paying the yearly subscription, but if you have created a tree in it and then stop paying the subscription your tree remains for others to find. I have found a few relatives with my subscription and so I keep it up but I haven’t put much detail on my tree and so it keeps sending me hints that are completely irrelevant.

Another one is FamilyTreeLink from the World Vital Records people. This one is free, and allows a gedcom to be uploaded. I can see who else is researching people from the same places as my people, and I can add photos, stories, documents and headstones (presumably photos). It has some different features such as the ability to request lookups from people. I haven’t been into this one for a while and when I just tried to see a tree diagram with more than the default number of 4 generations it seemed to kill my web browser (which is Firefox V3). No, it just gave it a scare, it’s working again now.

What I like about Ancestry is the ability to link records that you find with the relevant person in your tree. If you find your great-grandfather in the 1930 Census you can link the page to him. You can also upload pictures and multimedia, share it with others and even give them the ability to add to it. In theory members of different branches of your family could all be working on the same tree, but in practice I think I would want to check things for myself before allowing it on my tree.

You can also create a book that can be printed, which is a great idea. A family can collaborate and print a number of books to distribute amongst family members, or you can do it by yourself.

What worries me about these things is that there are so many of them. You need to be on as many of them as possible to have a chance of catching other relatives. I don’t know about you, but after I’ve gone to the trouble of entering the details of all of my ancestors individually and adding photos and stories and the like I’m not likely to do the same in another site. If any of my living relatives have started using another site then we won’t find each other.

The social networking sites such as FaceBook have family tree applications as well. You can upload gedcoms to these instead of entering them from scratch, which makes them more appealing to me, at least.

Is there any sense in using a new one that has just started? I certainly won’t be unless I can upload a gedcom; there aren’t enough hours in the day to enter the data into the ones I use now without starting again with another one. If I can’t upload a gedcom directly it isn’t worth the time for me. I’m afraid that It’s Our Tree may be too late.

My experience this afternoon with FamilyTreeLink leads me to another issue. It is difficult, perhaps impossible, to build a web application that will work perfectly with all web browsers and all computer configurations, and each new application has to do it themselves. A bad experience with one of these new ones can turn you off it for good. And then the browser will come out with a new version, as Mozilla has with Firefox 3, and suddenly things that used to work don’t any more.

The answer to this one, I guess, is to stick with a site that has been around for a while and has a large development team behind it. I’m not advocating Ancestry specifically but I have to confess that it’s the one I am spending more time entering data and linking records.

Which one do you use? Do you use any of them? Have you found any relatives?

This afternoon James Valentine on ABC Sydney Local Radio (702 AM) continued his phone-in collection of world record holders. Claimants this afternoon included a man who forgets that he’s wearing the wrong glasses up to three times per night and has to go back upstairs to retrieve them, and a high score on a game that I’ve already forgotten the name of.

Last week a lady rang in to say that her grandfather was born in 1833, thus claiming the record for the longest span between a living person and the birth of a grandparent. She won without any contest.

That record stood until this afternoon, when another lady, who turns 77 in December, claimed a grandfather born in 1803.

1803!!! It doesn’t seem possible, and yet there it is.

Her grandfather, born in 1803 somewhere in what is now Northern Ireland, fathered her father when he was 58 years old. This gives an approximate year of 1861.

Her father then fathered her when he was 73 years old, presumably in 1934. Work it out. Does it add up? No, it doesn’t exactly, because if she’s 77 she should have been born in 1931, not 1934, but it’s close enough.

So the record stands at 1803. Such a long span of history these three people have seen between them.

My four grandparents were born between 1897 and 1901 and had their children at a more usual age. My mother, who is still alive, has four grandparents who were born between 1867 and 1875, with the men older by just a few years than the women. So she wouldn’t have a hope of winning a medal in this event!

I guess it has to do with the age discrepancy between the parents because, let’s face it, 73-year-old women don’t have children, and very few 58-year-old women manage it. If men marry much younger women who then have children then this sort of range is possible. Pablo Picasso, born in 1881, famously fathered his youngest child, Paloma, when he was 67 or 68. (Source: Wikipedia).

What’s your record?

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).

23andMe just announced that the price of their service has dropped from $999 to $399.  According to an article in the San Francisco Chronicle, the company lowered the price of testing to attract more customers and increase the size of their database.  The article maintains that 23andMe will still bring in profit from the lower membership price, which is made possible by a “new, higher-density gene-scanning chip made by Illumina Inc. of San Diego.”  From the press release:

“The new Beadchip, called the HumanHap550-Quad+, makes use of a four-sample format. 23andMe also has added improved custom content to the new Beadchip, which will include a broader range of Single Nucleotide Polymorphism (SNP) variations and rare mutations not found on the previous Beadchip, thereby providing more relevant data on published associations, as well as maternal and paternal ancestry.”

Since 23andMe launched nearly a year ago, I’ve said that genealogists are a huge potential market for 23andMe’s services.  Undoubtedly, the company has recognized the value of marketing their product to genealogists.  Indeed, 23andMe’s blog, the Spittoon, announced today that the company has partnered with Ancestry.com to provide ancestry-related content from 23andMe to customers who have their DNA analyzed by Ancestry.com:

“We’re also very pleased to announce a new partnership between 23andMe and Ancestry.com, the world’s largest online source of family history information. As part of this arrangement, customers who have their DNA analyzed for genealogical purposes by Ancestry.com will also have access to ancestry-related content from 23andMe.”

You can learn more about the partnership by reading 23andMe’s press release.  As of Tuesday morning, I don’t see any press release at Ancestry.com or DNA Ancestry.

This lower price is only slightly more than many current genetic genealogy tests (some of which only sequence a few thousand bases rather than the 1,000,000+ SNPs tested by 23andMe’s SNP Chip). Will this lower price spur you to sign up for 23andMe’s services?  Will other companies such as deCODEme lower their prices in response?  What do you think?