The Genetic Genealogist

An Updated Y-DNA Tree at ISOGG

The International Society of Genetic Genealogy (ISOGG) announced today that their Tree Team has completed the 2008 version of the Y-DNA Haplogroup Tree. This revision was a major undertaking, because, as ISOGG states in the version history, “[t]he Karafet et al paper (2008) required a significant revision to the tree and affected all haplogroups.” The reference for this paper is (Karafet T M, Mendez F L, Meilerman M B, Underhill P A, Zegura S L, Hammer M F, (2008).
New Binary Polymorphisms Reshape and Increase Resolution of the Human Y-Chromosomal Haplogroup Tree. Abstract. Genome Research, published online April 2, 2008. Supplementary Material.). From ISOGG’s official release:

MAY 04, 2008 – The 2008 version of the ISOGG Y-DNA Haplogroup Tree is now available online: http://www.isogg.org/tree/. New to the tree is a haplogroup conversion table which is downloadable in MS Word. If you do not have MS Word/MS Office, you can download openoffice.org for a compatible word processing program. Appreciation goes to Richard Kenyon and Charles Moore for their work on compiling this table.

Thanks to Alice Fairhurst and the entire ISOGG Tree Team for all of their hard work and dedication. Added thanks for consultation goes to Jim Wilson, Dennis Garvey, Ken Nordtvedt, and Natalie Myres on various haplogroups. Additional appreciation to Charles Moore (Hg D) and Vincent Vizachero (Hg R) for joining the Content Team Experts.

The site also has a Haplogroup Conversion Table (MS Word) to convert a 2007 haplogroup to an updated 2008 haplogroup.

Updates at FTDNA and ySearch

The Karafet et al paper also resulted in updates to haplogroup designations at Family Tree DNA and ySearch. Users who have tested their Y-DNA through FTDNA or have created a profile at ySearch automatically had their haplogroup designation updated this morning (May 5th, 2008). For instance, before the update my haplogroup was R1b1c9a. After the update, the haplogroup is called R1b12a1c.

New Deep Clade Tests Reflects Changes

As a result of the SNPs analyzed in the Karafet et al paper, Family Tree DNA has updated their “Deep Clade” SNP tests. From the official announcement this morning:

New SNPs and haplogroup branches have been discovered and published, which have now been integrated into the Deep Clade testing panels. Customers who are currently waiting for Deep Clade test results will automatically be upgraded to the new testing panels at no additional fee. Participants who previously ordered Deep Clade tests and for whom some new SNPs may be informative will be offered a Deep Clade test extension, as applicable.

The new Deep Clade testing system is designed to determine a participant’s placement on the haplogroup tree. The test begins with their predicted haplogroup and tests whatever SNPs are necessary in order to determine their haplogroup assignment on the tree. Results of all SNPs tested are reported to the customer as they are completed.

Deep Clade tests are available for haplogroups E1b1b, G, I, J, and R (includes R1a, R1b, and integrates the U series SNPs within R1b).

To order the test, FTDNA users should check under the “Haplogroup” page on the left side of their personal page. Note that the FTDNA tests do not incorporate all the SNPs used by the ISOGG Tree Team to create the updated 2008 Y-DNA Tree. The ISOGG tree uses some SNPs that are new, provisional, or private and are not yet used by testing companies.

Here is the abstract of today’s Y-chromosome haplogroup tree paper in Genome Research, I’m still working to get a copy of the actual paper (unfortunately, it’s not open access at this time):

Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.

Karafet, T.M., Mendez, F.L., Meilerman, M.B., Underhill, P.A., Zegura, S.L., and Hammer, M.F. New binary polymorphisms reshape and increase resolution of the human Y-chromosomal haplogroup tree. Genome Res. doi:10.1101/gr.7172008.

[This is a repost of an article that appeared on May 29, 2007. Since I’m knee-deep in final projects and exams, I thought I’d pull out a popular article from the archives. I hope you enjoy it (again)]:

In Part I, Part II, and Part III of the “You and the $1000 Genome” series we’ve examined the Archon X PRIZE for Genomics, the International HapMap Project, and the ethical issues associated with both. In this final installment of the series we will examine the potential impact of genomic or SNP sequencing and interpretation on both medicine and genealogy (finally, some genealogy for you patient genealogists out there!).

I believe that whole genome sequencing will have myriad uses. In the paper mentioned in Part III of the series (John A. Robertson, “The $1000 Genome: Ethical and Legal Issues in Whole Genome Sequencing of Individuals (pdf).” 2003 The American Journal of Bioethics 3(3):InFocus), Mr. Robertson suggests that demand for personal genome sequencing outside of the medical context could be quite limited. But that view might fail to take into account uses of genomic information other than identifying or predicting disease, such as the genetic genealogy setting. Very few could have predicted 10 years ago that thousands of genealogists would be submitting their DNA for limited sequencing as they are doing today. If information from whole genome sequencing can be used to analyze genealogy (which it surely will be), then this will create an entire niche that will increase commercial demand outside of the medical context. And this is only one such niche. There might be many many more, some of which will only develop after whole genome sequencing becomes economically available.

Here is a list of just a few of the uses of genomic sequencing:

1.Identification of genes involved in disease – scientists are far from understanding the genetic basis of most human conditions, both normal and disease. Having thousands of genomes in research databases will give researchers the ability to make these types of associations through comparative genomics.

2.Tailored preventative medicine – knowing one’s propensity for disease(s) will allow scientists and medical specialists to attempt to prevent the formation of these diseases. So see more about personalized genetics, read this informative interview at ScienceRoll with Steven Murphy, MD of the Gene Sherpa. If tailored preventative medicine is to come about, it will require the education of all healthcare specialists in genetics and the relationship between genetics and disease.

3.Genealogical research – whole genome sequencing will greatly advance the ability of genealogists to use DNA to study ancestral relationships. This will have a big effect on both autosomal and Y chromosome studies. Genealogical testing using autosomal markers is limited by both the low number of identified markers and the unknown frequency of sequences across all populations. Cheap and efficient genomic sequencing could alleviate both these limitations. Y chromosome studies will greatly benefit by a huge increase in the number of STR markers that could be used for relationship comparisons. Currently companies such as Family Tree DNA offer 67-marker tests. In a few years we will be able to compare all the STRs in the Y chromosome rather than just a few of them.

Recognizing the impact that cheap and efficient whole genome sequencing will have on science and society, Nature Genetics‘ ‘Question of the Year’ is “What would you do if this sequencing capacity were available immediately?” The website has numerous replies from prominent geneticists and presents a number of interesting thoughts on the topic. evolgen, another member of The DNA Network, has also provided an answer to the question on the evolgen blog. In addition, DNA Direct Talk has a round-up of recent blog discussions regarding the $1000 genome.

Here is a quote from Professor Stephen Hawking in support of the X PRIZE in Genomics:

“As you may know, I have recently expressed my belief that space exploration and the eventual colonization of space is critical for humanity’s survival. To bring about breakthroughs for personal spaceflight is a laudable aim and it is work done by the X PRIZE Foundation that will eventually unleash humanity from the gravitational bonds of earth. You may also know that I am suffering from what is known as Amyotrophic Lateral Sclerosis (ALS), or Lou Gehrig’s Disease, which is thought to have a genetic component to its origin. It is for this reason that I am a supporter of the $10M Archon X PRIZE for Genomics to drive rapid human genome sequencing. This prize and the resulting technology can help bring about an era of personalized medicine. It is my sincere hope that the Archon X PRIZE for Genomics can help drive breakthroughs in diseases like ALS at the same time that future X PRIZEs for space travel help humanity to become a galactic species.”

Well there you have it! It is probably quite obvious that I have high hopes for efficient and inexpensive genome sequencing and subsequent interpretation. Although the necessary technology is still a few years away, it is important that we as a society address the many issues that will result from these technologies. As always, I would appreciate any comments that you many have on this topic, or any thoughts you may have had while reading this series.

P.S. – I just stumbled across an interesting article at In the Pipeline about the use of cheap(er) genomic sequencing to follow the development of antibiotic resistance in bacteria (S. aureus). I don’t have access to the PNAS paper, but it appears that the genome (which is tiny compared to ours) was completely sequenced twice, once before treatment and once after treatment failed due to the development of resistance. The strain had developed a total of 35 mutations! The author makes a great statement at the end:

“The technology involved here is worth thinking about. Even now, this was a rather costly experiment as these things go, and it’s worth a paper in a good journal. But a few years ago, needless to say, it would have been a borderline-insane idea, and a few years before that it would have been flatly impossible. A few years from now it’ll be routine, and a few years after that it probably won’t be done at all, having been superseded by something more elegant that no one’s come up with yet. But for now, we’re entering the age where wildly sequence-intensive experiments, many of which no one even bothered to think about before, will start to run.”

Other Posts in the Series:
You and the $1000 Genome – Part I: The Archon X PRIZE for Genomics
You and the $1000 Genome – Part II: The International HapMap Project
You and the $1000 Genome – Part III: The Ethical Issues

[This is a repost of an article that appeared on May 22, 2007. Since I'm knee-deep in final projects and exams, I thought I'd pull out a popular article from the archives. I hope you enjoy it (again)]:

Over the next week and a half I will be examining the Archon X PRIZE for Genomics, a challenge from the Archon X PRIZE Foundation to foster the development of efficient and inexpensive genomic sequencing. Not only will the X PRIZE for Genomics change the face of medicine, but it will also have an ENORMOUS impact on the field of genetic genealogy, which we’ll discuss in Part IV of the series. Stay tuned for all the information you need to know about the prize, and if you have any thoughts or questions please leave a comment!

History of the Archon X PRIZE for Genomics:
In 2003 the J. Craig Venter Science Foundation announced a $500,000 Genomic Technology Prize that would be awarded to an the group whose technology significantly enhanced “the field of high throughput DNA sequencing by enabling a human genome to be sequenced for $1,000 or less.” The Foundation believed that crossing this threshold would enable the majority of individuals to afford genomic sequencing as part of medical treatment.

By 2006, Dr. Ventor’s $1000 genome challenge was picked up by the X PRIZE Foundation to create the Archon X PRIZE for Genomics, a $10 million dollar incentive for the first successful team. To win the prize purse, the registered group must build a device and use it to sequence 100 human genomes within 10 days or less, with an accuracy of no more than one error in every 100,000 bases sequenced (that’s just 0.001%) for no more than $10,000 per genome. As of May 2007 there are three teams registered for the competition; VisiGen, 454 Life Sciences, The Foundation for Applied Molecular Evolution (FfAME), and Reveo, Inc. If you’re curious, Genomics & Proteomics Magazine has summarized a number of the leading technologies that are being developed in pursuit of the X PRIZE (very technical information).

In August 2005, the National Human Genome Research Institute announced that it had awarded grants in excess of $32 million to promote the development of sequencing technologies that would significantly lower the cost of whole-genome sequencing. At the time, it cost roughly $10 million to sequence a human genome (a 50-fold decrease from the previous decade), and the NHGRI set a final goal of $1000 or less for an entire genome. As the NHGRI pointed out, “the ability to sequence an individual genome cost-effectively could enable health care professionals to tailor diagnosis, treatment, and prevention to each person’s unique genetic profile.”

Four years later, has there been progress?
454 Life Sciences, for example, has just announced in March that they have essentially completed sequencing of James Watson’s genome, arguably the first time a single person’s genome has been sequenced (the Human Genome Project’s source of DNA was reportedly an amalgam of different sources). For those that don’t know (can there be anyone?), James Watson is famous for having discovered the structure of DNA over 50 years ago. Interestingly, Watson has asked 454 to withhold his results for the apoE gene – associated with Alzheimer’s disease – as well as a number of other results, citing privacy concerns. Watson, after all, has a son who received 50% of his genetic makeup from Watson’s genome. In light of this, 454 has decided to hand over the results to Watson, who will then decided what to release to the public. (See Marshall, Eliot, “Sequencers of a Famous Genome Confront Privacy Issues” Science 30 March 2007:Vol. 315. no. 5820, p. 1780DOI: 10.1126/science.315.5820.1780). 454 estimates that the six-fold coverage of Watson’s genome cost an estimated $1 million. Still a long way to go to reach the $1000 goal.

Meanwhile, Reveo, Inc. just joined the competition on April 30^th of this year, but Reveo’s founder, Dr. Sadeg M. Faris, believes that their technology will eventually be able to read an entire human genome “in minutes for pennies per genome.”

In the next post I will be examining whether or not the $1000 genome is really necessary considering recent developments in a related field.

The X PRIZE Foundation has released a video that explains the aims of the project.

[Since this article posted on May 22, 2007, there have been MANY developments towards the $1,000 genome. To learn more, visit the archives here at TGG, or search using the search box in the sidebar.]

I’m sorry if I’ve overloaded you on the recent launches of 23andMe and deCODEme, but I think there’s so much to talk about. For a little lightheartedness, read “23andMe Party” from How to Change the World by Guy Kawasaki. Kawasaki describes a friends and family “Spit Party” hosted by 23andMe, and even has a number of pictures from the event.

The party offered attendees the chance to submit their DNA for analysis at a discounted rate. Some of the attendees included co-founders Linda Avey and Anne Wojcicki, at least one Nobel Prize winner, and celebrities Goldie Hawn and Kurt Russell.

Would you like your genome sequenced in a matter of hours for under $100?

An article from GenomeWeb last week, “Complete Genomics, BioNanomatrix to Use $8.8M NIST Grant to Develop ‘$100 Genome’ Platform,” reveals that BioNanomatrix and Complete Genomics have partnered together to share an $8.8 million grant from the U.S. National Institute of Standards and Technology to “develop technology that will be able to sequence a human genome in eight hours for less than $100.”

From the article (don’t worry, I have no idea how these technologies really work either):

“The proposed sequencing platform will use Complete Genomics’ sequencing chemistry and BioNanomatrix’ nanofluidic technology. The companies said they plan to adapt DNA sequencing chemistry with “linearized nanoscale DNA imaging”to create a system that can read DNA sequences longer than 100,000 bases quickly and with accuracy “exceeding the current industry standard.””

So what does this mean for genetic genealogists? Well, considering many genetic genealogy tests cost substantially more than $100 and return a much smaller amount of sequencing, whole genome sequencing for $100 would have a pretty strong impact. Although this technology requires a considerable amount of development, there has been a lot of recent investment and remarkable progress in this area.

Ancestry.com has established a new blog, located at blogs.ancestry.com.  Let me just say that they have excellent taste in WordPress themes (it’s the same as mine)!

If you’re interested, here’s a link to a document from the Edge Foundation, a group designed to promote the discussion of intellectual pursuits. The document is a summary (including video links) of a casual meeting between some fantastic scientific minds (Craig Venter, Freeman Dyson, Robert Shapiro, Dimitar Sasselov, and Seth Lloyd) which took place in late August.

Although Dr. Church doesn’t discuss the Personal Genome Project, his brief discussion about our past and our future is very interesting.  There’s also a summary of the meeting from Gregory T. Huang, an invited journalist.  I see that one of the invited guests was Ting Wu, a researcher at Harvard who has initiated the pgEd (personal genetics education project).

I have to say, I am so tired of the United States Postal Service always losing my invitations.

Yesterday was another big day for genetic genealogy, with two major announcements. First, as I have previously mentioned, Ancestry.com teamed up with Sorenson Genomics to offer DNA testing. The results of that testing can be, at the owner’s discretion, tied into a new DNA database as well as their massive collection of genealogical source materials. Here’s the official announcement from PRNewswire: “Ancestry.com Enters DNA Genealogy Field Through Exclusive Partnership With Sorenson Genomics: Combines Three Major Pillars of Family History Research – Historical Records, DNA and Family Trees.” Here’s another blurb at Family Tree Magazine. According to one source (CNET News), the $200 test will examine both Y DNA and mtDNA, but that hasn’t been confirmed. It only makes sense to test both, however, especially at that price.

In other news, DNAPrint Genomics (aka AncestryByDNA) announced the release of a new autosomal test, EuroDNA 2.0. Where EuroDNA 1.0 used just 320 SNPs to delineate people of European ancestry into four groups – Northern European, Southeastern European, Middle Eastern, and South Asian – EuroDNA 2.0 uses 1,349 SNPs.

The test is based on a recently published paper using DNA chips to compare populations from around the world: Bauchet M, McEvoy B, Pearson L, Quillen E, Sarkisian T, Hovhannesyan K, Deka R, Bradley D, Shriver M. 2007. Measuring European population stratification with microarray genotype data. American Journal of Human Genetics 80(5): 948-956.

DNAPrint(R)’s EuroDNA(TM) 2.0 clarifies European sub-ancestry by using 1,349 European Ancestry Informative Markers (AIMs). This test reports a person’s proportional basic continental European ancestry using several categories: Southeastern Europe (Armenian, Jewish, Greek and some Italians); Iberian (Spanish, Portuguese); Basque (Spanish/French Pyrenees border); Continental European (German, Irish, English, Polish, Some French and Italian); and North Eastern European (Finnish). The EuroDNA(TM) 2.0 test is by far the most advanced genetic ancestry test yet to be offered to the public.

“The paper resolved 5 fundamental and ancient types of European ancestry – Southeastern European (Armenian, Jewish, Greek, some Italians), Iberian (Spanish, Portuguese), Basque, Continental European (German, Irish, English, Polish, some French and Italian, and North Eastern European (Finnish)). Many ethnogeographic populations show interesting mixes as a function of their history and geography.

In collaboration with the Shriver lab, which published the Bauchet et al., 2007 paper, DNAPrint® mined the chip marker used to create the Bauchet et al., 2007 paper, looking for the SNPs that provided most of the European Ancestry Information.

We found that 1,349 of the 11,071 chips SNPs, provided most of the within-Europe ancestry information.EuroDNAâ„¢2.0 measures each of these 1,349 European Ancestry Informative Markers (AIMs) for each customer, and using a Bayesian algorithm, reports a customer’s proportional Southeastern European, Iberian, Basque, Continental European and Northeastern European ancestry.”

All the technical information is available on the EuroDNA 2.0 Manual Page. I previously reviewed AncestryByDNA here on the blog.

Ancestry.com, one of the largest online sources of family trees and genealogy source material, is teaming up with Sorenson Genomics to offer DNA testing.

Ancestry.com has more than 14 million users, meaning that genetic genealogy will be introduced to a huge new group of individuals. Additionally, Ancestry can use the results of this testing to enhance the other databases they already offer – something that the other big testing companies lack.

As of now, the rumored price is to be $200, with no mention of the type of testing to be offered. There’s a lot more information available at Eastman’s Online Genealogy Newsletter, The Jerusalem Post, The Times Daily.com, The Salt Lake Tribune, and The Deseret News.com. Look for the announcement to be made sometime today.

A huge thanks to Tim at Genealogy Reviews Online!