R1b YSNP Project
Principal Investigator: Brian Kemp
Co-Investigators: Dennis Garvey and Cara Monroe
Project contact email: YSNPs@yahoo.com
May 15, 2009:
Dear R1b YSNP Study participants,
Dr. Kemp and I would like to thank you for participating in the R1b YSNP study. However we regret to inform you that earlier in the semester the difficult decision was made to shutdown the project, and all samples have been destroyed. This decision was based on what we came to perceive as an error in how the study was structured.
The problem involved the fact that the study's Informed Consent Form guaranteed that we would release results to participants as we learned them ourselves. However it has since become apparent that making the results public while the study is still underway seriously threatens the timeliness of the work - and therefore the chance of publication. However all the conditions and rules stated in the Informed Consent Form must be followed. Changing the conditions regarding the release of study results would require another round of sample collection with a new Informed Consent Form worded to that effect. Therefore the decision was made to shutdown the project and destroy those samples. Unfortunately none of the new candidate YSNPs had yet been found to be derived among the donor samples by the close of the study.
We want to thank you for your help and we apologize for the disappointment. We will keep your contact information on file in case the study is restarted at some point in the future.
Dr. Dennis Garvey
February 17, 2009:
The quantity of DNA collected using swabs was found to often be insufficient for the large number of candidate YSNPs that are being examined. Therefore a collection kit using mouthwash has been developed in-house and will be used in future collection kits.
Likewise, it has been found that traditional genotyping methods are also proving cumbersome for the large number of YSNPs to be examined. Therefore the next stage of the study will be to begin testing YSNPs using a form of mass spectrometry known as MALDI-TOF. This will allow large scale multiplexing and should speed up the project greatly.
Collection kits not returned: Y-188, Y-202
Next project update: May 15, 2009
The Y chromosome is passed down from father to son in exactly the same manner as surnames. Therefore over the last decade genetic testing of the Y has become a valuable new tool for genealogists. While any two human Y chromosomes are more than 99.99% identical, Y chromosomes from different lineages can be distinguished from one another based on that 0.01% difference. A selection of these 0.01% differences have been characterized by population geneticists and are referred to as markers. The major branches of the human Y family tree are called haplogroups, and each is designated with a capital letter (followed with a series of numbers and small case letters to indicate subgroups). The most common haplogroup among men of European descent is R1b. The aim of the R1b YSNP Project is to characterize new Y chromosome markers that will allow new subgroups of R1b to be identified.
Y chromosomes are useful for tracing "direct paternal lineages" (your father's father's father's father, etc). Most Y chromosome testing done for genealogy involves a kind of Y marker known as an STR. These markers mutate at a relatively fast rate, and so are useful for identifying connections between direct paternal lines that share a common ancestor within the last several hundreds of years (a genealogically useful timeframe). However there is another kind of Y marker known as a SNP (pronounced "snip") that mutates at a much slower rate, and allows connections between paternal lines to be identified over timescales of thousands, or even tens of thousands of years. For example, since the 2002 paper by Semino et al, it has generally been believed that R1b men are the direct paternal descendants of the first anatomically modern humans who expanded into Europe about 40,000 years ago. R1b is still the dominant Y lineage among men of European descent with frequencies of R1b approaching two-thirds of the men in some populations.
The usefulness of YSNPs for genetic-genealogy has been limited by the relative scarcity of R1b YSNP markers seen in any substantial fraction of R1b men. Previous to the release of the 2007 Sims et al study, more than 90% of R1b men would have had identical YSNP testing results. However the marker U106 has proven to be useful in singling out a group of more than 25% of the R1b men who share a more recent ancestor with other U106+ men (U106 derived) than they do with all other R1bs.
The aim of the R1b Project is to characterize new YSNP markers that will split haplogroup R1b into other significant subdivisions. The technical description of our goal is that we will phylogenetically characterize a subset of the YSNPs listed in the NCBI database dbSNP to identify new U-series YSNPs that may be useful to further subdivide the R1b haplogroup. The "Holy Grail" of this line of inquiry would be to identify SNPs that not only distinguish one R1b from another, but would be useful for identifying men with one region of European geographic origin from another.
Volunteers for the R1b YSNP Project are being recruited in early Fall 2008 through the public genetic-genealogy database www.YSearch.org. Participants will be able to track the progress of the study on this website. The results will be shown in a similar manner to the results shown above for the Sims et al study (with participants identified only by a Study ID Number like "EA-142"). Updates to the site will be made on a quarterly basis.
Frequently asked questions
Can I volunteer for the R1b YSNP Project?
We are sorry - but the recruitment phase of the project is closed.
When should I expect results?
Please try to think of us in the same way the genealogy community thinks of testing with the Sorenson Molecular Genealogy Foundation. Doing science is the SMGF's first priority, and that's why they do not give a time frame to their donors. We face even greater challenges than the SMGF in that all markers we test will be "first time science". The only solid deadline for the project is that the official end date of the R1b YSNP Project is August of 2010. But we do expect the final results to be available to volunteers long before then.
How often should I check back for new results?
The webpage will be updated every three months. The date of the next update will always be given at the end of the most recent update.
Are you aware that genetic genealogists are now able to test thousands of YSNPs commercially?
Yes we are. That's why we chose to limit ourselves to the remaining 25 million basepairs in the euchromatic portion of the human Y chromosome that are not commercially available. We assume that the public will do a good job of testing the markers available to them. We intend to take care of the rest.
I just heard about a great new YSNP called rs123456789. Will you be adding that to the markers you test now?
In September 2008 we purchased the primer pairs for a few dozen candidate YSNPs. The rest of the project will be many months of hard work in the lab to test what we already have on hand. So thank you for your suggestions, but we are already knee-deep in our own YSNP ideas. As mentioned above, we have avoided SNPs available to the public. That means that we really have no need to hear about the latest, greatest YSNP in the genetic-genealogy community (which would likely have come from the limited commercially available selection).
Can I email you and ask more questions about how the study is going?
Please keep in mind that time spent answering emails is time away from testing. Therefore we feel that it is in everyone's best interest that the only information available to the public about the project's progress is the information on the project webpage.