Ancestry SNPs galore

Today sees the launch of  Geno 2.0, an exciting new DNA test which marks phase two of the Genographic Project, a scientific research project run by National Geographic in partnership with Family Tree DNA and IBM. The launch has been covered by a number of bloggers in America who attended the pre-launch presentation. They each cover the test from slightly different perspectives and all the posts are well worth reading.

- Roberta Estes     National Geographic Geno 2 announcement - the human story
- Roberta Estes     Geno 2.0 - Q&A with Bennett Greenspan
- CeCe Moore        National Geographic and Family Tree DNA announce Geno 2.0 
- Blaine Bettinger   National Geographic and Family Tree DNA announce Geno 2.0
- Judy Russell       Geno 2.0 launches 
- Emily Aulicino     National Geographic announces new DNA test
- Razib Khan        The Genographic Project: on to the autosome!

The new Geno 2.0 test is a deep ancestry test. It complements the existing DNA tests that are traditionally used by genealogists and does not replace them. The new test is looking at special markers known as SNPs (pronounced 'snips'). These markers can tell us how much of our DNA we share in common with other populations from around the world. Both males and females will discover their mitochondrial DNA haplogroup. Males will discover their Y-DNA haplogroup. Haplogroups represent branches of the human family tree. The inclusion of new SNPs in the Geno 2.0 test will allow scientists to define not just the branches of the family tree, but also the twigs (subclades) which make up those branches.

For surname projects we use a different marker known as a Y-STR marker. Y-STR markers are like the leaves on a tree and we use Y-STR tests to place the leaves on the tree by grouping matching results in genetic families. If you are a male and are interested in using a DNA test to help with your genealogy research you should take a Y-STR test with one of the many surname or geographical projects at Family Tree DNA.

The new Geno 2.0 test will, however, effectively serve as a replacement for the old Y-DNA deep clade test from Family Tree DNA which provided detailed subclade assignments. The old deep clade test looked at a small handful of SNPs and it was necessary to order new SNPs à la carte as and when they were discovered. For just a little bit more money the new Geno 2.0 test covers 12,000 Y-DNA SNPs all in one go, and includes many new SNPs that were not previously available. It is set to transform our knowledge of the Y-DNA haplogroups.

The Geno 2.0 test covers 3,200 mitochondrial SNPs (about 19% of the mitochondrial genome). If you are only interested in learning your mtDNA haplogroup assignment then you should take the Geno 2.0 test. If you are interested in using mtDNA for matches within a genealogical timeframe (within the last 400 years) or if you are interested in participating in mtDNA scientific research then you will need to order a full mitochondrial sequence (FMS) test from Family Tree DNA. The FMS test sequences the entire mitochondrial genome (100%) which consists of 16,569 bases.

It will be interesting to see how the new Genographic Project test impacts on the other SNP tests that are currently available. Autosomal SNP testing is currently offered by 23andMe, Family Tree DNA and Ancestry.com. Their tests look at many more SNP markers than the new Geno 2.0 test. 23andMe tests one million SNPs. Family Finder and Ancestry test around 700,000 SNPs, I have written previously about my experiences with the 23andMe test and the Family Finder test. Both these tests can be used to find matches with genetic cousins within the last five generations or so. The 23andMe test also provides information on health issues. Ancestry.com have recently launched their own autosomal DNA test. I am currently waiting to receive my results, and will be reporting on this test in due course. The Geno 2.0 test cannot be used for cousin matching as it does not test enough SNPs to make confident relationship predictions so these tests will continue to be useful for genealogical purposes.

The new Geno 2.0 test will, however, be the test of choice for anyone interested in learning about their ethnicity. The existing autosomal DNA tests only provide very vague information on ethnicity giving percentages of Asian, European and African admixture. The Genographic Project, with the power of its huge database (524,000 tests from 140 countries) and the focus on ancestry informative markers, should in theory be able to provide highly detailed ethnicity breakdowns and they will effectively wipe out all the competition. This new test might hit Ancestry particularly hard. Ancestry have invested a huge amount of money in their new autosomal DNA test and have specifically targeted their test at the large American market, where there is a lot of interest in ethnicity testing. Despite the large investment the early reports suggest that there are many problems with the Ancestry.com tests which have yet to be ironed out.

The British company BritainsDNA offers a deep ancestry SNP test which looks at just 200 Y-DNA and 200 mtDNA SNPs for £200 (no autosomal SNPs are included). In comparison the Geno 2.0 test covers 143,000 SNPs (including 12,000 Y-DNA SNPs and 3,200 mtDNA SNPs) and costs just $199.95  (£128). It is difficult to see how BritainsDNA can possibly compete with the Genographic Project.

Further details about the Geno 2.0 test can be found on the Genographic Project website. Pre-orders are now being accepted. If you try to place an order you are told that the kit will be shipped on 30th October 2012.

See also my blog post dated 18th August which provides additional information on Geno 2.0.  

© 2012 Debbie Kennett

Illuminating Blogger Award

I was surprised and delighted to receive an email from Nicola Elsom at The Genealogy Workshop at the weekend, informing me that she had nominated me for an Illuminating Blogger Award. As a blogger it means everything to me to know that someone has read and remembered my blog posts!

If you haven’t come across it before, the award was initiated by Food Stories, and is awarded by bloggers to bloggers, for illuminating, informative blog content. Check out the Winners Blogroll and you need never be short of good reading material again!

As a recipient, I now have the privilege of nominating five blogs for the award myself. I have selected a diverse range of blogs from both sides of the Atlantic that I always enjoy reading and are always particularly informative. I have tried to avoid nominating previous recipients and have focused on individual blogs rather than those produced by professionals and companies.

Nominations

Your Genetic Genealogist

CeCe Moore shares my passion for genetic genealogy and is a fellow member of  ISOGG. She has a particular interest in autosomal DNA testing and is always up to date with the latest developments. She has tested numerous close family members and her posts are well illustrated with real-life examples.

Genealogic Blog
Emma Jolly is not one of the most prolific of bloggers but her posts are always very detailed, scholarly and interesting, covering a wide range of topics but with a particular focus on London. As someone who has always had a fascination with names I found her recent post on Naming for empire of particular interest.

The Legal Genealogist
Judy Russell has only been blogging since the beginning of the year but she has already found her own particular niche writing about the legal issues affecting genealogists. Although many of the issues she covers deal with access to records in America there are also important implications for us here in the UK.  Judy is also an avid genetic genealogist and regularly writes about her experiences of DNA testing.

Cumpston Research
Glenys Marriott has a lively blog devoted to her Cumpston one-name study. She shares stories of the exploits of the more interesting Cumpston name-bearers who feature in her study, but her blog is also of more general interest to genealogists as she often highlights websites of interest, many of which are not so well known.

Anglers Rests
Julie Goucher has a wonderfully eclectic blog which covers a wide variety of subjects from genealogy to book reviews and anything else which she finds of interest. Julie is half-Italian and she is doing a one-name study on the Sicilian surname Orlando.

My interesting fact
As part of my nomination I am supposed to share one interesting thing about myself. I am always fascinated by the way that we tend to follow in the footsteps of our ancestors. When I first lived in London I rented a flat in Hammersmith Grove in Hammersmith. When I started my family history research I was very surprised to learn that my great-grandfather George William Thorne Wiggins owed a property in "The Grove" in the very same street where I had been living. Another great-grandfather Frederick Cruwys was a tailor and at one time he had a shop in King Street in Hammersmith where I used to go every Saturday to get my shopping. Is is just a coincidence or is there something in the genes that attracts us to the same places as our ancestors?

If you are nominated, then you have received the Illuminating Blogger Award Please follow these steps:

1. The nominee should visit the award site (http://foodstoriesblog.com/illuminating-blogger-award/) and leave a comment indicating that they have been nominated and by whom. (This step is so important because it’s the only way that we can create a blogroll of award winners).

2. The Nominee should thank the person that nominated them by posting and including a link to their blog.

3. The Nominee should include a courtesy link back to the official award site (http://foodstoriesblog.com/illuminating-blogger-award/) in their blog post.

4. Share one random thing about yourself in your blog post.

5. Select at least five other bloggers that you enjoy reading for their illuminating, informative posts and nominate them for the award. Many people indicate that they wish they could nominate more so please feel free to nominate all your favourites.

6. Notify your nominees by leaving a comment on their blog, including a link to the award site (http://foodstoriesblog.com/illuminating-blogger-award/).

And you don’t need to wait to be nominated to give your favourite blog an award.  Just visit the award site and see how to do it.

© Debbie Kennett 2012

Update on SMGF and GeneTree

In May this year Ancestry.com announced the launch of their new autosomal DNA testing service. The launch was also accompanied by the news that Ancestry had acquired the DNA assets of the Sorenson Molecular Genealogy Foundation (SMGF). The full press release from Ancestry can be seen here. Although not mentioned in the press release the DNA assets acquired by Ancestry also included the DNA testing company GeneTree, which was the commercial arm of SMGF. GeneTree is now no longer accepting orders for DNA kits and the website will be closed down at the end of the year. Anyone who has tested with GeneTree is encouraged to download their results and transfer them elsewhere. GeneTree has provided instructions here on how to download your data.
GeneTree Y-DNA and mitochondrial DNA (mtDNA) results can be transferred free of charge to AncestryDNA. You will need to set up a free Ancestry account if you don't already have one to upload your results. Y-DNA results can also be transferred free of charge to Ysearch, a free public database of Y-DNA results. mtDNA results can be uploaded free of charge to Mitosearch. Both Ysearch and Mitosearch are sponsored by Family Tree DNA but accept results from all testing companies and allow you to search the databases for matches.

Only a small proportion of FTDNA customers upload their results to Ysearch and Mitosearch and for most former GeneTree customers in the long run the best option would be to join the FTDNA database. All the large haplogroup and geographical projects are at Family Tree DNA along with over 90% of all the surname projects, including almost all the projects for the very common surnames. FTDNA are also now the only company which offer advanced marker tests (SNP testing) for people who are interested in exploring their deep ancestry. Y-DNA results can be transferred to FTDNA on the payment of a small fee as part of FTDNA's Third Party Y-DNA Transfer Programme. There is no similar scheme to transfer mtDNA results to the FTDNA database, and you would have to buy a new mtDNA test from FTDNA to be included in their mtDNA database.

There has been considerable uncertainty over the fate of the Sorenson Molecular Genealogy Foundation database following the acquisition by Ancestry. SMGF has now announced that the site "will continue to operate for the foreseeable future as a freely accessible tool for the genetic genealogy community". The full text of the announcement can be read here. It is, however, still unclear what exactly Ancestry intends to do with the SMGF data. The genealogical information and DNA data were contributed by genealogists on the understanding that they were contributing to a non-profit research project. It would be a different matter entirely if this information were to be included in a commercial genealogy database and presumably Ancestry would be required to gain the consent of all SMGF participants if they wished to re-use their data in the Ancestry database, though the legal position in the US is not clear. If you are at all concerned about Ancestry having access to your data you can choose to have your data removed from the SMGF database. Details are provided on the SMGF consent form.

I will be reporting on the new Ancestry autosomal DNA test in a future blog post. The kits were initially restricted to residents of the US and it is not yet known if the test will be marketed in other countries. However, as an Ancestry subscriber I have now been able to buy a kit from the US at the introductory price of $99. I returned the kit this week and hope to have some results in the next few weeks. It will be interesting to see how it compares with the 23andMe test and Family Tree DNA's Family Finder test which I have already reported on.

© Debbie Kennett 2012

Family Tree DNA Summer Sale

Family Tree DNA has just announced its summer sale which starts today and ends in one week's time on Sunday 15th July at 11.59 pm Texas time. The sale prices are shown below. Kits can be ordered direct from Family Tree DNA at http://www.familytreedna.com.

NEW KITS	Current Group Price	SALE PRICE
Y-DNA 12	$99	$59
Y-DNA 37	$149	$129
Y-DNA 67	$239	$199
Family Finder	$289	$199
mtFullSequence (FMS)	$299	$219
FF+ Y-DNA 37	$438	$328
FF + mtDNAPlus	$438	$328
Comprehensive (FF + FMS + Y-DNA 67)	$797	$617
SuperDNA	$518	$428
UPGRADES
12 to 37	$109	$70
25 to 37	$59	$35
25 to 67	$159	$114
37 to 67	$109	$79
37 to 111	$220	$188
67 to 111	$129	$109
mtHVR1 to Mega	$269	$209
mtHVR2 to Mega	$239	$199

People of the British Isles Project

I had the opportunity yesterday to attend the Royal Society’s Summer Science Exhibition. My main interest in attending was to find out more about the People of the British Isles Project, who had been invited to take a stand at the exhibition to present their work. The exhibition was packed out all day and there seemed to be a constant crowd of people around the People of the British Isles exhibit as can be seen from the photos below.

I did manage to have a brief chat with some of the scientists who are working on the project, including Bruce Winney and Simon Leslie, to find out what progress has been made since June when I attended the Ancient Britons conference in Cardiff where the genetic map of Britain was presented for the first time. The People of the British Isles Project has now taken DNA samples from 4,371 volunteers. To participate in the project volunteers must live in a rural area and all four of their grandparents must have been born in the same county.  The DNA of 2,031 of the volunteers has now been sampled extensively using modern chip-based sequencing technology, which is the same methodology used for the 23andMe test and Family Tree DNA's Family Finder test. The People of the British Project has looked at 600,000 different markers known as SNPs (single-nucleotide polymorphisms) for their analysis. Although the chip contains both Y-chromosome (Y-DNA) SNPs and mtDNA (mitochondrial DNA) SNPs, they have so far only analysed the autosomal SNPs. Autosomal DNA is shuffled up and recombined with each new generation and provides a picture of the genetic make up of all our ancestors, whereas Y-DNA and mtDNA only tell us about our direct paternal and maternal lines respectively.

The researchers analysed the DNA using a technique known as linkage disequilibrium. They are essentially looking for motifs or patterns within the DNA which are specific to whole populations or sub-populations. The DNA data was analysed using a computer program called Fine Structure, which places the results in clusters based on their genetic similarity. This process requires an astonishing amount of computer power and it apparently took a week to run all the UK samples through the program. Once the clustering had been completed, the researchers added the geographical data to the samples and plotted the co-ordinates on a map using an average derived from the birth place of each individual's four grandparents. The resultant genetic map of the British population that was on display at the exhibition can be seen on the Royal Society's website. The colours shown on the map represent distinct genetic clusters. This was essentially the same map that we saw at the Ancient Britons conference. It can be seen that certain parts of the British Isles, such as Devon and Cornwall, are genetically quite distinct, whereas others, such as the whole of the south-east of England, are a homogenous mass. In some places distinctions have even been found within regions. In Orkney, for example,  the people of Westray were distinct from those on the Mainland. There is a particularly large cluster in Anglesey but this is apparently because samples were taken at an agricultural fair on the island and the researchers were inundated with people wishing to take part in the project!

The researchers have compared the results of the British samples with a collection of European samples. They have access to genetic data from 6,300 people in Europe. The samples were taken from projects such as the International Multiple Sclerosis Genetics Consortium and other data which is included in the Wellcome Trust Case Control Consortium 2. These samples were originally collected for medical studies and the researchers do not know the place of birth of the four grandparents or have any other ancestral information from the participants. However, they do know the name of the hospital or centre where the samples were taken which has enabled them to provide some geographical context. It was found, perhaps not surprisingly, that people in the south-west of England in particular were genetically quite similar to the people of north-western France. In the north people showed greater similarity with Scandinavian populations. I was understandably not allowed to photograph the European maps in close-up but a view of the display is shown below where you can just about distinguish the different-coloured clusters in Europe.

A paper will be submitted for publication in the next month, probably to Nature. All the maps on display at the exhibition will be included in the paper, and additional maps will also be included showing the different levels of clustering analysis. Some of the genomes from the project (some from Cornwall and for one other county) have apparently been uploaded to the 1000 Genomes Project. The raw data from the project will not be published with the forthcoming paper but will eventually be submitted to the Wellcome Trust Case Control Consortium. Researchers wishing to use the data will have to submit an application to be granted access. The data will be made available to population geneticists and not just medical researchers.

Although Y-DNA and mtDNA SNPs are included on the chip used by the project, the researchers have not yet started analysing these data. I was told that Professor Mark Jobling at the University of Leicester will probably be doing the Y-DNA analysis. A D.Phil. is also due to join the project in the autumn to help with this work. The project is also hoping to do some ancient DNA analysis as a comparison, but nothing has as yet been planned. The project still has two more years to run, and there will no doubt be other interesting papers published in the next few years.

© Debbie Kennett 2012