Friday, 10 May 2013

Mitochondrial DNA testing at a new low price

Family Tree DNA have announced a new permanent low price of US $49 (about £32for their entry-level mitochondrial DNA test. The new low pricing has been made possible thanks to a change to next generation sequencing technology, and brings the starter price for mtDNA testing in line with the new low-cost 12-marker Y-DNA that was introduced on 1st April this year. The $49 price applies to the mtDNAPlus test (HVR1 + HVR2). The basic HVR1 test, which used to be the cheapest available mtDNA test, has now been discontinued. FTDNA have also announced a temporary reduction in the price of their full sequence test which is currently on offer for just $199 or £130 (reduced from $299 or £194). Family Finder, FTDNA's autosomal DNA test, has also temporarily been reduced in price from $289 (£187) to $199 (£130). In an e-mail to group administrators FTDNA have cautioned that the "prices may go up on different tests at any time based on lab volume". Let's hope that the new low prices will attract sufficient sales to make such an increase unnecessary.

A mitochondrial DNA test will tell you about your direct maternal line (ie, your mother, your mother's mother, your mother's mother's mother, and so on back in time). The path of mtDNA transmission can be seen in this diagram on the ISOGG website. An mtDNA test can be used to find genealogical matches on the direct maternal line but also gives you a haplogroup assignment which tells you about your deep ancestry. Haplogroups are the branches of the human mtDNA tree, and the haplogroups all tend to have different geographical distribution patterns. Information on the distribution of the major European mtDNA haplogroups can be found on the Eupedia website.

The choice of mtDNA test will depend on your testing objectives. The mtDNAPlus test sequences the two hypervariable regions - HVR1 and HVR2 - where mutations are more likely to occur. There are 1,143 base pairs in the hypervariable region comprising around 6% of the mtDNA genome. The full mitochondrial sequence (FMS) test sequences all 16,569 base pairs in the mtDNA genome - HVR1, HVR2, plus the coding region where all the genes are found. With both tests your results go into FTDNA's large genealogical matching database and you will be notified of any matches at the three different levels - HVR1, HVR1+HVR2, and HVR1, HVR2 plus the coding region.

The number of matches that you can expect to have varies considerably. Some people like me have no HVR1 matches at all. At the other extreme some people, particularly in haplogroup H, the most common European haplogroup, can have over 12,000 matches at HVR1 and over 2,500 matches at the HVR1+HVR2 level. The full sequence test has only been available at an affordable price for the last few years and consequently there are currently fewer people in the database who have tested at this level. However, the matching criteria are more relaxed at the full sequence level so it is possible to have FMS matches despite having no matches at the lower resolutions. I have no HVR1 or HVR2 matches but I have two full sequence matches. Family Tree DNA have the world's largest collection of mtDNA sequences both at low resolution (HVR1 and HVR2) and at the full sequence level.1   As of today's date FTDNA have 159,015 mtDNA records in their database, of which 24,579 are FMS tests. With the price reductions we can expect the database to grow at a rapid pace.

The full sequence test is needed for matches in a genealogical timeframe. FTDNA estimate that 90% of exact full sequence matches will fall within 16 generations (around 400 years).2  However, lower resolution matches can sometimes provide clues for further genealogical research if your matches have ancestors from the same geographical area. If you start with the mtDNAPlus test you can always upgrade to the full sequence test at a later date.

For deep ancestry purposes the mtDNAPlus test will give you a base haplogroup assignment (eg, haplogroup H, haplogroup I, haplogroup U4, haplogroup U5, etc). The full sequence test will give you a more detailed haplogroup assignment with lots of extra letters and numbers after the base haplogroup. For example, I am a U4c1a and my dad is a U5a2b3. The most up-to-date version of the mtDNA tree is maintained by Phylotree. You can expect to see your haplogroup updated as new branches are discovered on the mtDNA tree.  If you take the full sequence test you can also contribute your results to scientific research, and you might find that your results help to define a new branch on the tree. My own full sequence results were used in the 2012 paper by Dr Doron Behar et al which provided a major update to the mtDNA tree and introduced the concept of the Reconstructed Sapiens Reference Sequence.3

For assistance with understanding mtDNA results it's a good idea to join the relevant mtDNA haplogroup project at FTDNA. In some cases the project administrators will be able to provide you with a more detailed haplogroup assignment than that provided by FTDNA. It should be remembered that all the administrators are volunteers and some have more time than others to devote to their projects. A full list of mtDNA haplogroup projects can be found in the ISOGG Wiki.

It is astonishing to see how the cost of mtDNA testing has plummeted in the last few years. Family Tree DNA introduced the full mitochondrial sequence test (formerly known as the full genomic sequence test) in 2005 and the test was initially sold for $895 (£580). By 2009 the price had dropped to $439 (£284). Now it is possible to buy the full sequence test for roughly the same price that I paid to purchase the mtDNAPlus test in a sale back in December 2007.

FTDNA are of course not the only company offering mtDNA tests but they are now the clear market leader and offer by far the most competitive prices as well as having the advantage of the largest and most international mtDNA database. While it would be nice to support the British DNA testing companies unfortunately their prices are prohibitively expensive. Oxford Ancestors now charge £199 ($306) for a very basic HVR1 test with no facility to upgrade. BritainsDNA (which also trades as ScotlandsDNA, IrelandsDNA, and YorkshiresDNA) offer a chip-based testing service which looks at just 400 mtDNA markers from across the mtDNA genome. For a female this test costs £170 ($261). This is sufficient to give you a haplogroup assignment but the results cannot be used to check for matches and the test therefore has no genealogical utility. The BritainsDNA test is slightly better value for males as an mtDNA analysis can be purchased for £30 (446) on top of the Y-SNP test which costs £170 ($261) and analyses around 400 Y-SNPs for deep ancestry purposes. However, if you are interested in your deep ancestry the new Geno 2.0 test from the Genographic Project is a much better investment as it tests over 12,000 Y-SNPs along with over 3000 mtDNA markers at a much lower price than the BritainsDNA test. The Geno 2.0 chip also includes autosomal and X-chromosome SNPs. Geno 2.0 Y-DNA and mtDNA results can be transferred to FTDNA free of charge, where you can join the relevant haplogroup, surname and geographical projects. The 23andMe test is a good alternative to the Geno 2.0 test at a reasonable price if you just wish to know your mtDNA haplogroup, and your Y-DNA haplogroup if you are a male. The 23andMe test has the benefit of providing additional health and ancestry information. Both the Geno 2.0 test and the 23andMe test will give you reasonably detailed haplogroup assignments. Note, however, that, like the BritainsDNA test, neither the Geno 2.0 test nor the 23andMe test can be used for genealogical matching purposes on the maternal or paternal lines. For further information on the tests offered by the major genetic genealogy companies see the comparison charts in the ISOGG Wiki:

ISOGG mtDNA testing comparison chart
ISOGG autosomal DNA testing comparison chart.
ISOGG Y-DNA testing comparison chart

It is certainly an exciting time to be involved in the world of DNA testing. The new low introductory prices mean that price is no longer a barrier. No doubt many new people will be added to the FTDNA database who hadn't previously considered testing. If you've not yet had your DNA tested then there is now no excuse for delaying! I will of course be delighted to welcome new members to my Devon DNA Project and my Cruse/Cruise/Crews/Cruwys DNA Project. I'm also hoping that one day someone will take an mtDNA test and will be an exact match for my rare U4c1a haplotype.

References
1. Congiu A, Anagnostou P, Milia N et al. Online databases for mtDNA and Y chromosome polymorphisms in human populations. Journal of Anthropological Sciences 2012 90; 1-15.
2. How do I tell how closely I am related to a mitochondrial DNA (mtDNA) match?  FTDNA FAQ ID 2140.
3. Behar DM, Van Oven M, Rosset S et al. A “Copernican” reassessment of the human mitochondrial DNA tree from its root. American Journal of Human Genetics, Volume 90, Issue 4, 6 April 2012, Pages 675-684.

The following is the official press release from Family Tree DNA:

Family Tree DNA Offers mtDNA Test For $49
Groundbreaking low pricing made possible by cutting-edge Next Generation Sequencing technology that is dramatically driving down costs
HOUSTON, May 9, 2013 /PRNewswire/ -- FamilyTreeDNA.com, the genetic genealogy arm of Gene By Gene, Ltd., has lowered the price of its mid-level maternal line mtDNA test to $49, effective immediately.  The company announced it will offer its mtDNAPlus product at a two-third price reduction permanently, in just its latest step toward universal access by individuals to their personal genetic data. 
"This groundbreaking pricing illustrates how next generation sequencing (NGS) is changing the DNA testing landscape," Gene By Gene President Bennett Greenspan said.  "For Family Tree DNA to be able to offer this test at such an affordable price would have been unheard of before NGS.  We're hopeful that by lowering the price of products like our mtDNAPlus, we'll be able to expand the horizon of DNA testing and, importantly, grow our database to fuel future genetic discoveries."
Earlier this year, Family Tree DNA -- the world's largest processor of Y-DNA and full mitochondrial sequences -- dropped the price of its basic Y-DNA test for males by 60 percent, in order to eliminate cost as a barrier to individuals interested in learning more about their personal genetic and genomic data. 
Since then, the company has been working to do the same with its mtDNA test, which is applicable to both males and females and provides data on the direct maternal line by testing the mitochondria.  The mtDNAPlus product tests Hypervariable Regions 1 and 2, or HVR1 and HVR2, providing individuals with both anthropological and genealogical information. 
With the largest DNA database in the world, Family Tree DNA has processed over 5 million discrete tests for more than 700,000 individuals and organizations since it introduced its Y-DNA test in 2000.  Data gathered from the mtDNAPlus test will be stored, free of charge, in the company's database. If customers are interested in performing any other DNA tests that the company offers in the future, they won't be required to resubmit DNA samples.
Customer Inquiries Individuals interested in Family Tree DNA's $49 mtDNA test, or any of its ancestral testing products, can visit www.familytreedna.com or call (713) 868-1438 for more information.
About Gene By Gene, Ltd. Founded in 2000, Gene By Gene, Ltd. provides reliable DNA testing to a wide range of consumer and institutional customers through its four divisions focusing on ancestry, health, research and paternity.  Gene By Gene provides DNA tests through its Family Tree DNA division, which pioneered the concept of direct-to-consumer testing in the field of genetic genealogy more than a decade ago.  Gene by Gene is CLIA registered and through its clinical-health division DNA Traits offers regulated diagnostic tests.  DNA DTC is the Research Use Only (RUO) division serving both direct-to-consumer and institutional clients worldwide.  Gene By Gene offers AABB certified relationship tests through its paternity testing division, DNA Findings. The privately held company is headquartered in Houston, which is also home to its state-of-the-art Genomics Research Center. 
Media Contact:
Kate Croft
for Gene By Gene, Ltd.
Casteel Schoenborn
888-609-8351
croft@csirfirm.com

Tuesday, 9 April 2013

Tom Cruise's Irish ancestry

Researchers in Ireland have been exploring the family tree of the Hollywood actor Tom Cruise. His line has been traced back to Andrew Cruise (d. 1780) who married Bridget Russell on 23rd January 1766 in Swords parish, County Dublin. The research can be found on the Eneclann website. The official press release from Tourism Ireland can be found here. Tom Cruise was in Dublin for the premiere of his new film Oblivion and he was presented with a copy of his family tree and his Certificate of Irish Heritage. You can see the video of the presentation here. My earlier blog post on the Cruise surname provides information on some of the early references to the surname in Ireland, a number of which have been used in the current research.

Tuesday, 26 March 2013

Citizen science discovery rewrites human Y-DNA tree

The following press release was received from Family Tree DNA and relates to the news announced at Who Do You Think You Are? Live in February 2013 of the citizen science discovery of the new ancient root of the human Y-chromosome tree. Family Tree DNA have announced to project administrators that the 12-marker Y-DNA test will be sold at the new permanent low price of $49 (£32) with effect from 1st April 2013. The 12-marker test is currently on sale at a special low price of $39 (£26).  FTDNA already have the world's largest Y-chromosome database with almost 250,000 samples from around the world. However, with a world population of over seven billion people there is still much to be learnt about our genetic heritage and we can expect many more exciting discoveries in the months and years to come as more people get their DNA tested.

Family Tree DNA's Genomics Research Center Facilitates Discovery of Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree

-- By Offering Low Cost DNA Test, Family Tree DNA Aims to Expand Reach of DNA Testing to Encourage Further Exciting Discoveries About Human Origins --

HOUSTON, March 26, 2013 /PRNewswire/ -- Gene By Gene, Ltd., the Houston-based genomics and genetics testing company, announced that a unique DNA sample submitted via National Geographic's Genographic Project to its genetic genealogy subsidiary, Family Tree DNA, led to the discovery that the most recent common ancestor for the Y chromosome lineage tree is potentially as old as 338,000 years. This new information indicates that the last common ancestor of all modern Y chromosomes is 70 percent older than previously thought.

The surprising findings were published in the report "An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree" in The American Journal of Human Genetics earlier this month. The study was conducted by a team of top research scientists, including lead scientist Dr. Michael F. Hammer of the University of Arizona, who currently serves on Gene By Gene's advisory board, and two of the company's staff scientists, Drs. Thomas and Astrid-Maria Krahn.
The DNA sample had originally been submitted to National Geographic's Genographic Project, the world's largest "citizen science" genetic research effort with more than 500,000 public participants to date, and was later transferred to Family Tree DNA's database for genealogical research. Once in Family Tree DNA's database, long-time project administrator Bonnie Schrack noticed that the sample was very unique and advocated for further testing to be done.

"This whole discovery began, really, with a citizen scientist – someone very similar to our many customers who are interested in learning more about their family roots using one of our genealogy products," said Gene By Gene President Bennett Greenspan. "While reviewing samples in our database, she recognized that this specific sample was unique and brought it to the attention of our scientists to do further testing. The results were astounding and show the value of individuals undergoing DNA testing so that we can continue to grow our databases and discover additional critical information about human origins and evolution."

The discovery took place at Family Tree DNA's Genomic Research Center, a CLIA registered lab in Houston which has processed more than 5 million discrete DNA tests from more than 700,000 individuals and organizations, including participants in the Genographic Project. Drs. Thomas and Astrid-Maria Krahn of Family Tree DNA conducted the company's Walk-Through-Y test on the sample and during the scoring process, quickly realized the unique nature of the sample, given the vast number of mutations. Following their initial findings, Dr. Hammer and others joined to conduct a formal study, sequencing ~240 kb of the chromosome sample to identify private, derived mutations on this lineage, which has been named A00.

"Our findings indicate that the last common Y chromosome ancestor may have lived long before the first anatomically modern humans appeared in Africa about 195,000 years ago," said Dr. Michael Hammer. "Furthermore, the sample, which came from an African American man living in South Carolina, matched Y chromosome DNA of males from a very small area in western Cameroon, indicating that the lineage is extremely rare in Africa today, and its presence in the US is likely due to the Atlantic slave trade. This is a huge discovery for our field and shows the critical role direct-to-consumer DNA testing companies can play in science; this might not have been known otherwise."

Family Tree DNA recently dramatically reduced the price of its basic Y-DNA test by approximately 50%. By offering the lowest-cost DNA test available on the market today, Gene By Gene and Family Tree DNA are working to eliminate cost as a barrier to individuals introducing themselves to personal genetic and genomic research. They hope that expanding the pool of DNA samples in their database will lead to future important scientific discoveries.

About Gene By Gene, Ltd. Founded in 2000, Gene By Gene, Ltd. provides reliable DNA testing to a wide range of consumer and institutional customers through its four divisions focusing on ancestry, health, research and paternity. Gene By Gene provides DNA tests through its Family Tree DNA division, which pioneered the concept of direct-to-consumer testing in the field of genetic genealogy more than a decade ago. Gene by Gene is CLIA registered and through its clinical-health division DNA Traits offers regulated diagnostic tests. DNA DTC is the Research Use Only (RUO) division serving both direct-to-consumer and institutional clients worldwide. Gene By Gene offers AABB certified relationship tests through its paternity testing division, DNA Findings. The privately held company is headquartered in Houston, which is also home to its state-of-the-art Genomics Research Center.

Friday, 22 March 2013

AncestryDNA updates

I wrote previously of my experiences with the AncestryDNA autosomal DNA test. I covered the consent forms and the admixture analyses in my first article. In a second article I looked at the matching process. One of the big criticisms that I and many others had with regard to the AncestryDNA test was the fact that the company, unlike 23andMe and Family Tree DNA, did not allow customers access to their raw genetic data. I am now pleased to advise that Ancestry have listened to the feedback and have finally made the raw data accessible.

The data can be accessed by logging into your AncestryDNA account and clicking on "Manage Test Settings". Before downloading the data it is necessary to re-enter your password. There are notices to advise that the downloaded data is subject to the AncestryDNA Terms and Conditions and the AncestryDNA Privacy Statement. The Terms and Conditions were revised on 20th March 2013 and now include what appears to be a new section laying out the Rules of Conduct. These state among other things that "You must also agree that you will provide valid and complete contact information, and that you will always have a valid email address on file with AncestryDNA." In addition the rules include the following somewhat puzzling condition: "You must not use the information from the AncestryDNA website or DNA tests (including any downloaded raw DNA data) in whole, in part and/or in combination with any other database for any discriminatory, breach of privacy or otherwise illegal activity (for example, to re-identify any anonymous donor or to make insurance or employment decisions)."

The Rules of Conduct conclude with the following paragraph: "These Rules of Conduct are not exclusive. If we believe, in our sole discretion, that you are in breach of this Agreement, are acting inconsistently with the letter or spirit of this Agreement or otherwise interfering with the efficient management or delivery of the AncestryDNA Website, Service or Content, we may limit, suspend or terminate your access to our AncestryDNA Website. In such a case, no portion of your subscription payment will be refunded. Should we decide to suspend or terminate your access for any reason other than your actions or omissions which we believe to be inconsistent with this Agreement we will refund to you any unused portion of your payment, which will be your sole and exclusive remedy upon such a suspension."

I am not at all clear how someone can use their own genetic data in any type of illegal activity and it seems to me that it is entirely my business what I do with my own genetic data and has nothing to do with AncestryDNA at all. The requirement to maintain a valid e-mail address is of some concern as this rather suggests that any account that does not have a valid e-mail address will be excluded from the AncestryDNA database. Inevitably subscriptions will lapse over time. People become ill and are no longer able to continue their family history research or they die and their account is not passed on to a relative. Does this mean that all these results will be removed from AncestryDNA because the accounts no longer comply with the Rules of Conduct?

The AncestryDNA Privacy Statement has been similarly updated with effect from 20th March 2013. Interestingly I note that Ancestry have now signed up to the Safe Harbor program which relates to the "collection, use and retention of personal data from European Union member countries and Switzerland". Does this mean that Ancestry are gearing up to make their test available in Europe? In section 3 "How does AncestryDNA use your personal information?" there is what appears to be a new addition and by testing with Ancestry you are now giving them permission to use "your personal information" to "research human genetic diversity". From what I can gather this permission applies even if you have, like me, not signed the separate AncestryDNA Consent Form.

Having gone through the instructions on the AncestryDNA website you are sent an e-mail to confirm the download. The e-mail is reproduced below.
Having confirmed the data download you are taken back to the AncestryDNA website and taken to a page where you can download the raw data. I have provided a screenshot below.
The data is downloaded as a zip file and when the file is unzipped it opens up in Notepad. The many citizen scientists in the genetic genealogy world are currently trying to examine and make sense of the raw data. It is likely that third party websites such as Gedmatch will provide a facility to upload AncestryDNA data. Support will no doubt also be provided for the other third-party tools which are listed on the autosomal DNA tools page in the ISOGG Wiki.

Interestingly, although Ancestry do not provide information on the X-chromosome and Y-chromosome SNPs on their chip or use these results for matching purposes, the raw data is included in the download file so by downloading the data it will be possible to get more value out of the test. It is not yet known which Y-SNPs are included on the chip but this information could potentially be of great value for anyone who has taken a Y-STR test and who wishes to learn more about their deep ancestry by participating in a Y-DNA haplogroup project.

Another big announcement about the AncestryDNA testing service was made today at Roostech by Tim Sullivan, Ancestry's President and Chief Executive Officer. He advised that the the Ancestry DNA is now available at the new low price of $99 to both subscribers and non-subscribers. The test was originally offered at $99 in the beta-testing period. The price was subsequently raised to $199 for non-subscribers and $129 for subscribers. The latest reduction means that the AncestryDNA test is now the same price as the 23andMe test. However, the 23andMe test provides many additional features, including health and trait information, which are not available from Ancestry.  Tim Sullivan also announced that Ancestry have over 120,000 autosomal results in their database. He promised that improved ethnicity results and improved cousin matches are on the way but no specifics were given.

Note that the AncestryDNA test is only available to US residents. Although I live in the UK, for some reason I was able to order the AncestryDNA test during the beta-testing phase, but I am one of only a tiny handful of non-US people in their database at present. It is not yet known when or if Ancestry will make their test available in other countries. For those of us who do not live in the US there is a straightforward choice between 23andMe and FTDNA's Family Finder test. Currently the most cost-effective way to get your results in both databases is to test with 23andMe and then transfer your results to FTDNA.

Family Tree DNA's Family Finder test is now much more expensive at $289 than the comparative offerings from 23andMe and AncestryDNA. The US is the prime market for all three companies. It will, therefore, be interesting to see how FTDNA respond to the competition. At the very least, it would be very useful if FTDNA could follow Ancestry's example and allow their customers access to their raw Y-SNP data. In theory FTDNA should be able to add AncestryDNA to their third-party transfer program, but the transfer currently costs $89, which is only $10 short of the cost of the 23andMe and AncestryDNA tests. Will FTDNA reduce the cost of the transfer to encourage more people to transfer their results and to widen their database? Whatever happens the competition will be very beneficial for the genetic genealogy community and we can no doubt look forward to many exciting developments in the next few years.

*Update 23rd March 2013*
I've now transferred my raw data from AncestryDNA into a spreadsheet. The file header contains the following information:
AncestryDNA raw data download
This file was generated by AncestryDNA at: 03/22/2013 10:39:55 MDT
Data was collected using AncestryDNA array version: V1.0
Data is formatted using AncestryDNA converter version: V1.0
Below is a text version of your DNA file from Ancestry.com DNA, LLC.  THIS INFORMATION IS FOR YOUR PERSONAL USE AND IS INTENDED FOR GENEALOGICAL RESEARCH ONLY. IT IS NOT INTENDED FOR MEDICAL OR HEALTH PURPOSES. THE EXPORTED DATA IS SUBJECT TO THE AncestryDNA TERMS AND CONDITIONS, BUT PLEASE BE AWARE THAT THE DOWNLOADED DATA WILL NO LONGER BE PROTECTED BY OUR SECURITY MEASURES. 
Genetic data is provided below as five TAB delimited columns. Each line corresponds to a SNP. Column one provides the SNP identifier (rsID where possible). Columns two and three contain the chromosome and basepair position of the SNP using human reference build 37.1 coordinates. Columns four and five contain the two alleles observed at this SNP (genotype). The genotype is reported on the forward (+) strand with respect to the human reference.
My AncestryDNA raw date file contains information on 701,478 SNPs divided into 25 chromosomes. I have data for:

- 17604 SNPs on chromosome 23
- 885 SNPs on chromosome 24
- 440 SNPs on chromosome 25

We of course only have 23 pairs of chromosomes. Ann Turner has clarified on the Genealogy DNA list that chromosome 23 is the X chromosome, chromosome 24 is the Y-chromosome, and chromosome 25 "is for XY SNPs, where the SNP is also found on the pseudo-autosomal regions (PAR) at the tips of the Y". As a female I do not have a Y-chromosome and most of my results for the Y are no calls (zeros). However, I do have results reported for 93 Y-SNPs. Apparently this is something to be expected for reasons which are not yet clear to me.

CeCe Moore was one of a number of genetic genealogists who had a meeting with the AncestryDNA people at Rootstech and she has advised on the Genealogy DNA list that Ancestry are working on a search function filtered by surname or user name. She further advises that Family Tree DNA are hoping to accept AncestryDNA uploads from the beginning of May and that Gedmatch will be able to accept AncestryDNA uploads in a couple of weeks.

*Update 24th March*
AncestryDNA have now added a section on raw data downloads to their FAQs which can be read here. Ancestry seem to be overly concerned about their customers misusing their data in some unforeseen way and provide a number of cautionary warnings about using your data on third-party websites.

*Update 25th March*
For a detailed report on AncestryDNA's plans see CeCe Moore's blog post on "AncestryDNA, Raw Data and Rootstech".

© 2013 Debbie Kennett