Showing posts with label 23andMe. Show all posts
Showing posts with label 23andMe. Show all posts

Thursday, 12 June 2014

Genetic genealogy hits the big time! Family Tree DNA are the first DNA company to pass the one million milestone

Family Tree DNA have announced that they have reached a significant milestone and have now processed over one million DNA tests for genealogy and anthropology purposes. This figure includes tests sold by Family Tree DNA as well as tests processed by FTDNA for the National Geographic's Genographic Project. This significant milestone was achieved in the current Father's Day sale during which the Family Finder test has been on offer at the lowest ever price of $79 (£47). FTDNA are the first DNA testing company to break through the one million milestone.

FTDNA also passed another major milestone in the last week which seems to have been completely unheralded. It was noted on 7th June that they had over half a million Y-DNA records in their database, though the exact date when this milestone was achieved is not known. FTDNA also have the honour of holding the world's largest repository of full mitochondrial sequences with the total currently standing at 39,518.

Family Tree DNA were founded in the year 2000. It took nine years for them to process 500,000 kits. This milestone was achieved in February 2009. It's taken just over five years to add the next half million tests. I wonder how long it will take to reach the two million milestone.

The other big two DNA companies, 23andMe and AncestryDNA, have also recently passed significant milestones. 23andMe now have over 700,000 "genotyped customers", and will surely pass the one million mark some time later this year. AncestryDNA announced in April that they had now genotyped over 400,000 members, which is a very impressive number considering that their test is only sold in the US.

The full press release from Family Tree DNA can be seen below.

Family Tree DNA Reaches a Historic Milestone: Over 1,000,000 DNA Tests Processed (via PRWeb)
Family Tree DNA, the genetic genealogy arm of Gene by Gene and the world leader in the field, announced today that it has processed over 1,000,000 DNA test kits results for genealogy and anthropology purposes. Houston, TX (PRWEB) June 12, 2014 This…

Friday, 6 December 2013

23andMe update, third party tools and alternative personal genomics companies

Following on from the warning letter received by 23andMe from the FDA, the company have now announced that in order to comply with the FDA's requirements new customers will not receive health reports "while the company moves forward with the agency’s regulatory review". The ancestry reports are not affected, and new customers will also have access to their raw data files. Raw data files can be uploaded to third-party services such as Promethease or Interpretome where you can generate your own health reports. A full list of autosomal DNA tools can be found in the ISOGG Wiki:

www.isogg.org/wiki/Autosomal DNA tools

The FDA is not concerned with customers interpreting their own raw data and as far I understand these third-party tools do not fall under the FDA's remit.

The health reports have only been withdrawn for customers who have ordered a 23andMe test from 22nd November onwards.  This was the date when the warning letter was received from the FDA. Existing customers who ordered a test before 22nd November will continue to have access to their health reports.

Anne Wojcicki of 23andMe has posted a personal message to 23andMe users on the company blog:

http://blog.23andme.com/news/23andme-provides-an-update-regarding-fdas-review/

More detailed FAQs can be found on the 23andMe website:

https://23andme.zendesk.com/entries/23273619-FDA-Update-December-5th

The official press release can be found here:

http://mediacenter.23andme.com/press-releases/23andme-inc-provides-update-on-fda-regulatory-review/

Blaine Bettinger, who writes the Genetic Genealogist blog, has provided some useful commentary on the latest developments and links to other posts on the subject:

http://www.thegeneticgenealogist.com/2013/12/06/23andme-will-continue-to-sell-genetic-tests-for-ancestry/

Margaret A. Hamburg, a Commissioner for Food and Drugs at the FDA, has written a letter to the Wall Street Journal in which she states that the FDA "remain committed to continuing our ongoing dialogue with the company in order to bring a safe, effective and trusted product to the market". The full letter can be read here:

http://online.wsj.com/news/articles/SB10001424052702304011304579222111609444156

It is not yet known how long the regulatory process will take but I hope that a resolution will be reached sooner rather than later and that 23andMe will once again be able to market their DNA testing service.

In the meantime if you are interested in getting your DNA tested for the health reports there are a number of different companies outside the US which offer a similar service to 23andMe. A full list can be found in the ISOGG Wiki:

www.isogg.org/wiki/List of personal genomics companies

All the other American companies now require that the testing is done through a doctor. However, many of the companies in other countries still offer a direct-to-consumer service. Unfortunately, none of the other personal genomics companies have the advantage of a large database and a vibrant community forum which are the biggest benefits of the 23andMe service.

For the background on the 23andMe story read my earlier blog post on 23andMe and the FDA.

© 2013 Debbie Kennett

Friday, 29 November 2013

23andMe and the FDA

The big news in the genetic genealogy world this week is the announcement that the personal genomics company 23andMe have received a stern warning letter from the FDA in which they were told that they "must immediately discontinue marketing the PGS [Personal Genome Service] until such time as it receives FDA marketing authorization for the device". However,  I note that despite the warning letter 23andMe have not withdrawn their test from sale.

This is the 23andMe ad which has been shown on national TV in the US which probably sparked the FDA's action. It seems to me inappropriate to advertise such a product on the television and I can understand the FDA's concern.

There have been many excellent articles and blog posts covering all sides of the debate so I won't comment here but will instead refer you to the best resources for further reading.

Blaine Bettinger, who writes The Genetic Genealogist blog, has given his take on the story and provided a very useful selection of links to the most interesting commentary on the subject. His post can be found here. If you are interested in the implications of the FDA's actions it's well worth reading all these links.

The journalist David Dobbs has also been tracking the coverage of the story and he has summarised all the different viewpoints and provided an extensive selection of links in his blog post FDA muzzles 23andMe after talks break down.

If you only have time to read one article on the subject I recommend reading Michael Eisen's thoughtful post FDA vs. 23andMe: how do we want genetic testing to be regulated. Michael Eisen's views most closely align with my own thoughts on the matter.

It will be interesting to see what happens in the next couple of weeks. I'm not expecting the FDA to shut down 23andMe but it might be that some of the health reports are redacted until such time as an agreement can be reached. Nevertheless it's a good idea to ensure that you have downloaded your raw data and saved the health reports that are of particular relevance. Some of the health reports can be saved as PDF files. For other reports you will need to save screenshots. If you've tested with 23andMe for genealogy purposes you might also like to take advantage of the Family Tree DNA sale to transfer your results to the FTDNA's Family Finder database. The transfer will cost $49 until the end of the year (the usual price is $69).

You can read my series of articles on my own 23andMe test using the links on this page.

Wednesday, 7 August 2013

Autosomal DNA testing is now affordable for all

Family Tree DNA announced last week that they will be keeping the price of their Family Finder test at $99 (£64) following the end of their successful summer sale. There does not appear to have been an official press release but the news was announced on their Facebook page. The Family Finder test cost $289 (£188) when it was first introduced in the spring of 2010. It has been possible to buy the test for $199 (£130) if you took advantage of a sale, but the high price was still a major disincentive for most people.

The price reduction has no doubt been prompted by competition from both 23andMe and Ancestry, the only other two companies who offer an autosomal DNA cousin-finding test. 23andMe reduced the cost of their test to $99 in December 2012 after receiving $50 million in investment funding. AncestryDNA followed suit soon afterwards. Family Tree DNA really had no alternative but to reduce their test to keep the price in line with the competition. It may well be that all three companies are effectively selling the test at less than the cost price, but whatever the reality it is good news for the consumer.

The AncestryDNA test is only on sale in the US so for the rest of the world, there is now a straightforward choice between the 23andMe test and the Family Finder test. While both companies charge the same price for their tests there are considerable differences in the postage costs. FTDNA charge just $7 to ship their kits overseas. In contrast 23andMe charge $79.95 for shipping to the UK as their kits are sent by courier and there is no option to have the kits sent out by ordinary post. The comparative prices therefore work out as follows:

Family Finder   $99 + $7        = $106       (£69)
23andMe          $99 + $79.95 = $178.95 (£117)

23andMe offer a 20% reduction for each additional kit ordered but much of this saving is wiped out because it's still necessary to pay an additional shipping fee for each extra kit ordered, albeit at a reduced price of $49. Family Tree sell DNA kits in theory to every country in the world. 23andMe currently only ship their kits to 56 countries, nearly all of which are in Europe or North America. So if you are interested in taking an autosomal DNA test and you live in South Africa, Brazil, India or Thailand or any of the many other countries not on the 23andMe list then the Family Finder test is your only option.

Price is of course not the only consideration. The 23andMe test is not just a genealogical DNA test but also provides health and trait information which is very interesting in its own right. 23andMe have a much larger autosomal database than FTDNA. They currently claim to have over 300,000 genotyped customers in their database. However, many of the people at 23andMe have taken the test for health reasons and are not interested in genealogy so the response rate when contacting matches is low. 23andMe have made little attempt to market their test outside the US, and probably about 90% of their customers are in the US. Nevertheless, there are growing numbers of British people in the 23andMe database as well as customers from countries such as Australia, Canada and New Zealand.

Family Tree DNA are a dedicated genetic genealogy company so their customers are more likely to respond to match requests. FTDNA also have the advantage of a much more international database. Probably only around 60%-70% of their customers are in the US. They have a huge range of geographical DNA projects covering most of the regions of the world. FTDNA are also much more well known in the genealogy world in the UK. They sponsor the DNA workshop each year at Who Do You Think You Are? Live, the big family history show which takes place at Olympia in London. While FTDNA have the world's largest Y-DNA and mtDNA databases, they have never disclosed the size of their autosomal database. We estimate that they probably had somewhere in the region of 60,000 autosomal test results in their database before the start of their sale in July. With the new low price we can expect to see the database grow very rapidly.

The choice of company will very much depend on your testing objectives. If you can afford it I recommend testing at both 23andMe and Family Tree DNA. It's an interesting exercise to explore your genome with 23andMe and it is an advantage to have your results in two different databases. If you do want to test with both companies, the most economical way to do so is to test first with 23andMe, and then do the FTDNA third-party transfer to add your autosomal results to the Family Finder database. The transfer currently costs $69 (£45). Further details can be found in the FTDNA FAQs. 23andMe do not accept transfers from other companies so if you test first at FTDNA you will have to pay for a new test at 23andMe. However, if you are only interested in finding genetic cousins then Family Finder is the test of choice.

Although my American friends have been finding lots of connections in the autosomal databases for the rest of us it's much more of a waiting game. I've yet to find a genealogical connection with any of my matches at FTDNA or 23andMe. I hope that with the new low price of the Family Finder test and the low shipping costs many more people outside the US will be tempted to explore their autosomal DNA. I'm looking forward to making my first genealogical connection with autosomal DNA testing.

Further reading
- The new Family Finder test from Family Tree DNA
- My first autosomal DNA success story
- My series of articles on my 23andMe test
- ISOGG Wiki Autosomal DNA Testing Comparison Chart
- ISOGG Wiki guide to autosomal DNA

© 2013 Debbie Kennett

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 around 300 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.  [*Update 18 June 2013: BritainsDNA introduced a new Chromo 2 test on 14 June. The mtDNA Chromo 2 test looks at around 3000 mt SNPs and costs £189 ($299). A new Y-DNA test is also available looking at over 15,000 Y-SNPs.]  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, 11 December 2012

23andMe test now down to $99

The personal genomics company 23andMe has just announced that it has reduced the cost of its test from $299 to $99. The new price has been made possible following the company's announcement today that it has raised more than $50 million of funding with the aim of helping them to achieve their growth goal of one million customers. The full press release can be read here.

Note that postage for the 23andMe kits in the US costs just $9.95 but is significantly more expensive in other countries as the kits are sent not by post but by courier although a prepaid return service is included in the cost. In some countries there are additional customs charges. Shipping to the UK costs $79.95. It costs $59.95 to send the kits to Canada, and $74.95 for Australia and New Zealand. I have not checked all the prices but I noticed that 23andMe charge $94.95 to ship to Cyprus, Malta and Iceland and $118.95 to send kits to Bosnia and Belarus. For a list of countries that 23andMe will ship to see this FAQ on their website.

Note that if you test with 23andMe you can also transfer your results to Family Tree DNA's Family Finder database for genealogical matches. Note however that the Y-DNA and mtDNA results from 23andMe are not included in the transfer as these results are not compatible with FTDNA's genealogical matching database. Although the 23andMe test includes a Relative Finder feature many of the people who test with 23andMe do so for health reasons and aren't interested in researching their family tree. Family Tree DNA also has a much more international database than 23andMe, largely thanks to its association with the Genographic Project. FTDNA will in theory send kits to any country in the world and charge a flat rate of just $6 for international postage. For information on the process of transferring kits to FTDNA please read the FAQs on Third-Party Transfers.

For further information on the 23andMe test read my four-part feature on "Exploring my genome with 23andMe":

Part 1 Disease risks
Part 2 Carrier status and drug responses
Part 3 Traits
Part 4 Ancestry

See also my blog post on 23andMe's new Ancestry Composition - a British perspective.

Saturday, 8 December 2012

23andMe's new Ancestry Composition - a British perspective

23andMe's new Ancestry Painting feature, now known as Ancestry Composition, has just been launched. The old Ancestry Painting was only able to distinguish between three continental population groupings - European, Asian and African. I was a very boring and predictable 100% European.
Ancestry Composition provides a biogeographical analysis based on 22 reference populations. 23andMe have provided an excellent guide to the science behind Ancestry Composition which is well worth reading in order to get an understanding of how the analysis works. Ancestry Composition provides a number of different views showing your comparisons with global, regional and subregional populations at three different confidence thresholds - speculative (50%), standard (75%), and conservative (90%).

My documented ancestry is all from the British Isles. I know the names and birth places of 15 of my 16 great-great-grandparents and they are all English. In this generation I have one illegitimate line which has prevented from me finding out the name of the remaining ancestor. The birthplaces of these 15 great-great-grandparents are: Burrington, Devon; Bristol (2); Thornbury, Gloucestershire; Clapham, London; Colchester, Essex; Sandon, Hertfordshire; Limehouse, London; Bermondsey, London; Merriott, Somerset; Sydenham, Kent; Sydmonton, Hampshire; Kintbury, Berkshire; Westminster, London; Sherston, Wiltshire.

I know the names of 27 of my 32 great-great-great-grandparents, but I only know the birth places of 21 of these ancestors. All of my known ancestors are from the British Isles. These are the birth places where known: Ashreigney, Devon; Mariansleigh, Devon; Thornbury, Gloucestershire; Bristol; Great Yeldham, Essex; Preston, Hertfordshire; Sandon, Hertfordshire; Scotland (place not known); Hackney, London; Laverstoke, Hampshire; County Kerry, Ireland; Merriott, Somerset; Rickmansworth, Hertfordshire; Shoreditch, London; Ecchinswell, Hampshire; Welford, Berkshire; Kintbury, Berkshire; Salford, Bedfordshire; Holborn, London; Leighterton, Gloucestershire; Purton, Wiltshire.

Ancestry Composition gives me the following percentages:

Sub-regional Resolution
Standard Estimate
17.4% British and Irish
1.6% French and German
74.2% Nonspecific Northern European
0.1% Sardinian
0.2% Nonspecific Southern European
6.5% Nonspecific European
0.1% Unassigned

Conservative Estimate 
0.3% British and Irish
71.1% Nonspecific Northern European
0.1% Nonspecific Southern European
28.0% Nonspecific European
0.5% Unassigned

Speculative Estimate
56.7% British and Irish
10.7% French and German
0.1% Scandinavian
31.2% Nonspecific Northern European
0.3% Sardinian
0.5% Nonspecific Southern European
0.4% Nonspecific European

The Sardinian and Southern European percentages are undoubtedly false positives. It is not clear if the French and German admixture appears because of the difficulties in distinguishing between British, French and German populations or if this is a reflection of more distant admixture from the Normans and Saxons.

This screenshot shows the much improved Ancestry Composition with a view of my Speculative Estimate.
These are my percentages for the Regional and Global Resolutions:

Regional Resolution
Standard Estimate
93.2 % Northern European
0.2% Southern European
6.5% Nonspecific European
0.1% Unassigned

Conservative Estimate
71.4% Northern European
0.1% Southern European
28% Nonspecific European
0.5% Unassigned

Speculative Estimate
98.8% Northern European
0.9% Southern European
0.4% Nonspecific European

Global Resolution
Conservative Estimate
99.5% European
0.5% Unassigned

Standard Estimate
99.9% European
0.1% Unassigned

Speculative Estimate
100% European

Although the subregional representations do not assign me with as much British ancestry as might be expected it is worth bearing in mind that these analyses are still in their infancy. 23andMe explain in their Ancestry Composition guide that their reference populations are largely drawn from their customer base and are supplemented from public reference datasets such as the Human Genome Diversity Project, HapMap, and the 1000 Genomes project.1 However, only a small number of genomes are as yet available in the public datasets. The 23andMe customers who are included in the reference dataset are required to have four grandparents born in the same non-colonial country. Although 23andMe were reported to have 180,000 paying customers in their database as of 9th October 2012, their customers are mostly Americans of mixed ancestry, few of whom will meet the qualifying criteria.2 Not all of the 23andMe customers will in any case have filled out the ancestry questionnaire. With the combination of 23andMe customers and public datasets there are just 7,868 people in the reference dataset used for Ancestry Composition. As all four of my grandparents were born in the UK I presume my own results have been included in this reference dataset.  I think it is a shame that 23andMe's questionnaire does not split up the United Kingdom into the four constituent countries as it would be more interesting to see if differences could be found between England, Scotland, Wales and Northern Ireland, rather than lumping all four very different countries together.

23andMe very helpfully provide details of the reference populations that they have used in their analysis. Below are screenshots showing the figures for the reference populations which appear in my Speculative Estimate.




As can be seen, the numbers are very small, but 23andMe have designed the Ancestry Composition tool in such a way that the results can be updated on a regular basis as and when more populations are added to the reference databases so no doubt the accuracy of the predictions will improve over time. For those of us from the British Isles we can probably expect to see big improvements when the datasets from the People of the British Isles Project become available. This project has tested over 4,500 people from the UK.3 To be eligible for the project people must have not just four grandparents from the same country but four grandparents from the same rural county. It might, therefore, one day be possible to assign percentages of DNA to specific English counties or regions.

"British/Irish" DNA seems to have been a particular problem with Ancestry Composition. Although the tool has a very high accuracy rate for the DNA which is assigned as British and Irish in their validation tests (a "precision" level of 0.90), they are much less successful at identifying all British/Irish DNA as British/Irish. The technical term for this is the recall rate. The recall rate for British and Irish DNA in the 23andMe validation tests was 0.32%, meaning that 68% of British and Irish DNA will not be picked up.1 The recall rate will no doubt improve as more reference samples are added to the database. However, it is difficult to quantify British or Irish DNA because we are an admixed population, comprising a mixture of DNA from many different groups such as the Saxons, Celts, Vikings, Picts, Normans, Bretons and Romans.

Chromosome view
As well as the map view there are two alternative views: split view and chromosome view. To use the split view it is necessary to have one parent in the 23andMe database. As my parents have not tested with 23andMe I cannot make use of this feature. I can, however, access the chromosome view which provides an interesting breakdown of the various percentages on the individual chromosomes. The screen shot below shows my Speculative Estimate.
With so many similar shades of blue it's quite difficult to distinguish the individual populations that make up each chromosome, though you can hover over a specific population to get a clearer picture. The screenshot below picks out the chromosomes where 23andMe speculates that I match with French and German populations.
As can be seen, whole chromosomes seem to have been matched with French and German populations which I don't quite understand. I don't have any French or German ancestry within the last several hundred years, though at the population level all British people would be expected to share many markers in common with the French and the Germans, but after several hundred years have passed I would have thought that there would only be tiny segments of "French" and "German" scattered throughout my genome.

Neanderthal DNA
In addition to Ancestry Composition another interesting and fun feature of the 23andMe test is that it will give you your percentage of Neanderthal admixture. This feature was introduced in December 2011.4 23andMe estimate that 2.5% of my DNA is inherited from Neanderthals.
Neanderthal percentages are also provided by the new Geno 2.0 test from the Genographic Project, which also provides percentages of Denisovan DNA. I imagine that 23andMe will eventually update their test to provide Denisovan percentages.

Conclusion
Ancestry Composition is a great improvement on 23andMe's Ancestry Painting. The percentages seem to be much more accurate than those provided by AncestryDNA. 23andMe also benefits by providing technical information on the methodology used by the scientists and they also provide valuable details of the reference populations used for the analysis, features which are notably absent at AncestryDNA. Family Tree DNA's Family Finder test includes a tool known as Population Finder. An update to Population Finder is expected in the New Year and it will be interesting to see how this compares with Ancestry Composition.

Other blog posts on Ancestry Composition
A number of other bloggers have written about their experiences with Ancestry Composition or provided commentary. Here is a list of the posts I have found to date. I will update the list as and when new posts are discovered:
- 23andMe's new Ancestry Painting - first look! by CeCe Moore. This post includes screenshots showing statistics on all the reference populations used by the Ancestry Composition tool.
- 23andMe Ancestry Composition Examples Part 1 by Andrea Badger. This post includes a magnificent selection of screenshots from people with a variety of mixed heritage producing a wonderful rainbow of colours.
- New worldview at 23andMe by Roberta Estes.
- My Ancestry Composition from 23andMe by Aidan Byrne.
- 23andMe Ancestry Composition by Dienekes Pontikos.
- Admixture advances by Judy Russell
- 23andMe adds ancestry composition by John Reid
- Is Daniel MacArthur 'desi' by Razib Khan

References
1. Ancestry Composition: 23andMe's State-of-the Art Geographic Ancestry Analysis. Anonymous article on the 23andMe website. Accessed 8th December 2012.
2.  How many paying customers does 23andMe have? Answer provided on Quora.com website by 23andMe software developer Alex Kohmenko on 9th October 2012.
3. The website of the People of the British Isles Project Project keeps track of the collection progress. As of 8th December 2012 it was reported that 4,538 samples had been collected.
4. Find your inner Neanderthal. 23andMe blog post by Scott H, 15th December 2011.

See also
My four part feature on "Exploring my genome with 23andMe":
Part 1 Disease risks
Part 2 Carrier status and drug responses
Part 3 Traits
Part 4 Ancestry

© 2012 Debbie Kennett

Monday, 11 April 2011

DNA article and Family Finder competition in Family History Monthly

The May issue of Family History Monthly is out now and contains an article by yours truly entitled "Cousins reunited" which explains how to use the latest autosomal DNA tests to find matches with your close relatives. Family Tree DNA and 23andMe are currently the only companies which offer this test. The Family Tree DNA test is known as the Family Finder. 23andMe's Relative Finder feature is a part of its personal genomics service. There was no room to include screenshots from the tests in the article but if you are interested in learning more about these new tests you might like to read the reviews I wrote for this blog last year.  My four-part review of the 23andMe service can be found here. My Family Finder review can be found here.

There is also an exciting competition in the May issue to win a free Family Finder test, worth around £180, from Family Tree DNA. Further details of the competition can be found on the Family History Monthly website.

Tuesday, 3 August 2010

Exploring my genome with 23andMe - ancestry

This is the fourth and final article in my short series of reviews on my personal genomics test with 23andMe. I wrote last week about my disease riskscarrier status and drug responses, and traits. I'm now going to look at the ancestry part of the service, which as a family historian, was my primary motivation for taking the test.

23andMe provides three different types of ancestry information. For deep ancestry purposes you are given a haplogroup assignment for your mitochondrial DNA and, if you are male, for your Y-chromosome. An Ancestry Painting gives you broad details of your ethnic percentages - African, European and Asian. Finally, the Relative Finder service identifies your close cousins in the 23andMe database and allows you to make contact with them.

I have already had a full mitochondrial sequence (FMS) test at Family Tree DNA and this aspect of the 23andMe test was therefore somewhat redundant for me, but I was nevertheless interested to see how the two results would compare. The FTDNA FMS test looks at all 16,569 base pairs in the mitochondrial genome whereas 23andMe test just 3,000 SNPs. I wrote previously about my unique mtDNA results and my rare U4 haplogroup. When I received my FMS results earlier this year FTDNA refined my haplogroup to U4c1. I have the advantage that I am the co-administrator of the mtDNA haplogroup U4 project at FTDNA. Within the U4 project we have a large body of FMS results and, using these results in conjunction with published sequences on Phylotree and GenBank, my co-admin, Ron Scott, has been able to refine the haplogroups for many of our project members, including me. Within the U4 project I am now classified as a U4c1a1b. 23andMe have also placed me in haplogroup U4. They have however allocated me to a different subclade - U4a2b. I'm not yet certain of the reasons for the discrepancy, but suspect that 23andMe have not tested enough SNPs to provide an accurate haplogroup assignment. This is a very new science, and the haplogroup nomenclature is in a constant state of revision so it is understandable that in the early days there will be discrepancies. Haplogroup prediction is also particularly difficult for rare subclades like U4c. For all practical purposes at this stage knowing the subclade does not tell me very much as so little is known about haplogroup U4. As a bonus, 23andMe do however provide some very interesting background information on haplogroup U4, whereas FTDNA provided hardly anything at all and we have had to work hard instead to build up a list of resources on the U4 project website.

I already know from my family history research that all my lines going back at least to the 1800s, and in some cases for many hundreds of years previously, are from the UK. It was therefore no surprise that my Ancestry Painting showed that I am 100% European.
This feature is probably of more interest to people of mixed ancestry where, for example, Aboriginal or Native American ancestry will show up as "Asian". A new feature, Ancestry Finder, has been introduced in the last few weeks which will tell you which countries your ancestors might have lived in. As I already know that all my ancestors are from the UK this feature again did not really tell me very much. I was however somewhat surprised when I lowered the threshold to five centiMorgans (a measure of matching DNA segments) to see that I matched people with four grandparents from Romania, Switzerland, Spain, the Netherlands and Sweden, with just 0.3% of my genome from the UK. This result is probably more of a reflection of the lack of UK testees in the 23andMe database. It is also possible that some of the participants have provided incorrect information on their ancestry (the country information is taken from a customer survey).

Relative Finder is an opt-in feature of the 23andMe service. It works by detecting shared segments of autosomal DNA and predicting the relationship based on the number and size of the shared segments. I currently have 151 matches in the Relative Finder database. Twelve of these matches are predicted to be fourth cousins, and the remainder are predicted to be fifth cousins or distant cousins. For each prediction a relationship range is given. Some of my fifth cousins could be third to sixth cousins; others could be third to tenth cousins. The names and contact details of your matches are not made available to you. You are instead given information on their haplogroups, and, if they have filled in the information on their profile, their country of residence and number of surnames listed.
You can contact your matches but are restricted to contacting just five people per day. Over the last few weeks I have religiously contacted all 151 of my matches, but have been very disappointed that so far only 14 people have accepted contact, a mere 9% response rate. Much to my surprise two people have actually declined contact, which was somewhat unexpected for what is meant to be an opt-in service. Of the 14 people who responded 13 are in the United States and just one is in the UK. Although I've exchanged details with all of these people we've not been able to find our common ancestor. American research is particularly challenging and American researchers are rarely able to trace their lines to a specific location in the UK. Without a surname in common there is, therefore, little hope of finding the link in the paper trail. My sole UK match had taken advantage of the special offer for Parkinson's disease patients, and had only just started to research her family history.

All in all the ancestry part of the 23andMe service has not been particularly informative. I am pleased that I was able to purchase the Complete Edition as, much to my surprise, I've found it far more rewarding than I expected exploring my health and traits with 23andMe than my ancestry. Relative Finder is however still very new and it is quite possible that I will have more responses and more meaningful matches in the future as the database grows. 23andMe currently have in excess of 50,000 people in their database. The company does not however disclose how many people have opted to use the Relative Finder feature. Other genetic genealogists have reported a similar problem with a lack of response to Relative Finder requests with response rates ranging from about 10% to 30%. From a British perspective another problem with the Relative Finder test is that the vast majority of the 23andMe customer base, probably well in excess of 90%, is in America. While it is interesting to know that I have lots of distant genetic cousins in America it is not going to help my family history research if there is no way of finding the connection in the paper trail.

For ancestry testing the Family Finder test from Family Tree DNA is likely to be a much better option. FTDNA have a very large customer base who are primarily interested in genealogy. In contrast, it would appear that the majority of 23andMe customers have tested primarily for health reasons and have little interest in, or knowledge of, their family history. In addition, Family Tree DNA, thanks to their partnership with the Genographic Project and their sponsorship of Who do you think you are? Live, have a much more international customer base and, more importantly from my point of view, more customers in the UK. I've already had Family Finder tests done on both my mum and dad, and I wrote previously about my dad's Family Finder test. My mum's results have just come in and I will write more about this test in future posts.

Autosomal DNA testing for ancestry purposes is still in its infancy. Whether you test with 23andMe or Family Tree DNA such a test should be considered as more of a long term investment. In the short term the test is best used to prove or disprove a particular hypothesis, such as whether or not two people share a common great-grandparent. The cost of the test is still a formidable barrier, especially for those of us in the UK where the weak pound makes the tests comparatively more expensive. However, as the cost of the tests come down and the databases grow in size, autosomal DNA testing will become an increasingly useful tool for family history research.

See also

Part 1 Disease risks

Part 2 Carrier status and drug responses

Part 3 Traits

*Updates*
- The cost of autosomal DNA testing tumbled in 2013 and the three providers now charge just $99 for the test. There are significant differences in the features offered, the international availability and the shipping costs. For an up-to-date comparison see the ISOGG autosomal DNA testing comparison chart.

- 23andMe updated their ethnicity predictions in December 2012. See my post on 23andMe's new Ancestry Composition - a British perspective for a review.

© Debbie Kennett 2010

Wednesday, 28 July 2010

Exploring my genome with 23andMe - traits

This is the third in my series of articles on my experiences of testing with 23andMe. I wrote yesterday about my carrier status and drug responses, and on Monday I discussed my disease risks. I'm now going to look at my results for the various traits. The 23andMe test currently covers 40 traits from the mundane, such as eye colour, hair curl and height, to the obscure such as "asparagus metabolite detection" (the ability to detect a distinct smell in your urine after eating asparagus). The screenshot below shows a selection of my results. (Click on the screenshot to enlarge it.)
One of the useful aspects of the data on traits is that you have the opportunity to see how your genetic predictions match the reality. According to my genotype I have a 72% chance of having blue eyes, a 27% chance of having green eyes and a mere 1% chance of having brown eyes. My eyes are actually green so the prediction is accurate, but this is also a useful reminder that the most probable prediction is not necessarily the reality.

For many of the traits 23andMe provides reports on more than one marker. The results can often be contradictory, again reflecting the complex pattern of genetic inheritance. There are for instance two reports on hair curl.  The confirmed research report suggests that I should have "slightly curlier hair on average" whereas according to the preliminary research report I am predicted to have only a typical amount of hair curl. In reality I have a mop of thick curly hair. The reports do explain that "this biological trait has a strong genetic component, although a simply inherited 'hair curl gene' that completely determines hair texture has not been found and likely does not exist. Instead, variations in several genes affecting different aspects of hair development probably combine together to determine the shape of your 'do". (I've never heard the expression 'do before but I presume it is perhaps an abbreviation for hairdo.) My sons have both inherited my thick curly hair so there is a strong possibility that they will also have inherited my marker for male pattern baldness. According to the preliminary report: "Sons of women with this genotype have a 50% chance of inheriting greatly decreased odds of male pattern baldness."

As another example, 23andMe provides preliminary reports on two markers for longevity. I have one marker which gives me higher odds of living to 100 and another marker which gives me typical odds of living to 95. The reported studies were however both very small – a study of 212 Ashkenazi Jews and a study of 615 Japanese men.

I have never been particularly athletic so it is no surprise to learn that I do not have "fast-twitch muscle fibre" and am therefore unlikely to be a fast sprinter. I didn't really need a DNA test to tell me that I have wet earwax, but on reading the report I now have a new word cerumen - the technical term for earwax - to add to my vocabulary!

One of the most interesting findings in my traits reports was the discovery that I have a genotype which makes me resistant to the most common strain of norovirus. Apparently because I have two As on this particular SNP I lack a functioning FUT2 gene. I was fascinated to learn that about 20% of people with European or African ancestry, but very few people with Asian ancestry, share this trait. I'm not however in any great hurry to go on a cruise to test my resistance!
The most innovative feature of the 23andMe service is that customers are given the opportunity to participate in the company's research programme, 23andWe. The company's first scientific paper, Web-Based, Participant-Driven Studies Yield Novel Genetic Associations for Common Traits, was published in June this year in the open-access peer-reviewed journal PLoS Genetics. The data on some of the traits on which the company reports, such as "photic sneeze reaction" and the above-mentioned asparagus metabolite detection, are taken from this paper. While the traits are somewhat trivial and insignificant, the open web-based research model has been validated and there will no doubt be many interesting discoveries in years to come. It is very exciting to be able to engage with your data in such a way and to have the opportunity to find out how your results compare with those of other participants and to see how your data has been used.

One of the best features of the test is the interactive nature of the website and the fact that your results are constantly updated. I've already had a number of new results in the last few weeks, the most recent of which was for leprosy susceptibility. Not all of the information will necessarily have any practical application. I am highly unlikely ever to contract leprosy and probably many of the other diseases for which I have reports. However, new studies are being reported every week and the value of the test will grow over time. Although I was primarily motivated to purchase a 23andMe test for the ancestry aspects I have found the medical aspects very interesting and educational. There is no better way to understand genetics than to have the opportunity to explore your own genome.

See also

Part 1 Disease risks

Part 2 Carrier status and drug responses

Part 4 Ancestry

© Debbie Kennett 2010

Tuesday, 27 July 2010

Exploring my genome with 23andMe -
carrier status and drug responses

This is the second in my series of articles on my test with 23andMe. I wrote yesterday about my disease risks. I am now going to look at my carrier status reports and my drug responses. 23andMe provides information on your carrier status for 24 diseases and conditions. Fortunately I tested negative for all 24 diseases. I must confess that I had not heard of the majority of diseases listed. When I explored further it transpired that many of the diseases were quite rare, and a surprisingly large number were particularly prevalent in the Ashkenazi Jewish community (eg, Bloom's syndrome, Canavan disease, mucolipidosis IV and the wonderfully named Maple syrup urine disease type 1B). I don't know whether the SNPs (single-nucleotide polymorphisms) chosen for the 23andMe test are a reflection of 23andMe's customer base or if it is simply that more research has been done into the inheritance of diseases in the Ashkenazi community.

It is important to remember that there are often a large number of SNPs associated with particular diseases and 23andMe only tests a small fraction of these SNPs. It is therefore quite possible to test negative for a particular disease but still to be a carrier.  To its credit, 23andMe does a commendable job of educating its customers. There is an excellent post on their blog, Absence of evidence is not evidence of absence: understanding what genetic testing can (and can’t) tell you, which explains the problem of interpretation very succinctly.

One of the most controversial aspects of the 23andMe test is the inclusion of the SNPs for three BRCA breast cancer mutations. The company make it very clear that "the absence of these mutations does not rule out the possibility that a person may carry another genetic variation that increases the risk of these diseases". (See screenshot below - you will need to click on the image to enlarge it.)
Interestingly again, the SNPs selected account for the majority of breast cancer cases in Ashkenazi Jewish women. Only a tiny proportion (0.2%) of 23andMe customers test positive for the BRCA mutations. Anne Wojcicki's presentation to the Food and Drug Administration last week provides statistics on the prevalence of some of the diseases and conditions in the 23andMe database. 

My only quibble with the presentation of the carrier status data is that you are urged to consult a genetics counsellor if you have any questions about your results. The link provided is to a commercial genetics counselling organisation in America. This might be appropriate for an American customer who presumably has to pay to see a doctor and for whom a genetics counsellor might be a cheaper option.  It is however not much help if you don't live in the US. For customers in the UK it would be more appropriate to make an appointment with a general practitioner for which of course there is no charge.

The drug responses are probably the most useful part of my 23andMe data. I have learnt that my genetics indicate that I might possibly have a reduced response to hepatitis C treatment and an increased sensitivity to warfarin. It is of course quite possible that I will never need either of these treatments but if I should do so then I am sure that the information will be beneficial to my general practitioner who might then be able to target the dosage accordingly and perhaps save the National Health Service some money in the process.
I was intrigued to learn from a preliminary research report that I have a marker which means that I might be a fast metaboliser of caffeine. This would give me a reduced risk of a heart attack from drinking coffee. Although I don't like coffee I do consume large quantities of tea every day!

Of no practical use, but interesting nonetheless, one preliminary research report suggests that I have a genotype which puts me at substantially higher odds of becoming addicted to heroin! The study was carried out on just 139 heroin addicts primarily of Swedish origin and it remains to be seen if these results can be replicated.
Although I've not made any major discoveries about my health it has been very interesting exploring the wealth of data on the 23andMe website. The value of the test will grow over time as more studies are published and the results are incorporated into the 23andMe database.

See also

Part 1 Disease risks

Part 3 Traits

Part 4 Ancestry

© Debbie Kennett 2010

Monday, 26 July 2010

Exploring my genome with 23andMe - disease risks

In recent months I have been following with interest the experiences of my friends in the genetic genealogy community who have tested with the personal genomics company 23andMe. The 23andMe test looks at over 500,000 SNPs (pronounced snips) - markers in your DNA known as single-nucleotide polymorphisms - and provides you with information on your ancestry and your predisposition to 163 traits and diseases. The Complete Edition 23andMe test normally costs US $499 (about £321). It is also possible to purchase separately the Ancestry Edition at $399 or the Health Edition at $429. The Complete Edition is however the only 23andMe test which gives you access to your raw data, and is therefore the most useful. Although I have been curious about the process I really could not justify spending nearly £400 on such a test. However, when 23andMe had a one-off sale on DNA Day at the end of April I jumped at the opportunity to purchase the Complete Edition test for just $99 (£63). I had to pay an additional $70 for Fedex delivery. The total cost charged to my credit card was £117. I have had my results for several weeks now but it has taken me a while to explore and digest all the information. I will share my experiences of my 23andMe test in a series of  blog posts, and will focus first of all on my disease risks. I should caution that I have no scientific or medical qualifications. There is a growing body of healthcare professionals and government agencies in America who believe that consumers such as me should not be permitted to purchase these tests without the intermediary of a doctor or genetics counsellor because we are supposedly incapable of understanding the results and, despite lack of evidence, there is a theoretical risk that we might make inappropriate health care decisions based on our findings.

By far the hardest part of the test was grappling with the packaging and then working out how to send the kit back to America. The Fedex instructions were very confusing, and no UK contact details were given. I eventually found a UK telephone number on the Fedex website and was then able to ring up and make arrangements for a courier to come and collect the kit. Before my test could be processed I was required to read and agree to a very lengthy and thorough consent document which reminded me first and foremost that it is "not a test or kit designed to diagnose disease or medical conditions, and it is not intended to be medical advice". The full text of the consent form can be read on the 23andMe website.

The results are all made available through a personal account on the 23andMe website. I have provided below a few sample screenshots. You will need to click on the images to enlarge them. 23andMe distinguishes between "established research" and "preliminary research". For results to be classified as  "established research" (shown on the screenshots with four yellow stars) the association must be widely accepted in the scientific community or validated by at least two studies on more than 750 people with the trait or condition. "Preliminary research" reports are shown with grey stars and are graded depending on the size of the study or studies in question. These findings have not been replicated in other studies and have therefore not yet been confirmed by the scientific community. The results for Parkinson's disease and breast cancer are initially locked, and you are required to read the warnings before deciding whether or not to access these results.
My most elevated risk was for type 2 diabetes, for which 23andMe tell me that I have a 23.6% risk versus an average risk of 18.2%. The screenshot below shows the way that my diabetes risk is presented and explained.
As an illustration of the complexity of so many diseases 23andMe reports on nine markers which have been associated with type 2 diabetes. I have a slightly increased risk on five of those markers but a slightly decreased risk on the remaining four markers. It is however still possible to contract a disease even if you have a reduced risk or, conversely, you might have a higher than normal risk of a disease but never suffer from the condition. For each disease or trait a large amount of information is given which is explained very clearly and presented in a way which makes it very easy to understand. My only criticism is that in the resources section all the links are specific to the US. The majority of 23andMe's customers are in the US so this is understandable, but it is not particularly helpful for those of us who do not live in America. You are also encouraged to consult with a genetic counsellor about your results and a link is provided to a commercial company in America which charges between $99 and $375 for a consultation. Although there is nothing in my results which gives me any cause for concern, if I did have any worries it would have been useful to know who to approach. I'm not aware that we have similar networks of private genetic counsellors in the UK and presumably access to a counsellor would only be possible on the National Health Service with a referral from a general practitioner.

My results also show that I have a slightly elevated risk of age-related macular degeneration and exfoliation glaucoma. I have no family history of either condition and I have never smoked, both of which can be contributory factors.  I have been short-sighted since childhood and, because I wear contact lenses, I go for regular check-ups with my optician. I will be therefore be able to alert my optician to the report, and ask her advice when I next go for a check-up.

Amongst the preliminary research reports I was particularly interested to see that I have a genotype which, if the results of the preliminary study on just one marker can be replicated, would put me at substantially higher odds of contracting diffuse-type stomach cancer. My maternal grandmother died of stomach cancer, albeit at the advanced age of 89, so I quite possibly do have a genetic predisposition. The study cited looked at 925 patients and 1,396 healthy controls from Japan. It will be interesting to see if these results can be replicated in other studies and particularly in European populations. One of the most useful features of the 23andMe service is that your results are continually updated with new findings from published papers.

The remaining results are organised into two further sections - those for which I have a decreased risk and those for which I have a typical risk. The way that the risks are presented is somewhat confusing. According to 23andMe my biggest risk is for obesity. I have a typical risk of 50.6% which is slightly lower than the average of 59%. It seems odd that obesity, my highest risk factor, is not highlighted in red at the top of the page whereas bipolar disease, for which I have only a 0.2% risk versus the average of 0.1% is flagged in red.
I was also very surprised at the figures that 23andMe quotes for obesity. I am advised that on average "59.0 out of 100 women of European ethnicity will get obesity between the ages of 13 and 59". The source for this figure is not given but I rather suspect the figure applies to American women of European ethnicity and not to the European population as a whole, especially as the obesity page is accompanied by a map of America with a breakdown of the obesity levels in each individual state. If so then the percentages for my other disease risks, and especially diabetes which has a strong association with obesity, would need to be suitably adjusted.

I have had no big surprises from the 23andMe test, but it has certainly been an interesting experience exploring my results. I will write more about some of the other features in future posts.
Update 31 July 2010
In today's Times newspaper there was a report from Mark Henderson, the Science Correspondent, on the contradictory population risk data provided by the leading personal genetics companies. If you have a subscription to The Times (you can sign up for a weekly subscription for a nominal fee) you can read the full story here along with the associated commentary from Daniel MacArthur here. Mark had his DNA tested with three different companies: 23andMe, deCODEme and Pathway Genomics. He discusses his results here and in a blog posting hereThe Times story begins: 
Personal genetic testing companies are to change the way that they present health risks after an investigation by The Times exposed how they can mislead people about their chances of developing disease. Three services have agreed to correct problems that can produce confusing and potentially inaccurate personal risk predictions for serious conditions such as heart attacks and diabetes.
The companies are giving the same individuals widely different risk estimates for some diseases because of uncertainty about how widespread the conditions are in the general population. This uncertainty affects the personal risks sent to customers but is not declared in their results... 
All three companies have announced that they will be reviewing their services and have said that "they would provide clear sources for population risk of diseases, and warn customers that the personal risks calculated might not be accurate for everybody." 23andMe have advised that they would "make adjustments within weeks".  I have been very impressed by the commendable way in which the companies have responded to these concerns and I look forward to seeing the amendments to my 23andMe results in due course.

See also

Part 2 Carrier status and drug responses

Part 3 Traits

Part 4 Ancestry

© Debbie Kennett 2010