In November I attend the Royal Society's two-day meeting on Ancient DNA. The recordings of the presentations are now available online on the Society's website:
http://royalsociety.org/events/2013/ancient-dna/
I previously posted my notes from the meeting which might help you to decide which talks you would like to listen to:
- Day 1 at the Royal Society's Ancient DNA meeting
- Day 2 at the Royal Society's Ancient DNA meeting
My personal favourites were the talks by Carles Lalueza Fox, David Reich, Johannes Krause, Greger Larson and Alice Storey.
Thursday, 12 December 2013
Sunday, 8 December 2013
Setting the record straight about Sara Sheridan’s “Japanese” DNA
I’ve previously written about the exaggerated and misleading haplogroup stories provided by some DNA testing companies. BritainsDNA, which also trades under the names ScotlandsDNA, IrelandsDNA and YorkshiresDNA, has been one of the worst offenders in this regard in the last year or so. I commented previously on the problems with their story about Prince William’s supposed Indian ancestry. In May this year a Scottish novelist by the name of Sara Sheridan told the story of the unusual findings from her ScotlandsDNA test in an article for the Huffington Post. She was informed by ScotlandsDNA that, despite her family history of Jewish ancestry, she descends “from a female line called 9Na [sic] that developed 17000 years ago in the area around Japan's most northerly island and on the mainland just opposite”. 9NA is a typo in the article and does in fact refer to N9a which is a mitochondrial DNA haplogroup. While haplogroup N9a might well have arisen 17,000 years ago, plus or minus several thousand years, determining precisely where a haplogroup originated is a different matter altogether. We are mostly reliant on the mtDNA of living people to make inferences about the genetic make-up of our matrilineal ancestors, but the present-day location of the bearers of a specific haplogroup does not necessarily correlate with its ancient origins. An awful lot of migration can happen in 17,000 years! In addition, the population today will probably only represent a tiny fraction of the mtDNA diversity of our distant ancestors because so many lineages will have become extinct. It is therefore quite preposterous to propose such a precise origin for a haplogroup so many thousands of years ago. Any theories on the origins of the various haplogroups should be regarded as highly speculative and should not be taken too seriously. They most certainly should not be presented as fact as they were here.
The test Sara would have taken with ScotlandsDNA is what they now call their Standard mtDNA Test. This test looks at just 300 mtDNA markers – known as SNPs (single-nucleotide polymorphisms) – from across the mtDNA genome and costs £170. An improved higher-resolution test known as Chromo 2 was introduced by the company in June 2013. The newer test looks at around 3000 mt SNPs and costs £189 (males also benefit from a Y-chromosome analysis from the same test). The 300 mt SNPs covered in Sara Sheridan’s ScotlandsDNA test represent just under 2% of the mtDNA genome. The new Chromo 2 test covers around 18% of the mt genome.
There are in fact many daughter branches below N9a as can be seen from the most up-to-date version of the mtDNA tree on Phylotree. However, in order to determine the sub-branch it is necessary to test many more than the 300 mt SNPs covered by ScotlandsDNA, and ideally the whole mtDNA genome (all 16569 base pairs) should be sequenced. The sub-branches are of more recent origin and can sometimes provide better geographical resolution, though there are currently not enough full mtDNA sequences available in the literature to draw reasonable conclusions.
For females the ScotlandsDNA/BritainsDNA mitochondrial DNA tests are very poor value for money. Sara Sheridan could have had her entire mitochondrial genome tested at Family Tree DNA, the market leader for mtDNA testing, for much less than the price she paid for her low-resolution and very expensive mtDNA test from ScotlandsDNA. The full mitochondrial sequence (FMS), which literally sequences all 16569 base pairs in the mt genome, normally costs $199 (about £122) and is currently on offer for $169 (about £103) in the FTDNA sale which closes at the end of December. FTDNA are currently the only company to offer a full mitochondrial sequence test direct to the consumer. The FMS test gives you the most detailed possible haplogroup assignment, which can be further refined as new sub-branches are discovered. FTDNA also have the advantage of a large genealogical matching database and the ability to join the appropriate mtDNA haplogroup project for further comparisons.
Note that although the BritainsDNA/ScotlandsDNA Chromo 2 test is poor value for females it is a useful test for males of British ancestry who wish to have a detailed Y-DNA haplogroup assignment (females do not of course have a Y-chromosome). For a comparison of the different Y-SNP tests on the market see the ISOGG Y-SNP testing chart.
When the news of Sara Sheridan’s supposed “Japanese” ancestry was first published I discussed the story with Jill Whitehead who, like Sara, has Ashkenazi Jewish ancestry from Scotland. As the Jewish community is very inter-connected it is highly likely that Jill and Sara are related within a fairly recent time frame, so Jill took a particular interest in this case. Jill is one of the pioneers in the genetic genealogy community. She had her mitochondrial DNA tested with Family Tree DNA back in 2003, and has also tested with 23andMe. Jill is a member of the Jewish Genealogical Society of Great Britain and has written several articles on Jewish genetic genealogy for the society’s journal. Jill wanted to have the opportunity to set the record straight about Sara Sheridan’s erroneous haplogroup interpretation, and has kindly provided below a much more plausible explanation of Sara's matrilineal origins:
A paper by Tian et al published in February 2015 in Scientific Reports documented four Ashekenazi Jewish individuals who were assigned to haplogroup N9A
The test Sara would have taken with ScotlandsDNA is what they now call their Standard mtDNA Test. This test looks at just 300 mtDNA markers – known as SNPs (single-nucleotide polymorphisms) – from across the mtDNA genome and costs £170. An improved higher-resolution test known as Chromo 2 was introduced by the company in June 2013. The newer test looks at around 3000 mt SNPs and costs £189 (males also benefit from a Y-chromosome analysis from the same test). The 300 mt SNPs covered in Sara Sheridan’s ScotlandsDNA test represent just under 2% of the mtDNA genome. The new Chromo 2 test covers around 18% of the mt genome.
There are in fact many daughter branches below N9a as can be seen from the most up-to-date version of the mtDNA tree on Phylotree. However, in order to determine the sub-branch it is necessary to test many more than the 300 mt SNPs covered by ScotlandsDNA, and ideally the whole mtDNA genome (all 16569 base pairs) should be sequenced. The sub-branches are of more recent origin and can sometimes provide better geographical resolution, though there are currently not enough full mtDNA sequences available in the literature to draw reasonable conclusions.
For females the ScotlandsDNA/BritainsDNA mitochondrial DNA tests are very poor value for money. Sara Sheridan could have had her entire mitochondrial genome tested at Family Tree DNA, the market leader for mtDNA testing, for much less than the price she paid for her low-resolution and very expensive mtDNA test from ScotlandsDNA. The full mitochondrial sequence (FMS), which literally sequences all 16569 base pairs in the mt genome, normally costs $199 (about £122) and is currently on offer for $169 (about £103) in the FTDNA sale which closes at the end of December. FTDNA are currently the only company to offer a full mitochondrial sequence test direct to the consumer. The FMS test gives you the most detailed possible haplogroup assignment, which can be further refined as new sub-branches are discovered. FTDNA also have the advantage of a large genealogical matching database and the ability to join the appropriate mtDNA haplogroup project for further comparisons.
Note that although the BritainsDNA/ScotlandsDNA Chromo 2 test is poor value for females it is a useful test for males of British ancestry who wish to have a detailed Y-DNA haplogroup assignment (females do not of course have a Y-chromosome). For a comparison of the different Y-SNP tests on the market see the ISOGG Y-SNP testing chart.
When the news of Sara Sheridan’s supposed “Japanese” ancestry was first published I discussed the story with Jill Whitehead who, like Sara, has Ashkenazi Jewish ancestry from Scotland. As the Jewish community is very inter-connected it is highly likely that Jill and Sara are related within a fairly recent time frame, so Jill took a particular interest in this case. Jill is one of the pioneers in the genetic genealogy community. She had her mitochondrial DNA tested with Family Tree DNA back in 2003, and has also tested with 23andMe. Jill is a member of the Jewish Genealogical Society of Great Britain and has written several articles on Jewish genetic genealogy for the society’s journal. Jill wanted to have the opportunity to set the record straight about Sara Sheridan’s erroneous haplogroup interpretation, and has kindly provided below a much more plausible explanation of Sara's matrilineal origins:
A number of us in the DNA community are aware of the presentation of DNA results used by the company BritainsDNA/ScotlandsDNA. These have been cursory to say the least, especially in terms of unusual DNA haplogroups that are not of British origins. ScotlandsDNA advised the Scottish author Sara Sheridan that her N9a haplogroup was Japanese or Korean even though she was of Jewish Ashkenazi origins. Surely alarm bells should have rung? Instead of paying for an expensive DNA test (and ScotlandsDNA can be pricey in comparison with others) she would have been better advised to carry out a paper trail search first.
I traced her family back through the ScotlandsPeople website, and also using the naturalisation records on the National Archives website and the JewishGen shtetl finder. I found her ancestral town of origin in Belarus within half an hour of searching. The cost was only £14 worth of credits on ScotlandsPeople. If you can get back to a naturalisation record, and bearing in mind that Scottish records show dates and places of marriages of parents (even those overseas), then it is quite a simple process to trace Jewish families (provided the name is not a common one). This was how I found my own Jewish Brown family of Edinburgh twenty years ago, before I tried DNA testing eleven years ago now.
I could not believe the description of the N9 haplogroup given by BritainsDNA. I match up with several thousand Ashkenazi Jews on both FTDNA's Family Finder and 23andMe's DNA Relatives feature. Their tests are much more sensitive and they recognise that the Jewish sub-haplogroup of N9 is in fact N9a3. I match half a dozen people of Ashkenazi Jewish origin who are also haplogroup N9a3. There has also been quite a bit of recent international research on N9 haplogroups, and FTDNA for one always publishes recent research papers. ScotlandsDNA obviously had no idea this research existed otherwise they would have known the difference between a Jewish N9 and a non-Jewish N9.
I reproduce below the comments I made on the Scotsman newspaper website after an article appeared in that newspaper which again described Ms Sheridan's haplogroup as being Japanese/Korean:
"I come from a prominent Edinburgh Jewish family that came to the city in the 1860s. I have also been interested in genetic genealogy for over ten years having published articles on this for Shemot, the Journal of the Jewish Genealogical Society of Great Britain, e.g. their recent specialist Jewish Genetics edition.
I was somewhat surprised to read the description of Sara Sheridan's N9a3 maternal mtdna haplogroup. The Japanese make up only one small part of N9, there are many other N9s to be found throughout the world, as shown in a number of academic genetics journals recently. I have never come across a Japanese Jew, but there is a Jewish subclade of N called N9a3 with recent origins in Poland/ Belarus/ Lithuania. In fact, a very recent academic paper from 2012 by Derenko et al from the Russian Academy of Sciences points to a series of Neolithic skeletons found in Hungary as being N9a3.
To add to that, I have no less than four assigned third cousins on the DNA testing site 23andMe, who are all N9a3, and they are all American Ashkenazi Jews originally from Poland/Lithuania/Belarus, who are related to me some time back in about the late 18th/early 19th century. I think ScotlandsDNA needs to be more accurate in its assessment and description of haplogroups. When haplogroups were being formed in ancient times, not all humans went in one direction, they scattered east and west. That is why we have Hungarian Neolithic skeletons, East European Jews and Asian populations who make up N9 haplogroups."Update 30 May 2015
A paper by Tian et al published in February 2015 in Scientific Reports documented four Ashekenazi Jewish individuals who were assigned to haplogroup N9A
Update 15th May 2022
Jill Whitehead has alerted me to an article written by Sara Sheridan for Historic Environment Scotland about her Jewish heritage. Her grandmother (presumably her maternal grandmother) was Jewish which would be consistent with the N9a3 mtDNA haplogroup designation she received from BritainsDNA.
Further reading and resources
- A list of Jewish DNA projects provided by JewishGen
- The Haplogroup N Project at Family Tree DNA
- The ISOGG list of mtDNA haplogroup projects
- The ISOGG mtDNA testing comparison chart
- The Jewish Genealogical Society of Great Britain. The April 2013 issue of the society's journal Shemot was a special edition devoted to DNA testing and provides a useful introduction to Jewish genetic genealogy.
Scientific papers
- Costa MD, Pereira JB, and Pala M. A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages. Nature Communications 2013; 4 (2543).
- Ostrer H and Skorecki S. The population genetics of the Jewish people. Human Genetics 2013; 132 (2): 119-127.
- Derenko M, Malyarchuk B, Denisova G et al. Complete mitochondrial DNA analysis of eastern Eurasian haplogroups rarely found in populations of northern Asia and eastern Europe. PLoS One 2012;7(2).
See also
- Mitochondrial DNA testing at a new low price
Further reading and resources
- A list of Jewish DNA projects provided by JewishGen
- The Haplogroup N Project at Family Tree DNA
- The ISOGG list of mtDNA haplogroup projects
- The ISOGG mtDNA testing comparison chart
- The Jewish Genealogical Society of Great Britain. The April 2013 issue of the society's journal Shemot was a special edition devoted to DNA testing and provides a useful introduction to Jewish genetic genealogy.
Scientific papers
- Costa MD, Pereira JB, and Pala M. A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages. Nature Communications 2013; 4 (2543).
- Ostrer H and Skorecki S. The population genetics of the Jewish people. Human Genetics 2013; 132 (2): 119-127.
- Derenko M, Malyarchuk B, Denisova G et al. Complete mitochondrial DNA analysis of eastern Eurasian haplogroups rarely found in populations of northern Asia and eastern Europe. PLoS One 2012;7(2).
- Behar DM, Yunusbayev B, Metspalu M et al. The genome-wide structure of the Jewish people. Nature 2010; 466 (7303): 238-242.
- Atzmon G, Hao L, Li Hao, Pe’er I et al. Abraham’s children in the genome era: major Jewish Diaspora populations comprise distinct genetic clusters with shared Middle Eastern ancestry. American Journal of Human Genetics 2010;
86 (6):
- Feder J, Ovadia O, Glaser B and Mishmar D. Ashkenazi Jewish mtDNA haplogroup distribution varies among distinct subpopulations: lessons of population substructure in a closed group. PLoS One. 2008 3 (4): e2062.
- Behar DM, Metspalu E, Kivisild T et al. Counting the founders: the matrilineal genetic ancestry of the Jewish Diaspora. American
Journal of Human Genetics 2006 78 (3): 487-497.
- Behar DM, Metspalu E, Kivisild T et al. The matrilineal ancestry of Ashkenazi Jewry: portrait of a recent founder event. American Journal of Human Genetics 2006; 78 (3): 487-497.
- Shriver MD, Kittles RA. Genetic ancestry and the search for personalized genetic histories. Nature Reviews Genetics 2004; 5: 611-618.
- Shriver MD, Kittles RA. Genetic ancestry and the search for personalized genetic histories. Nature Reviews Genetics 2004; 5: 611-618.
Books
Ostrer H. Legacy: A Genetic History of the Jewish People.
Oxford University Press, 2012.
Abulafia D. The Great Sea: A Human History of the
Mediterranean. Allen Lane/Penguin, 2011.
Goldstein D. Jacob’s Legacy: A Genetic View of Jewish History. Yale University Press. 2008.
Entine J. Abraham’s Children: Race, Identity and the DNA of
the Chosen People. Grand Central Publishing, 2007.
- Mitochondrial DNA testing at a new low price
Friday, 6 December 2013
23andMe update, third party tools and alternative personal genomics companies
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.
Update December 2014
The 23andMe health reports are now available once again in the UK and in Canada though in a somewhat pared down form. For further information see my blog post 23andMe relaunches health reports in the UK. See also the article 23andMe launches personal genome service in the UK by Philippa Brice of the PHG Foundation.
Tuesday, 3 December 2013
A new exome sequencing and interpretation service from Belgian company Gentle Labs
While the spotlight has been very much on 23andMe and the FDA this last week the launch of a new high-end genomics service has attracted little attention. Gentle Labs is a new company based in Belgium. They are offering an exome sequencing service with interpretation for
$1990. The results are provided through a doctor. This is from their FAQs:
Why would I pay $1990 if I can get my DNA sequenced for $99? Some companies are offering 'insights into your DNA' for only $99. These tests, however, are only based on 0.03% of your genome (corresponding with 1.9 % of your genes). It's like reading a novel by reading a letter on every page: you won't get much of the story. These cheaper tests do not allow for accurate or complete results or interpretation: some of these tests have false negative rates of 50% or more! In fact, companies offering these tests admit this themselves. One company clearly displays on their website that "The information on this page is intended for research and educational purposes only, and is not for diagnostic use." In other words: these tests should not be relied on for any medical purposes, nor for diagnostic use.
In contrast, our Gentle test not only offers complete coverage of all your genes, it also includes counseling with some of the world's best medical geneticists provided by Royal Doctors. Other advantages include:
* a free subscription service through which we will keep you informed about your DNA as science evolves
* free DNA data storage (so that you can provide your medical doctors access to your DNA data in case of a health issue or emergency)
* user friendly iPad and web apps to explore your genetic results and - in the end - yourself
The Royal Doctors have no connection with royalty but offer a network of doctors who will provide advice for a fee of one Euro per day. Their website can be found at www.royaldoctors.com
Dr. Bertalan Meskó, who writes the Science Roll blog, has signed up for the Gentle service and has published an interview with Peter Schols, the CEO of Gentle Labs, which can be found here.
The launch of Gentle Labs was covered by GenomeWeb but the story is behind a paywall.
Interestingly 23andMe launched their own exome sequencing pilot programme back in 2011. Exome sequencing is the logical next step for personal genomics tests but the costs are still prohibitively high for the average consumer. It will be interesting to see what transpires in the next five years.
The launch of Gentle Labs was covered by GenomeWeb but the story is behind a paywall.
Interestingly 23andMe launched their own exome sequencing pilot programme back in 2011. Exome sequencing is the logical next step for personal genomics tests but the costs are still prohibitively high for the average consumer. It will be interesting to see what transpires in the next five years.
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