Friday, 20 December 2013

A first look at the BritainsDNA Chromo 2 Y-DNA and mtDNA tests

Larry Vick has kindly shared screenshots of the results from his Chromo 2 test from BritainsDNA*. I wrote in my previous blog post about the results from his All My Ancestry admixture test. We will now have a look at his Y-DNA and mtDNA test results. The Chromo 2 test is a useful product for anyone wishing to have a detailed Y-DNA haplogroup assignment but who doesn't wish to pay out for one of the new but much more expensive comprehensive Y-chromosome sequencing tests. The test looks at around 15,000 Y-SNPs. For anyone with ancestry from the British Isles the Chromo 2 Y-DNA test is currently probably a better choice than the Geno 2.0 test from the Genographic Project. However, this is a rapidly changing market, and there are indications that the Genographic Project will be offering a new chip in 2014. For up-to-date comparisons of the various Y-SNP tests on the market see the Y-DNA SNP testing chart in the ISOGG Wiki.

There are a number of different options for the Chromo 2 test. The Chromo 2 Y-DNA test costs £189 ($299). A cheaper option is to purchase the Raw Y-DNA test for £129 ($199) which gives you your raw Y-DNA results without the ancestral and interpretative reports. If you are ordering the Raw Y test you will need to ensure that you share your results with the relevant haplogroup project administrators so that they can determine where your SNPs are placed on the Y-SNP tree as the position of many of the SNPs on the Chromo 2 chip is not yet known. The Chromo 2 test can also be purchased in packages in combination with the All My Ancestry test and a mitochondrial DNA haplogroup test. Larry had previously tested with Ethnoancestry (the former name of BritainsDNA) and was able to upgrade to the new test at a discounted price so he opted to have the full works. Make sure you click on all the images below to enlarge them to see the full details of each report.

The following screenshot shows the Y-DNA results welcome screen. Larry is haplogroup Q and BritainsDNA have identified his most downstream SNP as S324 (also known as L56). Larry tells me that he got a much better haplogroup assignment from BritainsDNA than he did from the Geno 2.0 test, and Chromo 2 has confirmed everything he already knew about his haplogroup except for what he has now discovered from the Full Genomes comprehensive sequencing test.

The Genetic Signature Report lists all the SNPs on the Chromo 2 chip for which Larry tested positive. Not all of these SNPs have been placed on the Y-tree and it is possible that his subclade assignment will be updated in future as the structure of the tree becomes clearer.

The Haplogroup Story provides a somewhat fanciful narrative about the origins of haplogroup Q which is defined by the SNP M242. It is of course mere speculation that haplogroup Q originated in the Altai mountains in Central Asia as they suggest. BritainsDNA give nicknames to the base haplogroups, and Altai is the name they have chosen in this case to represent haplogroup Q. Note that these nicknames have no scientific basis and should not be taken literally.

The World Distribution Map shows the percentage distribution of haplogroup Q in various populations around the world. BritainsDNA tell us that "the results for the world distribution have been brought to you from a combination of the published literature, our own data, and databases available from other research projects". It would have been helpful to have the full details of the sources used but unfortunately this information has not been provided. You can zoom in and out of the map to see the distribution of your haplogroup in different countries.

The Regional Distribution Map provides a breakdown of the distribution of haplogroup Q in the British Isles. The map represents "the locations of lineages 100 years ago" and is seemingly based on information provided by BritainsDNA customers who have been asked to give the birth place of their paternal grandfather.
This is an interesting feature which is not provided by any other companies. However, it would have been useful to have more details of the sampling process and, more specifically, the number of people sampled in each country. The date when the map was generated is not given and there is no indication as to how often the company plan to update the map.

The Four Nations map shows the distribution of Larry's haplogroup in the four countries that make up the British Isles. The company tell us: "The ancestral data that you and all of our customers provided on ordering has informed both the regional distribution across Britain and Ireland and uncovered the frequencies across our four home nations." The grandparents' place of birth is used for this chart which is again intended to represent "the location of lineages 100 years ago or more". As with the maps, this chart would have been more meaningful if details of the number of samples in each country had been provided. Presumably such information is considered to be commercially sensitive.

The Phylogenetic Tree shows the position of Larry's haplogroup in relation to the full Y-SNP tree. There is a slider to zoom around the tree, and a red line allows Larry to trace his lineage back to the root of the tree. With the anticipated SNP tsunami in 2014 the Y-tree is likely to undergo major restructuring, and this tree is likely to become out of date very quickly. ISOGG maintains the most up-to-date version of the Y-SNP tree.

The Y-DNA haplogroup frequencies chart shows the percentage of BritainsDNA customers who belong to each haplogroup.  Again, the underlying data are not provided, and it is not clear whether these frequencies include the whole customer base or just those customers who have a paternal grandfather who was born in the British Isles. The haplogroups are identified by their name and also by their BritainsDNA nickname. Note that the ISOGG Wiki has a chart which lists all these nicknames and the alternative SNP names.

BritainsDNA also offer the option to download the raw Y-SNP data. Larry sent me his raw data file which is in the form of a Notepad file with a list of all the SNPs tested. The results show whether Larry was positive or negative for each SNP tested and the genotype (the A, C, T and G letters) for each SNP. The file is provided in tab-delimited text file which can be opened up in a spreadsheet program.

Larry's mtDNA results follow the same format. Here is a screenshot of his mtDNA results welcome page.

Larry has been assigned to haplogroup H212b4, which is the same assignment he received for his full mitochondrial sequence test from Family Tree DNA. The Chromo 2 test covers around 3000 mt SNPs, and provides the same coverage as the Geno 2.0 chip. There are 16,569 base pairs in the full mitochondrial genome. 3000 SNPs is usually sufficient to give a reasonably detailed haplogroup assignment, but interpretation errors can occur and it is then necessary to have access to the raw data. There is, however, no option to download the raw mtDNA data. Larry tells me that BritainsDNA have advised him that they will not be providing the raw mtDNA data or indeed the raw autosomal DNA data. I would suggest that anyone who has taken an mtDNA or autosomal test with BritainsDNA should write to the company and ask for their raw data, and perhaps they will eventually change their mind. For a comparison of the mtDNA tests available see the ISOGG mtDNA testing comparison chart.

All in all I think the Chromo 2 test is a useful product for males wishing to have a detailed Y-DNA haplogroup assignment. It is certainly a big improvement on the previous offering from BritainsDNA/ScotlandsDNA which tested only 300 Y-DNA SNPs and 300 mtDNA SNPs, and was accompanied by a generic, melodramatic and fanciful narrative story with tales of the eruption of Mount Toba and ridiculous statements such as the supposed "fact" that "what directly caused populations to expand rapidly was the invention of porridge". The new haplogroup frequency charts and maps provide much more useful information, though the reports would have been more informative if details of the sample sizes had been provided. The experienced genetic genealogist is probably best advised to stick with the Raw Y test, unless he has a particular desire to have the charts and maps. If you've already taken a standard Y-STR test it is always best to seek advice first from the haplogroup project administrators or the relevant haplogroup-specific mailing list. In some cases it's possible to predict the most downstream Y-SNP with high confidence from a Y-STR signature and it is then only necessary to order a single SNP for $39 to confirm your placement on the Y-tree. It is also worth keeping up with the various genetic genealogy mailing lists and Facebook groups because there are likely to be many exciting new developments in 2014.

*Note that BritainsDNA also trades as ScotlandsDNA, IrelandsDNA and YorkshiresDNA.

Related blog posts
- A first look at the Chromo 2 All My Ancestry test from BritainsDNA
Alistair Moffat, BritainsDNA and the BBC - a "uniquely British farce"
- More pseudoscience from Alistair Moffat on the BBC
BritainsDNA, the BBC and Eddie Izzard
The British: a genetic muddle by Alistair Moffat
BritainsDNA, The Times and Prince William: the perils of publication by press release

© 2013 Debbie Kennett

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