Sunday, 30 July 2017

Living DNA updates and GEDmatch Genesis

While I was away on holiday in California in June Living DNA rolled out a couple of updates.

They have now provided us with the facility to download our raw data. You will find the new menu when you log into your Living DNA account.

We can use the raw data to do our own analyses and to upload the results to third-party sites to get additional interpretations. However, Living DNA uses a different chip from the other main testing companies (23andMe, AncestryDNA, Family Tree DNA and MyHeritage). The Living DNA test is run on the new Illumina Global Screening Array chip whereas the other companies are currently using the Illumina OmniExpress chip. As a result the Living DNA raw data is not compatible with other sites as there are not enough overlapping SNPs (markers) to make reliable relationship predictions. (Note, however, that if you are interested in getting health reports, you can upload your Living DNA raw data to Promethease.)

It's already been announced that 23andMe will be moving over to the GSA chip in due course, and it's likely that the other companies will eventually follow suit as the Illumina OmniExpress is being phased out. The GSA chip is designed for imputation. This is the process of inferring missing markers using statistical algorithms. Imputation can be done with a high degree of accuracy provided that sufficient reference populations are available. We will need to wait and see how the companies cope with the change but in theory the GSA chip is backwardly compatible with the OmniExpress. Much will depend on the quality of the imputation.

In the meantime the wonderful team at GEDmatch have come to the rescue. They are now beta-testing a new service called Genesis which will allow people to upload kits using formats that are not compatible with the main GEDmatch database. This includes Living DNA kits and exome sequences. The intention is that eventually the two databases will be merged.

GEDmatch are also in the process of developing an exciting new Genesis Algorithm which promises to provide more accurate matches. This is what the new Genesis home page looks like.

Here is a screenshot of the upload page.

I was successfully able to upload my Living DNA raw data to GEDmatch Genesis. When uploading your Living DNA data make sure you use the link for "Generic uploads (23andMe, FTDNA, Ancestry, most others)". Within a few minutes of uploading my raw data I was able to use the Genesis site to look at the various admixture calculators.

Here is a report using my Living DNA data with the Eurogenes K13 report. There are just 58623 SNPs used in this report.

When using the same Eurogenes K13 calculator on my standard GEDmatch kit 181512 SNPs are used in the comparison. However, as you can see from the screenshot below, the two reports are remarkably similar, despite the reduced number of SNPs used for the Living DNA comparison.

A few hours after I'd uploaded my results I was able to access my matches. Here is a screenshot of my matches with the kit numbers, names and e-mail addresses blurred out. Click on the image to enlarge it.

We are given information on the largest shared segment, the total cMs shared and the number of overlapping SNPs. Information is also provided about the confidence of the results. Confidence is very high for comparisons between two Living DNA kits but very low for comparisons with other companies.

All my matches are currently very low resolution and they go right down to matches that share a total of just 5 cMs. Few if any of these matches are likely to fall into a genealogical timeframe. Interestingly I've already spotted the names of four people I know amongst my Living DNA matches! As more people add their results to the Genesis database it will be a very useful way of making connections and doing comparisons across different testing companies. I look forward with interest to seeing how the Genesis algorithm develops.

The other new feature that Living DNA have rolled is what they call Family Views, which allows you to view your admixture results in Complete, Standard and Cautious modes. With the launch of this feature all our admixture results were completely rerun. This is because of teething problems with the new GSA chip. After initial quality control checks Illumina issued a new validation file to correct the errors. As validation continues it's possible that there will be further changes in the future. I will write separately about my updated Living DNA results in a future blog post.

There are also other updates in the pipeline as I learned at the Southern California Genealogical Society's Jamboree conference in June when a group of us attended a get-together with David Nicholson and Martin Blythe from Living DNA.

Living DNA should be able to accept uploads from other companies by the end of July. However, there are only a few days of July left and this hasn't yet happened so perhaps the launch of this feature has been delayed.

Living DNA are also working on a matching programme which they hope to start beta-testing in September.

A big update to our admixture results can be expected by the end of the year as more reference datasets are added to the collection. They will be including data from the Symons Genome Diversity Project, data from Asia and data from Aboriginals in Australia. Their Irish DNA Research Project is going well and they already have 1200 samples. They now have 450 people in their German DNA Research Project. Further projects are planned for France, Portugal, Austria, Belgium and the Netherlands.

We can look forward to some very exciting new developments in the next six months.

Further reading

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