Thursday, 22 November 2018

The complete guide to DNA testing kits - my article in Who Do You Think You Are? Magazine

There only just over four weeks to go until Christmas. If you're thinking of buying a DNA test as a Christmas present or if you just want to stock up on kits to test your relatives, now is a good time to buy as there are lots of sales for Black Friday and Cyber Monday. To help you to decide which test to buy I have written a guide to DNA testing for the Christmas issue of Who Do You Think You Are? Magazine. You can read a preview of the article here but you'll need to buy the magazine to read the full article.

The magazine is on sale in W H Smith's and other newsagents in the UK. You can also buy a digital version of the magazine here.

There is also a special offer on annual subscriptions to Who Do You Think You Are? Magazine with 49% off the usual price until 27th November. The print edition is just £34.99 and the digital edition is £33.26. You will receive 13 copies of the magazine each year.

I've provided below a quick round-up of the DNA sales. These details were updated on 23rd November 2018.

Black Friday DNA sales
Family Tree DNA's Family Finder test is on sale for Black Friday weekend for just $39 (£30), the lowest price ever for this test and for any autosomal DNA test.  The offer ends on 26th November.

You can also buy the Family Finder test in special "bundles" with other tests and get a 40% saving.

If you buy a Family Finder test you can add on a 37-marker Y-DNA test for just  $99 (about £77). If you order a Y-DNA test make sure you join the relevant surname and/or geographical project. You can find a full list here.

The mtDNA full sequence test is just $139 (£109) when purchased with the Family Finder test.

On top of all the above savings at FTDNA, shipping is just $9.95 for all kits both domestic and international for the sale period.

The AncestryDNA test is on offer until 26th November for just £49 exccluding shipping.

The MyHeritage DNA test is also on sale for £49 and their sale ends on 23rd November at 11.59 pm.

Living DNA have now teamed up with Findmypast and you can buy the newly branded Findmypast DNA test for just £59, the lowest price ever. The offer includes 14 days of free access to Findmypast's entire archive of more than 9 billion records and historical newspapers. The sale ends at midnight (GMT) on Monday 26th November. Note that Y-DNA and mtDNA are not included in this offer and will need to be purchased as add ons for £19.50. If you want Y-DNA and mtDNA haplogroups you'll need to buy direct from the Living DNA website where the 3-in-1 test is on offer for £69.

Living DNA are gradually rolling out their relative-matching Family Networks feature to beta testers. I just got access today though so far I don't match anyone else other than my parents.

The 23andMe Ancestry test is on sale for £59 and the Health and Ancestry service is on sale for £94. The offer ends on 26th November at 5 am GMT.

Note that there is an additional charge for postage and packing for all the above tests.

There are similar offers in other countries so check out the company websites to find out the prices in your local currency. Even better, check out this article from Michelle Leonard on the Ancestry Hour blog which provides a detailed overview of all the Black Friday offers.

Sunday, 18 November 2018

A 30x whole genome sequence from Dante Laboratories for €169 (£150 or $199)


Dante Laboratories have announced a special one-off promotion for Black Friday week. They are offering a next generation sequencing whole genome sequence (WGS) test at 30x coverage for just €169 (£150 or $199). The offer will end at midnight US Pacific time on Monday 26th November. Customers will also receive their raw data and a customised report without extra cost.

30x is the standard medical-grade coverage and this is the lowest price I've ever seen for 30x WGS.

The cost of the test includes the provision of a VCF file which can be downloaded from your account. There will be an option to download the BAM file from the cloud free of charge. Alternatively the FASTQ and BAM files can be sent on a 500 gigabyte hard disk for an additional fee of €59.00 ($69).

For further details visit the Dante Labs websites in the EU and the US:

https://us.dantelabs.com (US website)

The offer is also available through the Amazon market place in the US only.

There is a link to download a sample customised report on this page on the Dante Labs website.

See also the FAQs relating to this special offer.

Dante Labs introduced whole genome sequencing to the European market for €850 in May 2017. The price subsequently dropped to €449 (£400 or $499). There was a special offer in the US on Amazon Prime Day when the WGS test was on sale for $349.

What you can do with your whole genome data?
If you have your whole genome sequenced what can you do with the data? There are currently no companies that offer a relative-matching service using WGS. If you want to use a WGS test to search for relative matches you will need to extract the relevant SNPs to create a kit suitable for upload to GEDmatch. Thomas Krahn from YSEQ has provided some free code on Github to extract a 23andMe (v3) style file from a whole genome sequence BAM file (raw data file). Make sure you check out GEDmatch's revised terms of service first.

If you are interesting in discovering new SNPs from your WGS Y-chromosome data there are various tools that allow you to work with BAM files. YFull is already able to process BAM files from Dante Labs. Full Genomes Corporation offers a whole genome sequencing interpretation service for $75 and an advanced analysis for $250. The R1b Data Warehouse submission process has already been reconfigured to accept VCF files from Dante Labs and they can process WGS BAMs submitted to http://haplogroup-r.org/submit.html, However, at the moment no one appears to be working with these files.

You can also upload your whole genome sequence to the literature retrieval service Promethease to get a range of health and trait reports.

Dante Labs WGS data can also be uploaded to Sequencing.com where you can share your data for research and purchase reports from their app store.

There are also many other sites where you can share or upload your raw data. See the list of raw DNA data  tools in the ISOGG Wiki.

Other whole genome sequencing providers
Direct-to-the-consumer whole genome sequencing is available from Thomas Krahn's company YSEQ at 15x, 30x and 50x. The 15x test currently costs $740. There is an additional fee of $600 for a 30x test and a $100 fee for Sanger sequencing confirmation if required. The YSEQ test includes genealogically relevant reports for the Y-chromosome and mitochondrial DNA. YSEQ ships worldwide.

Full Genomes Corporation also provides a range of direct-to-the-consumer whole genome sequencing services as well as Y-chromosome sequencing options but sadly they stopped selling to European Union countries in May as a result of the EU's new General Data Protection Regulation (GDPR).

Nebula Genomics announced this week that they were offering low coverage 0.4x whole genome sequencing for $99. They are testing a model using cryptography and blockchain technology which will allow consumers to sell their health data to researchers and choose which research they would like to participate in. If you want a medical grade 30x sequence you would have to hope that a company or research organisation would be sufficiently interested in your data to pay for the sequencing.

There are various American companies that sell whole genome sequencing such as Veritas Genetics and Sure Genomics but they don't sell their tests outside the US and you also need to order through a doctor.

There were rumours circulating on Twitter last week that Illumina would be announcing a $100 genome in the next few months. We might therefore see other companies trying to jump on the WGS bandwagon in the next few months or additional offers in the run-up to Christmas. However, I understand that Dante are using BGI sequencing technology and not Illumina. It will be interesting to see how the market plays out.

See also this discussion A 30x full-genome sequence for $199 (€169 £150) on the Wikitree G2G forum.

Further reading
Dante Labs and the $1000 genome by Rebekah Canada

Acknowledgements
Thanks to Thomas Krahn for the information about the BGI sequencing technology used by Dante Labs. Thanks to James Kane for the information about the R1b Data Warehouse and Sequencing.com.

Thursday, 13 September 2018

MyHeritage now accepts transfers from Living DNA and 23andMe but will soon start charging for some features

MyHeritage have announced that they can now accept uploads from people who have tested at Living DNA and on the 23andMe v5 chip. Both these companies currently use the Illumina Global Screening Array chip, which has very limited overlap with the chips used by the other testing companies.

MyHeritage have also announced that they will soon be introducing charges to access some features. Here's an extract from their blog.
As of December 1, 2018, our policy regarding DNA uploads will change: DNA Matching will remain free for uploaded DNA data, but unlocking additional DNA features (for example, ethnicity estimate, chromosome browser, and some others) will require an extra payment for DNA files uploaded after this date. We will announce the full details of the new policy once it is finalized, closer to December 1st. All DNA data that was uploaded to MyHeritage in the past, and all DNA data that is uploaded now and prior to December 1, 2018, will continue to enjoy full access to all DNA features for free. These uploads will be grandfathered in and will remain free.
To read the full article click here.

If you've not yet added your kit to the MyHeritage database make sure you do so before the deadline. MyHeritage have some useful features for interpreting results, and they are also promoting their tests in some European countries, such as Germany and the Netherlands, that are poorly represented in the other company databases. MyHeritage also have a useful feature which allows you to see the countries where your matches live. Although my match list is still dominated by distant matches with Americans I now have 368 matches with people living in Britain as well as 130 Australian matches. I have quite a few cousins in Australia that I'm hoping to make connections with. It's always a good idea to have your DNA represented in all the databases as you never know where you're going to get the breakthrough matches.


Updated Ethnicity Estimates now available for everyone at AncestryDNA

I wrote back in June about my updated Ethnicity Estimate at AncestryDNA. Yesterday AncestryDNA rolled out the updates to everyone in their database. Many people will find that the changes are quite dramatic. I went from being just 21% Great Britain to 94% England and Wales, and my results are now a much better reflection of my recent ancestry within the last few hundred years. There have been a few tweaks since I got my results and the England and Wales cluster has now been renamed as England, Wales and Northwestern Europe.


The improvements have been made possible by the inclusion of many more people in the reference panel, which has now gone up from 3,000 to 16,000 samples. Previously Ancestry had just 111 samples from Great Britain, 138 from Ireland and 166 from Europe West. Now they have 1,519 samples from England, Wales and Northwestern Europe, 500 from Ireland and Scotland, 1,407 from France and 2072 from Germanic Europe. AncestryDNA are also using a different methodology and are comparing long stretches of linked markers rather than single markers in isolation. This means that the results are a reflection of our more recent ancestry within the last 500 to 1000 years rather than our distant ancestry from one thousand or more years ago.

AncestryDNA have written a White Paper explaining the methodology, which includes details of all the reference populations used. They will also be publishing a scientific paper about their methods.

Most people with British and Irish ancestry have found that their results are greatly improved and are much more in line with their known ancestry. The results will be more mixed for people from other countries. You can only be matched to the populations in the reference panel so if your country is not represented you will be matched to the next closest population. For example, AncestryDNA now has reference populations for Norway, Sweden and Finland but no distinct dataset for Denmark. Danes are therefore likely to get matched with Norway and Sweden or England, Wales and Northwestern Europe.

India, with a vast and diverse population of over 1.3 billion people, is poorly represented with just 65 samples from Western and Central India. There is also still a long way to go to get more meaningful results for people with African ancestry. There is more genetic diversity in Africa than in the rest of the world combined, which means that much larger reference panels are needed to capture this diversity. Ancestry are addressing this problem by starting an African Diversity Project, and we can look forward to further improvements in the years to come.

I always used to say that "ethnicity" estimates should be taken with a large pinch of salt and are really only of entertainment value, but we are now starting to get the stage where the results for some people can provide a reasonable approximation of their ancestry. If you've already done your family history research, the results won't tell you anything more than you already know, but at least there should now be a lot less confusion. As more populations are added to the reference panels we can expect to see similar improvements for other populations.

Update 15th September 2018
AncestryDNA will be presenting a poster at the ASHG conference in San Diego in October on Polly, the algorithm they are using for their updated ethnicity estimates. Here are the details:
PgmNr 2772/W: High-throughput local ancestry inference reveals fine-scale population history 
Authors:A. Sedghifar1; S. Song1; Y. Wang1; K. Noto1; J. Byrnes1; E.L. Hong1; K.G. Chahine1; C.A. Ball2 
Affiliations:
1) AncestryDNA, San Francisco, CA.; 2) AncestryDNA, Lehi, UT.  
An individual’s genome can be viewed as a mosaic of haplotype blocks from different ancestral origins, the sizes of which depend on the timing of admixture events. Recovering the length of these local ancestry blocks, together with their ethnic origin, provides information on the admixture and recombination events that shape current day genomes, thus shedding light on personal history as well as population history. As genomic databases rapidly approach sizes on the order of millions of genomes, there is an increased demand for super efficient approaches to identifying local ancestry blocks. Our team has developed Polly, an ultra fast algorithm for estimating genome-wide ancestry proportions in admixed individuals. Here, we present a modification of the Polly algorithm for accurately inferring local ancestry blocks. We evaluated the performance of our algorithm on simulated admixed individuals, and also assessed accuracy of estimated tract length distributions in admixed populations. Finally, we applied our method to estimate tract length distributions in historically admixed African American and Latin American populations.
The poster can be seen here.

The ASHG abstracts can be searched here.

Further reading
I've provided links below to the various official documents from AncestryDNA along with links to a few other blogs which might be of interest.

AncestryDNA links
Blogs