Thursday, 3 January 2019

What we learned about fighting bad science by taking on a genetic ancestry testing company

The following blog post was written by David Balding and Debbie Kennett. It is based on an article written in collaboration with Mark Thomas and Adrian Timpson entitled The rise and fall of BritainsDNA: a tale of misleading claims, media manipulation and threats to academic freedompublished in the peer-reviewed journal Genealogy. In just a few weeks the article has achieved the distinction of being the most viewed article in the journal's history. As of today's date it has been seen 3,658 times, and 2,190 people have downloaded a copy of the article. The blog post was originally intended for publication in The Conversation. However, the piece was subsequently rejected because the website's lawyer considered that it was "potentially defamatory in its current state". The Defamation Act of 2013 includes a provision for matters of public interest and provides special privileges for statements published in peer-reviewed journals. We believe that there is a strong public interest in highlighting this story. It is important that academic debate is not stifled by legal threats. There is nothing in the blog post which is not already referenced in our peer-reviewed article. We have therefore published it below in its entirety. 

The worlds of academia and industry are getting closer than ever before. Academic scientists are encouraged to engage directly with industry through consultancy roles, and to commercialise their research through the creation of new enterprises. At the same time, research institutions encourage promotion of resulting new findings to a broad public through the news media.

These trends can lead to conflicts of interest. Media savvy companies can and do attract free coverage for their science-related business under the guise of a public interest science story. It is possible that universities could collude with this deception in their eagerness to attract media attention by allowing a scientist to use the university brand in media presentations, without acknowledging the business motivation.

Our new case study of the former consumer genetic ancestry testing company BritainsDNA, published in the journal Genealogy, sheds light on how conflicts of interests can play out in reality.

Genetic ancestry tests are important tools for genealogists when used in combination with documentary and historical records. Y-chromosome DNA (Y-DNA) tests can be used to trace a man’s paternal ancestry, while mitochondrial DNA (mtDNA) provides information about ancestry on the direct maternal line. There are also autosomal DNA tests (the autosomes are the chromosomes other than the X, Y and mtDNA, and contain most of your DNA) which are useful in finding matches with genetic relatives in a database. Autosomal DNA tests are now the most popular tests. Ancestry testing is a multi-million-dollar industry, and around 18m people have now tested worldwide.

Such tests can be very reliable to reveal ancestry in recent generations. However, once you go beyond about 10 generations back, only a small fraction of the DNA of ancestors will have contributed to a living individual’s DNA. So while there’s a lot of research on human history through DNA, there is little that can be said that is specific to the customer. That means these tests cannot be used on their own to determine exactly where you came from.

The case of BritainsDNA
BritainsDNA was active before the growth of the autosomal DNA databases and focused on Y-DNA and mtDNA testing. They were able to achieve substantial favourable coverage in newspapers, radio and television, with stories drawing questionable links for example between contemporary British people and the Queen of Sheba.

In another promotion, the public service Welsh-language TV channel S4C ran a five-part series called “DNA Cymru” investigating the question of “Who are the Welsh?”. To participate, members of the public were invited to buy a Y-DNA or mtDNA test from the company’s Welsh website.

But the results of this “research” were not published in a scientific journal. Instead viewers were regaled with stories about the ancestry of celebrities, for example, that their Y-DNA or mtDNA results indicated they were ancient Welsh, pioneers or Rhinelanders. Yet these descriptions are so generic that they apply to ancestors of almost anyone: they are essentially meaningless. Y-DNA and mtDNA comprise just 2% of our DNA, and convey very limited information about the history of a nation.

So how could this happen? Two principal actors in the company were a geneticist from The University of Edinburgh and an historian and former television executive who at the time held an unpaid position as Rector of St Andrews University.

The university roles of the company’s directors were used to lend credibility to the promotions. The media outlets did not seek the views of other scientists, who would have contested many of the claims. Few journalists have scientific training, which can allow sensationalised or unbalanced reporting. And while most scientists can be relied upon to be objective, journalists need to be aware that research-related commercial interests can affect scientists’ motivations.

Challenging the claims
We formed part of a small group of concerned scientists who tried to challenge this avalanche of marketing disguised as science. This was prompted by an interview on the prestigious BBC Radio 4 Today programme, which described a “massively subsidised” project to study the DNA of Britons as “bringing the Bible to life”. In fact, the interviewee was there to sell DNA tests and the BBC interviewer turned out to be an old chum. Our challenges were met with legal threats from the company, and resistance to acknowledging editorial failure from the BBC and other media.

Many scientists don’t speak out because of a fear of legal action. We were fortunate to have strong support from the then UCL Provost, and from many colleagues. So we decided to continue to challenge the misleading claims. We were also encouraged by the science writer Simon Singh, who had himself been sued by the British Chiropractic Association for critical comments made in The Guardian. Although the case against Singh was eventually dropped, he suffered years of personal stress and substantial unrecovered legal costs. We also received support from the charity Sense About Science, and we worked with them to prepare the pamphlet Sense about Genetic Ancestry Testing and an article on Sense about Genealogical DNA Testing.

The satirical magazine Private Eye was the only media outlet to see through the company’s misleading media campaign from the start. But eventually we had complaints upheld by the BBC, which also aired a radio documentary that partly corrected previous claims.

Over a period of years we got the upper hand. The company did not pursue its legal threat and eventually went out of business. With a move to genome-wide genetic data, containing more information than is available from Y-DNA and mtDNA, there is reduced scope for fanciful storytelling today. However, there remain problems with ancestry companies failing to reveal limitations of their analyses or to indicate uncertainty in inferences. The population labels that are used are not well defined and can conform to outdated notions of race and identity.

Our story has wider implications about the relationships between business and academia and the reporting of science stories in the media. We hope that our case study will be used to inform media training and education programmes, and that universities monitor the abuse of academic position to advance business interests. Most importantly, we hope that other scientists will be encouraged by our experience and will not be afraid to speak out against bad science.

Further reading
Academics pan Melrose-based DNA business  an overview of our paper from Ewan Lamb on the Not Just Sheep and Rugby blog.
Talking Headlines with Debbie Kennett - My interview with Talking Headlines about our BritainsDNA paper, the lessons learnt and how to detect fake science news.

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.