Wednesday, 19 February 2020

30x whole genome sequencing from Nebula Genomics for $299

The cost of whole genome sequencing has been slowly coming down to an affordable level. Dante Laboratories had a special offer on their direct-to-consumer (DTC) whole genome service (WGS) in November 2018 when the test was priced at €169 (£150 or $199). They now offer a 30x whole genome test for €289 (reduced from €599). 30x refers to the coverage of the test  the number of reads at each position. 30x is now the standard coverage for medical purposes. Dante are based in Italy and initially focused on the European market but now sell their test globally. They had sequenced over 10,000 genomes by the end of 2019 and are currently processing 600 to 700 genomes per week.

DTC whole genome sequencing has also been offered for several years by Full Genomes Corporation though they no longer sell their tests in the European Union. FGC offer a range of tests at different coverage as well as a long-read whole genome test for $2900. A range of DTC WGS tests is also available at varying levels of coverage from the German company YSEQ. The British company SanoGenetics launched a DTC whole genome sequence test priced at £950 at the end of 2019 with an emphasis on data security. They hope to provide access to genetic counsellors, a doctor and good links to the UK's National Health Service but it is likely to be more than a year before they are in a position to deliver on this promise.

The market is now hotting up with the announcement that Nebula Genomics have launched a new 30x whole genome sequencing service for $299 (£231 or €277). The Nebula product will be available in 188 countries. Nebula are based in the US with offices in San Francisco and Boston. The sequencing is currently being done by BGI in Hong Kong. Nebula have partnered with FamilyTreeDNA to provide an analysis of the Y-chromosome and mitochondrial DNA sequences which are included with the service. The following information about the Y-DNA and mtDNA ancestry analysis is provided in Nebula's FAQs.
It is not clear how the transfer process will work but I presume that the sequences will be uploaded to FTDNA's BigY database and mitochondrial DNA database in order to receive genealogical matches. I suspect the promise of additional ancestry reporting will be in the form of an option to transfer a Family Finder-compatible file to FTDNA's autosomal DNA database.

On top of the cost of the testing it is necessary to pay a subscription for access to Nebula's reports which are updated on a weekly basis. You can choose a monthly, annual or lifetime subscription.

It doesn't seem to be possible to order a test without paying for a subscription so it appears that you would have to sign up for at least a single subscription for one month once you have received your results.

There is further information about Nebula Genomics in this article from OneZero.

Whole genome sequencing is not likely to be of interest for the average genealogist in the immediate future. To use a WGS test for genealogy we would need to have a WGS database so that we can be matched with our genetic cousins. No such database currently exists though I suspect it's only a matter of time before an enterprising company decides to take the initiative and set up a service. For now WGS is likely to be of most interest for genealogical purposes for the Y-chromosome data to see how the sequencing compares with other sequencing products such as FamilyTreeDNA's BigY test. WGS will also appeal to advanced genetic genealogists who like manipulating and playing with big data files. For example Louis Kessler, a genetic genealogist with a background in computer programming, has purchased a number of WGS tests and has had great fun analysing the files out of sheer scientific curiosity.

None of the major genetic genealogy companies currently offers a WGS test but I suspect it's only a matter of time.

Tuesday, 7 January 2020

The end of an era: goodbye to the Rootsweb mailing lists

It was announced today that the Rootsweb genealogy mailing lists will be discontinued and archived. Here is the e-mail I received from the Rootsweb Listowners list.
Beginning March 2nd, 2020 the Mailing Lists functionality on RootsWeb will be discontinued. Users will no longer be able to send outgoing emails or accept incoming emails. Additionally, administration tools will no longer be available to list administrators and mailing lists will be put into an archival state.

Administrators may save the emails in their list prior to March 2nd. After that, mailing list archives will remain available and searchable on RootsWeb.

As an alternative to RootsWeb Mailing Lists, Ancestry message boards are a great option to network with others in the genealogy community. Message boards are available for free with an Ancestry registered account.

Thank you for being part of the RootsWeb family and contributing to this community.


The RootsWeb team
When I first started my family history research nearly 20 years ago I found that the regional Rootsweb mailing lists were an invaluable source of education and assistance, and I made many friends on these lists. Unfortunately the functionality of the lists has been greatly reduced for many years now. The lists were offline for a considerable time as a result of security issues and they were eventually transferred to a new host in July 2018. It was perhaps inevitable that with all these problems discussions would move elsewhere.

While mailing lists used to be the central focus of genealogical life, they are becoming used much less often and I find that most of my genealogy and DNA conversations now take place in the various Facebook groups and also on Twitter. I am the admin of a few surname lists on Rootsweb but no one has posted on these lists for many months. If a service is not supported it is inevitable that it will eventually disappear. The demise of the Rootsweb lists is not a big surprise, but it does feel like the end of an era.

The decline in the use of mailing lists was no doubt also a factor in the decision by Yahoo to shut down all the web hosting for their Yahoo Groups. Yahoo hosted many of the popular DNA lists as well as a number of genealogy lists. The Yahoo lists will continue to function as email lists but without any archiving facility. All the old conversations have been deleted. This is a salutary lesson that all websites need to be backed up and archived in order to ensure their preservation. I suspect a huge amount of knowledge and history has already been lost as many groups have disappeared without back ups being made.

No doubt some of the Rootsweb lists and Yahoo Groups will find a new home elsewhere. Some mailing lists have now moved over to IO Groups. I am one of the admins of the Haplogroup R1b-U016 list and we moved our U106 list from Yahoo to IO Groups. We have been very pleased with the service from IO Groups. There is a lot of additional functionality which we have found very useful. If you have been hosting a list on Rootsweb and are looking for a new platform then IO Groups would be a good alternative.

Facebook is not everyone's cup of tea but it is home to a vibrant genealogy community. Katherine Willson does a brilliant job of tracking and categorising all the genealogy and history groups on Facebook. Do check out her Genealogy on Facebook list. At the last update in May 2019 it included over 14,500 links.

If you are particularly interested in genetic genealogy check out the ISOGG Wiki list of genetic genealogy mailing lists and Facebook groups.

Facebook has over two billion users around the world so it's not going away any time soon – or at least not until the next big thing comes along and who knows what that might be?

Saturday, 4 January 2020

New lower pricing structure at FamilyTreeDNA

The FTDNA sale has now ended but the good news is that the prices haven’t gone back up to the old pricing levels and the new prices are now much lower. When ordering direct from the FTDNA home page there are now only five tests available:
  • Y-37 $119 (previously $169)
  • Y-111 $249 (previously $359)
  • BigY-700 $449 (previously $649)
  • mtDNA full sequence $159 (previously $199)
  • Family Finder autosomal DNA test $79 (no change)
The old price of the BigY-700 test included access to the raw data file (the BAM file). However, most people did not want the raw data file which meant that the price was artificially inflated for the benefit of the few. If you do want your BAM file you can now purchase it as an add on for $100.

Shipping costs $9.95 in the US and $12.95 to most international destinations.

The 25-marker test and the 67-marker test have now been discontinued. The 12-marker test is still available for $59 but can only be ordered through a project. You can access the project search menu here.

There used to be discounts available when ordering kits through projects but these discounts are no longer available. However, with the new lower prices I would hope that all of us with projects at FTDNA will see renewed interests in our projects in 2020.

In addition to the reduced prices for new tests there are also big reductions in the upgrade prices for Y-DNA tests. Dave Nicolson compiled a spreadsheet showing the new pricing which he shared in the Only FTDNA Project Administrators Group on Facebook. He has kindly given me permission to reproduce his chart below.

Discounts for members of the Guild of One-Name Studies
If you are a member of the Guild of One-Name Studies note that you can buy 37-marker tests and Family Finder tests at discounted prices from the Guild.

The Y-DNA test is currently £88 from the Guild. The cost from FTDNA is £91 at current exchange rates. Postage rates are calculated individually by the Guild and you would need to pay return postage for the kit to Texas but for most people, especially outside the US, it is likely to be cheaper to buy a 37-marker test from the Guild, and especially so if you can pick up a kit at one of the Guild events. 

You can also buy FTDNA Family Finder kits direct from the Guild for £40. This is a considerable saving on the current price of $79 from FTDNA which works out at £60 at current exchange rates. Postage would again be extra.

For further details see the page on the Guild website on DNA kits available from the Guild.

Tuesday, 17 December 2019

An update on EU kits at GEDmatch and a message from Curtis Rogers

We learnt last week that GEDmatch has been acquired by the forensics company Verogen. I now have some further information about the handling of European Union users at GEDmatch. When the sale first went through only a small number of EU users were presented with a consent form in order to access the website. We thought at the time that the form was only being shown to those who had an identifiable e-mail address in the EU. I did not have to re-consent when I first tried to log onto GEDmatch, presumably because my e-mail address had a .com suffix and not a suffix. That all changed some time last week, and Verogen are now identifying EU users by their IP address. As a result I found that I had to re-consent to use the site. Below are screenshots of the data transfer form which all EU users are now required to sign.

Having signed the form you are then presented with this screen.

You are then given the option to decide on a kit by basis which kits you would like to transfer to Verogen, which kits you would like to delete and which kits you would like to decide about later.

Many people have been reporting that they've lost a lot of matches at GEDmatch and that some of their kits have disappeared. Genetic genealogist Paul Watkins contacted Verogen and he has given me permission to share the contents of the reply he received which explains what has been happening:
While we did have issues with Kits “disappearing” this week from UK users, the main reason that matches are looking like they disappear is that people who are subject to European General Data Privacy Regulations (GDPR) have been pulled out of the database temporarily, as we are legally required to obtain consent to transfer control of users data to Verogen.

Unfortunately, in addition, to known EU users, there are also many users that we do not know their location (we use the IP address of the user when they login to determine the country of origin). This group contains a mix of users from different countries (EU, US, and ex-US users). However, because there is most certainly EU users in this unknown location group, the legal ramification of violating European GDPR is severe, and this has forced us to pull these people out of the database until they log in and consent. 
Users from the EU and those with an unknown location are logging back in, and we expect that these matches will repopulate over time. We are also reaching out proactively to these users to ask them to log in to confirm their location and accept the new terms of service.
The issue of disappearing kits appears to have been resolved and the following notice now appears when you log into GEDmatch.
Meanwhile it has been reported in the official GEDmatch Facebook group that Curtis Rogers will be sending out an e-mail to all GEDmatch users. I've copied the text of the e-mail below for reference:
To GEDmatch users, 
As you may know, on December 9 we shared the news that GEDmatch has been purchased by Verogen, Inc., a forensic genomics company whose focus is human ID. This sale took place only because I know it is a big step forward for GEDmatch, its users, and the genetic genealogical community. Since the announcement, there has been speculation about a number of things, much of it unfounded. 
There has been concern that law enforcement will have greater access to GEDmatch user information. The opposite is true. Verogen has firmly and repeatedly stated that it will fight all unauthorized law enforcement use and any warrants that may be issued. This is a stronger position than GEDmatch was previously able to implement. 
There has been concern that Verogen will eliminate GEDmatch free tools and raise Tier 1 rates. In fact, Verogen has made it clear that the free tools will remain, and there are no immediate plans to raise Tier 1 rates. 
It has been reported on social media that there is a mass exodus of kits from the GEDmatch database. There has been a temporary drop in the database size only because privacy policies in place in the various countries where our users reside require citizens to specifically approve the transfer of their data to Verogen. As users grant permission, that data will again be visible on the site. We are proactively reaching out to these users to encourage them to consent to the transfer. 
The sale to Verogen will be a tremendous benefit to genealogists. Verogen has pledged to continue the GEDmatch philosophy of providing free services. It recognizes that all information belongs to the users who have placed it on GEDmatch, that this information may be removed by the users at any time, and that strong privacy protections need to be in place. It is to Verogen’s advantage to build the consumer database, meaning more and better matches for users. Verogen recognizes that law enforcement use of genetic genealogy is here to stay and is in a better position to prevent abuses and protect privacy than GEDmatch ever could have done on its own. 
Bottom line: I am thrilled that the ideal company has purchased GEDmatch. The baby I created will now mature for the benefit of all involved. If anyone has any doubts, I may be reached at [email address redacted]. I will do my best to personally respond to all concerns. 
Curtis Rogers
It will take time for GEDmatch to settle back down after the sale but I would urge everyone to give the new owners the benefit of the doubt and to see how it all works out in the months to come.