Friday, 12 May 2017

New issue of the revived Journal of Genetic Genealogy


The first issue (Volume 8 Number 1) of the newly relaunched Journal of Genetic Genealogy (JoGG) is now available online. Some of the articles were published online as preprints towards the end of last year but this is now the complete issue.

JOGG is a free open access peer reviewed journal which provides a much-needed platform for publication of articles on all aspects of genetic genealogy. Here is a description of the journal's aims and scope:
Topics include, but are not limited to, autosomal DNA inheritance, surname DNA projects, geographic patterns in genetic data, phylogenetic analyses, haplogroup categorization, and mutation rates. Genetic genealogists have access to larger datasets with more markers than are usually available to genetic researchers, although the sampling may not be random (e.g., surname studies) and the datasets may vary in quality (e.g., inconsistent marker sampling). Therefore, JoGG is a forum for research that may not fall within the scope of more genetically oriented journals. The journal is likely to have an audience in both the lay and academic communities.
Thank you to Leah Larkin for taking on the role of editor and thank you to Linda Magellan for all her hard work on the website and preparing the content for online publication.

Contributions for future issues of the journal are welcome. Detailed instructions can be found on the Instructions for authors page.

Here is a list of contents for the new issue:

Reports
Y-DNA Testing of a Paper Trail - The Fox Surname Project
By Joseph M. Fox III and David E. Fox

Evidence of early gene flow between Ashkenazi Jews and non-Jewish European inmictochondral DNA haplogroup H7
By Doron Yacobi and Felice L. Bedford, Ph.D.

Columns, Editorials and Features

Editor's Corner
Leah Larkin, Ph.D.
Welcome to the new Journal of Genetic Genealogy

Satiable Curiosity
Ann Turner, M.D.
Generation Gaps: A Sign of Microdeletions?

CeCe Moore
The History of Genetic Genealogy and Unknown Parentage Research: AnInsider's View

Blaine T. Bettinger, Ph.D., J.D.
The Shared cM Project: A Demonstration of the Power of Citizen Science

Reviews and announcements

Review By:  Leah Larkin, Ph.D.
App:  Genome Mate Pro 

Review By:  Jennifer Armstrong Zinck
Book:  Genetic Genealogy in Practice
Authors:  Blaine T. Bettinger and Debbie Parker Wayne

Further reading
The Journal of Genetic Genealogy and scientific publishing by Leah Larkin. The DNA Geek, 12 May 2017.

UCL workshop on "Personal Genetic Testing: Challenges, Pitfalls, and Benefits in and Beyond the Clinic"

The front entrance of UCL. Photo by Neil Turner.
Originally published on Flickr under a Creative Commons Licence.
We are hosting a workshop at University College London (UCL) on 27th June on “Personal Genetic Testing: Challenges, Pitfalls, and Benefits in and Beyond the Clinic”

It will take place between 09.45 and 19.30 at the UCL Anthropology Department, 14 Taviton Street, London.
The event is free to attend but there are only a limited number of spaces at the venue so if you are interested in coming along make sure you register at EventBrite:

https://www.eventbrite.co.uk/e/personal-genetic-testing-challenges-and-benefits-in-and-beyond-the-clinic-tickets-34145019673

Here is the timetable for the meeting:

09.45. Welcome

10.00. Keynote Speech: Genetics and Identity - Adam Rutherford (BBC)

11.00-11.20. ~ Coffee Break ~

11.20. Science of Ancestry Testing, Focus Group - Garrett Hellenthal (UCL), Debbie Kennett (UCL), Turi King (University of Leicester), David Nicholson (Living DNA), Mike Mulligan (AncestryDNA), Mark Thomas (Moderator, UCL)

12.20-13.30. ~ Lunch ~

13.30. Ethical Issues in Personal Genetic Testing, Panel - Ernesto Schwartz-Marin (Durham University), Speaker TBC, Matthias Wienroth (Moderator, Northumbria University)

14.30. Social Science Perspectives on Personal Genetic Testing and Identity, Panel - Catherine Nash (Queen Mary University), Speaker TBC, Sahra Gibbon (Moderator, UCL)

15.30-16.00. ~ Coffee break ~

16.00. Security and Privacy Challenges in Genomics, Tutorial - Emiliano De Cristofaro (UCL)

17.00. Medical and Research Aspects of Personal Genetic Testing, Short Talks - Stephen Beck (UCL), David Bentley (Illumina), Joyce Harper (UCL, moderator)

18.00. Reception

Please note that the agenda may change and will be confirmed a few days before the event as we are still finalising some invitations. Please check the Eventbrite page for updates.

Abstract
The rapid growth of the Personal Genetic Testing (PGT) market raises a number of important scientific, ethical, legal and social concerns, including data security, privacy, and identity, as well as issues around the accuracy, utility, and communication of inferences regarding ancestry, biological predispositions, disease vulnerability, and the sharing of personal data with third parties.

At the same time, PGT has great potential value to individuals and healthcare providers. Realising this potential requires evidence-based standards for translating commercial genetic testing data into actionable medical information, and educating clinicians and the public on what can and cannot be inferred from personal genomes.

Sponsored by the UCL Grand Challenges Initiative, this workshop aims at establishing a highly interdisciplinary, highly engaged UK-based community of researchers and practitioners that are eager to tackle the various challenges associated with personal genetic testing and inform policymakers, clinicians, and companies.

Monday, 8 May 2017

Dante Labs offers whole genome sequencing to European market for €850


A new biotech start-up by the name of Dante Labs is joining a growing number of companies who are offering whole genome sequencing at ever more competitive prices. Dante is a global company based in the US but with an office in Italy. They are catering specifically for the European market and are offering a high-coverage (30x) whole genome sequencing test with interpretation for €850 (about £718 or US $929 at current exchange rates). Customers can have access to their raw data on request.

It is not clear what is provided with the Dante Laboratories interpretation service. There are no sample reports available on the website and no details are provided of the scientific personnel who will be doing the analysis.

Many of the companies selling whole genome sequencing tests (eg, Veritas Genetics and Sure Genomics) only sell their test in the US and require the customer to order through a doctor whereas the test from Dante is available direct to the consumer. There are two companies  Full Genomes Corporation and YSEQ  which sell whole genome testing worldwide for the genetic genealogy market. Both companies specialise in the interpretation of Y-chromosome results and do not provide medical reports.

For details of other companies offering whole genome sequencing see the list of DNA testing companies in the ISOGG Wiki.

Below is the press release I received from Dante Labs.
Dante Labs offers EUR 850 Whole Genome Sequencing 
THE INTERNATIONAL BIOTECH COMPANY OFFERS FOR THE FIRST TIME IN THE WORLD WHOLE GENOME SEQUENCING AND INTERPRETATION AT ONLY EUR 850, MARKING A HISTORIC STEP IN THE DEMOCRATIZATION OF GENETICS. 
New York, NY April 18, 2017 – Dante Labs today announced that they are offering 
Whole Genome Sequencing (WGS) and interpretation at only EUR 850 (ca. $900). While American individuals were able to access whole genome sequencing at $1,000, this innovation marks the first time Europeans can access whole genome sequencing below EUR 1,000. 
The sequencing includes bioinformatics analysis and interpretation, which are crucial to leverage genetic information and apply it into decisions about disease monitoring, prevention, nutrition, exercise, health monitoring and more. 
The Whole Genome Sequencing is run at 30X, which makes the achievement even more impressive. 
Dante Labs has chosen a selected list of partners to develop DNA sequencing services “accessible to everyone”. “By leveraging only the world’s best genetic technologies, we ensure that our customers have access to the best in the world of genetics,” says Dante Labs co-founder Andrea Riposati. “Genetics has seen tremendous developments in the last decade. Just think that the first whole genome sequencing cost north of $2.4 billion. For too long, only few people could benefit from the impact of genetic research. It’s healthcare, so I say it is important everyone benefits from it. The key to empower everyone with high-quality, advanced genetics it is to decrease the price. By integrating in the value chain, removing unnecessary intermediaries, developing synergies with strategic partners and leveraging economies of scale, we are able to offer the whole genome sequencing at only EUR 850.” 
Dante Labs offers a suite of direct-to-consumer DNA tests, including BRCA1 and BRAC2 sequencing, Whole Exome Sequencing and Common Hereditary Cancer. 
About Dante Labs
Founded in 2016, Dante Labs is a global pioneer in developing direct-to-consumer genetic services. The company mission is to empower people with knowledge and insights about their own genetic information so that they can live healthy, long and happy lives. Dante Labs has offices in the US and Europe.

Saturday, 29 April 2017

Who Do You Think You Are? Live 2017

It has been a very busy April. At the beginning of the month I was away for the weekend at the Guild of One-Name Studies conference in Boorley Green, SouthamptonWho Do You Think You Are? Live was held the following weekend at the NEC in Birmingham. We then went away for a short family break in Dorset. As a result I've had a lot of catching up to do and I've only just had the chance to do my usual write-up of WDYTYA Live.

WDYTYA is always the highlight of the genealogical calendar in the UK. It's the largest family history show in the UK and in Europe, and is the one event that is not to be missed. It's always good to catch up with friends, and meet new people, but three days is never enough, especially when you are giving talks, organising speakers and helping out on a stand. There were many people I would like to have seen but didn't get a chance to speak to.

In one of my volunteer roles for ISOGG (the International Society of Genetic Genealogy) I once again helped to organise the lecture schedule for the DNA workshop. Family Tree DNA very kindly provided sponsorship for the lecture theatre. We had another great line-up of speakers. We are very grateful to the genetic genealogists and academics who gave so generously of their free time, and especially so as none of the speakers receives an honorarium or reimbursement of expenses.

Thanks to the sterling efforts of Maurice Gleeson, most of the talks have been recorded and will be uploaded to the Who Do You Think You Are? DNA Lectures channel on YouTube over the course of the next couple of weeks. To get an idea of the delights in store you can check out the DNA lecture schedule here.

I presented a talk on autosomal DNA demystified, and was very pleased that Tony Wood, a member of my Devon DNA Project, was able to join me and share his story with the audience. Tony has been using both Y-DNA and autosomal DNA to try to identify the father of his illegitimate great-grandfather James Polyblank Wood. James was born on 15th July 1870 in Kingsbridge Union Workhouse in Devon and was the son of Sarah Wood. Previously genealogists would struggle to identify the father in such situations but genetic genealogy is now starting to provide answers.

Tony belongs to haplogroup N-P189.2, which is rarely seen in the for UK and occurs today at the highest frequency in Serbia. Uros Uzelac, the volunteer administrator of the Haplogroup N-P189.2 Project at Family Tree DNA, has taken a special interest in Tony's Y-DNA results, and was able to come along to WDYTYA to meet Tony. The photo below shows Tony and Uros meeting Max Blankfeld, Vice President of Operations and Marketing at Family Tree DNA.

Uros Uzelac, Max Blankfeld and Tony Wood
DNA testing had a major presence at WDYTYA this year and seemed to be a major topic of conversation. There were four companies selling DNA tests: Family Tree DNA, AncestryDNA, Living DNA and MyHeritage DNA. All the companies had special show prices, and there were lots of people stocking up and buying multiple DNA kits. We can look forward to many more matches once these tests have been processed. BritainsDNA (now trading under the name MyDNA.Global) were noticeable for their absence for the second year running.

I'd written a buyer's guide to DNA testing for the May issue of Who Do You Think You Are? Magazine. With immaculate timing early issues of the magazine had arrived at the NEC just in time for the opening. I was delighted to discover that my article is featured on the front cover. There is a preview of my article on the WDYTYA Magazine website but you'll need to buy the magazine to see the testing company comparisons.



Family Tree DNA
Family Tree DNA had a stand opposite the DNA lecture area. The were selling their Family Finder test for just £40, and had special offers on their Y-DNA and mtDNA tests too. The BigY test was on sale for existing customers, and a number of people took the opportunity to upgrade their kits. There seemed to be a constant crowd of people around the FTDNA stand.


I was delighted to see Princess Maria Sviatopolk-Mirski again. We first met at WDYTYA Live in 2010 when the show was held at Olympia in London. I wrote about Princess Maria's interesting mtDNA results here. She had made a special visit to WDYTYA so that she could upgrade her mtDNA test to the full mitochondrial sequence. She belongs to the very rare haplogroup R0a, and it will be interesting to see what her full sequence test reveals.

Living DNA
Living DNA had by far and away the most impressive stand at the show with a big flashing screen with an ever-changing array of images. They were selling their DNA test for £99, and seemed to be attracting a lot of interest.



On Thursday evening Living DNA invited about twenty or so genetic genealogists to a special meeting at the Hilton Metropole Hotel where we had the opportunity to learn more about their plans and to ask questions. Here are a few insights I gleaned from that meeting and from other conversations at WDYTYA:
  • The Irish grandparents' project has been going well. They have collected about 1200 samples, and an update should be ready in the next month or so.
  • Living DNA have now launched a German DNA Project. For details see my blog post A DNA Day sale at  Living DNA and the launch of a new German People Project.
  • A Scottish Project is due to launch in June. They are hoping to do similar projects in other European countries.
  • Autosomal matching is being worked on, and two different systems are currently being tested.
  • The autosomal transfers will be coming in two to three months' time for a fee. They want to make sharing and transferring from other companies very easy. The idea is that it would be done with a quick click through.
  • Living DNA hope to collaborate with other companies on trees rather than coming up with their own system.
  • Raw data downloads should be available in the next few months. They are still in the process of validating all the data from the new Illumina GSA chip.
Nick Thorne, the "Nosey Genealogist", did an interview with David Nicholson of Living DNA which can be seen on YouTube.

AncestryDNA
AncestryDNA had a major presence at WDYTYA, and were the overall sponsor of the show. They sponsored the lectures in the Celebrity Theatre, which included two DNA lectures each day. The AncestryDNA test was on sale for just £49, which was a huge saving on the usual price of £79. By picking up kits at the show visitors were also able to save on the £20 shipping fee. There seemed to be a lot of people buying multiple Ancestry kits to test their friends and relatives.


AncestryDNA had their own lecture area on their stand, where their scientists and genealogists presented a series of talks. The last session each day provided an opportunity to learn more about their new Genetic Communities feature. I didn't have the chance to attend one of these sessions but I did have a chat with Mike Mulligan, AncestryDNA's Product Manager, who was able to get answers to some of the questions that I had:
  • The threshold for matching in the Genetic Communities is currently set at 16 cMs, though it's possible that the threshold will be lowered in the future. (In the scientific paper which provided proof of concept of Genetic Communities a threshold of 12 cMs was used.)
  •  New communities will be added as they are identified rather than being rolled out all once in a big upgrade.
  • Ancestry apply a special algorithm known as Timber to downweight "pile-up regions" (sections of the genome where large numbers of people match as a result of shared human history, shared population history or some other reason). Timber wasn't mentioned in the scientific paper but I received confirmation that Timber is applied before the communities are identified. The communities work with the match data which means that the feature is only applied after the phasing and IBD identification has already taken place.
MyHeritage
I paid a visit to the MyHeritage DNA stand and had a chat with Daniel Horowitz, their Chief Genealogical Officer. I've taken advantage of the free autosomal DNA transfer to MyHeritage. At the moment the transfers are not receiving admixture reports but Daniel very kindly gave me a sneak preview of my own report. He explained that these results are not being rolled out to the people who've done the transfers. The company have been collecting reference samples and are working on providing regional breakdowns. The transfer kits will receive an admixture report once the regional breakdowns are ready to be rolled out. They are also trying to work on a chromosome browser.

I've had a lot of problems with the MyHeritage trees. I'd previously received a free three-year PremiumPlus MyHeritage subscription courtesy of a special offer from the Guild of One-Name Studies. However, once this offer expired I found that I was locked out of my account because I'd added more than 250 people to my tree. In order to transfer my DNA to MyHeritage I had to set up a new account under a different e-mail address. Daniel merged the two accounts together for me and very kindly gave me a free MyHeritage PremiumPlus subscription in consideration of my status as a "DNA expert".


Attendance
I've not yet seen the figures for the attendance at this year's show but it was my impression and that of other people I spoke to that the numbers were down on last year. A number of exhibitors from last year did not make the return trip including big names like The National Archives, Eneclann, and the National Library and Archives of Ireland. A number of family history societies who attended last year were also missing this year including the Gloucestershire Family History Society, the Hampshire Genealogical Society, the Huguenot Society, the Jersey Family History Forum, the Peterborough and District FHS and the Wharfedale FHS. There seemed to be more stands than usual given over to charities, most of which seemed to be related to dogs and cats. Perhaps they think family historians are more likely to be pet owners. Presumably these charities were given discounts to fill up some of the spaces but it would have been better to offer reduced rates to the family history societies who often struggle to pay the high costs of a stand at the show. In addition they have to pay travel expenses and provide accommodation for their volunteers so that they can man their stands for three days. I also think that the organisers could do a lot more to advertise the show, particularly in the national press.

The NEC has a spacious comfortable exhibition hall with good facilities but the venue is in the middle of a large industrial estate which is totally lacking in atmosphere and designed for cars not pedestrians. Because so many people travel to Birmingham by car or by bus, they all leave early to avoid the rush hour traffic so by mid afternoon each day the crowds start to thin out, and it becomes very quiet. I know some people prefer being in Birmingham but I would much rather that WDYTYA returned to London.

Other blog posts
A number of other bloggers have written about their experiences at WDYTYA Live:
Other resources
WDYTYA 2018
Who Do You Think You Are? Live will take place next year from 26th to 28th April 2018 at the NEC, Birmingham, so put the dates in your diary now. See you all there!

In the meantime you can enjoy some more photos from this year's show below.

Update 3rd May 2017
Immediate Media have announced that Who Do You Think You Are? Live will no longer take place for "financial reasons". The event has been running at a considerable loss and it has not been possible to bring into profit. See this blog post from Who Do You Think You Are Magazine for further details. The Society of Genealogists are hoping to arrange a replacement event. See the SOG blog for further information.

I've been advised by Else Churchill of the Society of Genealogists that attendance this year was 13,500 which was slightly up on last year, but clearly not enough to make a difference.

The long queue of people outside the NEC waiting for the doors to open.
Linda Magellan - DNA for beginners
Katherine Borges - The benefits of being a DNA project administrator
Garrett Hellenthal - The science of admixture percentages. Photo by Joss ar Gall.
Julia Bell - The strange affair of the Kings Cross baby and other mysteries solved with autosomal DNA
Maurice Gleeson - Researching your surname with Y-DNA. Photo by Joss ar Gall.
Emily Aulicino - Finding your way through DNA. Photo by Joss ar Gall.
John Cleary - What is SNP testing and how can it enhance a Y DNA surname or genealogy project? Photo by Joss ar Gall.
Mark Jobling - The Y-DNA and mtDNA landscape of Britain and Europe
Brian Swann - DNA emigration and shipping
Graham Holton - Y-chromosome SNPs in the historical era: discovering cascading hierarchies of SNPs
Linda Kerr - DNA for absolute beginners. Photo by Joss ar Gall
Michelle Leonard - What can autosomal DNA testing do for your family tree? Photo by Joss ar Gall
Dan Bradley - Recent findings in ancient Irish DNA
Mark Thomas - Ancient DNA and British genetic history.
Andrew Millard - Digging up your ancestors. Photo by Joss ar Gall
Victoria Moore - Applying forensic DNA techniques and applications to historical casework. Photo by Joss ar Gall.
Adam Rutherford - A brief history of everyone who ever lived
Debbie Kennett, Mark Thomas, Dan Bradley and Adam Rutherford
The Guild of One-Name Studies stand.
From left to right: Peggy Homans Chapman, Geoff Giles, Paul Featherstone, Sue Swalwell and Cliff Kemball.
Katherine Borges, Director of ISOGG with (left) Uros Uzelac, group administrator, N-P189.2 Project, and Gareth Henson, group administrator, Haplogroup T Project, and a member of the  ISOGG SNP tree team.
The Devon Family History Society's stand.
The ISOGG stand. Photo by Joss ar Gall.
Who Do You Think You Are? Magazine.