Wednesday, February 29, 2012

Exome Testing at 23andMe - For Genetic Genealogy?

Since I have been curious about this project, but am not personally participating, Dr. Tim Janzen kindly wrote an update on 23andMe's Exome Testing for the readers of this blog:

In November 2011 the genetic testing company 23andMe rolled out a pilot project to sequence the exomes of project participants as a complement to its current test that analyzes approximately 1,000,000 SNPs.  The exome project is detailed at www.23andMe.com/exome.  The cost for participating in this project is $999.  23andMe is using an Agilent exome capture system and an Illumina HiSeq 2000 machine to sequence the DNA in the exome at approximately 80 times coverage.  The exome comprises about 1.5% of the entire human genome and includes approximately 50,000,000 base pairs.  The exome includes all of the coding portions of the genes that are used to make proteins.  23andMe customers who enrolled in the project had to submit additional DNA as saliva samples.  The earliest participants in the project received their special exome DNA collection kits in December 2011. The data for those people who have returned their kits is now starting to come back from the lab to 23andMe's headquarters.  One of 23andMe's specialists in bioinformatics, Brian Naughton, is heading up the exome project.  Brian has sent two e-mails to the project's participants updating them about the project, one in January and the most recent one on February 17.  No customers have yet received their exome results, but it seems probable that within the next several months at least some project participants will be receiving their results.  Brian estimates that the size of the data file including all of the variants (SNPs, insertions, and deletions) will be approximately 10-20 MB in size.
 
So how is exome testing going to be helpful for the typical genetic genealogist?  It is still somewhat early to say for sure, but exome testing will without doubt reveal specific autosomal SNPs and other variants (insertions and deletions) that are unique to specific family lines.  These SNPs in some cases will have occurred within the past one to two generations, but in other cases they will have occurred hundreds or even thousands of years ago.  These autosomal SNPs will likely help us trace specific ancestral lines once we can link specific SNPs to specific ancestors.  Once a SNP has been linked to a particular ancestor then essentially any person who carries that specific SNP will be established as a descendant of the first ancestor in which that mutation occurred (unless the mutation in question has occurred more than once in human history). Each autosomal SNP that is found in the exome should be cataloged and an attempt should be made to determine which ancestor the SNP was inherited from.  It seems highly probable that autosomal SNPs will be used in conjunction with matching half identical regions (HIRs) to help map segments of chromosomes to specific ancestors.  Autosomal SNPs could also be used to map very tiny segments of DNA (under one to two cMs in length) that are too small to be identified via the typical mapping procedure for larger DNA segments.  
Exome testing is simply the first step toward complete genome sequencing.  It seems likely that 23andMe at some point in the future will begin offering complete genome sequencing.  Relatively few people in the genetic genealogy community have done complete genome sequencing up to this point in time.  However, within the next 5 years it will be commonplace for genetic genealogists to do complete genome sequencing.  Ideally, autosomal DNA data will be pooled and will be matched with pedigree charts so that DNA segments can be accurately linked to specific ancestors.  It will be exciting to watch this unfold in the coming years and to see how exome testing and complete genome testing impacts genealogical research!

 
Tim Janzen is a family practice physician in Portland, Oregon and a long-time genetic genealogist. He serves as one of six 23andMe Ancestry Ambassadors as well as on the ISOGG Y-DNA Haplogroup Tree committee. He is a leading researcher in autosomal DNA for genealogy.

Sunday, February 26, 2012

"SNiP of the Week" - News from the World of Genetic Genealogy

This week in genetic genealogy:

1. On Friday night, the long-anticipated episode of Who Do You Think You Are? featuring Blair Underwood and Ancestry.com's new autosomal DNA test finally aired. As expected, there has been some controversy regarding the apparent specificity of the prediction of Blair's "10th cousin" from Cameroon (read Blaine Bettinger's take on it here). As I have expressed on various forums over the last couple weeks, it is my opinion that it is impossible to accurately predict the level of relationship past 4th cousins using autosomal DNA exclusively. After about five or six generations of random recombination, the autosomal DNA is so mixed up that there is just no way to determine if a matching block of DNA came from your fourth great grandparents or your tenth great grandparents without extensive testing of other parties. My guess is that Ancestry.com was using Y-DNA in this prediction since the "cousin" stated that he tested back in 2005 and twice it is mentioned that this match is on Blair's paternal side. Perhaps, they got really lucky and he matched the Cameroon cousin on both atDNA and Y-DNA, which helped them to come to this conclusion. Regardless, the specificity of the prediction seems overly confident. 
The links on the interface to "Contact" the match or "View tree" looked promising. 
The biogeographical ancestral breakdown that Blair received from Ancestry.com was quite impressive, with the inclusion of several specific African tribes. Since Blair's "cousin" Eric Sonjowoh stated that he donated his DNA in 2005, then it has been suggested that, perhaps, he was tested originally by Sorenson. However, there is no one with the surname Sonjowoh listed on their site (thanks to Dr. Ann Turner for pointing this out). This leaves the possibility that he may have been tested by African Ancestry or even the Genographic Project which launched in 2005. Could the "guy" Eric referred to who took his DNA be Spencer Wells? In his book, Deep Ancestry, Dr. Wells mentions a trip he took to Chad in October and November of 2005 (page 172) to collect samples from the indigenous African population there. Since Chad lies adjacent to Cameroon, perhaps his team ventured over the border to collect samples in that country too. Who knows? The anticipation for the release of this new offering from AncestryDNA and the associated details is ever increasing.  [Update - Judy Russell from "The Legal Genealogist" blog points out that the sample can't be from the Genographic Project due to their privacy policy.]


2. This weekend the "world's largest genealogy conference" Who Do You Think You Are Live! was held in London. We had several International Society Of Genetic Genealogy (ISOGG) representatives there educating the Brits on genetic genealogy. Dick Eastman reports that the Family Tree DNA and ISOGG booths were "constantly crowded". He states regarding the dedicated genetic genealogy area, "...the lecture area was packed and a few times people were standing in the back and along the side, listening to DNA lectures." ISOGG Director Katherine Borges reports that "Friday was a smash! FTDNA went through a whole bag of kits (and) passed out 500 flyers..." Debbie Kennett, author of DNA and Social Networking, was working at the ISOGG booth and says it was "much busier" than last year and FTDNA ended the show with only three DNA collection kits remaining! Derrell Teat reported that ISOGG signed up 83 new members and many testers took advantage of the offers of free testing that were sponsored by various surname projects with the hope of getting the US testers' genealogy extended "across the pond". Debbie also reported that she, Brian Swann, Katherine Borges, Emily Aulicino, James Irvine, Chris Pomery and Geoff Swinfield met up with Dr. Bruce Winney from the People of the British Isles Project and Dr. Turi King. She tells me, "They have some very interesting results showing distinct DNA regions within the UK. They're finding ancient haploblocks that are specific to particular areas. There will be some papers coming out soon but it will be a while before the testing companies will be able to incorporate the results in their admixture analyses."
It is encouraging that WDYTYA Live! was such a success this year and that the interest in genetic genealogy appears to be ever increasing. 


3. This week the OpenSNP blog announced the opportunity to apply for free genotyping from 23andMe. Phillipp from the study tells me, "First, we're looking for people who pass the tiny true/false test (and thus know a bit about the potential consequences of an open genotyping). We don't have any specific targets in genotypings - we thought that the more interesting, rare or unresearched a phenotype is, the more 'points' that person will get in the end. Then we have to adjust the amount of genotypings we can give out to 23andMe's delivery costs which seem to vary greatly by country." Not surprisingly, underrepresented types will get priority over "WEIRDS". Here is a video that has more details on their work.

4. 23andMe announced that Muhammad Ali has joined their efforts to research Parkinson's Disease and premiered their new video, featuring Ali, at his 70th birthday celebration last weekend. The 23andMe Parkinson's Initiative, launched in 2009, has the goal of genotyping 10,000 Parkinson's suffers to advance the research on the disease and "accelerate the search for a cure". Presently, they have 6,710 participants and are hoping that this new partnership will increase visibility and enrollment in the study. If you or someone you care about has been diagnosed with Parkinson's, please encourage them to join the fight against this terrible disease by applying for a free lifetime membership to 23andMe. (This initiative is close to my heart since my father died from Parkinson's in 2008.)

5. Happily, the results for the majority of the 23andMe raw data transfers to Family Tree DNA finally came in this week. Many customers experienced new genealogical successes with the resulting matches, including myself. I was excited to find a new Hemings-Jefferson descendant for my autosomal DNA Project.

Another banner week for genetic genealogy!

[Disclosure - my company StudioINTV has an existing production agreement with FTDNA that has no bearing on the opinions I express. I also receive a small commission from FTDNA on non-sale orders through my affiliate link, which I use to fund DNA tests. I am currently serving in a volunteer advisory position for 23andMe, for which I may receive a small number of 23andMe kits for my DNA research.  Any opinions that I express here on my blog are my own and do not reflect those of management at either company.  I receive no other compensation in relation to any of the companies or products referenced in my blog.]

Monday, February 20, 2012

Opportunity to Apply for OpenSNP's Free 23andMe Genotyping

I'm passing along this great opportunity to my readers. If interested, please click through to the OpenSNP blog to apply and ask questions. Good luck!


New post on openSNP

Apply now for a free genotyping

by Bastian
At the end of last year we announced that we've got some funding from the German WikiMedia foundation to get more people – who are willing to share their results – genotyped. We have now settled on a process that should allow us to perform the project without too many problems. Starting today, you can apply for one of the free genotypings. The deadline for applications is Sunday, 03/25/12 23:59 o'clock, so you still have some time to think about an application. In the two weeks following the deadline, we will select as many participants as we can afford to get genotyped using the 5000 Euros we received from Wikimedia. We'll get in contact with everybody who has sent an application to let all applicants know whether their application was successful or not.
The genotyping will be done through 23andMe. We will order you a gift kit which will be delivered to your address. These gift kits include prepaid access to the 23andMe website for 12 months, so you can check up on the latest findings about your genetic variation as well. After this 12 month period, those features will expire automatically, you don't have to cancel any subscriptions.
Our application form contains some standard questions (Where do you live? Does 23andMe deliver to your country? etc.) but also some details about your motivation, why you want to make your dataset available to the public and why your data might be of great interest (For example: Do you have a rare disease where research is lacking?). Additionally, we will also try to get people genotyped who are currently under-represented in publicly available data sets. Most data up to now is from WEIRDs: Western, Educated, Industrialized, Rich and Democratic people (most are probably male, too).
We would like you to deposit the final raw data, which you will then be able to download from 23andMe, into the openSNP database, ideally along with some phenotypic information about yourself. So please think about the possible consequences which may arise by doing so before you apply for one of the genotypings. The application process has some questions about possible consequences as well (just so we get a feeling of whether you know what you are doing). If you get your results, but then find the results too problematic to publish: That is fine. We are aware of this possibility and while it would suck for us as it means less data, you are the one who has the last word in this matter. Some information that might make you a bit more comfortable with the idea of sharing data: We won't release the names of any applicants (whether successful or unsuccessful) and you can sign up to openSNP using a pseudonym, plus we don't log any IPs used to access openSNP.

We offer you the chance to get genotyped through 23andMe for free if you are willing to share the data with the public. Here's the planned schedule:
  • Until 03/25/12 23:59 o'clock you can apply for a genotyping using this application form
  • We select the lucky winners between 03/26/12 and 04/08/12 and get in contact with every applicant.
  • Mid-April: You should receive the 23andMe-kits in your mail.
  • End of May: You should receive the results of the genotyping, so you can upload the results to openSNP.
If you've got any questions regarding the application process, the schedule etc., just let us know using the comments or write us an email to info@opensnp.org. We will try to answer all of your questions as fast as possible.
Good luck,
your openSNP-team!
Bastian | February 20, 2012 at 4:34 pm | Categories: Uncategorized | URL: http://wp.me/p1Ruc7-2B

Friday, February 17, 2012

News from the World of Genetic Genealogy - "SNiP of the Week"

There have been a few developments of note in the last few days in the world of genetic genealogy. I feel these are worth mention and demonstrate beneficial progress for all of us interested in the advancement of genetic genealogy. "SNiP of the Week - News from the World of Genetic Genealogy" is a new weekly feature of this blog.

1. MyHeritage has announced a partnership with Family Tree DNA:
MyHeritage is now offering FTDNA kits to their 62 million international customer base. MyHeritage users will receive discounts and will be encouraged to utilize DNA testing to find related individuals and grow their family trees. The testers from MyHeritage will be added to the FTDNA database and matched with already existing FTDNA customers. MyHeritage will even alert their customers if a surname project exists at FTDNA for their last name and encourage them to join (great news!). The announcement on the MyHeritage blog explains the new offerings thoroughly. In answer to a question about transferring in already existing FTDNA results to MyHeritage, "Ania" had this response: "...if you use the Family Tree Builder, you may enter the results right on there. Currently it is not possible to enter them in the site but we are working on to (sic) make this possible. We will keep you updated." The company is not currently offering the option to import DNA results from other testing companies, but says they are planning to in the future. For more information the FAQs can be accessed here.
This is definitely a step in the right direction since it is my strong belief that combining autosomal DNA test results with family trees is a necessity to further our collective research.

2. 23andMe has announced the removal of the five per day limit on sending out Relative Finder invitations:
This is the first change resulting from the new advisory panel of which I am a contributor. Although it is an incremental change and it is my understanding that it is intended only as a temporary fix while 23andMe considers solutions to the larger issues that have been brought to their attention, it does demonstrate that they are listening to their genetic genealogy customers and making an effort to improve our experience there.

3. FTDNA has announced a delay in the new Family Finder results from the recent 23andMe uploads:
"We apologize for the delay in posting your results. These last two weeks have produced some of our biggest batches of Family Finder orders ever. After the second of those batches is uploaded, we will be processing your transferred results, and expect to post them to the website next week."
Although this minor delay is unfortunate, the fact that we are seeing more autosomal DNA testing participants is great news for the genetic genealogy world.

4. Another update (and reversal) on Ancestry.com's rumored genotyping chip:
I have very good reason to believe that Ancestry.com is indeed using an Illumina OmniExpress Plus Genotyping Beadchip for their new autosomal test as I initially speculated and contrary to the information that I previously reported from an Illumina employee. If true, this is good news because it will ensure compatibility with other testing platforms. A direct quote from the Illumina CEO Jay Flatley on the February 7th earnings call regarding array orders seems to verify this, "Two large consumer orders were placed in Q4 as well, including one from ancestry.com for approximately $7 million."
I also hear rumors that Ancestry.com may be utilizing the services of Illumina's competitor Life Technologies as well.


[Disclosure - my company StudioINTV has an existing production agreement with FTDNA that has no bearing on the opinions I express. I also receive a small commission from FTDNA on non-sale orders through my affiliate link, which I use to fund DNA tests. I am currently serving in a volunteer advisory position for 23andMe, for which I may receive a small number of 23andMe kits for my DNA research.  Any opinions that I express here on my blog are my own and do not reflect those of management at either company.  I receive no other compensation in relation to any of the companies or products referenced in my blog.]