Upcoming Presentations: November 8th and 14th

I am speaking twice in the next week and a half - once locally and once in Austin, Texas. I hope to see some of you there! Details follow:

• November 8, 2013 - Adoption Knowledge Affiliates Conference, Austin, TX.   

1:15 – 2:45pm, Session A: Using DNA Testing to Discover the Genealogical Roots of Adoptees
Due to recent technological advances, adoptees and individuals without knowledge of their genealogy are increasingly turning to DNA testing to discover their genetic roots. The tight-knit AdoptionDNA community has been in the forefront of innovation in this area, helping many adoptees rediscover their birth families and ancestral origins. Attendees will learn some of the techniques and tools successfully used.

• November 14, 2013 - Diamond Gateway Women's Club at 6:30pm, Penasquitos, CA. Reservations required, contact Dael at 619-252-0804 or daelnk612@yahoo.com. There is a $5 fee. Mt. Carmel Church of the Nazarene, 10060 Carmel Mt. Rd., San Diego, 92129.

First Look at the Full Genomes Y-Sequencing Results from Itaï Perez

(**Warning - Advanced Content**)

Guest Blogger, Itaï Perez, reviews his Full Genome results for my readers:

For those wondering what the results from Full Genomes look like, here’s a first look.  

After a long wait while my kit was sequenced and analysed, I finally received an email from Full Genomes with an attached rar archive containing 9 files.

Almost all these files are in a formatted text format, and can easily be converted to an excel table (which I did).

Here’s the description of the 9 files, as much as I understand it, one by one:

File #1 -  PrivateSNPs

This one is easy to understand. It is a list of all Private SNPs discovered in my sequencing. Here is the description found in the beginning of the file (which I removed when converting to Excel).

#based on 20131001 variantCompare analysis using PGP083013.filt.pyfilt.1kGfilt.vcf and ALL.1kG.samplelist.redo.sorted.paths.20130812.curated_pm.filt2.called.pyfilterCG2k.vcf reference files

And here is the file itself:

The columns are SNP name, position, ancestral and derived base. The position of these new SNPs have been removed from each image in order to give the Full Genomes team time to register and name them.

File #2 -   yknot

This is the only file which is not a table. This text file includes a tree, following my positive SNPs from Y-Adam to my current most recent SNP, as defined in the ISOGG Y-tree.

 

File #3 - variantCompare

This file is more complex. Here is the description in the beginning of the file:

#FGC report: Analysis of Called Variants

#this report analyzes variants called as differing from the GRCh37 reference sequence

#for best viewing, open with tab-delimiting in a spreadsheet viewer

#reliability flag key: no flag: over 99% likely genuine; *: over 95% likely genuine; **: about 40% likely genuine; ***: about 10% likely genuine

#it is strongly suggested that results analysis be restricted to variants with zero or one asterisks

#citations for reference data include:

#            1000 Genomes Project: An integrated map of genetic variation from 1,092 human genomes, McVean et al., Nature 491, 56-65 (01 November 2012) doi: 10.11038/nature11632

#            Personal Genome Project: Ball, Madeleine P., et al. A public resource facilitating clinical use of genomes. Proceedings of the National Academy of Sciences 109.30 (2012): 11920-11927. http://www.pnas.org/content/109/30/11920.long

#            A High-Coverage Genome Sequence from an Archaic Denisovan Individual, Meyer et al. Science 338, 222-226 doi:10.1126/science.1224344

#            R. Drmanac, et. al. Science 327(5961), 78. [DOI: 10.1126/science.1181498]

GRCh37 is the Genome Reference Consortium human genome (build 37). I guess it is a reference genome similar to CRS or RSRS for mtDNA. This table lists all the SNPs which vary from this reference. The fields are position, base change, rsID, SNP name, reliability and a list of the reference genomes which share this change. There are four successive sections: shared SNPs, private SNPs, shared INDELs and pricate INDELs.

Here’s how the file looks:

I also received a small manual describing this file and how to use it:

File #4 - strcall203.lobystr203report

This table contains the list of all STRs.

Here’s the description in the file :

#FGC Y-STR report generated based on lobSTR pre-v2.0.3 (sourceforge git revision 34534b) processing

#lobSTR citation: Gymrek M, Golan D, Rosset S, & Erlich Y. lobSTR: A short tandem repeat profiler for personal genomes. Genome Research. 2012 April 22.

#Notes:

#Repeat counts reported according to lobSTR standards; conversion required in certain cases to produce results based on other counting standards

#chrY coordinates based on hg19 / b37 reference sequence

#Marker conversions to FTDNA standards for DYS448, DYS449, DYS607, DYS576, DYS511, DYS640, and DYS485 are provisional

#Marker results known to be unreliable include: DYS413a/b, DYS490, DYS572, DYS726, DYS534, DYS446, and DYS487

#default lobSTR database has been augmented with results for DYS540, DYS712, DYS593, DYS715, DYS513, DYS561, DYS497, DYS510, DYF385.1, and DYF385.2, which should be treated as provisional

#Only two copies of DYS464 and DYF371 are called here; fully-spanning read details can provide insight into additional copies

#DYF371 includes DYS425

#NR = not reported / no reads

#NA = not available

#call confidence: 1 corresponds to highest confidence, 0 corresponds to lowest confidence; results with call confidence below 0.2 should be considered very speculative

#conflict flags: ? = conflicting fully-spanning reads; * = conflicting partially-spanning reads; % = het result in diploid calling for marker not recognized as multicopy; & = not called in diploid calling

#read details: Format is [repeat count]|[number of reads supporting given repeat count], with different counts separated by ';'. In the case of multicopy markers like DYS464, the fully-spanning read details can be used to determine repeat counts for additional copies

And here is what the file looks like:

Now this gets very technical and I don’t understand everything, but from what I can figure out, first we have the STR name and the estimated result, and then follows information explaining how this result was found and how sure the program is of it.

File #5 - strcall203.lobystr203report ftdna

This table also lists the STRs, but in a much simpler form. You simply have the name and the results, and the STRs are in the order they are found at Family Tree DNA.

The description in the file is:

#Marker conversions to FTDNA standards for DYS448, DYS449, DYS607, DYS576, DYS511, DYS640, and DYS485 are provisional

#see main Y-STR report for further information regarding reliability, etc.

And here’s the table:

File #6 - mttype.RSRS.MT

This table gives the mtDNA results in RSRS format. It gives for each SNP the position and the ancestral and derived result.

Here’s the description:

#FGC mtDNA report

#Variants with respect to RSRS

And here is the file:

File #7 - mttype.rCRS.MT

This one is exactly the same, but using the CRS format.

#FGC mtDNA report

#Variants with respect to rCRS

File #8 - haplogroupCompare

This table lists my SNPs and compares them to some reference results from my haplogroup or close to it. It quite similar to the variantCompare file. The fields are position, base change, rsID, SNP name, reliability and the reference results mine is compared to. There are two successive sections: shared SNPs and private SNPs.

Here’s the description :

#FGC report: Detailed Analysis of Called SNPs

#refer to Analysis of Called Variants for citations and other details

#in the reporting below, it is assumed that the reference allele is ancestral ("-") and the sample allele is derived ("+"); "x"=ambiguous and "?"=no-read/no-call

#note that this report uses a different, simplified variant calling approach from that used in the Analysis of Called Variants report, so results may differ, especially for less-reliable variants

Haplogroups in the neighborhood of G-L91 being considered; includes: G-L91;G-L166;G-M286

And here’s the file: 

File #9 -  gtype

This one is also a bit complex. It lists the Y-SNPs and seems to detail how the results were determined.

Here’s what it looks like:

This ends the description of these nine analysis files. Note that I am still waiting for access to my results on the website and to my sequencing raw file. If you are interested I’ll write another article to show it to you then.

Thanks Itaï! 

These tools were developed by Dr. Greg Magoon with the supervision of Justin Loe. Justin tells us "these are not final versions and will be upgraded to a more user-friendly presentation by specialists in user-interfaces."  

BGI provided the sequencing services and developed the Y chromosome chip.

If you have any questions, please post them below and I will try to get them answered. I'm sure we will be seeing a lot more regarding the Full Genomes test soon...

AncestryDNA's New Ethnicity Predictions Rolling Out to Customers

AncestryDNA customers will be happy to see that the new ethnicity results are starting to appear in their DNA accounts today. If you haven't checked yours yet, be sure and do so. I have been working with the new predictions for a little over a month and feel that they are a huge improvement over the original version. That's not to say that they are perfect, but no admixture predictions are without weaknesses. As Dr. Catherine Ball emphasizes in the new introductory video that is why they are called estimates.

I have intended to write about this new feature ever since I was invited to participate in a webinar and conference call by AncestryDNA with a handful of other bloggers back in early September, but I have been overwhelmed with other work that I will write about soon. I plan to post a couple of upcoming blogs to catch up with all of the exciting genetic genealogy news, including additional coverage on AncestryDNA's advancements.

Is Ancestry Using the Sorenson Samples?
First,  I want to discuss the role of the Sorenson data in these updated and more refined predictions. There has been a lot of conflicting information shared on the blogs, in the forums and even by Ancestry.com employees in this regard. I spoke with Dr. Ken Chahine, AncestryDNA's General Manager, to clarify the role of the Sorenson data and the status of the DNA samples collected by Sorenson.

AncestryDNA's first version of their Genetic Ethnicity feature used public data sets for the reference populations. For the new version, Ken confirmed, they have transitioned to using Sorenson samples and the associated pedigree data "almost exclusively" (and not unsourced Ancestry.com personal member trees).

Contrary to what has been claimed by some and in agreement with what Ken has told me in the past, AncestryDNA does, in fact, have possession of the physical DNA samples. How else could they have been integrated into this new cutting-edge technology? They have been retesting an increasing number of those samples on the Illumina chip that they use for the AncestryDNA test in order to improve their ethnicity predictions. Upon hearing this, I know that many people will wish to test those samples of deceased family members who donated their DNA to Sorenson on the AncestryDNA platform, however it was explained to me that for legal reasons AncestryDNA is not currently able to allow that. They are attempting to work out the legalities involved, but cannot guarantee that this will be an option in the future. Ken said that he "definitely understands the desire, the need" to access these samples to take advantage of the more advanced genetic testing technology, but AncestryDNA is required ensure that everyone's privacy is protected and they, as a corporation, are covered legally. Ken explained that AncestryDNA would very much like to come up with a solution to be able to genotype these samples and deliver the results to their family members, but they just don't have an answer at this point as to if and when this will be possible. Further, he explained that it may turn out that AncestryDNA will not be able to overcome the legal difficulties involved with allowing third party access to these samples. Moving forward AncestryDNA is looking into creating an option for designating a beneficiary for current AncestryDNA accounts/samples in order to avoid this dilemma in the future.

Now, to discuss the details of the new release...

Transparency
What I like most about the presentation of these new ethnicity estimates is that AncestryDNA has worked very hard to make the science transparent, just as the genetic genealogy community has been requesting. They have released an extensive white paper delving into the minute details of their work. You can find it on your ethnicity estimate page by clicking on the little "i" in the upper right hand corner.

The New Ethnicity Estimate home page - click to enlarge

The have also provided the option to click through to simpler explanations throughout the interface. I recommend that everyone takes the time to go through and read each of these in order to get a better understanding of how this feature works. They do such a good job of this, that it is probably unnecessary for me to go into extensive details here. 

As you will see, the graphics are extremely well done in these explanations. For example, the Regional Overlap Chart (below)  helps to explain why it is so difficult to break continental regions into sub-regional categories.

Additionally, the AncestryDNA team has done a very good job of illustrating the reality of this challenge with the graphic depictions of the ranges integrated with the estimates.

 

There is more detail offered for the customers who wish to "dive down" into the technical details in the click-thru explanations. 

New Home Page
I also like the updated look for the new home page. It summarizes the important details of your results in an easy-to-understand format.

Some customer's pages are really colorful now!

Increased Resolution and Detail
All of the results in my account are much more accurate based on the research that I have done both on my traditional genealogy and in working with my autosomal DNA matches over the last several years. I also got a couple of surprises with the enhanced resolution of this test.

AncestryDNA has increased their coverage tenfold by analyzing 300,000 SNPs in their predictions as compared to the 30,000 that they were using previously. The new version of their reference panel uses "3,000 DNA samples from people in 26 global regions".  In an ambitious attempt, they are the first company to offer customers with African ancestry an estimate of the specific regions in Africa to which their DNA can be traced. I will look forward to hearing the opinions from the African Americans in our community on how well they think AncestryDNA has done with this first attempt. (23andMe will be releasing their own effort soon.)

Coming Soon...
I will examine my results in more depth and share some thoughts and interesting details from my conversation with Ken Chahine.


Disclosure of Material Connection: Some of the links in the post above are “affiliate links.” This means if you click on the link and purchase the item, I will receive an affiliate commission. Regardless, I only recommend products or services I use personally and believe will add value to my readers. I am disclosing this in accordance with the Federal Trade Commission’s 16 CFR, Part 255: “Guides Concerning the Use of Endorsements and Testimonials in Advertising.”

Ask Your Geno 2.0 Questions Friday, September 13th on Twitter

I received an email from National Geographic announcing an exciting opportunity to interact directly with Dr. Spencer Wells:

National Geographic is offering the opportunity for people interested in the field of genetics to ask questions directly to The Genographic Project and Spencer Wells in a live Twitter chat on September 13 at 12pm ET. Spencer will be tweeting from his twitter handle @spwells and participants may ask questions using the hashtag #NatGeoLive.

 
I strongly encourage anyone who has questions about the Genogrpahic Project and/or their Geno 2.0 results to join in on Friday at 9am PST/12pm EST and ask Dr. Wells. 

You can learn more here.

Kelly Wheaton's Beginners' Guide to Genetic Genealogy

Genetic genealogist Kelly Wheaton has been hard at work on a beginner's guide to genetic genealogy for the last couple of weeks. She was inspired to share her extensive knowledge by a thread on the ISOGG DNA Newbie mailing list asking (begging!) for easier to understand resources. Since my readers are always clamoring for more educational resources as well, I am very happy to be able to introduce it to you all.

Kelly doesn't draw a lot of attention to herself, but she has been a long-time contributor to the DNA Newbie list and a frequent poster on the 23andMe forums. She has always generously shared her knowledge through these forums and on her website. I consider her to be a very valuable asset to our community. I'm sure you will agree after reading her new guide.

Kelly Wheaton

The guide has received unanimously good reviews from those of us who have read it. One of the nice things about it is that it breaks the instruction into easily digestible pieces, by keeping each lesson short and concise. There are thirteen lessons so far and Kelly says that she will continue to add to it. As she was writing, Kelly had the foresight to share it with "newbies" to receive feedback and make sure that it is understandable for the beginner. This has resulted in a very easy-to-understand resource. Kelly is continuing to accept suggestions for improvements and additions.

You can find this wonderful guide here. Thank you Kelly for all of your hard work and valuable contributions to our community.

Debbie Kennett has just created a page on the ISOGG Wiki with links to beginners' guides here. Right now it only has Kelly's guide and my series for Geni.com. Please add to it if you find basic resources which are helpful to you and, while you are there, look around. The Wiki is a great resource in itself!

Autosomal DNA: A Revelation for African Americans Searching for their Roots

Lately, I have been having great success with autosomal DNA for African American genealogy research. This has been especially true at AncestryDNA with the plethora of trees attached to the DNA matches and the ease of identifying and analyzing patterns with the new search filters and Jeff Snavely's great tool. What was once a dream for African Americans searching for their roots prior to Emancipation is finally becoming a reality. 

Last week I came across a very meaningful example of this and wanted to share it with you. Over at the 23andMe forum, there is a 14 part thread (must be logged in to access) started by genetic genealogist extraordinaire Kelly Wheaton discussing AncestryDNA. Kelly asked the following question of the participants:

"Did AncestryDNA prove to be genealogical helpful? Would you recommend it to others in spite of its shortcomings?" 

One of the responses was so beautifully written and powerful that I wanted to share it with you. With permission, it follows:

"I’ve thought long and hard about this question. For me, AncestryDNA restored my lost heritage and helped me complete an important journey I began many years ago.

For years beginning in the mid 1960s I was the only African American male in my school in central Michigan.  It was difficult and on more than one occasion I endured being called the “N” word, but in the 5th grade I had an exceptional white teacher who cared more about teaching than anything else. She took an interest in me that no other teacher had. I remember her excitedly telling me something about my score on some intelligence test and that she moved me into advanced classes. Years later, I earned a bachelors degree from the University of Michigan Ann Arbor at the age of 19 and eventually became one of the youngest lawyers in my state.

Anyway, one of the assignments that this teacher gave the class was to go home and find out why our ancestors had come to America. I had never thought about that one, but I was later disappointed to hear my parents tell me that we were just “American Negroes” and we came here as slaves. The depiction of slaves in my school books from which they were teaching mainly white, northern children was that slaves were badly clothed, unkempt people with smiling, but dumb expressions on their faces. Supposedly they were slaves because they liked the hot sun and weren’t good for much else. What a horrible and false image to put in a book for children! And how many people still believe that image because that’s what they were taught in school?

When I returned to class the teacher asked each of us what we’d learned. My sense of embarrassment and inferiority deepened. Some kids had ancestors from wonderful sounding places like Ireland and France. Some had ancestors who came on the Mayflower. Others had ancestors who fought for independence. I had no countries of origin of which to boast, only negative, stereotypical images taught to us in our school books.

My parents were concerned. A few years later in the early 1970s or late 60s, my step dad saw an article in the newspaper that a man named Alex Haley was coming to speak on tracing your family tree. The epic Roots had not been completed and most people would not have recognized Haley’s name. I went to hear him and learned much. I followed his advice for years afterward and learned of my courageous slave ancestors who escaped to Canada on the Underground Railroad and who helped free others. I also learned of my mother’s grandfather who was born a slave but became a newspaper publisher and one of the first black lawyers in his state. And there were many others who clearly debunked the monstrous lies behind the negative images of slaves they taught me and the largely white student body in my school.

But even with what Haley taught me, there were many, many brick walls. I couldn’t discover where in Africa my ancestors came from or when. Then came AncestryDNA. First it revealed to me that my ancestry was almost equally divided between Europe and West Africa. It told me of ancestral origins in Benin or Cameroon. Other services also identified Senegal. But AncestryDNA also revealed the family connection between my slave ancestors and those who enslaved them. It brought me full circle back to the fifth grade in revealing ancestors in my past just like the other kids boasted of all those years ago. It led me to my ancestors from England, Ireland, France and other places. There was a Mayflower passenger. There were ancestors I shared in common with George Washington, Thomas Jefferson and even President Obama.

So, in answer to your question, is AncestryDNA worth it? Absolutely! For me, it's a life changer and one of the most important things I've ever experienced. 

--- Charles Holman

Charles with his cousins Lynne Goransson and her daughter Dr. Leslie Goransson

Charles met his previously unknown cousins Lynne Goransson and her daughter Dr. Leslie Goransson through Ancestry.com. They are related through a slaveholding ancestor.

Family Tree DNA Will Keep $99 Price for Family Finder

I just received the GREAT news from Max Blankfeld that Family Tree DNA will be able to keep the low and competitive price of $99 for Family Finder:

Family Tree DNA Will Keep Reduced Prices

One month ago Family Tree DNA reduced its Family Finder price to $99 with the promise that if we achieved a minimum volume of orders during our Sizzling Summer Promotion, Illumina would help us keep this price moving forward. We are happy to announce that the genetic genealogy community responded in a big way, and thanks to you we are maintaining the price of the Family Finder test at $99.

We hope that with this price reduction you can reach out to family and friends, so that more and more people can join our growing database and find new matches.

Thank you for your continued support!

Max Blankfeld, Vice-President and COO

http://www.GeneByGene.com

max@genebygene.com

713-868-1438

This development has leveled the playing field for all three companies offering autosomal DNA tests to the genealogy community and allows those who prefer not to receive health results and/or wish to have their DNA sample stored for 25 years to affordably do so. I hope that this will encourage more genealogists to get themselves and their families into the Family Tree DNA Family Finder database. It benefits all of us to have genealogists with well-documented family trees participating in our groundbreaking autosomal DNA research. These price drops are really helping us to get to the critical mass that we need to get the most out of these databases. Recently, I have seen great strides in this regard in my research. Thank you to everyone who ordered tests during this trial run and to FTDNA and Illumina for making this possible.