Yesterday, at Health 2.0 in San Francisco, 23andMe announced that it will be offering sequencing of exomes with 80x coverage for $999. At Exome 80x, 23andMe discusses their test:
Your exome is the 50 million DNA bases of your genome containing the information necessary to encode all your proteins. Informally, you can think of the exome as the DNA sequence of your genes.
Your entire genome is made up of your exome plus other DNA, consisting of three billion bases with repetitive sequences, sequences of unknown function, and DNA that does not code for proteins.
Note that the Exome 80x test is only available to current customers, and is determined on a “first come, first served” basis. Further, test-takers will initially only receive their raw data of 50 million DNA bases at 80x coverage, but 23andMe plans to develop new tools to take advantage of exome sequencing.
Direct-to-consumer DNA testing has led to the re-joining of yet another family.
Y-DNA and autosomal testing by Family Tree DNA has revealed that two NFL players , Xavier Omon (San Francisco 49ers)) and Ogemdi Nwagbuo (San Diego Chargers), are half-brothers. ESPN has a long write-up of the story at “A brothers’ tale for Omon, Nwagbuo.”
Meeting for the First Time
The brothers had planned to meet face-to-face yesterday, September 1, 2011, as their teams met on the field. Turns out Omon’s team, the 49ers, were victorious, meaning that if he’s anything like my brothers, he gave Nwagbuo a hard time about it! The Mercury News has a story about the brothers’ first meeting at “Omon meets half-brother (a Charger) for first time,” and the SF Gate has a story at “49ers’ Xavier Omon meets half-brother.”
Lone Frank, a journalist and author with a Ph.D. in neurobiology, has just published her fourth book, entitled “My Beautiful Genome: Exposing Our Genetic Future, One Quirk at a Time” (available for pre-order at Amazon). A chapter of the book is available here (pdf).
Frank describes her book thusly: “This book is my very personal take on personal genomics. It chronicles my meetings and interviews with leading scientists and lays out the – somtimes [sic] disquieting – discoveries I make in my own genome.”
The book is described as follows at Amazon:
“Internationally acclaimed science writer Lone Frank swabs up her DNA to provide the first truly intimate account of the new science of consumer-led genomics. She challenges the scientists and business mavericks intent on mapping every baby’s genome, ponders the consequences of biological fortune-telling, and prods the psychologists who hope to uncover just how important our environment really is – a quest made all the more gripping as Frank considers her family’s and her own struggles with depression.”
Family Tree DNA has announced the 7th Genetic Genealogy Conference for Family Tree DNA Group Administrators, to be held in Houston, Texas on November 5th and 6th, 2011.
Featured speakers at the meeting include the following:
Another interesting speaker at the meeting will be Jessica L. Roberts, J.D., an Assistant Professor of Law at the University of Houston Law Center (recent C.V. here (pdf)). Although it’s not clear what Roberts will be speaking about, her recent publications (pdf) focus on genetics and the law, including the Genetic Information Nondiscrimination Act. Kudos to Family Tree DNA for again bringing together a wide array of viewpoints and opinions at the conference.
Daniel MacArthur tweeted this morning about “Interpretome,” which is browser-based software that can be used to examine autosomal testing results from 23andMe and Lumigenix. There is also an interesting blog post about the software at the blog of Konrad J. Karczewski, one of the co-creators of the software, and one by Daniel at Genomes Unzipped.
Users load their raw data files, and then can use that information to explore their genome. There are a number of different exercises that a user can run through with their data, including health issues (diabetes, warfarin sensitivity, many other diseases, etc.), ancestry analyses, and determination of “Neanderthal SNPs,” which are SNPs that have been suggested to derive from Neanderthal ancestry (note that this science is still VERY early stage and subject to change OFTEN!).
As you may have heard, I recently made my 23andMe and Family Tree DNA autosomal testing results available for download online at “mygenotype,” and dedicated the information to the public domain (if dedicating DNA sequence to the public domain is even possible – I’m currently doing some research in this area and expect to write more in the future).
At “mygenotype” you can download the following:
My Family Tree DNA Results:
- Affymetrix Autosomal DNA Results (2010)
- Affymetrix X-Chromosome DNA Results (2010)
- Illumina Autosomal DNA Results (2011)
- Illumina X-Chromosome DNA Results (2011)
My 23andMe Results:
- V2 Results (2008)
- V3 Results (2010)
- Y-DNA Results (2010)
- mtDNA Results (2010)
You can also find my SNPedia Promethease reports:
In addition to my genome, Razib Khan of Gene Expression has a spreadsheet of approximately 48 other genomes that are available for download online.
A Challenge To YOU
Now that the information is out there, available to anyone who might be interested, it remains to be seen who might be interested in the information.
Helen Marley Johnson, my great-grandmother, was born to unidentified parents on March 3, 1889, in Oswego County, New York. Although I didn’t really know Marley, I remember meeting her when I was very, very young, just before she died in 1983.
Marley lived in Oswego and Jefferson counties for all her long life. She was married twice, had two children, and today has numerous descendants located throughout the United States and the world. However, by the time Marley was 13 years old, she had been adopted by at least three different families, eventually marrying into the last family that adopted her.
Since I began my genealogical research more than 20 years ago, I’ve worked to find the parents of Marley Johnson, without much success. I have a plethora of data about the entire remainder of her life, but almost nothing about her ancestry. For example, although I’ve found her birth certificate, it lists her mother as Minerva Johnson (a name that may or may not be real, and which I’ve found nothing on) and lists her father as “unknown.”
DNA Heritage, a popular genetic genealogy company intiated in 2002, has ceased operations (although pending orders will be fulfilled). The company’s website announced today that it is in the process of transferring their database and domains to Family Tree DNA.
Family Tree DNA, meanwhile, has announced that it records in the DNA Heritage database will only be placed into FTDNA’s database if the owner agrees to opt-in. FTDNA has a series of FAQs related to the transfer available here.
The full text of the announcement is below:
As of April 19 2011, DNA Heritage has ceased its operations and is in the process of transferring the domains DNAHeritage.com and Ybase.org to Family Tree DNA.
All the tests in progress will be processed by our current lab and the results will be delivered to our customers.
An independent group of scientists has recommended that the Department of Defense (“DoD”) obtain and sequence the genomes of members of the military.
JASON, a group of between 30 and 60 scientists and created in 1960 which advises the U.S. government on scientific and technological issues, authored the report entitled “The $100 Genome: Implications for the DoD,” (pdf) which was released on January 13, 2011.
In the report, the scientists provided the following recommendation:
“The DoD should establish policies that result in the collection of genotype and phenotype data, the application of bioinformatics tools to support the health and effectiveness of military personnel, and the resolution of ethical and social issues that arise from these activities. The DoD and the VA should affiliate with or stand up a genotype/phenotype analysis program that addresses their respective needs. Waiting even two years to initiate this process may place them unrecoverably behind in the race for personal genomics information and applications.”
Robert Estes of DNAeXplain announces the discovery of a previously-undiscovered Native American haplogroup. Up to the current point, research had found only two Y-DNA haplogroups in the Native peoples of North and South America – C3b and Q1a3a (aka Q1a3a1). However, new research described in the accompanying paper (here (pdf)) uncovers a third haplogroup found in Native peoples.
From the paper:
“For the past decade, since the advent of genetic genealogy, it has been accepted that subgroups of haplogroup C and Q were indicative of Native American ancestry. Specifically, subgroups C3b and Q1a3a, alone, are found among the Native peoples of North and South America. Other subgroups of haplogroup C and Q are found elsewhere in the world, not in North or South American, and conversely, C3b and Q1a3a are not found in other locations in the world. This makes it very easy to determine if your direct paternal ancestor was, or was not, Native American. Or so it seemed.”