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.
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.”
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 MacArthurtweeted 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!).
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.
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.”
“Interest in personal DNA analysis is growing, as the number of genomic retailers multiply. Navigenics is the first to obtain a license in New York state, last December, and other companies are going through the approval process now. A course at Syracuse’s Upstate Medical University prepares doctors for the new medical world, where patients arrive for appointments not just with symptoms and complaints, but with a list of personal genetic variants — and concerns about what it means.”
PLEASE NOTE: This post is a parody, and has two purposes: (1) simply for the sake of light-hearted fun; and (2) to provoke conversation with geneticists and researchers in this field (not that it will do so anyway!). So many of the recent studies about consumer reactions and/or guidelines for DTC testing have been released without any data at all, or have been studies involving a handful of test-takers. I believe that further studies are absolutely vital, but they should be an in-depth analysis rather than the curt and superficial write-ups that have been done to date. Rather than contribute to solving issues related to DTC testing, these incomplete studies add to the confusion surrounding the field.
So, ASHG geneticists, if you can see the humor in things and are willing to accept challenges to your way of thinking, read the post below! Otherwise, click here: http://www.ashg.org.
This morning, a single tweet sent me on a 2-hour tour (more, if you count drafting this post!) of my genome.
In the tweet, Mary Carmichael expressed interest in a potential book regarding the orchid/dandelion theory recently described in a December 2009 article in The Atlantic “The Science of Success.” Before this morning, I was not familiar with either the article or the theory.
The introduction to the article, reproduced below, does a good job of summarizing the main thrust of the very long (but extremely interested and worthwhile) report:
“Most of us have genes that make us as hardy as dandelions: able to take root and survive almost anywhere. A few of us, however, are more like the orchid: fragile and fickle, but capable of blooming spectacularly if given greenhouse care. So holds a provocative new theory of genetics, which asserts that the very genes that give us the most trouble as a species, causing behaviors that are self-destructive and antisocial, also underlie humankind’s phenomenal adaptability and evolutionary success. With a bad environment and poor parenting, orchid children can end up depressed, drug-addicted, or in jail—but with the right environment and good parenting, they can grow up to be society’s most creative, successful, and happy people.”