In Part I, Part II, and Part III of the “You and the $1000 Genome” series we’ve examined the Archon X PRIZE for Genomics, the International HapMap Project, and the ethical issues associated with both. In this final installment of the series we will examine the potential impact of genomic or SNP sequencing and interpretation on both medicine and genealogy (finally, some genealogy for you patient genealogists out there!).
I believe that whole genome sequencing will have myriad uses. In the paper mentioned in Part III of the series (John A. Robertson, “The $1000 Genome: Ethical and Legal Issues in Whole Genome Sequencing of Individuals (pdf).” 2003 The American Journal of Bioethics 3(3):InFocus), Mr. Robertson suggests that demand for personal genome sequencing outside of the medical context could be quite limited. But that view might fail to take into account uses of genomic information other than identifying or predicting disease, such as the genetic genealogy setting. Very few could have predicted 10 years ago that thousands of genealogists would be submitting their DNA for limited sequencing as they are doing today. If information from whole genome sequencing can be used to analyze genealogy (which it surely will be), then this will create an entire niche that will increase commercial demand outside of the medical context. And this is only one such niche. There might be many many more, some of which will only develop after whole genome sequencing becomes economically available.
In Part I and Part II of the “You and the $1000 Genome” series we examined the history of the Archon X PRIZE for Genomics and the success of the International HapMap Project. Today we’ll talk about some of the ethical issues associated with efficient and inexpensive genome sequencing. The value of whole genome sequencing will only be realized if individuals believe they have complete and legal control over their genetic information. I am greatly indebted to a thorough analysis of this issue by John A. Robertson at the University of Texas School of Law (“The $1000 Genome: Ethical and Legal Issues in Whole Genome Sequencing of Individuals (pdf).” 2003 The American Journal of Bioethics 3(3):InFocus). Note that this analysis is not intended to constitute answers to any of the ethical questions – it is only meant to be part of the discourse.
In Part I of the “You and the $1000 Genome” series we examined the Archon X PRIZE for Genomics, a $10 million purse for the group that can sequence 100 genomes in 10 days for no more than $10,000/genome with an error rate below 0.001%. With today’s technology this goal is still a few years away.
But do we need an entire genomic sequence to obtain all the relevant medical information that our DNA contains? After all, 99.9% of my DNA is exactly the same as everyone else’s! Why sequence that 99.9% over and over and over if the results are the same every time? Wouldn’t it be cheaper to just sequence and then decode the 0.1%?
Sequencing that 0.1% is the goal of the International HapMap Project. HapMap stands for “Haplotype Map”, and those of you who are genetic genealogists will instantly recognize the importance of the word haplotype. The goal of the HapMap Project, begun in 2002, is to identify SNP groups (haplotypes) from a total of 270 individuals representing the Yoruba people of Nigeria, the Han Chinese in Beijing, the Japanese, and U.S. residents with northern and western European ancestry. The HapMap is essentially a catalog of all the common genetic variants in human beings.
Speaking of the $1000 genome, if you haven’t visited the 23andMe main page recently, you’ll probably want to check it out. The site has been redesigned and includes links to an About page and a Press Release page, a Contact page, and the Jobs page. I love the fact that the job benefits include “free genotyping for you and a family member or friend”!!
The front page also has a new description of the company:
“23andMe is a privately held company developing new ways to help you make sense of your own genetic information.
“Even though your body contains trillions of copies of your genome, you’ve likely never read any of it. Our goal is to connect you to the 23 paired volumes of your own genetic blueprint (plus your mitochondrial DNA), bringing you personal insight into ancestry, genealogy, and inherited traits. By connecting you to others, we can also help put your genome into the larger context of human commonality and diversity.
Over the next week and a half I will be examining the Archon X PRIZE for Genomics, a challenge from the Archon X PRIZE Foundation to foster the development of efficient and inexpensive genomic sequencing. Not only will the X PRIZE for Genomics change the face of medicine, but it will also have an ENORMOUS impact on the field of genetic genealogy, which we’ll discuss in Part IV of the series. Stay tuned for all the information you need to know about the prize, and if you have any thoughts or questions please leave a comment!
History of the Archon X PRIZE for Genomics:
In 2003 the J. Craig Venter Science Foundation announced a $500,000 Genomic Technology Prize that would be awarded to an the group whose technology significantly enhanced “the field of high throughput DNA sequencing by enabling a human genome to be sequenced for $1,000 or less.” The Foundation believed that crossing this threshold would enable the majority of individuals to afford genomic sequencing as part of medical treatment.
Update: The podcast was updated to add the last 5 minutes of the interview (after the commercial break).Â As a result, the link to the podcast changed.Â I apologize to everyone who tried the old link – it should work fine now.
Market News First, a website dedicated to microcap markets, recently interviewed the CEO of DNAPrint Genomics, Inc.”Richard Gabriel, President and CEO of DNAPrint Genomics, Inc. spoke with MN1.com’s Rich Hancock on April 26th, 2007 about the Company’s innovative and cutting edge technology that aids law enforcement crime scene investigation (CSI) forensics, consumer applications in genealogy ancestry/genetic testing and its pharmaceutical and diagnostic applications. Mr. Gabriel highlights the Company’s recent advances in its pharmaceutical and diagnostic, and talks about its successes in both law enforcement and the growth market of DNAPrint’s consumer oriented products.”
I get visitors from search engines nearly everyday looking for information about the startup business 23andMe. Iâ€™ve briefly mentioned 23andMe before, but I thought Iâ€™d see how much information I could gather doing a brief online search.
The website describes the venture:
â€œ23andMe is an early stage startup developing tools and producing content to help people make sense of their genetic information. Our goal is to take advantage of new genotyping technologies and help consumers explore their genetics, informed by cutting edge science.
â€œCombining computer science, biology and informatics, we are at the cutting edge of a new era of genetics. Genome deciphering technologies have reached affordable levels, allowing consumer access. This information has the potential to empower both individuals and society in a way that will deliver tremendous value. For the individual, such information will provide personal insight into ancestry, genealogy and health. For society, the collection of genotypic and phenotypic information on a large scale will provide scientists with novel avenues for research.
Argus BioSciences, located in Belmont, California, is an up-and-coming company offering DNA sequencing for the study of genetic genealogy.Founded in 2003 by Dr. David Whyte, the company offers mtDNA sequencing and haplotype determination.
Although Argus is currently (as of March 2007) offering only mtDNA testing, all products are being offered at a greatly reduced rate.Sequencing of the hypervariable region (which includes HVR1-3) is offered for only $125.00 (regularly $149).You can compare this price to those offered by other companies in my DNA testing company comparison chart.Additionally, Argus is offering complete sequencing of the entire mitochondrial genome (16, 569 bases) for $345 (regularly $695).The company will also accept four monthly payments of $95 to pay for a full sequencing (to inquire, contact Argus at email@example.com).Currently only one other company (Family Tree DNA) offers complete mtDNA sequencing as a regular product.
The last time I counted there are at least 21 unique companies offering DNA testing for genealogical purposes, either Y-chromosome, mtDNA, or autosomal testing (see the Sidebar to the right for a listing).Â To get a clearer picture of what each company offers I created a master list of every company and the services they offer.Â See here.
While compiling the list I also gathered information about the markers that each Y-chromosome test analyzed.Â See here.Â There are of course the standard markers offered by most companies as well as the markers offered by only a single company.Â What company have you been tested by?
African Ancestry has had a very good year.Â The popular PBS series â€˜African American Livesâ€™, which analyzed the African roots of nine famous figures (such as Oprah, Quincy Jones, Whoopi Goldberg, Chris Tucker, and Dr. Sara Lawrence-Lightfoot), used the African Lineage Database developed by the Scientific Director of African Ancestry, Dr. Rick Kittles.Â This publicity has resulted in African Ancestry being featured in a wide array of newspaper and magazine articles around the world.
African Ancestry offers two types of DNA analysis, the Matriclan test and the Patriclan test.Â The Matriclan test sequences a portion of an individualâ€™s mtDNA to determine whether the ancestry of that lineage is African, European, or other ethnic group.Â If the ancestry is African the company will compare the sequence to the African Linage Database.Â This exclusive database is African Ancestryâ€™s strongest selling point.Â It contains lineages sampled from over 30 countries and 160 ethnic groups in Africa.Â The maternal lineage database, for example, contains almost 14,000 samples.