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.
In 2003, researchers from around the world released a paper that suggested that 8% of all Mongolian males have a common Y chromosome because they are the descendants of Genghis Khan (See â€œThe Genetic Legacy of the Mongols,â€ 2003, Zerjal, et. al., American Journal of Human Genetics, 72: 717-721).The researchers examined the Y chromosome variability of over 2000 people from different regions in Asia and discovered a grouping of closely related lines.The cluster is believed to have originated about 1,000 years ago in Mongolia and its distribution coincides with the boundaries of the Mongol Empire.
Genghis Khanâ€™s empire (he ruled from 1206 â€“ 1227) stretched across Asia from the Pacific Ocean to the Caspian Sea and was reportedly extremely prolific.Khanâ€™s son Tushi had as many as 40 sons.His grandson Kublai Khan is reported to have had as many as 22 sons, and perhaps many more.Together this family may have as many as 16 million descendants alive in Asia today.It is extremely important to note that until DNA can be extracted from Khanâ€™s bones (which have never been found), there is no definitive proof that this Y chromosome cluster is actually descended from Genghis Khan.
The Genetic Genealogist has been invited to be a member of the new genetics blogging group The DNA Network
, founded by Rick Vidal of My Biotech Life
and Hsien Lei of Eye on DNA
. The group is “a network (double helix?) composed of life science enthusiasts with specialized views in areas such as genetics, biology, biotechnology, health care, and much more.”
Not only is the network a great way to discover new blogs, but it is an opportunity to stay current on events and developments in the field of genetics. The following blogs are currently members of the network:
My Biotech Life
DNA Direct Talk
Eye on DNA
Gene Sherpas: Personalized Medicine and You
henry: the human evolution news relay (genetics)
Mary Meets Dolly
Microarray and Bioinformatics
And me, The Genetic Genealogist.
Thomas Jefferson, 3rd President of the United States, has been at the center of a DNA controversy for over 200 years.In September 1802 journalist James T. Callender wrote in Richmond Reporter that Jefferson had for many years â€œkept, as his concubine, one of his slaves.Her name is Sally [Hemmings].The name of her eldest son is Tom.His features are said to bear a striking though sable resemblance to those of the president himself.â€Although these rumors had reportedly already been passed around quietly, this article spread the rumor far and wide, setting off many years of debate.
In 1998 analysis of a male descendant of Jeffersonâ€™s paternal uncle showed that Jeffersonâ€™ Y chromosome belonged to haplogroup K2 (Thomas Jefferson did not have any male descendants to provide DNA.For more information, see: â€œJefferson fathered slaveâ€™s last child.” 1998. Nature 396 (6706): 27â€“28. PMID 9817200).Haplogroup K2 is rather rare, constituting just 1% of worldwide Y chromosomes (See â€œThomas Jeffersonâ€™s Y chromosome belongs to a rare European lineage.â€ Am J Phys Anthropol 132(4): 584-9.PMID 17274013 ).Surprisingly, or perhaps not-so-surprisingly depending on which side of the debate you stood, a male descendant of Sally named Easton Hemmings possessed the same K2 chromosome, suggesting a genetic link between Jefferson and Easton.Keep in mind, however, that this is not determinative since it is possible that any of Jeffersonâ€™s male relatives (who possessed the same Y chromosome) could have fathered Easton.And keeping in mind that non-paternal events are ALWAYS a possibility, nothing is 100% certain.Not until we can time-travel and obtain DNA samples from the source!
Some scientists have hypothesized that Australian aboriginals received a portion of their DNA from an ancient hominid species called Homo erectus, which for a short time was contemporaneous with modern man. A recent study published in PNAS (Proceedings of the National Academy of the Sciences) set out to answer this question by analyzing mtDNA and Y-chromosome samples from aboriginals.
A total of 172 mtDNA and 522 Y-chromosome previously published and new sequences from aboriginal Australians and New Guineans were analyzed for mtDNA and Y-chromosome variation and were compared to the current world haplogroup tree. All of the mtDNA sequences were members of the M and N founder branches, and all of the Y-chromosome sequences fell into the C and F founder branches.
FamilySearch (a nonprofit organization sponsored by The Church of Jesus Christ of Latter-day Saints) announced today that it will provide FREE services to any and all archives and records custodians who wish to digitize, index, publish, and preserve their collections.This is, of course, on top of the ambitious project already underway to digitize and make freely available the 2 million rolls of microfilm stored in the Granite Mountain Records Vault.
This is a huge benefit for genealogists, since many more records will be freely available online.This is also a huge benefit for archivists and record depositories, since they can digitize and make available their collections for free using FamilySearchâ€™s many years of scanning experience.
I spent the morning doing a redesign of the blog.Â I should have been studying, but I’ve been meaning to give the site a new look for a while now.Â My goals were (1) to make the content the center of attention; (2) to quickly and easily provide information about the blog and subscription options to newcomers; (3) to minimize the impact of advertising (since I don’t make that much anyway!); and (4) to make the site more visually pleasing and professional.Â If you have any problems accessing information or using the site, please be sure to let me know.Â If you like the new design, let me know that too!
Do you have a burning question about genetics that’s been keeping you up at night? Ever wonder why the combination of red hair and brown eyes is so rare? There are two great resources currently available online for anyone who is curious about genetics.
AsktheGeneticist is a partnership between the Department of Human Genetics at Emory University and theDepartment of Genetics at the University of Alabama at Birmingham.The mission of AsktheGeneticist â€œis to answer questions about genetic concepts, and the etiology, treatment, research, testing, and predisposition to genetic disorders.â€ AsktheGeneticist has a genetic genealogy section, but itâ€™s pretty sparse.
The Tech Museum of Innovation in San Jose, California has partnered with the Department of Genetics at Stanford University to present â€œGenetics: Technology with a Twist.â€The interactive site has an â€˜Ask The Geneticistâ€™ section where you can ask a Stanford geneticist a question.