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You and the $1000 Genome – Part IV: The Impact

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.

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Celebrity Genomes on DVD

As I mentioned recently, James Watson is about to be the first person to have his entire genomic information handed to him. According to this article in Today’s issue of the Observer, Watson “has decided to go ahead and have his entire genome put on the internet this week.” I’m not sure what the Observer used as its source – according to my research Watson hadn’t yet decided what he was going to do with the sequence. Update: A huge story from Newsweek states that Watson has decided to release his entire genome to a NIH database (minus the ApoE gene)!

I hope this gets lots of media coverage. This is a HUGE moment for genetics, one that we will all look back on. And I have to admit, I am very jealous of Watson’s opportunity! Here’s a great article on the subject, well worth a read!  Here are some highlights from the Observer article:

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You and the $1000 Genome – Part III: Ethical Issues

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.

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You and the $1000 Genome – Part II: The International HapMap Project

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.

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23andMe and Google

gumbert_mid.pngSpeaking 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.

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You and the $1000 Genome – Part I: The Archon X PRIZE for Genomics

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.

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Famous DNA Review, Part II – Genghis Khan

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 “The Genetic Legacy of the Mongols,” 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 Khan’s empire (he ruled from 1206 – 1227) stretched across Asia from the Pacific Ocean to the Caspian Sea and was reportedly extremely prolific.Khan’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 Khan’s bones (which have never been found), there is no definitive proof that this Y chromosome cluster is actually descended from Genghis Khan.

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The DNA Network

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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
Epidemix
Epigenetics News
evolgen
Eye on DNA
Gene Sherpas: Personalized Medicine and You
Genomicron
henry: the human evolution news relay (genetics)
Mary Meets Dolly
Microarray and Bioinformatics
Omics! Omics!
ScienceRoll
And me, The Genetic Genealogist.

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Famous DNA Review, Part I – Thomas Jefferson

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 “kept, 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.”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 Jefferson’s paternal uncle showed that Jefferson’ Y chromosome belonged to haplogroup K2 (Thomas Jefferson did not have any male descendants to provide DNA.For more information, see: “Jefferson fathered slave’s last child.” 1998. Nature 396 (6706): 27–28. PMID 9817200).Haplogroup K2 is rather rare, constituting just 1% of worldwide Y chromosomes (See “Thomas Jefferson’s Y chromosome belongs to a rare European lineage.” 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 Jefferson’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!

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Are aboriginal Australians and New Guineans the modern-day descendants of the extinct species Homo erectus?

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.

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