A Repost – The $1,000 Genome, Part IV

[This is a repost of an article that appeared on May 29, 2007. Since I’m knee-deep in final projects and exams, I thought I’d pull out a popular article from the archives. I hope you enjoy it (again)]:

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.

Here is a list of just a few of the uses of genomic sequencing:

1.Identification of genes involved in disease – scientists are far from understanding the genetic basis of most human conditions, both normal and disease. Having thousands of genomes in research databases will give researchers the ability to make these types of associations through comparative genomics.

2.Tailored preventative medicine – knowing one’s propensity for disease(s) will allow scientists and medical specialists to attempt to prevent the formation of these diseases. So see more about personalized genetics, read this informative interview at ScienceRoll with Steven Murphy, MD of the Gene Sherpa. If tailored preventative medicine is to come about, it will require the education of all healthcare specialists in genetics and the relationship between genetics and disease.

3.Genealogical research – whole genome sequencing will greatly advance the ability of genealogists to use DNA to study ancestral relationships. This will have a big effect on both autosomal and Y chromosome studies. Genealogical testing using autosomal markers is limited by both the low number of identified markers and the unknown frequency of sequences across all populations. Cheap and efficient genomic sequencing could alleviate both these limitations. Y chromosome studies will greatly benefit by a huge increase in the number of STR markers that could be used for relationship comparisons. Currently companies such as Family Tree DNA offer 67-marker tests. In a few years we will be able to compare all the STRs in the Y chromosome rather than just a few of them.

Recognizing the impact that cheap and efficient whole genome sequencing will have on science and society, Nature Genetics‘ ‘Question of the Year’ is “What would you do if this sequencing capacity were available immediately?” The website has numerous replies from prominent geneticists and presents a number of interesting thoughts on the topic. evolgen, another member of The DNA Network, has also provided an answer to the question on the evolgen blog. In addition, DNA Direct Talk has a round-up of recent blog discussions regarding the $1000 genome.

Here is a quote from Professor Stephen Hawking in support of the X PRIZE in Genomics:

“As you may know, I have recently expressed my belief that space exploration and the eventual colonization of space is critical for humanity’s survival. To bring about breakthroughs for personal spaceflight is a laudable aim and it is work done by the X PRIZE Foundation that will eventually unleash humanity from the gravitational bonds of earth. You may also know that I am suffering from what is known as Amyotrophic Lateral Sclerosis (ALS), or Lou Gehrig’s Disease, which is thought to have a genetic component to its origin. It is for this reason that I am a supporter of the $10M Archon X PRIZE for Genomics to drive rapid human genome sequencing. This prize and the resulting technology can help bring about an era of personalized medicine. It is my sincere hope that the Archon X PRIZE for Genomics can help drive breakthroughs in diseases like ALS at the same time that future X PRIZEs for space travel help humanity to become a galactic species.”

Well there you have it! It is probably quite obvious that I have high hopes for efficient and inexpensive genome sequencing and subsequent interpretation. Although the necessary technology is still a few years away, it is important that we as a society address the many issues that will result from these technologies. As always, I would appreciate any comments that you many have on this topic, or any thoughts you may have had while reading this series.

P.S. – I just stumbled across an interesting article at In the Pipeline about the use of cheap(er) genomic sequencing to follow the development of antibiotic resistance in bacteria (S. aureus). I don’t have access to the PNAS paper, but it appears that the genome (which is tiny compared to ours) was completely sequenced twice, once before treatment and once after treatment failed due to the development of resistance. The strain had developed a total of 35 mutations! The author makes a great statement at the end:

“The technology involved here is worth thinking about. Even now, this was a rather costly experiment as these things go, and it’s worth a paper in a good journal. But a few years ago, needless to say, it would have been a borderline-insane idea, and a few years before that it would have been flatly impossible. A few years from now it’ll be routine, and a few years after that it probably won’t be done at all, having been superseded by something more elegant that no one’s come up with yet. But for now, we’re entering the age where wildly sequence-intensive experiments, many of which no one even bothered to think about before, will start to run.”

Other Posts in the Series:
You and the $1000 Genome – Part I: The Archon X PRIZE for Genomics
You and the $1000 Genome – Part II: The International HapMap Project
You and the $1000 Genome – Part III: The Ethical Issues