Aliquot

A portion of science, at all intersections.

aliquot

aliquot
Location
Boston, Massachusetts, USA
Birthday
December 31
Title
Dr.
Bio
Neuroscience Ph.D. ************************** Passionate about science education and outreach; enjoys a great discussion about the intersection of science and everyday life *************************** Currently a biomedical researcher at a Harvard University hospital - Areas of expertise: endocrinology, appetite and metabolism, neuroscience, biochemistry, molecular biology *************************** Areas of interest: science and art, science and society, science policy, books/films/music, reading great magazines, travel, learning new things and sparking new ideas, gardening/nature *** All Content Copyright Aliquot - do not reproduce without express permission ***

Aliquot's Links

Science Resources
Earth Science
science and health
best of science
Do, Read, Listen, Go...
Basic Science
Research Findings
reviews
food and science
science and art
science at the borders
Links Recommended by Aliquot
science and society
Research Updates
science and the body
debunking science myths
More recommended links - education
JANUARY 6, 2010 5:15PM

Why sequence 10,000 genomes?

Rate: 2 Flag

  logo 10k

 

Since 1995, more than 180 species have had their entire genomes sequenced, including the human (Homo sapien).  These projects have provided valuable insight into human evolution by comparing our genomes to other species, but have also aided biomedical research which uses model species in research, such as the laboratory mouse (Mus musculus), the laboratory rat (Rattus norvegicus), the nematode (Caenorhabditis elegans), the mustard plant (Arabidopsis thaliana), and the fruit fly (Drosophila melanogaster) - all of which have been completely sequenced.

 Our genomes consist of the entire sequence of DNA bases (those As, Cs, Ts, and Gs) we have in the nuclei of each of our body's cells, including those pesky regions which differ even within a species (ie: SNPs, or single nucleotide polymorphisms, where just one base differs and can have a functional, and possibly detrimental, result).  These DNA sequences are the blueprint for our development, and the starting point for the majority of our functions and behaviors.

Recently, the Genome 10K project was launched, with the goal of sequencing 10,000 genomes - a feat that not so long ago would have seemed impossible, but today appears feasible due to the improvement and decreased cost of DNA sequencing technology.

From the project's website:

The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction in DNA sequencing suggests that this project will be feasible within a few years. Capturing the genetic diversity of vertebrate species would create an unprecedented resource for the life sciences and for worldwide conservation efforts.

The growing Genome 10K Community of Scientists (G10KCOS), made up of leading scientists representing major zoos, museums, research centers, and universities around the world, is dedicated to coordinating efforts in tissue specimen collection that will lay the groundwork for a large-scale sequencing and analysis project.

 Why do this?

 An excerpt from Science Magazine's coverage:

Ever since they finished the human genome sequence {in April 2003}, researchers have been champing at the bit to sequence other genomes to compare with human DNA. Such comparisons help identify conserved regions that likely serve key roles in survival and also regions that differ between species and likely represent adaptations to a particular way of life.

For example, research in comparative genomics has shown that the human and the fruit fly share 60% identity in their DNA sequences.  A full 2/3 of human genes known to be involved in cancer have homologs in the fruit fly, making cancer research faster and easier by using a model species.  In addition to providing novel information about human DNA and the functional implications of its sequence in physiology and disease, this project could also aid conservation efforts for endangered and dwindling species.  

Implications

The decreased cost of DNA sequencing has also brought us into the era of personalized medicine and personal DNA testing kits. Pharmacogenomics is one area of personalized medicine hoping to take advantage of our inherited differences in DNA sequence, which may predispose us to respond better or worse to pharmacological treatments for disease.

Personal DNA testing, however, runs the gamut from research-driven (the Personal Genome Project) to purely a fee-for-service approach (ie: 23 and Me, named for our 23 pairs of chromosomes).  And then we get into the realm of ethics, and whether the ability to determine SNPs that may predispose us to a disease leads to a necessity to know this information...but that is a post for another time!

 

References:

Sequencing:

Genome 10K: http://www.genome10k.org/

Science coverage of 10K: http://www.sciencemag.org/cgi/content/full/326/5954/794

Quick Guide to the sequenced genomes so far...

http://www.genomenewsnetwork.org/resources/sequenced_genomes/genome_guide_p1.shtml

Brief guide to genomics:

http://www.genome.gov (see Fact Sheets)

 Also see my post on the 2009 Nobel Prize, relating to DNA:

http://open.salon.com/blog/aliquot/2009/10/19/a_science_nobel_prize_explained

Pharmacogenomics introduction from the Mayo Clinic:

http://www.mayoclinic.com/health/personalized-medicine/CA00078

Personalized DNA testing:

Intro from Nova (PBS):

http://www.pbs.org/wgbh/nova/sciencenow/0302/01.html

Personal Genome Project:

http://www.personalgenomes.org/

23 and Me:

https://www.23andme.com/

Your tags:

TIP:

Enter the amount, and click "Tip" to submit!
Recipient's email address:
Personal message (optional):

Your email address:

Comments

Type your comment below:
I would also love to see them sequence 10,000 human sequences and compare them. Then we'd be able to pinpoint exactly how much of the DNA sequence defines us as individuals. A couple years ago, SNP/haplotype comparisons were made in batches of about 20 individuals, my lab had one of the largest cohorts of a couple thousand (at the time), but those were only portion sequences of candidate genes. Whole genomes would be fascinating to compare. Maybe we'd finally figure out what "junk DNA" is doing and get a better picture about genetic diseases.

I do see the value in sequencing other species, I just think they aren't thinking large enough :)
I agree Alicia. The SNP (and other human sequence comparison) projects I know about are definitely small in scope compared to this 10k project. And I do think we would learn more about human disease by comparing human sequences. The Personal Genome Project is one project hoping to do this via outreach to the public, an interesting approach!
What's the down side, if any? In other words, this seems like a no-brainer to me that, of course, we obviously should be doing this, and as Alicia says above, we should be doing sequencing of 10,000 humans to do a comparable across cultures to see disease across the spectrum of humanity
I guess potential downsides would be the same for any large scale experiment - time and money vs. potential knowledge gained. And why 10k species?? Is it a fancy sounding number, or is there logic behind a number that large?
Personally, I agree that this is a no brainer, though!
Wanted to add two great resources:
critique of personal genome services by New Scientist:
http://www.newscientist.com/article/dn17939-personal-genomics-firms-must-come-clean.html

Steven Pinker's personal genomics piece in the NYTimes:
http://www.nytimes.com/2009/01/11/magazine/11Genome-t.html?pagewanted=all
It would be great if the scientists would manage to capture the genetic diversity of vertebrate species, they still have a lot of work to do here but I am sure this project will be successful. First it was hard for me to believe this is possible but after making some research I found out scientists have been working on this for a long time.
Such studies help identify cures for complications from diabetes and vascular disorders by making an in-depth analysis of human genome and finding what causes to change it. I went to Wound Care Berlin Maryland center after my niece that works as a doctor told me they have the latest scientific advances in wound care, I bet such genome studies helped them to identify a potential wound complication.