Fwd: Personal Genome Project Newsletter
Bryan Bishop
From: Personal Genome Project <gen...@personalgenomes.org>
Date: Tue, Oct 13, 2009 at 11:07 AM
Subject: Personal Genome Project Newsletter
To: "kan...@gmail.com" <kan...@gmail.com>
Newsletter #2, October 2009. Read it online now.
Thank you for registering for updates about the Personal Genome
Project (PGP). Since our last newsletter in April, we have been busy
developing the infrastructure to support the next phase of enrollment
where we will scale the PGP from 10 participants ("PGP-10") to 100
participants ("PGP-100"). This newsletter highlights some of these
advancements.
PGP-100: Exomes vs. Whole Genomes
The cost of whole human genome sequencing is plummeting. In less than
2 years, we have witnessed prices drop from more than $1 million to
now less than $50,000 per genome, with some speculating that the
arrival of $5000 genomes is imminent. This is a trend that the PGP is
monitoring closely because it will impact our sequencing strategy for
the PGP-100.
The PGP's initial strategy for sequencing was to focus on "exomes".
Despite being only a fraction of a human genome, an exome contains all
20,500+ genes and therefore is information rich and (in theory) a more
economical alternative to whole genome sequencing. However, the cost
of exome sequencing has not fallen as rapidly as whole genome
sequencing. For the PGP-100, the decision to pursue whole genomes is
increasingly a viable option, but will ultimately depend on many
factors including the fundraising success of the non-profit
PersonalGenomes.org and the willingness of sequencing companies to
publicly showcase their technologies through sponsorship of PGP-100
genomes.
Trait-o-matic: PRR preview
Developed at the Church Lab at Harvard Medical School, the open source
Trait-o-matic tool automates the identification, filtering, and
annotation of genetic variants. Public datasets from the PGP and the
Trait-o-matic tool are intended to serve as foundational resources for
the development and evaluation of universal standards for genomic
interpretation.
In future releases, the Trait-o-matic functionality will be expanded
to enable a community of volunteers to annotate and interpret
integrated genomic and trait datasets from the PGP. The tools,
algorithms, and processes employed in the interpretation of these
datasets will be made available for the benefit of the general public,
so their strengths and weaknesses can be identified and improved over
time.
The PGP also plans to use the Trait-o-matic informatics tool to
generate "Preliminary Research Reports" (PRRs) for PGP participants.
PRRs will contain a non-comprehensive list of genetic variants present
in the participant’s DNA sequence data that may be of potential
significance and are intended to help each participant make a more
informed decision about whether to publicly release their PGP data.
The genomic datasets from the PGP-10 have been used to develop an
early prototype of what PRRs may look like for the PGP-100. You can
view these datasets and prototype PRRs via the Trait-o-matic website:
PGP participant #1: Whole genome sequence from Complete Genomics and
prototype PRR available here.
PGP participant #2 thru 10: Partial exome sequences (approximately
5-10% exome) and prototype PRRs available PGP #2, PGP #3 , PGP #4, PGP
#5, PGP #6, PGP #7 , PGP #8, PGP #9, PGP #10,
Legal Tools for Public Genomics
PersonalGenomes.org is committed to advancing the science of personal
genomics by making research data from the PGP freely available to the
public. The PGP has adopted the CC0 (“CC zero”) universal waiver to
help us accomplish this goal. Creative Commons developed the CC0
universal waiver to provide a method for dedicating copyrighted works
to the public domain. Read more about the CC0 waiver here.
Tissues, cell lines and DNA derived from PGP participants are stored
at the Coriell Institute for Medical Research biorepository and will
be distributed according to the Science Commons Open Use Material
Transfer Agreement (SC-OU MTA ). Science Commons, a project of
Creative Commons, has developed these contracts with the aim to reduce
the technical and legal hurdles investigators often face in the
transfer of physical biological materials. The MTA to be used by the
PGP is available on our consent forms page here. Read more about the
Science Commons Biological Materials Transfer Project here.
What ELSI is New?
This month the Genomics Law Report is featuring a series of guest
commentaries from industry, academic and thought leaders in the fields
of genomics and personalized medicine. Entitled "What ELSI is New?" ,
the series asks commentators to identify the most pressing ethical,
legal and social issues (ELSIs) confronting the fields of genomics and
personalized medicine and has already identified a wide range of ELSIs
that must be addressed to enable projects such as the PGP to fully
realize their potential.
Contributions thus far include:
"How will we handle the rapidly approaching flood of genomic
information on individual patients and consumers?", contributed by
Hank Greely of Stanford Law School.
"Dear Dr. Board-Certified Clinical Geneticist", contributed by Misha
Angrist of the Duke University Institute for Genome Sciences & Policy
and PGP-4.
"Genetic Exceptionalism and the Precautionary Principle", contributed
by Alan Dow of Complete Genomics.
"Personalized medicine, leave U.S. behind", contributed by David
Dooling of the Genome Center at Washington University in St. Louis.
Click here to read all of the previously published commentaries, and
check out the Genomics Law Report all month long for additional
commentaries, including several from current PGP participants.
Published research from the PGP
So far in 2009, there have been 4 published research articles that
used tissues derived from PGP participants:
Ball MP, Li JB, Gao Y, Lee J, LeProust E, Park I-H, Xie B, Daley GQ,
Church GM. Targeted and whole-genome methylomics reveals gene-body
signatures in human cell lines. Nature Biotechnol 27:361-8. (PDF)
Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon J-K,
Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, Church GM. Multiplex
padlock capturing and sequencing reveal human hypermutable CpG
variations. Genome Res 19(9):1606-15. (PDF)
Zhang K, Li JB, Gao Y, Egli D, Xie B, Lee JH, Aach J, LeProust E,
Eggan K, Church GM (20-Jul-2009) Digital RNA Allelotyping Reveals
Tissue-specific and Allele-specific Gene Expression in Human. Nature
Methods 6, 613 - 618. (abstract)
Sommer MO, Dantas G, Church GM. Functional characterization of the
antibiotic resistance reservoir in the human microflora. Science. 2009
Aug 28;325(5944):1128-31. (PDF)
Four additional research articles have been submitted for review and
publication. We have added a page on the website to track publications
that use PGP materials.
Webisodes from Documentary about the PGP
Did you know there is a documentary film being made about the Personal
Genome Project? Two-time Emmy Award-winning documentary producer
Marilyn Ness has been following around the Personal Genome Project
(PGP) staff and volunteers for the past several years. We're thrilled
to announce that she has released three webisodes featuring PGP-10
participants. Watch Webisode #1 featuring George Church; Webisode #2
featuring Rosalynn Gill; Webisode #3 featuring John Halamka.
Support PersonalGenomes.org
Contributors to PersonalGenomes.org who donate $50 or more between now
and December 1st 2009 will receive one our new PGP stickers. Donate
now.
In this issue
PGP-100: Exomes vs. Whole Genomes
Trait-o-matic: PRR Preview
Legal Tools for Public Genomics
What ELSI is New?
Published Research
Webisodes from Documentary
Support PersonalGenomes.org
Donate
PersonalGenomes.org is a 501(c)3 charitable organization that supports
the PGP. We need your support. Donate now.
Spotlight
Daniel Vorhaus is an attorney at the law firm of Robinson, Bradshaw &
Hinson in Charlotte, NC. He is also an ELSI advisor to the PGP and
Editor of the Genomics Law Report . Robinson, Bradshaw & Hinson
publishes the Genomics Law Report and serves as legal counsel to
PersonalGenomes.org.
Register Now
If you or someone you know would like to apply for enrollment in the
PGP, register now online.
Upcoming Events
We'll be speaking at the Pop!Tech conference in late October and the
HUGO Symposium on Genomics and Ethics, Law and Society in November.
Read More
Save the Date: DNA Day 2010
PersonalGenomes.org will be hosting several unique events scheduled
around DNA Day 2010 (Sunday April 25th). We are tentatively planning a
meeting that will bring together scientists, participants from the
PGP-10 and PGP-100, scholars from the ELSI community, companies, and
other stakeholders and contributors dedicated to the advancement of
personal genomics. More details will be released soon.
Connect
PersonalGenomes.org is now on Facebook and Twitter.
If you prefer not to receive updates from us, you may instantly unsubscribe now.
--
- Bryan
http://heybryan.org/
1 512 203 0507
JonathanCline
> The cost of whole human genome sequencing is plummeting. In less than
> 2 years, we have witnessed prices drop from more than $1 million to
> now less than $50,000 per genome, with some speculating that the
> arrival of $5000 genomes is imminent.
everyone on this list got a DVD-R in the mail with their entire genome
sequence. What would you look for in the data? Specific markers that
might point towards family-related medical conditions? Or ?? Anyone
have something specific they would love to be able to check in their
DNA, right now?
## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################
C.R.S.
Cathal Garvey
I'd probably hunt down all my gene variants for such poorly understood things, tack on a family history, and send them to research groups to help out. After that, I'd tinker with a recombination program with my and my Fiancé's genome to see how accurately I could predict our children! :P
fhapgood
immediately catalyze
a new field: recreational genomics: figuring out which genes were
associated with
reading science fiction, playing chess, and vacationing in Maine,
etc., etc.
Jay Woods
> I asked a long time ago, I've been wanting to ask again. Suppose
> everyone on this list got a DVD-R in the mail with their entire genome
> sequence. What would you look for in the data? Specific markers that
> might point towards family-related medical conditions? Or ?? Anyone
> have something specific they would love to be able to check in their
> DNA, right now?
>
The diabetes is likely inherited as it appeared in my Dad and both
Grandmothers. It would be worthwhile to know which of the varieties of Cystic
Fibrosis, several genes that vary the severity of Cystic Fibrosis, and the
several genes that go wrong on blood sugar control as well as vary the
severity of diabetes I carry. It would make drug choice easier.