Simona Volpi: Okay, good afternoon, everyone.
And so, yeah, I will be giving an update on GTEx, the genotype and tissue expression program.
So GTEx is a NIH Common Fund program, and the co-chairs are Dr. Green and Dr. Insel.
The two leading ICs are NHGRI and NIMH.
NCI has played a very important role in this project as well.
We have a very engaged working group at the NIH which has a lot of people -- a lot of
members from different ICs.
So the goal of GTEx is to establish a resource database and tissue bank in which we study
the relationship between genetic variation and gene expression in reference/non-diseased
human tissues.
Right now we are collecting over 30 tissues in a rapid autopsy setting.
And we are performing RNA sequencing on all the samples that are of enough good quality.
And while we expect at some point to probably do some sequencing of the blood DNA, we are
right now performing high density SNP genotyping.
And with the lumina fiber M [spelled phonetically] as well as an exome ChIP.
So GTEx started as a pilot in 2010; ended last year as a pilot in 2012.
And the recruitment and RNA quality goals, which were the main concern for full implementation
of this program, were met.
The goal for recruitment, for example, was to be able to enroll at least 10 donors by
the end of the pilot, by the end of the month of the pilot -- of the pilot.
And as you can see from this graph, really, which shows the numbers of donors by month,
we were able to achieve this goal on average.
And the RNA quality goals, which I mentioned before, were met as well, as measured by the
reen [spelled phonetically] values.
GTEx, at the end of the scale up, we can imagine a resource which will provide really an atlas
of human gene expression.
In addition to provide a comprehensive cis- and trans-eQTL results for these tissues.
The resource at the end will include around 900 post-mortem donors, completely genotyped.
We are expecting to collect over 25,000 tissues, and being able to hopefully perform RNA sequencing
on almost all of them.
We are also expecting to have associated clinical and histopathological data available for those
samples.
And being able to provide a system to access both data and samples.
We are also performing an ELSI study on donors' family, and results from that study will be
available as well.
Well, GTEx is a very complex program and has a lot of moving parts.
So I'm going to go briefly over the component of GTEx.
Organ donor enrollment is done through organ procurement organization and tissue banks.
We have, right now, two sites that are enrolling donors.
We have a sample and a data repository.
We have a very highly engaged team of pathologists which are reviewing each sample they receive.
These activities are coordinated and managed by NCI through the CA hub [spelled phonetically]
initiative.
We have also brain bank where the brains that are collected at the sort sites go, and there,
further dissection of the brain happens.
We have a centralized laboratory and data analysis and coordinating center, this is
the Broad Institute.
This place really does a lot of things, among which, performs the RNA sequencing, the SNP
genotyping, takes care of coordinating this project, and also performs data analysis.
Together with, actually, a very engaged group of geneticists, statistical geneticists, and
they basically tackle the data that have been generated by GTEx.
We also have, as I mentioned before, an ELSI study that is happening.
And NCBI is managing the GTEx database and the eQTL browser.
In addition to this, we are planning to add a new component, which is the enhanced GTEx.
And I will talk a little more about this later on in this presentation.
So let's look at the data that are available from GTEx.
GTEx data are housed in two places.
We have dbGaP, which has the control access data such as SNP genotyping files, as well
as BAM files from RNA-seq.
But we envision to be this place, also, an archive sometime in the future of all the
GTEx data.
We have then another place where GTEx data are available, and that is the GTEx portal.
It is housed at the Broad Institute; this is the URL.
And this has been designed with a different goal in mind, more as a place where user can
go and use the features that are available there in a user-friendly way.
And there are several ways the user can look at the data, display the data, search the
data.
In fact, we have -- I'm sorry -- we have several -- we have an option here where there is a
tab where they can go to the next page and can search, for example, eQTLs, either by
gene or by the SNP.
And this is also the place where other features area available and I'll talk a little bit
more later.
So look at the expression data production and release.
This is a graph that shows the number of cases analyzed and deposited into dbGaP by organ
site.
This is a list of organs that -- it's not the full list that we have.
In the red box, I have highlighted the brain areas.
And as you can see here, in the dark blue bars, we have the number of cases deposited
since last November.
We also have, in the light blue bars, cases that will be deposited by the end of this
month.
And the very light blue bars indicates the remaining of the pilot.
So if you look at it overall, you can notice that, basically, by the end of the pilot,
we will have -- the data set of the pilot, basically, will include seven sites with at
least 100 donors and two sites with at least 90 donors each.
In the scale up, we are planning to sequence all the samples that are coming in of enough
good quality and performing, hopefully, DNA sequencing of the blood samples, or at least
the ChIPs that we are actually doing right now.
So, I told you a little bit more about the data that are available.
Let's look at the samples now, what do we have?
GTEx has tissue that has been PAXgene fixed and frozen.
We have also PAXgene fixed tissues which have been paraffin embedded and stored.
And we have also some nucleic acid.
We have nucleic acid.
The brain is the only organ that has not been PAX fixed, PAXgene fixed, but has been -- it
is shipped on ice from the sort site to the brain bank.
At the brain bank, the group there further dissect the brain into 1.5 centimeter slabs.
And then those additional area, together with the remaining of the brain, are flash frozen
and stored.
We also have cell lines available.
We have lymphoblastoid and fibroblast cell lines.
The lymphoblastoid cell line are successful right now for 50 percent of the donors.
Whereas the fibroblast, they have a higher success rate.
Here you'll see another search capability of the portal at the Broad Institute where
user can go, after logging in, and search for samples, basically search the inventory
at the Broad.
They can look at the different material, different tissue site, and do a kind of mine of what
is available for GTEx.
So, now, how did we -- how are we making these samples available?
Well, last November, the NIH issued a RFA, the enhanced GTEx with molecular analysis
of stored biospecimen RFA.
This RFA has a receipt date of March 28.
We expect to have a summary review by CSR.
Those applications will come to this council next September for funding in early FY '14.
So you will see those applications.
And the Common Fund gave us $10 million over three years, with 3.8 in FY '14.
So the goal of this RFA, it's really to -- it's open, it's open to the most compelling ideas.
So we really want the scientists to leverage the uniqueness of GTEx and come up with ways
how to add value to this resource.
So, with this, I would like to thank all the institution that are part of this project
for the great support in achieving the goals that we had.
And I will be happy to take questions.
Sure.
Female Speaker: Could you speak just a little bit to what
the ELSI project is like that's part of this?
Simona Volpi: Sure.
The ELSI project is really looking the next of kin, how, you know, the family has felt
about the process of consenting for this program.
There is a group at University of Virginia Commonwealth that is highly engaged in this.
And so we had the donors' families interviewed after and asked questions about the consent
process.
How they felt, did they understand the process, did they understand what the study about?
There are a lot of questions that we asked them.
And we tried to incorporate their suggestions in the review that we do to the consent process
as well.
Robert Nussbaum: Could I ask a little bit about the ascertainment,
what's your acceptance and your rejection criteria for donors?
Simona Volpi: So donors are the -- we have a few, very few
criteria.
Donors' age has to be between 21 and 70 years old.
We have a limit on the BMI, between 18 and 35.
And the donors have to be free of major disease, among which, cancer.
One of the exclusion criteria, for example, is that they can't -- they couldn't receive
chemotherapy in the last couple of years.
And we also have to think about how these donors get to GTEx.
These donors are mainly recruited through organ procurement organizations.
So the criteria that stand for those basically stand also for GTEx.
Robert Nussbaum: Are living -- I mean, these are organ transplant.
Simona Volpi: Some cases -- most of the cases are.
Some are autopsy, rapid autopsy cases.
Robert Nussbaum: Do you find yourself sometimes in conflict
with the organ procurement process?
Simona Volpi: Well, these case go first to organ procurement
organizations, so if they qualify for that, then they pass and become GTEx cases.
Male Speaker: Okay, thank you very much, Simona.