**The Cancer Genome Atlas (TCGA)**

**Steering Committee**

*Thursday, November 2, 2006*

*4:00pm-6:00pm ET*

**ACTION ITEMS** *([not]{.underline} listed in order of importance)*

1.  Dr. Robert Penny will compile the Biospecimen Core Resource (BCR)
    biomolecule preparation protocols and e-mail them to the Cancer
    Genome Characterization Centers (CGCCs) and Genome Sequencing
    Centers (GSCs).

2.  The CGCCs and GSCs will e-mail Dr. Joe Vockley
    (<vockleyj@mail.nih.gov>) requesting test DNA/RNA and providing
    information on the concentrations that they would prefer.

3.  Each CGCC and GSC should send Patsy Folio (<pfolio@intgen.org>) the
    name and contact information of the person at the CGCC/GSC who will
    be responsible for accepting shipped biomolecule materials from the
    BCR.

4.  As soon as possible, the CGCCs/GSCs who have not already done so
    (*i.e.,* Baylor & UNC) should make sure that their Offices of
    Technology Transfer (OTTs) approve the draft Material Transfer
    Agreement (MTA) allowing for the shipment of biomolecules from the
    BCR to the centers. Dr. Gerhard should be e-mailed ASAP with this
    approval and any input regarding the MTA. Once Dr. Gerhard has
    received feedback from all of the CGCCs/GSCs regarding the MTA, a
    finalized version of the document will be distributed within
    approximately 1 week in order to obtain the appropriate signatures.

5.  Each center should provide at least two representatives for each
    working group.  By following that proviso, just in case one of those
    representatives is unable to attend a call, the center still should
    be able to be represented by the other person.

> **For the TCGA Steering Committee *Biospecimens & Biomolecules*
> Working Group:** Send additional names to the working group chair
> \[Dr. Robert Penny (<rpenny@intgen.org>)\], the NIH facilitators
> \[Drs. Brad Ozenberger (<bozenberger@mail.nih.gov>) and Carolyn Compon
> (<comptcar@mail.nih.gov)>\], and Jessica Melone
> (<jmelone@mail.nih.gov>).
>
> **For the TCGA Steering Committee *CGCC & GSC Production &
> Development* Working Group:** Send additional names to the working
> group co-chairs \[Drs. Charles Perou (cperou@med.unc.edu) and Rick
> Wilson (rwilson@watson.wustl.edu)\], the NIH facilitators \[Drs.
> Daniela Gerhard (gerhardd@mail.nih.gov) and Jane Peterson
> (<petersoj@mail.nih.gov)>\], and Jessica Melone
> (<jmelone@mail.nih.gov>).
>
> **For the TCGA Steering Committee *Informatics* Working Group:** Dr.
> Peter Good will e-mail centers that currently have only one
> representative on this working group for additional names.
>
> **For the TCGA Steering Committee *Analysis* Working Group:**
> Additional names should be sent to Jessica Melone
> (<jmelone@mail.nih.gov>).

6.  Suggestions of agenda items for the December 12^th^-13^th^ meeting
    should be sent to any NCI/NHGRI Project Team member.

7.  During the next Steering Committee call, the group will discuss the
    timeline for transferring 600-700 samples from the BCR to the
    CGCCs/GSCs.

> **[REMINDER (For those centers that have not already done
> so)]{.underline}**
>
> The Project Team requests that each component of the TCGA \[Cancer
> Genome Characterization Centers (CGCCS), Genome Sequencing Centers
> (GSCs), Biospecimen Core Resource (BCR), Data Coordination Center
> (DCC)\] submit a summary description of its organization/consortia,
> etc. as follows:

a.  Title of the center and overall role in TCGA (Production Centers,
    BCR, DCC, etc.)

b.  Organization and Principal Investigator

c.  Co-PIs (individuals and organizations)

d.  The director of the data production pipeline

e.  The director of the informatics for the project

f.  A short paragraph description of the specific functions, platforms
    and/or other activities that your center/component will be funded to
    accomplish as part of TCGA

**BIOSPECIMENS**

Dr. Robert Penny reported on the activities of the BCR. The BCR has
begun performing a dry run. The 40 samples for phase I of the dry run
were successfully shipped and have been received by the BCR. Ten of the
40 samples are extra ovarian tissue samples obtained from the
Gynecologic Oncology Group (GOG) in Ohio. Although similar, these
samples are not the "real" TCGA ovarian cancer samples that will be used
from the GOG tissue bank. Twenty of the 40 samples are from lung and
colon cancers, and the remaining ten samples of the 40 are from an
external source. The BCR has isolated molecular analytes (*e.g.*,
DNA/RNA) for the 40 dry run samples and an independent lab will perform
the same analyte isolation protocols as the BCR for quality control
comparison purposes. The BCR anticipates that it will be able to ship
the analytes in late November 2006 to the CGCCs/GSCs for testing. All of
the CGCCs/GSCs are interested in receiving these dry run biomolecules
since optimizing the BCR nucleic acid extraction protocols will be
integral to the success of the TCGA pipeline. To allow for the shipment
of the biomolecules amongst the centers, the CGCCs/GSCs should begin to
develop the appropriate Material Transfer Agreements (MTAs). Once the
MTAs are in place, the BCR expects to ship out all biomolecules in bulk
at once to the CGCCs/GSCs, rather than waiting for specimen requests
from the CGCCs/GSCs.

***Action:** Dr. Robert Penny will compile the Biospecimen Core Resource
(BCR) biomolecule preparation protocols and e-mail them to the Cancer
Genome Characterization Centers (CGCCs) and Genome Sequencing Centers
(GSCs).*

***Action:** The CGCCs and GSCs will e-mail Dr. Joe Vockley
(<vockleyj@mail.nih.gov>) requesting test DNA/RNA and providing
information on the concentrations that they would prefer.*

***Action:** As soon as possible, the CGCCs/GSCs who have not already
done so (i.e., Baylor & UNC) should make sure that their Offices of
Technology Transfer (OTTs) approve the draft Material Transfer Agreement
(MTA) allowing for the shipment of biomolecules from the BCR to the
centers. Dr. Gerhard should be e-mailed ASAP with this approval and any
input regarding the MTA. Once Dr. Gerhard has received feedback from all
of the CGCCs/GSCs regarding the MTA, a finalized version of the document
will be distributed within approximately 1 week in order to obtain the
appropriate signatures.*

The BCR shipping operations are set. Liquid nitrogen vapor shippers will
be used. These shippers can carry 75-500 vials. There is a 14-day
lifespan for keeping the vials frozen. Shipments can be made in bulk or
can be staggered. Over the past 2.5 years, the BCR has made more than
910 individual shipments and has never lost a sample using this
technology. The only modification that the BCR needed to make to its
shipping system is the ability for the BCR and receiving centers to
track the shipment. Consequently, the BCR tracking and LIMS systems are
being modified and upgraded for the purposes of the TCGA project. The
BCR is designing a single page with an executive view over the dry run
and, eventually, the "real" sample activities. From this site, any TCGA
member can access information as to how many samples passed quality
control analyses, how much DNA/RNA was distributed, etc. The site also
will have subsections relating pathology metrics, shipment tracking,
etc. This site should be ready within the next 10-14 days.

***Action:** Each CGCC and GSC should send Patsy Folio
(<pfolio@intgen.org>) the name and contact information of the person at
the CGCC/GSC who will be responsible for accepting shipped biomolecule
materials from the BCR.*

The MD Anderson Glioblastoma glioblastoma tissue bank will have Dr. Ken
Aldape, a board-certified neuropathologist, review the pathology of the
glioblastoma samples. The Glioblastoma samples will be 100% QC'd, with
15% further assessment by a blue-ribbon panel of national experts. The
squamous lung carcinoma samples were expected to be reviewed by a
general surgeon pathologist. However, it was strongly encouraged that a
subspecialist review the squamous lung carcinoma samples as well to
ensure 100% QC, and this suggestion was accepted. In addition, as a
general principle, the QC process will analyze tissue taken from the
actual samples that will be used for the TCGA pipeline.

**STEERING COMMITTEE WORKING GROUPS**

There currently are four TCGA Steering Committee working groups.
Although several of the working group aims overlap, the groups have been
divided into the following four categories:

(1) Biospecimens & Biomolecules

(2) CGCC & GSC Production & Development

(3) Informatics

(4) Analysis

These working groups will be charged with addressing the details of
pertinent TCGA concerns so that the umbrella Steering Committee can
engage in higher-order issues and decision-making.

***Action:** Each center should provide at least two representatives for
each working group.  By following that proviso, just in case one of
those representatives is unable to attend a call, the center still
should be able to be represented by the other person.*

> ***For the TCGA Steering Committee Biospecimens & Biomolecules Working
> Group:** Send additional names to the working group chair \[Dr. Robert
> Penny (<rpenny@intgen.org>)\], the NIH facilitators \[Drs. Brad
> Ozenberger (<bozenberger@mail.nih.gov>) and Carolyn Compon
> (<comptcar@mail.nih.gov)>\], and Jessica Melone
> (<jmelone@mail.nih.gov>).*
>
> ***For the TCGA Steering Committee CGCC & GSC Production & Development
> Working Group:** Send additional names to the working group co-chairs
> \[Drs. Charles Perou (cperou@med.unc.edu) and Rick Wilson
> (rwilson@watson.wustl.edu)\], the NIH facilitators \[Drs. Daniela
> Gerhard (gerhardd@mail.nih.gov) and Jane Peterson
> (<petersoj@mail.nih.gov)>\], and Jessica Melone
> (<jmelone@mail.nih.gov>).*
>
> ***For the TCGA Steering Committee Informatics Working Group:** Dr.
> Peter Good will e-mail centers that currently have only one
> representative on this working group for additional names.*

***For the TCGA Steering Committee Analysis Working Group:** Additional
names should be sent to Jessica Melone (jmelone@mail.nih.gov).*

**TARGET SELECTION**

Operating in parallel to the TCGA Steering Committee and its four
working groups is a TCGA Target Selection Committee, co-chaired by Drs.
Thea Tlsty and Rick Wilson. The Target Selection Committee will provide
feedback on the development of target lists for the three TCGA tumor
types, which will be analyzed *sequentially* in the TCGA pipeline. The
Target Selection Committee was provided with the initial NCICB drafts of
TCGA target gene lists. The Target Selection Committee was sectioned
into three subcommittees, each addressing one of the three TCGA tumor
types (Glioblastoma Multiforme, Squamous Lung Carcinoma, and Ovarian
Cancer). The NCI/NHGRI Project Team is awaiting responses from the
subcommittees regarding the content of the draft NCICB gene lists for
their assigned tumor types.

**MAY 2006 DATA RELEASE WORKSHOP**

The report from the May 2006 TCGA Data Release Workshop, co-chaired by
Drs. Rick Schilsky and Bob Waterston, has been released. The TCGA
website contains a link to the report
(<http://cancergenome.nih.gov/components/TCGA_101706.pdf>).

The workshop provided guidance regarding data release policy and
reinforced the notion that TCGA data should enable the broad research
community. The workshop encouraged adherence to the guiding data
policies of other large-scale projects (*e.g.*, the Fort Lauderdale
Principles followed by the Human Genome Project and the International
HapMap Project). Nevertheless, workshop participants recognized the
unique challenges faced by the TCGA project, notably the need to protect
patient identity and to abide by patient consent forms.

The workshop participants agreed that a two-tiered system of databases
was preferable: (1) An open-access database available to the public and
housing data that could not potentially identify any patient and (2) A
controlled-access database requiring NIH authorization for access and
housing any data that potentially could be used to identify a patient.
It was agreed that the data should be released rapidly and should be
considered pre-competitive. The workshop participants also reaffirmed
the need to use consent forms that clearly state potential risks to
patients.

**DECEMBER 2006 MEETING**

There will be a meeting of the TCGA External Consultant Panel (ECP),
Steering Committee, and NCI/NHGRI Project Team on December
12^th^-13^th^, 2006 at the Marriott in College Park, MD. The agenda for
the December meeting could include a discussion of the parameters for
using normal samples in the TCGA pipelines. In addition, the potential
for domestic and international collaborations could be addressed.

**Action:** *Suggestions of agenda items for the December 12^th^-13^th^
meeting should be sent to any NCI/NHGRI Project Team member.*

***Action:** During the next Steering Committee call, the group will
discuss the timeline for transferring 600-700 samples from the BCR to
the CGCCs/GSCs.*