# ICR Workspace Teleconference

## Meeting Information

Date: October 8, 2008

Time: 2-4 PM ET\
Moderator: Elaine Freund

#### 

## Executive Summary

Received updates from Working Groups in the regular rotation schedule

## Key Outcomes and Decisions

N/A

## Action Items

Table 1: Meeting Action Item List

  ------------------------------------------------------------------------
  **Assigned To**   **Description**                         **Due Date**
  ----------------- --------------------------------------- --------------
  Text                                                      

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## Meeting Notes

### EY1

There was a recent note from NCICB Deputy Director, George Komatsoulis
pointing out that September 30 marked the end of the initial period of
the caBIG® Cancer Center deployment activity.

From this morning there are currently\...

122 caBIG® Participants

107 grid services

77 data services

30 analytical services

For more information please visit
<http://cagrid-portal.nci.nih.gov/web/guest/discovery>

### Enterprise Support Network:

#### Knowledge Center

KC wiki: We regularly update the KC wiki to add additional information
and links.

KC forums: There is increasing usage of the KC forums on all four tools

a.  geWorkbench has announced the cut-over in September, 2008 and is
    using the KC forums exclusively.

b.  GenePattern has scheduled the switch from its existing Yahoo forum
    to the KC forum on October 14, 2008.

c.  caArray has announced the transition from its listserv to KC forums
    and the cut-over is on Oct 31, 2008. Currently all messages posted
    to the caArray listserv are copied to the KC caArray forums. This
    transition applies to both the caArray Users and Developers listserv
    and in the interim, responses on the forums are copied to the
    listserv as well.

The forum offers a number of important advantages over the listservs,
particularly the availably of organized, searchable message threads.  In
addition, you may subscribe to these forums and receive email
notifications of new postings that include the content of the posting in
the body of the email. 

After **Friday, October 31**, the caArray listservs will not be
available for general posting (though we may continue to send out
critical announcements via this mechanism).  In order to receive email
notification of caArray User and/or Developer forum postings, please do
the following:

1.  Request a Knowledge Center Web account at
    <http://wikiutils.nci.nih.gov/KC_signup>.  You will receive your
    username and password within one business day.

```{=html}
<!-- -->
```
1.  Go to the MAT-KC forum at
    <https://cabig-kc.nci.nih.gov/Molecular/forums/> and login (login
    link is at the upper right of the page).

2.  Once logged in, click on the forum of interest, for example "caArray
    End User Discussions".

3.  At the bottom of the page, click on "Subscribe Forum".  

4.  You will now receive email notifications for all postings to this
    forum, very analogous to how the listserv works. 

These directions, along with associated screenshots, are available in
the slide deck from this month's caArray Users meeting which are
available at
<https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/CaArray_Monthly_User_Meetings>.

#### First Licensed caBIG® Support Service Providers Now Available

The cancer Biomedical Informatics Grid^®^ (caBIG^®^) initiative
announces a milestone in its expansion of support alternatives for
end-users, IT staff and senior decision makers implementing caBIG^®^
tools and infrastructure. Three companies, 5AM Solutions, Inc., Ekagra
Software Technologies and SRA Corporation, are the first to be licensed
by the National Cancer Institute (NCI) to market their services as part
of the caBIG^®^ Support Service Providers Program. Other companies in
addition to 5AM, Ekagra and SRA are currently engaged in the licensing
process, and will be announced in the coming weeks.

caBIG^®^ Support Service Providers are independent entities that are
approved by NCI as meeting specific criteria for performance of support
services related to caBIG^®^ needs. There are four categories of
support: Help Desk Support; Adaptation and Enhancement of
caBIG^®^-Compatible Software Applications; Deployment Support for
caBIG^®^ Software Applications Deployment; and Documentation and
Training Materials and Services. Services rendered by caBIG^®^ Support
Service Providers to their clients are established under separate
business arrangements organized by and between the service provider and
its clients.

Visit <https://cabig.nci.nih.gov/esn/service_providers> to learn more
about caBIG^®^ Support Service Providers or access those Support Service
Providers that are currently licensed. If you are interested in applying
to become a Service Provider, you can access past and future
announcements for caBIG^®^ Support Service Provider at this site as
well.

### F2F Related:

#### Meeting presentations and Notes

-   Meeting presentations have been posted on the web
    <https://cabig.nci.nih.gov/workspaces/ICR/Meetings/index_html/ICR_F2F_Sept08>.

-   Meeting notes to listserv by COB Fri or SOB Tues.

#### Matthew Myerson Presentation Follow Up

In his plenary talk, Dr. Myerson presented his work showing a
correlation between specific EGFR mutations in lung adenocarcinoma and
response to a specific chemotherapy.

We were pleased to note the NCI announcement:

<http://www.cancer.gov/newscenter/pressreleases/MARVELrelease>

NCI Launches First-Ever Study to Determine if Biomarkers Can Help Guide
Treatment for Lung Cancer

Today, a large national clinical trial for non-small cell lung cancer
was launched to validate whether a biomarker can predict clinical
benefit in the treatment of this disease. Biomarkers, which are
molecules found in the body that can signal an abnormal process or
disease, would identify a target known as epidermal growth factor
receptor (EGFR). This receptor can be increased in some lung cancers due
to the presence of extra copies of its coding gene. These extra copies
can result in activation of tumor growth, so drugs that block this
activation could have a significant impact on lung cancer treatment.
This study, sponsored by the National Cancer Institute (NCI), part of
the National Institutes of Health, is called MARVEL (Marker Validation
for Erlotinib in Lung Cancer) and will attempt to definitively establish
the future value of selecting patients for treatment based on the
presence or absence of EGFR activation.

Approximately 1,200 lung cancer patients will be tested for the status
of this biomarker, and then will be randomly assigned to treatment based
on the test results. Both EGFR-positive and EGFR-negative patients will
receive either the chemotherapy drugs erlotinib (Tarceva ®, Genentech)
or pemetrexed (Alimta ®, Eli Lilly) after they have received their
initial, standard chemotherapy. Erlotinib specifically targets EGFR,
whereas pemetrexed blocks tumor cell growth by another mechanism.

It is hypothesized that erlotinib will be superior in the patients with
EGFR-positive lung cancer, whereas pemetrexed would be favored in
patients with EGFR-negative lung cancer, based on knowledge from
earlier, smaller studies. MARVEL will incorporate genetic studies for
erlotinib and pemetrexed that will be important to further identify
patients with different sensitivity and toxicity profiles to these
therapies.

Lung cancer is expected to claim 161,840 lives in 2008, and 215,020
people are expected to be diagnosed with the disease this year, making
it the number one cancer killer. Non-small cell lung cancer represents
about 85 to 90 percent of all lung cancers.

\"Because lung cancer is such a lethal disease and because it is
particularly difficult to treat, especially if diagnosed in its later
stages, the MARVEL trial is of major importance because it could define,
based on a single test, the best therapy for this disease. The future of
moving highly targeted agents from the lab to the clinic will be heavily
dependent on biomarkers for patient selection,\" said NCI director John
E. Niederhuber, M.D.

Both erlotinib and pemetrexed are approved treatments for advanced
non-small cell lung cancer. Among the factors that appear to influence
responsiveness to erlotinib, in addition to the level of EGFR
activation, are whether the resulting cancer cells are classified as
adenocarcinomas (as opposed to squamous or other types of cells), female
gender, Asian ethnicity, and whether the patient was ever a smoker.
However, no forward-looking study has been performed to definitively
address which factors are most important.

MARVEL, also known as N0723, is a phase III study that will be led by
the North Central Cancer Treatment Group (NCCTG) and include many other
NCI-sponsored clinical trial groups. The trial will enroll patients over
a four year period and test them for EGFR status. It will randomly
assign about 950 of the 1,200 tested patients to the treatment protocol
(assuming that 80 percent of the tests will successfully allow
classification of patients as either EGFR-positive or EGFR-negative),
and, after a minimum of one to two years of follow-up, accrue data on
disease-free and overall patient survival rates as well as determine if
markers are good predictive and prognostic tools. It will also establish
whether erlotinib provides a meaningful benefit over the patients\'
initial, standard chemotherapy.

This trial is the outcome of a unique and innovative collaboration,
formed in 2006, called the Oncology Biomarkers Qualification Initiative
(OBQI) between NCI, the U.S. Food and Drug Administration (FDA), and the
Centers for Medicare and Medicaid Services. OBQI was designed to qualify
biomarkers for use in clinical trials and, ultimately, to speed better
agents to cancer patients.

\"The MARVEL trial is unique and an important first because it is an
outgrowth of specific NCI initiatives designed to advance lung cancer
therapies and received broad input from the FDA, NCI cooperative groups,
the biomarker industry, and the pharmaceutical industry,\" said Alex A.
Adjei, M.D., Ph.D., senior vice president of Clinical Research at
Roswell Park Cancer Institute, Buffalo, N.Y., and chair of the study.

#### In addition to being chaired by the NCCTG, the trial represents a collaborative effort of many of NCI\'s cooperative groups who perform lung cancer research including the Cancer and Leukemia Group B (CALGB), the Eastern Cooperative Oncology Group (ECOG), the Southwest Oncology Group (SWOG), and the National Cancer Institute of Canada, Clinical Trials Group (NCIC CTG), as well as industry partners. For more information on MARVEL, please go to [**http://www.clinicaltrials.gov/ct2/show/NCT00738881?id=N0723&rank=1#desc**](http://www.clinicaltrials.gov/ct2/show/NCT00738881?id=N0723&rank=1#desc)

### caBIG Related Publication

### **September 2008: *Towards a Data Sharing Culture: Recommendations for Leadership from Academic Health Centers*, PLoS Medicine** **(Vol. 5, Issue 9)** - This article, written on behalf of the DSIC Workspace, discusses the critical roles Academic Health Centers (AHCs) can play by encouraging data sharing among their scientists and clinicians. These data exchanges can lead to improved patient outcomes, reduced research costs, and faster application of research technologies to clinical care. The benefits to both researchers and the AHCs themselves include an increased visibility of the research, opportunities for additional publications through collaboration, and potentially even increasing the citation rate of the primary publications. The full text of the article can be found at: [**http://medicine.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pmed.0050183**](http://medicine.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pmed.0050183)

### WORKING GROUP REPORTS

#### ASBP Working Group

> Please click the following link to review the ASBP Presentation:
> <https://gforge.nci.nih.gov/frs/download.php/5156/20081008_ASBPUpdateToICR.ppt>
>
> OCT 14 ad hoc to make up for the Columbus day holiday.
>
> Reviewed Shannon Hasting's talk at the ICR F2F Break-out
>
> Multidimensional arrays -- a solution is limited to 2 D arrays and is
> an interim solution for GenePattern. Long term solutions to be
> discussed with VCDE.

#### ICRi Working Group

> Please click the following link to review the ICRi Presentation:
> <https://gforge.nci.nih.gov/frs/download.php/5160/ICRi2ICR_2008-10-08c.ppt>
>
> Note on slide of presentation to deployment leads -- table of use
> cases

#### Information Representation Working Group

> Please click the following link to review the Information
> Representation Presentation:
> <https://gforge.nci.nih.gov/frs/download.php/5158/20081008_IRWG_ICR_WS_Presentation.ppt>

### Working Group Related Items

#### WG Communication 

> The proliferation of ad hoc meetings causing exclusion of key players
> has been a point of concern, especially with WG Leads who are trying
> to move projects forward and stay coordinated. During a recent
> discussion, we came to the following conclusions on a general path
> forward:

-   reduce ad hoc meetings

-   touch base through WG leads on specific themes

-   WG lead or a designee known to them to attend an ad hoc meeting
    should one need to occur

-   WG agendas to include reporting back on ad hoc meetings

-   can use WS Lead to assist

## Next Steps

Scheduled Speakers on ICBP (Thomas Deisboeck and Tahsin Kurc) need to
reschedule today's planned presentation.

## Next Meeting

October 22, 2008

## Attendees

Table 2: List of Meeting Attendees

  -----------------------------------------------------------------------
  **Affiliation**                     **Name**
  ----------------------------------- -----------------------------------
  Indiana U                           Ganesh Shankar

  Georgetown                          Baris Suzek

  Broad                               Ted Liefeld

  3^rd^ Mill                          Elaine Freund

  Baylor College of Medicine          David Steffen

  Dana Farber                         Deven Atnoor

  BAH                                 Li Kramer

  SAIC                                Donna Messersmith

  JAX                                 Grace Stafford

  NCI                                 Jim Sun

  NCI                                 Juli Klemm

  UNC                                 Leonard McMillan

  Fred Hutch                          Martin Morgan

  NCI                                 Mervi Heiskame

  Wash U                              Nathan Baker

  LabKey                              Peter Hussey

  Mayo                                Bob Freimuth

  Duke                                Sal Mungal

  Wash U                              Jahangheer Shaik

  MGH                                 Stanley Shaw

  NCI                                 Sue Pan

  Nartech                             Tom Boals

  FKH                                 Trey White

  UNC                                 Wei Wang

  Columbia                            Zhong Li

  IMS                                 Mary McAdams
  -----------------------------------------------------------------------