Summary![](media/image1.png){width="0.6118055555555556in"
height="0.5958333333333333in"} of the **2^nd^** MAQC Project Meeting

**The MAQC Project: Microarray QC Metrics and Thresholds**

Meeting Date: February 25, 2005, 11:00 am CST, teleconference

Summary Date: March 1, 2005

Author: Leming Shi, FDA/NCTR, 870-543-7387, <leming.shi@fda.hhs.gov>

**FIVE (5) WORKING GROUPS**

The following five working groups were established to coordinate the
MAQC study:

  -------------------- ----------------- --------------------------------- --------------------
  **Working Group**    **Coordinator**   **Contact Information**           **Responsibility**

  **RNA**              James Fuscoe      Division of Systems Toxicology,   Selecting two RNA
                                         FDA/NCTR, 3900 NCTR Rd., HFT-130, samples
                                         Jefferson, AR 72079.              
                                         870-543-7126, 870-543-7682(F),    
                                         <james.fuscoe@fda.hhs.gov>.       

  **Microarray**       Uwe Scherf        Division of Microbiology Devices, Designing the main
                                         FDA/CDRH/OIVD, OAK8, RM366,       study; generating
                                         HFZ-440, 2098 Gaither Road,       microarray datasets
                                         Rockville, MD 20850. 240-276-0496 
                                         Ext. 164, 301-594-5941(F),        
                                         <uwe.scherf@fda.hhs.gov>          

  **qRT-PCR**          Federico Goodsaid Office of Clinical Pharmacology   Selecting 1000 genes
                                         and Biopharmaceuticals, FDA/CDER, for qRT-PCR;
                                         HFD-860, 2078 Woodmont II Office  generating qRT-PCR
                                         Complex, 1451 Rockville Pike,     datasets
                                         Rockville, MD 20852.              
                                         301-827-5442, 301-480-6645(F),    
                                         <federico.goodsaid@fda.hhs.gov>   

  **Scanner**          Raj Puri / Jing   Division of Cellular and Gene     Comparing the
                       Han               Therapies, FDA/CBER/OCTGT, NIH    performances of
                                         Bldg N29B, Rm 2NN16, HFM-735, 29  commonly used
                                         Lincoln Drive, Bethesda, MD       microarray scanners
                                         20892. 301-827-1801,              
                                         301-827-0449(F),                  
                                         <jing.han@fda.hhs.gov>            

  **Bioinformatics**   Leming Shi        Division of Systems Toxicology,   Managing, sharing
                                         FDA/NCTR, 3900 NCTR Rd.,          and analyzing data
                                         Jefferson, AR 72079.              
                                         870-543-7387, 870-543-7382(F),    
                                         <leming.shi@fda.hhs.gov>.         
  -------------------- ----------------- --------------------------------- --------------------

If you are interested in participating in the working groups, please
contact the respective WG coordinator directly (and cc to me at
<leming.shi@fda.hhs.gov>).

**SIX (6) TEST SITES FOR THE PILOT STUDY**

+--------------+---------+---------+----------------------------------+
| **Platform** | **Test  | **Co    | **Shipping Address and Contact   |
|              | Site**  | ntact** | Information**                    |
+--------------+---------+---------+----------------------------------+
| Affymetrix   | **Affym | Chunmei | 3380 Central Expressway, Santa   |
|              | etrix** | Liu     | Clara, CA 95051. 408-731-5502,   |
| (U133        |         |         | 408-481-0422(F),                 |
| Plus2.0)     |         |         | <chunmei_liu@affymetrix.com>     |
+--------------+---------+---------+----------------------------------+
|              | **A     | Mike    | 2130 Woodward St., Austin, TX    |
|              | mbion** | Wilson  | 78744. 800-888-8804 or           |
|              |         |         | 512-651-0200 x6236,              |
|              |         | Sean    | 512-651-0201(F),                 |
|              |         | Banks   | <mwilson@ambion.com>             |
+--------------+---------+---------+----------------------------------+
| Agilent      | **Ag    | Jim     | 3500 Deer Creek Road, MS 25U-7,  |
|              | ilent** | Collins | Palo Alto, CA 94304.             |
| (G4112A)     |         |         | 650-485-5048, 650-485-8670(F),   |
|              |         |         | <jim_collins@agilent.com>        |
+--------------+---------+---------+----------------------------------+
|              | **FDA   | Tucker  | Division of Neurotoxicology,     |
|              | /NCTR** | Pa      | HFT-132, FDA/NCTR, 3900 NCTR     |
|              |         | tterson | Rd., Jefferson, AR 72079.        |
|              |         |         | 870-543-7427, 870-543-7745(F),   |
|              |         |         | <tucker.patterson@fda.hhs.gov>   |
+--------------+---------+---------+----------------------------------+
| GE           | Ambion  | Mike    | 2130 Woodward St., Austin, TX    |
| Healthcare   |         | Wilson  | 78744. 800-888-8804 or           |
|              |         |         | 512-651-0200 x6236,              |
| (300026-6PK) |         | Sean    | 512-651-0201(F),                 |
|              |         | Banks   | <mwilson@ambion.com>             |
+--------------+---------+---------+----------------------------------+
|              | **U     | Michael | Microarray Suite, Center for     |
|              | Mass    | L       | Environmental Health, Science    |
|              | B       | ombardi | and Technology, University of    |
|              | oston** |         | Massachusetts Boston, 100        |
|              |         |         | Morrissey Boulevard, S-4-023,    |
|              |         |         | Boston, MA 02125. 617-287-6084,  |
|              |         |         | 617-287-6053(F),                 |
|              |         |         | <mlombardi@rics.bwh.harvard.edu> |
+--------------+---------+---------+----------------------------------+
| Illumina     | **Ill   | Shawn   | 9885 Towne Centre Drive, San     |
|              | umina** | Baker   | Diego, CA 92121. 858-202-4597,   |
| (Sentrix®    |         |         | 858-202-4680(F),                 |
| Human-6)     |         |         | <scbaker@illumina.com>           |
+--------------+---------+---------+----------------------------------+

For information regarding GE Healthcare's arrays, contact Richard
Shippy, GE Healthcare, Molecular Diagnostics, 3200 W. Germann Rd.,
Chandler, AZ, 85248. 480-722-2339, <Richard.Shippy@ge.com>.

**DISTRIBUTION OF SIX (6) CANDIDATE RNA SAMPLES**

1.  Clontech ships 100μg of Universal Human Reference RNA (636538) to
    each test site, plus 800 μg to Ambion for mixing with Stratagene's
    UHRR *by March 3, 2005*. (Sample A)

2.  Stratagene ships 100μg of Universal Human Reference RNA (7400000) to
    each test site, plus 200μg to Ambion for mixing with Clontech's UHRR
    *by March 3, 2005*. (Sample B)

3.  Ambion mixes 800μg of Clontech UHRR with 200μg of Stratagene UHRR,
    and ships 100μg of the mixed UHRR to each test site *by March 7,
    2005*. (Sample C)

4.  Ambion ships 100μg of Human Brain RNA (cat#?) to each test site *by
    March 7, 2005*. (Sample D)

5.  Ambion ships 100μg of Human Liver RNA (cat#?) to each test site *by
    March 7, 2005*. (Sample E)

6.  Ambion ships 100μg of mixed Human Brain and Liver (20:80) RNA
    (cat#?) to each test site *by March 7, 2005*. (Sample F)

Each test site should conduct RNA QC upon receipt of samples and submit
QC data.

Contact Information of RNA Providers

+-----------+-----------+----------------------------------------------+
| **RNA     | **Contact | **Shipping Address and Contact Information** |
| P         | Person**  |                                              |
| rovider** |           |                                              |
+-----------+-----------+----------------------------------------------+
| Ambion    | Mike      | 2130 Woodward St., Austin, TX 78744.         |
|           | Wilson    | 800-888-8804 or 512-651-0200 x6236,          |
|           |           | 512-651-0201(F), <mwilson@ambion.com>        |
|           | Sean      |                                              |
|           | Banks     |                                              |
+-----------+-----------+----------------------------------------------+
| Clontech  | Laurence  | 1020 East Meadow Circle, Palo Alto, CA       |
|           | Lamarcq   | 94303. 650-739-7301, 650-354-0776(F).        |
|           |           | <laurence_lamarcq@bd.com>                    |
+-----------+-----------+----------------------------------------------+
| S         | Garvin    | 11011 North Torrey Pines Road, La Jolla , CA |
| tratagene | Fisher    | 92037. 858-535-5400 x13075, 858-535-0071(F), |
|           |           | <gavin.fischer@stratagene.com>               |
+-----------+-----------+----------------------------------------------+

**DISTRIBUTION OF ARRAYS**

1.  Affymetrix ships 60 arrays (U133 Plus2.0) to Ambion *by March 7,
    2005*.

2.  Agilent ships 60 arrays (G4112A) to FDA/NCTR *by March 7, 2005*.

3.  GE Healthcare ships 60 arrays (300026-6PK) to Ambion *by March 7,
    2005*.

4.  GE Healthcare ships 60 arrays (300026-6PK) to U Mass Boston *by
    March 7, 2005*.

**GENERATION OF MICROARRAY DATA**

-   For one-color platforms, each of the six samples will be processed
    in 10 replicates (with separate synthesis and labeling reactions) at
    each test site, resulting in a total of 60 hybridizations per
    platform per test site.

-   For the two-color (Agilent) platform, details of experimental design
    are being determined between Agilent and FDA/NCTR.

-   Each platform provider and its test sites should discuss with each
    other to decide on a common protocol.

**TENTATIVE TIMELINE OF THE PILOT STUDY**

[Task]{.underline} [Completion Date]{.underline}

RNA sample distribution: **March 3, 2005** (for Clontech/Stratagene's
UHRR to Ambion)

> **March 7, 2005** (for shipping RNA samples to all test sites)

Array distribution: **March 7, 2005** (for Affymetrix, Agilent and GE
Healthcare)

3^rd^ teleconference: March 11, 2005

4^rd^ teleconference: March 25, 2005

Array processing: **April 1, 2005**

Data sent to FDA/NCTR: **April 1, 2005**

5^th^ teleconference: April 8, 2005

Data-sharing with test sites: April 8, 2005

Data analysis: April 22, 2005

6^th^ teleconference: April 22, 2005

Face-to-face meeting: **April 29, 2005** (tentative, DC or CA)

> (Selection of two RNA samples and design of the Main Study)

MAQC Main study: May-July, 2005 (Generation of microarray and qRT-PCR
data)

October, 2005 (Face-to-face project meeting, DC or CA)

**CRITERIA FOR RNA SAMPLE SELECTION**

The purpose of the Pilot Study is to generate microarray data (regarding
gene coverage and ratio range) to aid the selection of two RNA samples
to be used in the Main Study. The following criteria have been proposed:

1.  Available in large quantity

2.  Reproducibility in production

3.  High quality

4.  Accessibility (commercial source)

5.  Wide gene presence

6.  Large fold changes for a number of genes

7.  The two RNA samples should not be selected from the same RNA
    provider.

**Notes:**

-   Criteria 1-6 were listed in slide #5 of Leming Shi's presentation on
    February 11, 2005.

-   Criterion 7 has been added after concerns were raised regarding the
    possibility of dominance by one RNA provider.

-   All MAQC participants are invited to suggest other criteria that
    should be considered in the selection of the two RNA samples.

-   It must be made clear that the six candidate RNA samples (A-F)
    should be treated equal and independent to each other. The best
    combination of any two candidates (according to the selection
    criteria) will be selected for the Main Study.

-   It must also be stressed that only two samples (from the six
    candidates) will be selected for the Main Study.

-   Assessment of "accuracy" is not the goal of the Pilot Study and
    should not be used as a criterion for RNA sample selection.

-   At the 3^rd^ MAQC teleconference (March 11, 2005, 11:00 am CST
    tentative), a formula for RNA sample selection (based on the
    proposed criteria) will be discussed.