Summary of the MAQC **May-19-2005** Teleconference

**The MAQC Project: Calibrated RNA Samples, Reference Datasets, and QC
Metrics/Thresholds for Microarray Quality Control**

Meeting Date: May 19, 2005 (9 am PDT / 11 am CDT / 12 pm EDT)

Meeting Place: Teleconference

Summary Date: May 22, 2005

Author: Leming Shi, FDA/NCTR, +1-870-543-7387, <leming.shi@fda.hhs.gov>

1.  **Review of May 2-3 meeting**: Leming Shi briefed the MAQC group of
    the conclusions of the MAQC face-to-face meeting on May 2-3, 2005
    (detailed meeting summary was set out on May 10, 2005). Briefly,
    each platform will be tested at three test sites (including the
    microarray manufacturer) with four RNA samples (*i.e*., Ambion brain
    RNA, Stratagene UHRR, and two mixtures of the brain RNA and UHRR in
    a mixing ratio to be determined by the MAQC Pilot Titration Study)
    and in five replicates per site, resulting in 20 arrays per test
    site per platform.

2.  **Availability of Brain RNA**: Bob Setterquist updated Ambion's
    progress towards manufacturing reasonably reproducible and larger
    batch of the brain RNA sample. It is expected that the brain RNA
    will be available within two months. Mike Wilson (Ambion) clarified
    that each batch would in a quantity of above 1 gram of brain RNA.

3.  **Pilot Titration Study**: Rich Shippy introduced the experimental
    design of the MAQC Pilot Titration Study (Table 1), which is to be
    conducted by the microarray manufacturers. Bob Setterquist and Mike
    Wilson will master mix the total RNA samples, split appropriately
    (approximately 10 ug per sample), and send to microarray
    manufacturers. The Ambion human brain RNA will be the same as in the
    MAQC pilot study. The Pilot Titration Study is expected to be
    completed within one month. The participating manufacturers will
    form a small group to develop strategies for analyzing the titration
    datasets. Everyone is encouraged to make suggestions on the analysis
    of the titration data.

Table 1: Experimental Design of the MAQC Pilot Titration Study

  ---------------- ----------------------- --------------------- --------------------
  No.              Ambion Brain RNA (%)    Stratagene UHRR (%)   Number of Replicates

  1                100                     0                     6

  2                99.5                    0.5                   3

  3                99                      1                     3

  4                95                      5                     3

  5                90                      10                    3

  6                75                      25                    3

  7                50                      50                    3

  8                25                      75                    3

  9                10                      90                    3

  10               5                       95                    3

  11               1                       99                    3

  12               0.5                     99.5                  3

  13               0                       100                   6

  Total number of                                                **45**
  arrays per site                                                
  (manufacturer)                                                 
  ---------------- ----------------------- --------------------- --------------------

4.  **Cross-platform analysis for selecting genes for validation**: The
    FDA/NCTR is conducting cross-platform comparison in order to provide
    information for selecting \~1,000 genes for validation by orthogonal
    technologies (*e.g*., TaqMan^®^ and QuantiGene^TM^) based on the
    mapping of RefSeq across the platforms. Microarray manufacturers
    will work together to reach a consensus gene mapping and will also
    provide sequence information to the MAQC group to conduct
    sequence-based gene mapping. Volunteers are needed to analyze the
    pilot study datasets for assessing cross-platform comparability and
    for selecting genes for validation. If interested, please contact
    <Leming.Shi@fda.hhs.gov>.

5.  **Publications**: It was suggested that the MAQC group should aim at
    publishing the major findings in a widely-read journals such as the
    *Nature* series (*e.g*., *Nature Methods*) in order to maximize the
    impact of the MAQC study on the microarray community.

6.  **Timeline**: Based on the projected timeline for the availability
    of the larger batch of Ambion's brain RNA sample (July 2005), it is
    possible that the microarray data generation phase of the MAQC main
    study can still be completed by ***[the end of August
    2005]{.underline}***, and the next face-to-face meeting on data
    analysis can be held in October (or November) in California (Bay
    area or San Diego).

7.  **Other issues**: The issue of including "day effect" in the MAQC
    main study was brought up by Leming Shi after concerns were raised
    by eliminating this factor in the main study. However, the majority
    of the MAQC group appeared to be happy with the decision on
    conducting five replicates within the same day. It was suggested
    that each test site should record the day on which a labeling
    reaction or a hybridization is conducted.

8.  **New participant**: Andy McShea (VP, <amcshea@combimatrix.com>)
    confirmed Combimatrix's participation in the MAQC main study by
    agreeing to run its platform(s) at three test sites (including
    Combimatrix) and to follow the design of the MAQC main study.
    Combimatrix may also participate in the MAQC Pilot Titration Study.

**Next MAQC Teleconference:**

Thursday, June 2, 2005 (9 am PDT / 11 am CDT / 12 pm EDT)