![](media/image1.jpeg){width="1.0791666666666666in"
height="0.26458333333333334in"}Summary of the 3^rd^ Face-to-face MAQC
Project Meeting

**December, 1-2, 2005**, Palo Alto, CA

**The MAQC Project: Calibrated RNA Samples, Reference Datasets, and**

**QC Metrics/Thresholds for Microarray Quality Control**

Meeting Date/Place: December 1-2, 2005, Palo Alto, CA

Summary Date: December 12, 2005

Author: Leming Shi, +1-870-543-7387,
[Leming.Shi@fda.hhs.gov](mailto:jfuscoe@nctr.fda.gov)

MAQC Website: <http://edkb.fda.gov/MAQC/>

1.  **Overall**: The MAQC project, which aims at establishing calibrated
    RNA samples, reference datasets, and QC metrics/thresholds for
    microarray quality control, successfully held its 3^rd^ face-to-face
    meting in Palo Alto, California on December 1-2, 2005. Over 100
    people from more than 50 organizations representing industry,
    academia, government agencies, and other stakeholders attended the
    meeting (see attached table for a list of meeting participants).
    More than 30 speakers presented their results during the meeting,
    and Dr. Ronald Davis of Stanford University gave an excellent
    keynote address on "Data Quality in Genomics", emphasizing the
    importance of high quality genomic data in research and clinical
    diagnostics.

2.  **The MAQC Project and FDA's VGDS**: FDA representatives from NCTR,
    CDER and CDRH clearly illustrated the importance of the MAQC project
    by discussing major challenges encountered in analyzing the VGDS
    (Voluntary Genomic Data Submission) datasets and the implications in
    regulatory uses of genomic data. A focus of the Palo Alto meeting
    was on the evaluation of various ways of analyzing microarray data
    and objective QC metrics for performance assessment. It was agreed
    that the MAQC datasets are important for the community to reach
    consensus on microarray data analysis.

3.  **The Quality of the MAQC Datasets**: The meeting extensively
    reviewed the quality of the large MAQC datasets (collected from 30
    test sites on seven microarray platforms and three alternative
    technology platforms) and agreed that the overall quality of the
    data was excellent. Quality problems with a few test sites were also
    discussed. Participants shared results and ideas about performance
    metrics for microarray quality control.

4.  **Data Integrity Check**: In order to avoid error propagation in
    data analysis, each manufacturer was strongly encouraged to
    double-check the integrity of the data from its platform and make
    sure that no clerical errors were introduced during the data
    transfer process.

5.  **Biogen Idec Was Accepted as an Official Data Analysis Site**: Lisa
    Croner of Biogen Idec gave a presentation on "An Extensive Survey of
    Analysis Methods" and illustrated the areas where Biogen Idec might
    contribute to the MAQC effort. A decision was made to include Biogen
    Idec as an additional MAQC data analysis site.

6.  **TeleChem ArrayIt Data Generation**: Mark Schena and Paul Haje from
    TeleCehm ArrayIt indicated that three test sites (TeleChem ArrayIt,
    Yale University, and Wake Forest University) were expected to finish
    generating data according the MAQC study guidance and submit the
    data to MAQC by the end of December.

7.  **Interest in Extending the MAQC Project to Rat**: There was a great
    interest in extending the current MAQC project, which uses human
    RNAs, to rat samples which are more frequently used in toxicogenomic
    studies. Implementation details regarding the rat MAQC will be
    worked out by surveying the needs of the toxicogenomics community.
    Federico Goodsaid (CDER) will be coordinating the rat MAQC effort.

8.  **Publication Plan with *Nature Biotechnology***: The meeting agreed
    that it is critical to make the MAQC datasets and results available
    to a greater scientific community as soon as possible. The proposal
    (listed in the MAQC-3 meeting Agenda) of publishing the MAQC results
    with a set of 12 manuscripts in a high-impact, peer-reviewed
    scientific journal was extensively discussed, and individual
    manuscript-drafting teams were assembled. Arrangement has been made
    with *Nature Biotechnology* to publish MAQC results in a
    supplemental issue (tentatively scheduled for September 2006).

9.  **Data Analysis and Manuscript-drafting Meeting in Boston**: It was
    emphasized that the results presented at the Palo Alto meeting
    should be considered preliminary because each data analysis site did
    not have much time to analyze the data before the meeting. Each
    analysis site should critically assess each other's assumptions and
    conclusions in data analysis. Thus, a data analysis meeting was
    proposed to be held at the University of Massachusetts in Boston in
    late January (Jan. 30-31) or early February (Feb. 3-4), 2006 to
    decide additional analyses that need to be performed for each
    manuscript and for the MAQC group to reach general consensus on data
    analysis practice. Detailed outline for each manuscript will also be
    discussed. Thanks to Rick Jensen for agreeing to host the meeting.

10. **Timeline for MAQC Manuscripts**: Each manuscript-drafting team
    should work according to the following tentative timeline:

> **Dec-23-05**: Detailed outline (for circulation within each
> manuscript-drafting team);
>
> **Jan-13-06**: Detailed outline (revised, for circulation within
> MAQC);
>
> **Feb-3/4-06**: Data analysis and manuscript-drafting meeting in
> Boston (tentative);
>
> **Feb-28-06**: Initial draft version of manuscripts (for circulation
> within each manuscript-drafting team);
>
> **Mar-15-06**: 1^st^ version of manuscripts (for circulation within
> MAQC);
>
> **Mar-22-06**: Discuss 1^st^ version of manuscripts in San Diego
> (after the MAQC panel discussion at the CHI QPCR meeting) (tentative);
>
> **Apr-10-06**: 2^nd^ version for internal review (many organizations);
>
> **May-10-06**: 3^rd^ version for internal review (many organizations);
>
> **May-31-06**: Submission of manuscripts;
>
> **Jun-Aug-06**: Peer review and revision;
>
> **Sep-06**: Publication

**The next MAQC Teleconference:**

Thursday, December 15, 2005 (9 am PST / 11 am CST / 12 pm EST / 17:00
GMT)

USA Toll Free Number: **888-566-5020**

International caller:     +1-210-795-9594

PASSCODE:               **79451**

![](media/image2.png){width="1.1847222222222222in"
height="0.2916666666666667in"}**MAQC-3 Meeting Participants, December
1-2, 2005, Palo Alto, CA**

  --------- ----------------- ------------------- --------------------------------------
  **No.**   **Name**          **Organization**    **E-mail**

  1         Aschheim, Kathy   *Nature             k.aschheim@naturesf.com
                              Biotechnology*      

  2         Austermiller,     Ohio Medical        
            Bradley           University          

  3         Baker, Shawn C.   Illumina            scbaker@illumina.com

  4         Bao, Wenjun       SAS                 wenjun.bao@sas.com

  5         Beneke, Ralph     Tecan               ralph.beneke@tecan.com

  6         Bertholet,        Eppendorf           bertholet.v@eppendorf.be
            Vincent                               

  7         Bigelow, Nancy    Health Canada       nancy_bigelow@hc-sc.gc.ca

  8         Bjeldanes, Erik   Agilent             erik_bjeldanes@agilent.com

  9         Blasband, Andy    AB Consulting       andyblasband@sbcglobal.net

  10        Boysen, Cecilie   ViaLogy             cecilie.boysen@vialogy.com

  11        Bremer, Eric      Northwestern        egbremer@northwestern.edu
                              University          

  12        Bromley, Bud      ViaLogy             bud.bromley@vialogy.com

  13        Chen, Luke        PhalanxBio          

  14        Chen, Rong        Stanford University rchen1@stanford.edu

  15        Chu, Tzu-Ming     SAS                 tzu-ming.chu@sas.com

  16        Chudin, Eugene    Illumina            echudin@illumina.com

  17        Coleman,          FDA/NCTR            jcoleman@nctr.fda.gov
            Jeannette F.                          

  18        Collins, Jim      Agilent             jim_collins@agilent.com

  19        Croner, Lisa J.   Biogen Idec         lisa.croner@biogenidec.com

  20        Davies,           Affymetrix          christopher_davies@affymetrix.com
            Christopher                           

  21        Davis, Ronald W.  Stanford University dbowe@stanford.edu

  22        de Longueville,   Eppendorf           delongueville.f@eppendorf.be
            Francoise                             

  23        DeSesa, Catherine Northwestern        cdesesa@luc.edu
                              University          

  24        Dick, Daren       TeleChem ArrayIt    daren@biosearchtech.com

  25        Dragan, Yvonne P. FDA/NCTR            yvonne.dragan@fda.hhs.gov

  26        Falduto, Mike     GenUs BioSystems    mfalduto@genusbiosystems.com

  27        Fischer, Gavin M. Stratagene          gavin.fischer@stratagene.com

  28        Flanagan, Steve   City of Hope        sflan@coh.org

  29        Foy, Carole       LGC                 carole.foy@lgc.co.uk

  30        Friedman, Milt    TeleChem ArrayIt    miltfriedman@earthlink.net

  31        Fuscoe, James C.  FDA/NCTR            james.fuscoe@fda.hhs.gov

  32        Goodsaid,         FDA/CDER            federico.goodsaid@fda.hhs.gov
            Federico M.                           

  33        Guo, Xu           Affymetrix          xu_guo@affymetrix.com

  34        Hager, Janet      Yale University     janet.hager@yale.edu

  35        Haje, Paul K.     TeleChem ArrayIt    paul@arrayit.com

  36        Herman, Damir     NIH/NCBI            herman@ncbi.nlm.nih.gov

  37        Jacobson, James   Luminex             jjacobson@luminexcorp.com
            W.                                    

  38        Jensen, Roderick  UMass Boston        roderick.jensen@umb.edu
            V.                                    

  39        Ji, Hanlee        Stanford University hanleeji@stanford.edu

  40        Jokhadze, George  PhalanxBio          

  41        Jones, Wendell    Expression Analysis wjones@expressionanalysis.com

  42        Kalush, Francis   FDA/CDRH            fxk@cdrh.fda.gov

  43        Kao, Paul         PhalanxBio          

  44        Kawasaki, Ernest  NIH/NCI             kawasake@mail.nih.gov
            S.                                    

  45        Knight, Charles   Ohio Medical        
                              University          

  46        Kohne, Connie     Jaden BioScience    ckohne@san.rr.com

  47        Kohne, David      Jaden BioScience    drkohne@gmail.com

  48        Kopf-Sill, Anne   Nugen               akopf-sill@nugeninc.com

  49        Kumm, Jochen      Stanford University jochen.kumm@stanford.edu

  50        Kunitake, Steve   Reametrix           steve@reametrix.com

  51        Kuo, Winston      Harvard University  wkuo@genetics.med.harvard.edu

  52        Lee, Kathy Y.     Applied Biosystems  kathy.y.lee@appliedbiosystems.com

  53        Li, Li            Stanford University l3li@stanford.edu

  54        Li, Quan          UT Southwestern     quan.li@utsouthwestern.edu

  55        Li, Rachel        Roche               rui.li@roche.com

  56        Liggett, Walter   NIST                walter.liggett@nist.gov

  57        Liu, Chunmei      Affymetrix          chunmei_liu@affymetrix.com

  58        Lobenhofer,       Icoria              elobenhofer@icoria.com
            Edward K.                             

  59        Luo, Yuling       Genospectra         yluo@genospectra.com

  60        Ma, Charles       PhalanxBio          charlesma@phalanxbiotech.com

  61        Ma, Yunqing       Genospectra         yma@genospectra.com

  62        Mansfield, Elaine Affymetrix          elaine_mansfield@affymetrix.com

  63        Mansfield,        Affymetrix          elizabeth_mansfield@affymetrix.com
            Elizabeth                             

  64        Odujinrin,        Customized          odujinrin@pol.net
            Oluwole           Therapeutics LLC    

  65        O\'Leary, Dan     Nichols Institute   olearyd@nicholsdiag.com
                              Diagnostics         

  66        Osborn, Terry W.  Gene Express        twosborn@geneexpressinc.com

  67        Peters, Elizabeth Gene Express        ehpeters@gmail.com
            H.                                    

  68        Peterson, Ron     Novartis            ron.peterson@novartis.com

  69        Pine, Scott       FDA/CDER            patrick.pine@fda.hhs.gov

  70        Reid, Laura       Expression Analysis lreid@expressionanalysis.com

  71        Ren, Hongzu       EPA                 ren.hongzu@epamail.epa.gov

  72        Retief, Jacques   Iconix              jretief@iconixpharm.com

  73        Salit, Marc       NIST                salit@nist.gov

  74        Samaha, Ray R.    Applied Biosystems  raymond.samaha@appliedbiosystems.com

  75        Schena, Mark      TeleChem ArrayIt    mark@arrayit.com

  76        Schroth, Gary P   Solexa              gschroth@solexa.com

  77        Setterquist,      Ambion              bsetterquist@ambion.com
            Robert A.                             

  78        Shchegrova,       Agilent             svetlana_shchegrova@agilent.com
            Svetlana                              

  79        Shi, Leming       FDA/NCTR            leming.shi@fda.hhs.gov

  80        Shippy, Richard   GE Healthcare       richard.shippy@ge.com

  81        Shreter, Rachel   Affymetrix          rachel_shreter@affymetrix.com

  82        Slikker, Jr.,     FDA/NCTR            william.slikker@fda.hhs.gov
            William                               

  83        Smith, Dave D.    Luminex             daves@luminexcorp.com

  84        Sun, Yongming     Applied Biosystems  sunya@appliedbiosystems.com

  85        Suzuki, Greg      TeleChem ArrayIt    greg@arrayit.com

  86        Thierry-Mieg,     NIH/NCBI            mieg@ncbi.nlm.nih.gov
            Jean                                  

  87        Thompson, Karol   FDA/CDER            karol.thompson@fda.hhs.gov
            L.                                    

  88        Tong, Weida       FDA/NCTR            weida.tong@fda.hhs.gov

  89        Turpaz, Yaron     Affymetrix          yaron_turpaz@affymetrix.com

  90        Walker, Stephen   Wake Forest         swalker@wfubmc.edu
            J.                University          

  91        Wang, Charles     UCLA/Cedars-Sinai   charles.wang@cshs.org

  92        Warrington, Janet Affymetrix          janet_warrington@affymetrix.com
            A.                                    

  93        Wicki, Roland     Applied Biosystems  roland.wicki@appliedbiosystems.com

  94        Willey, James C.  Gene Express (Ohio  jwilley@meduohio.edu
                              Med. U.)            

  95        Wilson, Mike      Ambion              mwilson@ambion.com

  96        Wolber, Paul K.   Agilent             paul_wolber@agilent.com

  97        Xiao, Chunlin     Applied Biosystems  chunlin.xiao@celera.com

  98        Yang, Jingping    SuperArray          jpyang@superarray.net

  99        Zhai, Jack        Applied Biosystems  jack.y.zhai@appliedbiosystems.com

  100       Zhang, Lu         Solexa              lzhang@solexa.com

  101       Zong, Sheng       UIUC                szhong@uiuc.edu

  102       Zong, Yaping      Full Moon           yaping_zong@fullmoonbio.com
                              BioSystems          
  --------- ----------------- ------------------- --------------------------------------