![](media/image1.png){width="0.9652777777777778in"
height="0.9395833333333333in"}**Project Meeting Agenda**

**Microarray QC Metrics and Thresholds:**

**Calibrated RNA Samples, Reference Datasets, and Standard Datasets**

**Friday, February 11, 2005**

Building 26 Room A103 (NCTR/ARL Videoconference Room)

National Center for Toxicological Research (NCTR), US FDA

3900 NCTR Road, Jefferson, Arkansas 72079

**Videoconference**:

8:30 am--12:00 pm CST

Conf. Room 2055, FDA White Oak Labs

**Teleconference**:

> 8:30 am--12:00 pm and 1:00--2:30 pm CST
>
> Access #: 888-664-9854; Passcode: 13344

8:30 am Welcome remarks and overview of NCTR's research activities
(**Dan Casciano**)

8:45 am Current genomics activities at

> CDER (**Felix Frueh/Federico Goodsaid**)
>
> CDRH (**Uwe Scherf**)
>
> CBER (**Jing Han**)

9:00 am Presentation on the *Microarray QC Metrics/Thresholds* project
(**Leming Shi**):

1.  Project overview

2.  Selection of RNA samples

3.  Microarray experimental design

4.  "Gold standards" (qRT-PCR)

5.  QC metrics and thresholds

6.  Data sharing, management, and analysis

7.  Timetable

8.  Logistics, challenges, and benefits

9.  Expectations from the meeting

9:30 am Application of a Cross-platform RNA Standard for Assessing
Microarray Data

> Comparability
>
> **Karol Thompson** (FDA/CDER)
>
> **Jacques Retief** (Affymetrix)

9:50 am Break

10:00 am Discussion session I (Chair: **Janet Warrington**)

*(Participants: Please state your name/affiliation before you speak.)*

RNA samples

Experimental design

"Gold standards" (qRT-PCR)

Data sharing, management, and analysis

QC metrics and thresholds

Task assignments

12:00 pm Lunch

Tour of NCTR (Division of Systems Toxicology, **Yvonne Dragan**)

1:00 pm Discussion session II (Co-chairs: **David Dorris** and **Bob
Setterquist**)

Logistics

Timetable

Working groups

2:15 pm Meeting summary and action plan (**Leming Shi**)

2:30 pm **Close of meeting**.

**List of Participants**

**At FDA/NCTR site (Building 26 Room A103):**

1.  Affymetrix: Janet Warrington VP (Emerging Markets and Molecular
    Diagnostics)

2.  Affymetrix: Jacques Retief Manager (Data Analysis, Genomic
    Collaborations)

3.  Ambion: David Dorris VP and GM (RNA Services)

4.  Ambion: Bob Setterquist Group Leader (RNA Ampl. and Microarray
    Products)

5.  Illumina: Shawn Baker Sr. Scientist (Expression Profiling)

6.  ViaLogy: Bud Bromley VP (Business Development)

7.  FDA/CBER: Jing Han Biologist (customized and Affymetrix microarrays)

8.  FDA/CDER: Federico Goodsaid Sr. Scientist (PGx data submissions)

9.  FDA/CDRH: Uwe Scherf Scientific Reviewer (microarrays)

> FDA/NCTR:

10. Dan Casciano, Director

11. Yvonne Dragan Director, Division of Systems Toxicology

12. Fred Kadlubar Director, Division of Pharmacogenomics and Molecular
    Epidemiology

13. Jim Fuscoe Director, Center for Functional Genomics

14. Luke Ratnasinghe Director, Center for Structural Genomics

15. Weida Tong Director, Center for Toxicoinformatics

16. John Bowyer Biologist (filter arrays)

17. Varsha Desai Biologist (customized oligoarrays)

18. Lei Guo Biologist (Applied Biosystems platform, qRT-PCR)

19. Tao Han Biologist (customized oligoarrays)

20. Tucker Patterson Biologist (Agilent platform)

21. Jim Chen Statistician (microarrays)

22. Hong Fang Bioinformatician (microarrays)

23. Leming Shi Computational Chemist (data mining and microarray QC)

**Via Videoconference** (FDA's White Oaks Labs):

1.  CDER: Felix Frueh Associate Director of Genomics, OCPB (PGx data
    submissions)

2.  CDER: Karol Thompson, Team Leader, Molecular Toxicology/DAPR

3.  CDER: Member from Dr. Karol Thompson's team

4.  CDER: Member from Dr. Karol Thompson's team

5.  CDRH: Maria Chan

6.  CDRH: Joe Hackett

7.  CDRH: Reena Philip

8.  CDRH: Kate Simon

9.  CDRH: Zivana Tezak

**Via Teleconference:**

1.  Agilent: Jim Collins Microarrays

2.  Applied Biosystems: Gary Schroth Microarrays, qRT-PCR

3.  Applied Biosystems: Lu Zhang Microarrays, qRT-PCR

4.  Applied Biosystems: Jack Zhai Microarrays, qRT-PCR

5.  GE Healthcare: Hrissi Samartzidou Microarrays

6.  GE Healthcare: Tim Sendera Microarrays

7.  GE Healthcare: Rich Shippy Microarrays

8.  Stratagene: Garvin Fisher RNA samples, qRT-PCR

9.  Stratagene: Natalia Novoradovskaya RNA samples, qRT-PCR

10. Full Moon: Youxiang Wang Microarray standardization

11. Full Moon: Yaping Zong Microarray standardization

12. Cedars-Sinai/UCLA: Charles Wang Microarrays, qRT-PCR

13. Children's Hospital/Harvard: Zoltan Szallasi Microarrays, data
    comparison

14. Children's Hospital/Harvard: Roderick Jensen Microarrays, qRT-PCR

15. EPA: Gregory Akerman Regulatory review

16. EPA: David Dix Genomic Effects / Reprod. Tox

17. EPA: J. Christopher Corton Research Biologist

18. EPA: A few others

19. FDACVM: Heather Harbottle Customized platforms

20. Naval Res. Lab: Baochuan Lin

21. NIH/NCI: Ernest Kawasaki (unavailable) Microarrays

22. NIST: David Duewer Data comparison

23. NIST: Marc Salit (unavailable) Standardization (ERCC & Metrology)

**Contact Information**

**FDA/NCTR/**

1-800-638-3321

**Leming Shi**

870-543-7387 (O), 501-227-8590 (H), 501-258-3615 (M),
<leming.shi@fda.hhs.gov>

**Weida Tong**

870-543-7142 (O), <weida.tong@fda.hhs.gov>

**Lee Ann Branch** (Secretary, Division of Systems Toxicology, NCTR)

870-543-7467 (O), 870-543-7686 fax, <leeann.branch@fda.hhs.gov>

**Gaucho's Grill**

3 Rahling Road, Little Rock, Arkansas 72223. 501-821-2818

(This is an informal restaurant so you can dress for your own comfort.)