2011 NYU NMVB Report2011 NYU NMVB Report

NYU Dept of Cardiothoracic SurgeryNYU Dept of Pathology

Monday November 7th, 2011

Personnel @ NYUPersonnel @ NYU

Dept. Pathology

Audrey Sorensen, RN(Research Nurse Coordinator)

Harvey Pass, MD(Surgeon, NYU Steering Committee Member & PI)

Dept. Cardiothoracic Surgery

Ryan Harrington(Lab Technician, Thoracic Lab)

Angela Pittman(Research Project Coordinator)

Ruth Pe Benito(Bioresource Manager)

Jonathan Melamed, MD(Pathologist, NYU Steering Committee Member)

Monica Gorman(Research Coordinator)

Rachel Ruoff(Lab Technician, Pathology Lab)

NYU MVB IRB Amendment ApprovalNYU MVB IRB Amendment Approval

Amendment to IRB (approved on 10/27 /11)

Amendment includes the following statement in the consent: “The NYU School of Medicine is collaborating with the University of Pittsburgh to create and maintain the Mesothelioma Virtual Bank (MVB). Clinical information and biologic samples that are free of any personal health identifiers are shared in accordance with HIPAA standards. This data is used to advance the scientific understanding of Mesothelioma. “

SPECIMENS COLLECTED

CATEGORY Serum Plasma Buffy Coat Paxgene Mono CPT Tumor Normal Effusion

Mesothelioma Follow-up (n=4) 3 3 3 3 2 2 1 0 1

Mesothelioma New (n=7) 7 7 7 7 7 7 7 4 1

NYU Additions to MVB 2011NYU Additions to MVB 2011

YearRetrospective

CasesProspective

CasesOverall Total

2007

157 31 188

2008

0 21 21

2009

0 11 11

2010

0 8 8

2011

0 11 11

Total: 239

NYU MVB Biospecimen AccrualNYU MVB Biospecimen Accrual

Year New cases collected

Collection Method

Frozen tissue only

Paraffin + Frozen tissue

Paraffin tissueonly

2008 7 0 6 1

2009 9 2 7 0

2010 6 0 4 2

2011 7 0 7 0

• Emphasis on accruing extrapleural pneumonectomy cases

NYU MVB tissue accrualNYU MVB tissue accrual

NYU MVB Paraffin TMA 1NYU MVB Paraffin TMA 1

• NYU MVB Paraffin TMA 1NYU MVB Paraffin TMA 1• 2 identical TMA Blocks• 37 cases - arrayed over 2 blocks• 37 Tumor + 4 Control• 8 Cell lines

• Supplementary TMA• 9 Cases (additional cores for TMA1)• 9 Tumor +1 Control Block A Block B

Map for Paraffin TMAMap for Paraffin TMA

Evaluation for presence of tissue and sampling accuracy based on tumor (9 of 37 cases missing across the two TMAs – added in supplementary block)

IHC stain to evaluate antigenicity of tissue: WT-1, Calretinin

QA Steps for TMA (slide A)QA Steps for TMA (slide A)

B- Benign TissueT-Tumor

A- Missing Core

MVB #Cores

on TMA out of 8

Tumor/Benign

2230 1 Tumor

2186 2 Tumor

2202 1 Tumor

2162 2 Tumor

2160 2 Benign

2187 1 Tumor

2163 1 Possible Tumor

2170 None

2231 3 1 Tumor/ 2 Benign

MVB #Cores on TMA Blocks out of

possible 8Tumor/Normal

2230 1 Tumor

2186 2 Tumor

2202 1 Tumor

2162 2 Tumor

2160 2 Normal

2187 1 Tumor

2163 1 Possible Tumor

2170 None

2231 3 1 Tumor/ 2 Normals

QA Table for TMAQA Table for TMA

0 1 2 3 4 5 6 7 8 9

0 Liver MVB 2230 MVB 2186 MVB 2160 MVB 2187 MVB 2163 MVB 2180 MVB 2230 MVB 2186 MVB 2186

1 Liver MVB 2202 MVB 2162 MVB 2231 MVB 2170 MVB 2231 MVB 2170 MVB 2202 MVB 2162 MVB 2202

2 Liver MVB 2160 MVB 2230 MVB 2180 MVB 2187 MVB 2163 MVB 2231 MVB 2160 MVB 2180

3 Liver

4 Liver MVB 2230 MVB 2186 MVB 2187 MVB 2163 MVB 2230 MVB 2186 MVB 2186

5 Liver MVB 2202 MVB 2162 MVB 2170 MVB 2231 MVB 2202 MVB 2162 MVB 2160

6 Liver MVB 2160 MVB 2230 MVB 2180 MVB 2187 MVB 2160 MVB 2202

7 Liver MVB 2162 MVB 2163 MVB 2170 MVB 2162

Map for Supplementary Paraffin TMAMap for Supplementary Paraffin TMA

Frozen TMAFrozen TMA

Normal lung tissue

Tumor tissue (mesothelioma)

MVB #s indicatedistinct patients

N=13 ptsmvb22

21mvb22

21          

mvb2189

mvb2215

mvb2219  

mvb2189

mvb2215

mvb2219

mvb2190

mvb2191

mvb2197  

mvb2190

mvb2191

mvb2197

mvb2217

mvb2214

mvb2199  

mvb2217

mvb2214

mvb2199

mvb2203

mvb2211

mvb2213  

mvb2203

mvb2211

mvb2213

mvb2212      

mvb2212    

High Density Frozen TMA: Construction High Density Frozen TMA: Construction

Frozen Array mold

2009-2010

2010-2011Oil

Ischemia-Fixation TMAIschemia-Fixation TMAPre-analytic variables in FFPEVaried duration from devascularization to preservation: ISCHEMIA time (minutes to hours)Varied duration of fixation: 0- 36 hoursVaried tissue processor protocols across institutions

Design: Timed experiment with varied ischemia/fixation times of tissue –constituted into TMA (n = 3+)

Outcome: TMA slides for 1) investigators to measure preservation of marker of interest against different pre-analytic variables2) NMVB biospecimen science – to determine biomarkers that reflect early ischemic effects for rating of core preservation on NMVB TMAs.

Ischemia-Fixation Meso TMAIschemia-Fixation Meso TMATime

Delay (hr)

Case 1 Case 2 Case 3Cell Line

Time Fixation

(hr)

0 + + 12

1 + + 12

2 + + 12

4 + + 12

6 + + 12

8 + + 12

12 + + 12

24 + + 12

36 + + 12

Diagnostic marker durability: Necrosis, ischemia, overfixation (WT-1, Calretinin)(autopsy vs biopsy material)

Impact of preanalytic variables: Tissue expression of current serum /pleural fluid biomarkers:

Tools: Frozen TMA & Ischemia/Fixation TMA

Biospecimen ScienceBiospecimen Science