Microscopic Level

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“TMAtrix” Tissue Array
Database Solution

APIII 2003, Pittsburgh

10/09/03


David Seligson, MD

UCLA Tissue Array Core Facility

Department of Pathology & Laboratory Medicine

INTRODUCTION

TMAtrix

Joint Project of the:


UCLA Tissue Array Core Facility,
Department of Pathology &
Laboratory Medicine


UCLA Computing Technologies
Research Lab (Ctrl).

TMA Process

Interdependant Processes

Layers of Personnel

Extended Time Periods

UCLA Tissue Array Core Facility
-

Services


Consultation regarding tissue


array project planning


Construction of tissue arrays


Construction of supporting datasets


In situ

assay workup and optimization


Array staining (H&E, IHC & FISH)


Array Imaging


Histopathologic evaluation of stained arrays


Array data analysis

Tissue Array Block

300 Blocks

1 Tissue Array


150 Patients

100 Array Slides

(60,000 Samples)

600

Cores

1,050 Blocks and Slides

(150 patient X 7)

4 cores

each case

Tissue Array Datasets

Project I

Project I

Project I

Project I

Project I

Array Library

Project I

Prostate

Block A

Project XXV

Brain

Block B

Block C

Block D

Block E

Block F

Block G

Tissue Array Datasets

Project I

Project I

Project I

Project I

Project I

Array Library

Project I

Prostate

Block A

Quadrant 1

Project XXV

Brain

Block B

Block C

Block D

Block E

Block F

Block G

Project I

Project I

Project I

Project I

Project I

Slide 200

Slide 1

Quadrant 2

Quadrant 3

Quadrant 4

Quadrant Scoring

Clinical Database

Pathology Database

Images

Layers of Data: Pathology Data Set:

“Reported, Reviewed, Target & Spot” Data

“ReportedCase”

Data Field

“Reviewed Case”

Data Field

“Target”

Data Field

“Spot”

Data Field

Surgical

Pathology


S95
-
000XX

TMAtrix Tissue
Array Database

UCLA TMA Core Facility


TMA projects = ~30 total (7 large projects)


150,000 cells of data average / large project, or
> 1,000,000 entries over 7 projects.


Currently archiving tissue materials of ~2,000
patients (~14,000 slides, 14,000 blocks)


TMA Blocks total in library = ~ 100


>20,000 individual tissue cores total to manage


At ~100 cuts of each = > 2,000,000 spots.


Generate potentially >5,000,000
scoring

data
points

What is Special About Tissue
Array Projects?


Volume of Data


Multi
-
personnel interactions and
interdependant processes which must
communicate to function efficiently
and safely


Complex data linkages

DATA MODEL / TECHNICAL

Design Philosophy


Open Source


Web
-
based


Multiple users


Relational database model


Scalable


Generic


Secure


IRB complient


Facilitate efficient core facility functionality

Main Database Components

Patients:


Demographic

Clinical

Pathology



Array Projects:


Construction

Administration



Array Studies:


H&E

IHC

FISH

TMAtrix Data Model
>700 Fields


Patients


Pathology

Demographics


Clinical

Array Studies


Array

Projects

TMA Core / Spot Data Hierarchy


Libraries


Projects


Array Blocks


Duplicate Blocks

»
Slides


Quadrant


Coordinate (row and column)


Unique

Core

Unique

Spot

TMAtrix Model System

Web Application:

Expresso (Java)


Framework

Apache Tomcat Server


Database:

Oracle 8i
Relational
Database
Management
System;
SUN
Enterprise
Server


Client:

Security:

Usernames and passwords

Audit trail

128
-
bit SSL

No patient identifier, no linked


codebook

Server

Pages

HIPAA Compliant


IRB
Approved


No patient identifiers or links to patient
identifiers will be included in the database


No patient names will be present


Patient medical record numbers and pathology
accession numbers will be randomly coded by
the computer on data entry


No research data will be stored with links to
patient identifiers

USER INTERFACE

TMAtrix Login Page

TMAtrix
-

Administrative

TMAtrix


Administrative

Block Layout

TMAtrix
-

Administrative

TMAtrix


Administrative

Array Core Thumbnail

TMAtrix
-

Patients

Patient Administration:


Search Patients / Cases


Detailed Patient Information


Detailed Pathology Information

TMAtrix
-

Patients

TMAtrix
-

Patients

Outcomes

Social History

Medical History

Surgical History

Treatment History

Family History

Lab Results

Radiography/


Imaging

To Detailed

Surgical Pathology
Data

Patients
-

Main Case Page

Overall Summary Pathology

Donor Block Detailed Pathology

Pathology Specimens

Case
Level

Macroscopic
Level
(Specimen)

Microscopic
Level

(Reported)

Macroscopic
Level
(Specimen)

Microscopic
Level

(Reported)

Microscopic
Level

(Reviewed)

Results of micro analysis
of each specimen

Specimen description,
procedure, macro analysis
of each specimen

Microscopic
Level

(Reviewed)

Overall Case
Identifiers

Patients


Specimen Macroscopic

Patients


Specimen Microscopic

TMAtrix
-

Projects

Array Administration:


Tissue array slide and
block inventory


Core coordinate maps
and histologic contents

Array Project Administration

Block Info

Section New

Slide

View
Block
Layout

List Slides

Used

Spot Data

TMAtrix
-

Studies

Studies Administrator:


List of Studies


Scoring Data


Links to Images

Studies Main Page

New


Existing

Types

(Templates)

New Study

Select Slides from Inventory

List Slides Chosen for Study

Score Study

Score Study

Spot Code


Active link to spots

(current spot blinks)

Core ‘Target’ and

‘Reviewed QC’ Histology

Supports multiple

histologies per spot

Scoring consecutive or random

IMAGING

Image Capture

Tissue Microarray Slide

Aperio

Image Segmentation

Segmented Image Viewing

TMAtrix Image Interface

1.

2.

3.

Scoring

CONCLUSION

Tasks for Completion



Defined query pages


Import / Export wizards

Interaction


Outside
Collaboration Potential


XML
-
based TMA Data Standard has been recently
published (Berman, J., Edgerton, M., Friedman B.
at http://biomedcentral.com/1472
-
6947/3/5).


Data standards will grow the use of the platform
for potential inter
-
institutional data sharing.


Java programs will be written to represent
TMAtrix data in extensible markup language
(XML) for this communication.

Acknowledgements

Tissue Array Core Facility


David Seligson
(Director)


Sheila Tze
(Data Manager,
Database Developer)


Interactive Media Group


Robert Dennis
(Director)


Khy Huang
(Programming)


Stefan Deusch
(Programming)


Val Stambolstain
(Imaging
Interface)


Nick Young
(Programming)


Gene Lacson
(Graphic Interface)


Aperio Technologies


Aperio Image Server and other
documentation


TMAtrix Team:

Donors



Ken and Wendy Ruby