Breast Center Biostatistics and Informatics Core

Tumor Banks and Descriptions

ARRAYS

Arrayed Dead End Bank (ADEB):
This bank contains breast cancer samples that were reconstituted into paraffin blocks from pulverized frozen tissue. There is no clinical, pathological or follow-up information about any of these tumors. They were originally collected between 1987 and 1998 for the NBCTR. As such, they can be requested by SPORE investigators.

There are 89 12-tumor arrays in this bank. The first 12 arrays contain in situ tumors and are released sparingly. Arrays 13-89 contain all histologies of infiltrating breast cancers. This resource is quite limited. The paraffin blocks in which these arrays are embedded are currently managed by the Pathology Core under D. Craig Allred, M.D. The quality control for all of these tissues was performed by D Craig Allred.

Arrayed Follow-up Bank (AFUB):
This bank contains breast cancer samples that were reconstituted into paraffin blocks from pulverized frozen tissue. They were originally collected between 1973 and 1993 for the MOPP and SPORE tumor banks. There are more MOPP tumors than SPORE tumors in this bank (these are the remains of the Node Positive and Node Negative Banks). The arrays are available only to Breast Center investigators and their collaborators. All of the tumors are those of patients who were abstracted and followed via one of the two old databases (oldMOPP, commonly referred to as the San Antonio database, and oldSPORE, commonly called the Nichols database). They consist of in situ and infiltrating breast carcinomas.

There are 133 12-specimen arrays in this bank. Though the arrays contain mostly followed breast cancer tumors, there are other tissues set on the arrays for control purposes (breast cancers without followup and normal tissues). The paraffin blocks in which these arrays are embedded are currently managed by the Pathology Core under D. Craig Allred, M.D. The quality control for all of these tissues was performed by D Craig Allred.

TransATAC (TA-01):
This bank contains specimens from patients enrolled in the Arimidex, Tamoxifen and Combination clinical trial. The Breast Center is creating and storing these samples for the international ATAC Committee, and cannot dispense them for research. Any requests for these samples must be addressed to the Pathology Subcommittee for the ATAC clinical trial. The samples are managed by Leslie Lopez.

PARAFFIN & FROZEN TISSUE BANK

oldMOPP/San Antonio Inventory:
FROZEN-This is tissue that was flash frozen at various hospitals around the U.S. It was pulverized for ligand-binding assay and flow cytometry, and the residual was kept at –70 degrees in vials. It has to be warmed to be aliquotted, so some samples have been warmed multiple times for short periods. In June 2000, all power was cut off to the freezers for a period of at least 48 hours, and most of the vials spent that time in hot water. They have been refrozen, but of course their utility is now severely limited.

These tumors were collected between 1970 and 1999 (most were collected before 1986) for ER/PgR and s-phase/ploidy assays. They were followed until 12/31/2002, when the old MOPP grant expired. More than half of the patients were from San Antonio and outlying towns in Texas, but a significant proportion came from different parts of the country: upstate New York, New Orleans (LA), Cleveland (OH) and other places. There are some powders left, but now most of them have been used. These tumors are managed by Bryant McCue.

PARAFFIN-Small portions of certain patients’ tumors (those patients whose frozen tumors were included in the Node Negative and Node Positive subbanks of the MOPP inventory) were converted into fixed paraffin-block specimens. A slide was read from each block, and information about the quality of the sample (assessed by Drs. Allred, Yu, and Libby) was entered into the database.

SPORE/NBCTR (National Breast Cancer Tissue Resource):
FROZEN-This tissue was flash frozen at various hospitals around the U.S. It was pulverized for ligand-binding assay and flow cytometry, and the residual was kept at –70 degrees in vials. It has to be warmed to be aliquotted, so some samples have been warmed multiple times for short periods. In June 2000, all power was cut off to the freezers for a period of at least 48 hours, and most of the vials spent that time in hot water. They have been refrozen, but of course their utility is now severely limited.

These tumors were collected between 1984 and 1999 for ER/PgR and s-phase/ploidy assays through the Nichols Institute Reference Laboratories (now Quest Diagnostics). They were followed until 12/31/2002, when the old SPORE grant expired. The patients were from different parts of the U.S., mostly California (39,034) and Texas (26, 181). There are some powders left, but not most of them have been used or were thrown away after the tropical storm in June 2000. Those which were kept after 6/00 were all frozen specimens from followed patients, patients whose tumors were used in a prior large study, and/or tumors that were suspected of being from the same patient (bilateral primaries, contralateral primaries and recurrent lesions). These tumors are managed by Bryant McCue.

PARAFFIN-Small portions of certain patients’ tumors (the ‘spore bank’ subset, which were the tumors with the best (cleanest) clinical and followup data in the nichols database) were converted into fixed paraffin-block specimens. A slide was read from each block, and information about the quality of the sample (assessed by Drs. Allred, Yu, and Libby) was entered into the database.

Ben Taub Breast Tissue Resource:
This resource is a collection of breast tissue (normal, premalignant and malignant) harvested at Ben Taub in the Harris County Hospital District. The patients have been diagnosed after 2000. Retrospective samples (paraffin blocks) will be collected for as many patients as possible. Prospective samples (flash-frozen in liquid nitrogen in the frozen section room at the time of surgery) are being collected for as many patients as possible after 11/2003. There will be associated followup with these samples, and followup is planned indefinitely. These tissues will be available to Breast Center investigators. This resource is managed by Bryant McCue.

Asterand Breast Tumor Bank:
The patients who contributed these tumors were diagnosed between 1975 and 1983 at several different sites in Detroit, Michigan. They were collected by the Michigan Cancer Foundation as part of a study of prognostic factors. The tumors were transferred to the Breast Center at Baylor College of Medicine when the currently-named Karmanos Cancer Center no longer had the funding to maintain the tumors and data. There is associated followup with these tumors, though the subjects and their tumors have been anonymized. This Bank may be utilized by Breast Center and other SPORE investigators.

FROZEN: The frozen samples are solid pieces of flash-frozen tissue. A small subset were frozen in OCT, but the majority were frozen using liquid.

PARAFFIN: At the time of surgery, half of the specimen not needed for diagnostic purposes was flash-frozen, while the other half was formalin-fixed and preserved in paraffin blocks. These are also solid tissue. This resource is managed by Bryant McCue.

Metastatic Tissue Bank:
This protocol proposes to collect tissue from metastases from breast primaries when they are biopsied. An extra core or two will be harvested and flash-frozen in the clinic, and paraffin blocks will also be collected after diagnosis is complete. There will be limited associated followup with these cases, maintained by Dr. Elledge’s research nurse. This resource is managed by Bryant McCue.

PARAFFIN ONLY

The RAHBT (referred to as “Rabbit”—“Repository of Archival Human Breast Tissue”):
The bank is the repository of all paraffin blocks of breast cancer patients whose breast tissue resides at Texas Methodist Hospital. The overall RAHBT is not a tumor bank—no specimens can be requested from it, though there are sub-banks in the RAHBT which can be accessed for research with the proper IRB and Tissue Use Committee approval. There are already 2 banks in the RAHBT which have been IRB-approved and are available for research requests (within their own limits): the Evolutionary Bank and the Garrett R. Lynch Tissue Resource. Due to certain political problems, no paraffin blocks may be requested at this time.

Evolutionary Bank (sub-bank of RAHBT):
D. Craig Allred began collecting tissue for this resource in c. July 1999, and continued to collect tissue specimens when they became available until about 2004. All of the specimens in this bank are very small. They are not breast malignancies; rather, they range from normal breast tissue through abnormal breast tissue and to pre-cancerous lesions. These lesions are managed by Craig Allred.

Garrett R. Lynch Tissue Resource (GRL/Retrospective) (sub-bank of RAHBT):
Begun in 2001, this resource is a retrospective study of breast cancer patients treated by Garrett R. Lynch. This was planned as exclusively a paraffin block resource, as it is entirely retrospective. All patients whose blocks are in this resource will be followed. The paraffin blocks have not been collected yet, but if they do join the inventory, they will be managed by Bryant McCue.

WESTERN BLOT

These specimens (called “proteins”) were derived from subsets of the Node Negative and Node Positive banks in the MOPP (which did contain some SPORE tumors, but not many). This was done in the mid 1990's by Suzanne Fuqua . They are stored frozen, in vials. They are not aliquoted—when somebody needs them, Irma Parra thaws them and measures out approximately 20 mg of each protein for the requestor. The WB freezer did not warm up significantly during the 6/00 power outage. There are very few proteins in this resource.

SERUM

The NSABP Serum Bank:
Comprised of sera from patients enrolled in all NSABP clinical trials performed since 1999. The Breast Center acts as a skilled storage facility for these samples, and cannot dispense them for research. Any requests for these samples must be addressed to the NSABP. The samples are managed by Bryant McCue.