Application for Tissue Microarrays

To receive tissue microarrays (TMAs) from the resource, you must first send an application that contains:

1. Your name, surface mail and email address, and telephone number.
2. Type of TMA requested (progression, prognostic, or both).
3. Scientific rationale: This section of the application (usually one page in length) should include the following:
   1. Concise introduction to the project concluding with a brief statement of the hypothesis of the proposed research.
   2. Specific aims of the work to be carried out with the TMAs.
   3. Information about the marker(s) to be evaluated - briefly describe each marker and why it was selected for testing including:
      1. Evidence that the marker(s) is relevant to breast cancer - describe preliminary data and cite published references suggesting the importance of each marker.
      2. If more than one marker will be included in the analysis, describe how the markers are related to each other.
4. Technical approach: This section of the application (usually about one page in length) should include the following:
   1. A brief description of the technical approach, the measurement technique(s) and reagent(s)
   2. Evidence that the specific techniques and reagents have been used successfully on paraffin-embedded sections in your laboratory. (We can provide test sections to optimize assay conditions.) We prefer to see photographs or figures generated in your own laboratory that are annotated with legends describing what tissues are assayed and what marker results (e.g., staining intensity) are exhibited.
   3. A description of the scoring system. For example, if results will be reported as "positive" or "negative," how will these be defined? What is the basis (preliminary data) for using this scoring system?
   4. Positive and negative controls to be used.
5. Statistical plan: This section of the application (usually about 0.5 page in length) should describe how the assay results obtained using the TMA will be analyzed and should include:

   1. In what form will the data be used in the analysis?

      Examples:
      • Binary assessments of marker positive/negative status
      • Categorical scale such as 0, 1+, 2+, 3+
      • Continuous measurements such as percent stained cells or output from a quantitative image analysis system

   2. A brief description of the statistical approach that will be used to test the hypothesis you stated above.

      Examples for the Progression TMA:
      • Chi-square test or Fisher’s exact test to test for differences in marker positivity rates between groups
      • T-tests to test for differences in mean marker levels between groups

      The Progression TMA was statistically designed to have good power to compare marker distributions (e.g., positivity rates) across stage groups. The CBCTR strongly recommends that you obtain the assistance of a statistician if you plan to conduct statistical analyses more complex than simple comparisons of categorical marker variables.

      Examples for the Prognostic TMA:
      • Log-rank test or Cox proportional hazards regression to test for associations between marker and recurrence or overall survival times

      The Prognostic TMAs are intended for studies examining the association of markers with survival outcomes in stage I invasive breast cancer. The survival data provided with these TMAs are overall survival and recurrence-free survival (see Hudis et al., Journal of Clinical Oncology, v. 25, no. 15, May 20, 2007 for definitions). The arrays were statistically designed to have at least 80% power in the subgroup of ductal cancers to detect a hazard ratio of 2 or greater for overall survival associated with a binary marker that has positivity rate between 20% and 80%. Additional detailed power calculations are provided in the Statistical Guidance.

      The CBCTR strongly recommends that if you are not familiar with statistical analysis methods for survival data you consult with a statistician to evaluate if the design of the TMA will be suitable for your study and to assist in the data analysis.

      If a prognostic TMA is requested, please indicate that the Statistical Guidance for the array was read.

6. Total number of sections requested

   This section of the application should provide a specific accounting and justification for the number of sections requested. For example, how many sections will be used for each assay, and how many sections will be used for positive and negative controls.

   For the progression TMA, each case set is arrayed in quadruplicate to address possible tissue heterogeneity: four cores are taken from each breast tissue specimen, with one core per specimen appearing in each of the four replicate tissue array blocks. A complete array set, representing the minimum number of cores recommended for an experiment, includes sections from three case sets. It is recommended by the CBCTR that each assay should be performed using a minimum of three case sets, with a minimum of two replicate sections per case set, for a total of six tissue microarray sections.

   The stage I prognostic TMA consists of five different cases sets, representing specimens from five non-overlapping groups of patients. Each case set is arrayed in quadruplicate to address possible tissue heterogeneity: four cores are taken from each breast tissue specimen, with one core per specimen appearing in each of the four replicate tissue array blocks. A complete array set, representing the minimum number of cores recommended for an experiment, includes sections from all five case sets. It is recommended by the CBCTR that each assay should be performed using a minimum of two replicate sections per case set, for a total of ten tissue microarray sections.

7. A Brief Biosketch (Please send as an attachment).

Please submit your application electronically.

If you choose to mail your application please be sure to send it in the same format as the electronic form and include all the required information. Incomplete applications will be returned for completion resulting in a delay in the evaluation and review of your request.

This page was last updated on:
Friday, February 6, 2009 at 08:01:32 AM

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