Tissue MicroArrayer for High Throughput Analysis of Pathology Tissue Samples

Project Collaborators (sorted by Institute): 
Genetics Branch, Center for Cancer Research, NCI
Cancer Genetics Branch, NHGRI
Project Brief: 

NIH researchers introduced an innovative technique for high density arraying of archival clinical tissue in the research and clinical laboratory. Consisting of an array of cylindrical cores extracted from formalin-fixed paraffin embedded tissue samples, tissue microarrays (TMA) have become widely used as a powerful validation tool for high throughput genomic screens. TMAs allow a researcher to quickly compare many different tumor types, a single tumor type over multiple patients, or tumor progression on a single pathology slide; significantly reducing the costs associated with reagents and processing, as well as improving analysis reproducibility. The original manual process uses a hollow needle to remove cores from standard pathology blocks (i.e., donor block) that are then deposited into a pre-made hole in a block of paraffin (i.e., recipient block). When completed, the recipient blocks are sectioned to create pathology slides for downstream analysis. While successful, the manual construction of the TMAs is time consuming and requires training to produce quality arrays.

In collaboration with NHGRI researchers and a commercial company, we designed and fabricated a robotic arrayer to semi-automate the TMA construction procedure.  The custom arraying apparatus, enabling automatic tissue core acquisition and deposition with X-Y-Z controls, provides a platform capacity for 21 recipient blocks and 4 donor blocks for large scale TMA production. To achieve higher specificity in choosing donor block tissue, a macroscopic method was employed to localize and mark desired targets in the donor block.  Specifically, the paraffin block sample sites are marked with an overlay of the corresponding glass slide H&E section over the transluminated donor block. While successful, this method can lead to inconsistently sampled microscopic lesions and non-informative TMA tissue section spots if the target area is not carefully chosen.

Using the semi-automated arrayer, collaborators in NHGRI developed a TMA which led to an important finding for BRAF mutations in nevi.

Automated robotic tissue microarrayer

Robotic tissue microarrayer: The robotic arrayer allows simultaneous construction of up to 21 replicate tissue microarrays. The XY platform movement is controlled by microprocessors, and needle position (Z) is guided by laser sensors. A camera provides video integration of donor block position and user selected regions of interest for targeted sampling.

Robotic TMA control software

Robotic TMA control software: The graphical user interface (UI) allows the user to enter various design parameters such as core spacing, number and location of recipient blocks, and size and design of the desired recipient arrays. At the core punching stage of the UI, the user marks regions of interest on donor blocks, sets punching depths of both recipient and donor blocks, enters comments and block IDs, and designates configuration of donor core placement in the recipient block. The UI also provides visual feedback on the progress of the array construction.

Block marking software and procedure

Block marking procedure: The main function of the block marking software is to allow for marking of histopathological regions of interest (ROI) on a magnified slide image, and then to supply coordinates for core extraction of the corresponding tissue locations from the donor block. (a) A magnified slide image is opened in the block marking software. Using the available software tools (e.g., polygon, single point), the user electronically marks the ROIs on the slide image. Aside from marking the ROIs, the user also denotes the location of reference points on the image. (b) An image of the donor block (i.e., positioned in the arrayer) is acquired via the overhead camera. The user marks the corresponding three reference points on the donor block image. The block marking software automates regeneration of ROIs on the donor block image, generates punch locations, and supplies the arrayer with the respective XY coordinates. (c) An image of the donor block after the completion of the tissue extraction.

Tech Transfer: 
  • Employee Invention Report. 2004. Tissue Microarray Technology. Method and system for processing regions of interest for objects comprising biological material. NHGRI, CIT.

  • Employee Invention Report. 2003. Tissue Microarray Technology. High-throughput tissue microarray technology and applications. NHGRI, CIT, Beecher Instruments Inc.