Enriching tumor content in FFPE sample dissections: A review of macro- and micro-dissection techniques

The traditional “manual macrodissection” method for dissecting formalin-fixed paraffin-embedded (FFPE) tumor slides is no simple task: Pathologists first determine where in an H&E-stained slide tumor cells abound, trace that area to demarcate it, and direct the lab to use that annotated slide as a reference for dissecting the area of interest (AOI) for serial slides. Subsequently, lab techs are expected to interpret and replicate the AOI specified by the pathologist faithfully: They place the reference slide underneath the serial section slide from the same paraffin block to align the two, then trace the AOI onto the serial slide with a marker pen, and finally use a scalpel to carefully scrape off the tissues within the marked AOI for downstream molecular analysis.1

Such a manual method for tumor dissection, though common, has several drawbacks. For starters, an innocuous factor such as the thickness of the marker pen used to trace can change the precision by a millimeter! The manual method, on top of being physically demanding, can also introduce errors from extrapolation during overlapping of slides, and can suffer from misinterpretation of hand-written notes and poor documentation practices.2

From "macro" to "micro"

A slightly improved method called manual microdissection entails using a needle or a scalpel for dissection with the aid of a light microscope. Though painful, this method works for the most part, especially when the required dissection area is at least a few millimeters and the required sensitivity for a downstream assay is at least 20%.2 However, there has been a dire need for a more precise and automated process for slides with very low tumor content or sections that cannot be easily dissected by hand. In such cases, sample recovery for further molecular analysis for targeted therapy becomes a challenge.

Toward sophisticated automation

Laser capture microdissection (LCM) is an automated technology meant to fulfill this gap. This highly precise technology can provide single-cell resolution and digital annotation.3 Although sophisticated, LCM still hasn’t been adopted widely in the clinical space due to several critical factors, such as high cost, low turnaround time, burning of precious tissue and specialized training requirement. In some cases, it has been reported that LCM was unable to retrieve sufficient and high quality sample for downstream analysis.1,4

Despite the availability of such wide-ranging technologies, current FFPE tissue dissection methods are still viewed as either too crude or too complex. In the next blog post, we will introduce an intermediate solution – a simple yet precise automated tissue dissection that could be just right.


  1. Geiersbach et al. Cancer Genet. 2016;209(0)42-49.
  2. Adey et al. BMC Clinical Pathology 2013;13:29.
  3. Emmert-Buck et al. Science 1996;274:998-1001
  4. Michel et al. Am J Pathol. 2003;163(6):2191-9.