Recognised Research Center Of Mysore University


Quality parameters for Sectioning of Paraffin and OCT Embedded Tissue

Set the section thickness at 4-5 microns for IHC or ISH advance staining and 10-20 microns for nucleic acid extraction samples.

General considerations for section review:

Morphologic review of tissue sections

Feedback about section quality to refine practices of Quality Control procedures

Issues concerning quality of sections:

Sections are made to eliminate or minimize nucleic acid contamination from equipment or other samples for PCR-based molecular studies.

Ensure that type of fixation, processing duration and temperatures used during the fixation and sectioning procedures minimize the antigen masking or deterioration of molecular components. This is important for certain proteins in assays such as immunohistochemistry.

Review of section hickness for consistency and appropriate for intended use.

Ensure that paraffin and frozen sections are stored at appropriate temperatures.

Review of 3, H&E slides

General considerations for morphological review
  • Assessment of morphologic review of all collected tissue.
  • Feedback about sample quality to refine collection and storage practices of Quality Control procedures.
  • Develop a defined scoring system that allows a ‘quality score' to be assigned to a tissue or molecular sample that has undergone assessment at a designated quality control laboratory. The score (assigned levels) will help in the interpretation of the quality assessment results and correlate to the suitability of the tested sample for specified research applications.
Levels of frozen tissue specimen

ANSA will recognize four levels of specimens based on time for freezing (for FROZEN TISSUE samples only) and these levels will determine the particular research application for which they may be utilized

Quality Assessment - Pathology Reviewue specimen

Quality control practice includes a morphologic review of formalin-fixed H&E stained slide, representative (mirror-image, adjacent) of the SNAP FROZEN or FORMALIN FIXED PARAFFIN EMBEDDED tissue samples.

The review must confirm and assess:

  • Tissue type and assessment of diagnosis
  • Tumor type
  • Tumor grade
  • Presence of tumor
  • Percent cellularity of tumor and stroma
  • Percent necrosis or signs of degradation
  • Presence of inflammatory cells
  • Microscopic examination of the slide and a digital image of an area representative of the tissue sample must be stored in the bank database.


Assessment of molecular integrity is always performed.

Feedback about sample quality to refine collection and storage practices and guide evolution of Quality Control procedures.

Defined scoring system that for a ‘quality score' to be assigned to a tissue or molecular sample.

Quality Assessment - DNA by spectrophotometric measurements, enzymatic digestion and gel electrophoresis.

The quality assessment includes testing the suitability of the test sample DNA for use in enzymatic reactions (such as Hind III digestion) and visual assessment following agarose gel electrophoresis. Use a control sample as a reference.

Assign a quality score to the tested sample based on DNA quantification analysis (OD 260/280 ratio, agarose gel electrophoresis and restriction digestion):

DNA quality based on UV spectrophotometry

OD 260/280 Ratio

Assigned Score









Less than 1.2


DNA quality based on electrophoresis of genomic DNA

Electrophoretic Integrity

Assigned Score

Discrete high MW band


10 kb smear


5 kb smear


2 kb smear


Less than 2 kb smear




The purity of the samples are checked by A260/A280 ratio.

The integrity of the samples are checked by Agilent Bioanalyser.

Data Management:

Data Management gives flexible choices to meet evolving needs and enhance the overall value by providing complete sample management along with inventory control. HMS allows for sample registration, collecting sample details based on forms, inventory control, cost/price management and MIS Reports. It also allows easy retrieval of sample data based on diagnosis and sample types, and has a full-fledged user and access control management.