The Availability and Type of FFPE Sample Collection Formats
Modern research efforts are fueled almost exclusively by the availability of human tissues. Tissue procurement is truly a fine-art or rather, a fine-science, however, you’d like to apply it. What is known about providing FFPE samples is that the research community demands the best quality assurance standards available. This is where partnering with a professional biorepository offers multiple layers of value to those within our industry platform.
FFPE Sample Collection Formats
Individual tissues: Diseased or normal from an individual donor
Four-tissue or quad combination sets: Fresh frozen, paraffin-embedded and formalin-fixed tumor and normal adjacent tissue specimens from one donor are available in combination sets
Matched pairs:
FFPE and fresh frozen tumor and normal adjacent tissue samples from one patient.
FFPE diseased/tumor and metastatic tissue samples from a single donor.
*Most FFPE procured specimens are sized at 0.5 x 1 x 1 cm. This can vary significantly depending on the nature of the disease and tissue type. The fixation agent and the embedding media might also vary depending upon requested customizations.
*Most tumor tissues offer a 60% tumor content.
FFPE Sample Collection Formats Used in Modern Applications
It is easy to understand the significance placed upon usable tissue quality and diversity in assay preparation when you take into consideration the role it plays in medical advancements. Biomedical research requires a large quantity of tissues to analyze and characterize care strategies based upon what Is identified diagnostically through FFPE tissues or frozen specimens.
Geneticist moved in a progressive way to provide a vast array of customized tissue assays. In doing so, we are able to respond to the needs of researchers in a few different positive ways:
The ability to offer an economic advantage for the researchers, as they can analyze multiple different tissues from different patients within the same assay.
It represents a global approach – availability and quantity matters. With customized tissue assays, we can arrange multiple assays in a way that represents a few different testing needs – this is especially true for advanced diseased research and best represented in quad tissue formatting.
Microarrays (TMA’s) are the preferred tool for large scale research efforts, as they allow the genome-wide measurement of transcription abundance.
There has been a huge shift in how tissue combination sets are used. Studies suggest that the consolidation of the four different tissue expression data sets can increase data quality which results in more meaningful interpretation.
FFPE sample collection formats are used in several different clinical applications such as:
Oncology: (cancer four-tissue set, cancer serum/plasma, blood in special tubes)
Inflammatory Disease: (synovial tissue synovial fluid, matching blood, serum, plasma)
Neurological Evaluation: (postmortem brain tissue from patients with PD and AD)
Normal Individualized Tissues: (4 - 12 hours postmortem and surgical collection)
Quality Assurance
Geneticist offers a full suite GMP certified specimen and/or tissue collection models that can be used in varying clinical capacities. Our team operates under the strictest SOP controls and we pair this methodology with IRB certified professionals for tissue procurement collection efforts.
FFPE (formalin-fixed, paraffin-embedded) is a form of preservation and preparation for biopsy specimens that aids in the examination, experimental research, and diagnostic/drug development. More specifically, it normally involves a piece of harvested human tissue prepared by a certified medical pathologist that is submerged in 10% neutral-buffered formalin for 18 - 24 hours and embedded in IHC-grade paraffin.
The harvest methods matter because the collection model is dependent upon viability. Storage and housing also matter, but the preservation of this type indicates FFPE is safely stored at room temperatures. However, all specimens are housed with specific adherence to GMP and other regulatory and laboratory best practices in mind.
Addressing the Concern: Obtaining Viable FFPE and Frozen Tissues from a Biorepository
The operational procedures of the biorepository must be well-trained in order to match that which is provided to the investigator versus the overall diagnosis of the specimen via a surgical pathology report. Specimen mismatching occurs in many instances such as in the case of necrosis, or unsuspected tumor invasion of seemingly normal tissues in which the specimen is mistaken grossly for tumor.
During the course of what may be called a huge push in genomics and other related “omic” genres, doubts and concerned have surfaced. The goal of obtaining viable FFPE tissues are centered around reproducibility making the procurement and handling methods a critical element. There are relevant studies which have raised eyebrows citing poor reliability of microarray data based upon incongruent preparation methods of varying TMA platforms.vii
The bottom line is there will always be factors to weigh in on such as TMA platform, tissue handling, RNA isolation method and hybridization procedure which have the potential to alter the results. We maintain at Geneticist that these factors are greatly minimized when the tissues are collected with a high level of acuity and applied to consistent levels of output.
References:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3445033/
https://www.ncbi.nlm.nih.gov/pubmed/21898218
https://www.ncbi.nlm.nih.gov/pubmed/15542899
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2664171/
https://www.sciencedirect.com/science/article/pii/S0888754318300995
