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Tissue procurement facilitates the progress of both basic and clinical research into a host of important diseases. Many studies depend on Formalin-fixed paraffin-embedded (FFPE) blocks to study DNA, RNA and proteins. FFPE blocks facilitate the study of a wide range of biomarkers. Recent research indicates that the storage time of such blocks has no significant effect on the quantity and quality of extracted nucleic acids and proteins. We discuss a study that demonstrates that for time periods of 11–12 years, 5–7 years, and 1–2 years, there were no significant differences between the extracted macromolecules for current year blocks. This study systematically examined the quality and quantity of nucleic acids and total protein in FFPE blocks of various malignant tumors that had been stored over periods of many years and compared the results to current blocks and concluded that no significant difference in extracted materials obtained.
Advances in molecular biological techniques have resulted in the ability to extract fragmented DNA, RNA and proteins from FFPE blocks. This is an important development as archived FFPE blocks now represent a source of materials that can facilitate the study of biomarkers for targeted therapies and prognosis. Fragmented macromolecules have been successfully used in downstream analyses where short fragments are all that is required. Fragmented DNA has been amplified via PCR, biomarker analysis has been facilitated via micro RNAs and fragmented proteins have been useful in mass spectrometry. Considering the large amount of archived material available in the form of FFPE blocks, questions have been raised as to whether the amount and quality of extracted macromolecules depend on storage time. Recent results indicate that across all previously mentioned time scales extracted DNA, RNA and proteins show no significant difference with frozen controls.
In the study researchers extracted RNA and DNA from a single sample of FFPE tissue curls. Protein was extracted from the additional tissue curls. Frozen tissues were used as controls. Frozen tissue was not matched across storage periods to the FFPE tissues. This reflected the clinical setting in which there are usually large samples of FFPE tissue but frozen material is collected as necessary. This is the first study to extract protein from the same tissue as DNA and RNA for comparison and it is the second study to report extraction of DNA and RNA from the a single set of FFPE curls.
The study of biomarkers taken from human tissue samples play a vital role in the study of disease. Tissue procurement from quality biorepositories facilitates such research. Human tissue samples in the form of FFPE blocks are some of the the raw materials necessary for developing novel therapies and refining prognoses. There are large archives of FFPE tissue blocks that can be made available for molecular biological applications. Using these sources reduces the cost of research for certain applications because specimens do not need to be frozen. For research that can use fragmented macromolecules in downstream analysis FFPE tissue blocks provide a reasonable alternative to frozen tissue samples.
- All formalin-fixed, paraffin-embedded (FFPE) tissue specimens are collected under IRB approval by certified medical pathologists.
- Tissues are fixed in 10% Neutral-Buffered Formalin (NBF) within 30 minutes of surgery excision.
- Tissues are fixed for 18 – 24 hours at room temperature, then embedded in IHC-grade paraffin.
- Standard sample size is 1 x 1 x 0.5 cm, but can vary based on the nature of the disease or tissue type.
- The fixation agent and embedding media can be customized upon request.
- FFPE tissue samples are stored at room temperature.
- Unless indicated, all FFPE tumor tissues have at least 50% tumor content.
squamous cell carcinoma, benign
adenocarcinoma, signet ring cell carcinoma, mucinous adenocarcinoma, GIST, benign
follicular carcinoma, papillary carcinoma, medullary carcinoma, benign
endometrioid adenocarcinoma, sarcoma, leiomyosarcoma, benign
squamous cell carcinoma, adenocarcinoma, benign
pigmented, non-pigmented, ulcerated, non-ulcerated
SOFT TISSUE SARCOMA
fibrosarcoma, leiomyosarcoma, rhabdomyosarcoma, liposarcoma
adenocarinoma, acinar cell carcinoma, ductal adenocarcinoma, cystadenocarcinoma
serous carcinoma, endometrioid, mucinous carcinoma, clear cell carcinoma, various benign
traditional cell carcinoma, adenocarcinoma, papillary carcinoma, benign
glioblastoma multiforme, anaplastic astrocytoma, anaplastic meningioma meningioma, oligodendroglioma
ductal carcinoma, lobular carcinoma, medullary carcinoma, mucinous carcinoma, paget’s disease, cribriform carcinoma, inflammatory, various benign
squamous cell carcinoma, clear cell type carcinoma, various benign
adenocarcinoma, GIST, squamous cell carcinoma, polyps, benign
HEAD AND NECK
squamous cell carcinoma, adenolymphoma, adenoid cystic carcinoma, benign
clear cell type carcinoma, oncocytoma, chromophobe, angiolipoma, benign
hepatocellular carcinoma, cholangiocarcinoma
adenocarcinoma, squamous cell carcinoma, bronchioloalveolar carcinoma, neuroendocrine carcinoma, large cell adenocarcinoma, small cell adenocarcinoma, basaloid squamous cell carcinoma, inflammatory myofibroblastic, mesothelioma, adenoid cystic carcinoma, infectious, COPD