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Academic literature on the topic 'Formalin-fixed, paraffin-embedded tissues- FFPE'

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Published: 11 March 2023

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Journal articles on the topic "Formalin-fixed, paraffin-embedded tissues- FFPE"

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Obi, Ekenedirichukwu N., Daniel A. Tellock, Gabriel J. Thomas, and Timothy D. Veenstra. "Biomarker Analysis of Formalin-Fixed Paraffin-Embedded Clinical Tissues Using Proteomics." Biomolecules 13, no. 1 (January 3, 2023): 96. http://dx.doi.org/10.3390/biom13010096.

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The relatively recent developments in mass spectrometry (MS) have provided novel opportunities for this technology to impact modern medicine. One of those opportunities is in biomarker discovery and diagnostics. Key developments in sample preparation have enabled a greater range of clinical samples to be characterized at a deeper level using MS. While most of these developments have focused on blood, tissues have also been an important resource. Fresh tissues, however, are difficult to obtain for research purposes and require significant resources for long-term storage. There are millions of archived formalin-fixed paraffin-embedded (FFPE) tissues within pathology departments worldwide representing every possible tissue type including tumors that are rare or very small. Owing to the chemical technique used to preserve FFPE tissues, they were considered intractable to many newer proteomics techniques and primarily only useful for immunohistochemistry. In the past couple of decades, however, researchers have been able to develop methods to extract proteins from FFPE tissues in a form making them analyzable using state-of-the-art technologies such as MS and protein arrays. This review will discuss the history of these developments and provide examples of how they are currently being used to identify biomarkers and diagnose diseases such as cancer.
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Magdeldin, Sameh, and Tadashi Yamamoto. "Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues." PROTEOMICS 12, no. 7 (April 2012): 1045–58. http://dx.doi.org/10.1002/pmic.201100550.

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Dear, Jonathan D., Jane E. Sykes, and Danika L. Bannasch. "Quality of DNA extracted from formalin-fixed, paraffin-embedded canine tissues." Journal of Veterinary Diagnostic Investigation 32, no. 4 (June 9, 2020): 556–59. http://dx.doi.org/10.1177/1040638720929637.

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Veterinary pathology tissue banks are valuable resources for genetic studies. However, limited data exist as to whether quality DNA can be extracted from these tissues for use in canine genotyping studies. We extracted DNA from 44 formalin-fixed, paraffin-embedded (FFPE) tissue blocks from dogs; 9 of these dogs had DNA available from whole blood samples that had been banked. We genotyped DNA from 30 of 44 tissue blocks and 9 whole blood samples on the Illumina CanineHD BeadChip; DNA quality was insufficient in 14 of 44 samples from tissue blocks. There was significant correlation between the 260/280 ratio and single-nucleotide variation (SNV) call rate ( p = 0.0276; r2 = 0.162); 23 of 30 samples from FFPE were genotyped with > 65% call rates. Median pairwise identical-by-state (IBS) analysis was 0.99 in 8 pairs of dogs with call rates > 65%. Neither age of tissue block nor specific tissue types were associated with significant differences in DNA concentration, 260/280 ratio, or SNV call rate. DNA extracted from tissue blocks can have variable quality, although comparable levels of homozygosity suggest that extracts from FFPE with call rates > 65% might provide similar results to samples from whole blood when analyzed on the Illumina CanineHD BeadChip.
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Michelsen, Nete V., Klaus Brusgaard, Qihua Tan, Mads Thomassen, Khalid Hussain, and Henrik T. Christesen. "Investigation of Archived Formalin-Fixed Paraffin-Embedded Pancreatic Tissue with Whole-Genome Gene Expression Microarray." ISRN Pathology 2011 (December 26, 2011): 1–12. http://dx.doi.org/10.5402/2011/275102.

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The use of formalin-fixed, paraffin-embedded (FFPE) tissue overcomes the most prominent issues related to research on relatively rare diseases: limited sample size, availability of control tissue, and time frame. The use of FFPE pancreatic tissue in GEM may be especially challenging due to its very high amounts of ribonucleases compared to other tissues/organs. In choosing pancreatic tissue, we therefore indirectly address the applicability of other FFPE tissues to gene expression microarray (GEM). GEM was performed on archived, routinely fixed, FFPE pancreatic tissue from patients with congenital hyperinsulinism (CHI), insulinoma, and deceased age-appropriate neonates, using whole-genome arrays. Although ribonuclease-rich, we obtained biologically relevant and disease-specific, significant genes; cancer-related genes; genes involved in (a) the regulation of insulin secretion and synthesis, (b) amino acid metabolism, and (c) calcium ion homeostasis. These results should encourage future research and GEM studies on FFPE tissue from the invaluable biobanks available at the departments of pathology worldwide.
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Guo, Tong, Weijie Wang, Paul A. Rudnick, Tao Song, Jie Li, Zhengping Zhuang, Robert J. Weil, Don L. DeVoe, Cheng S. Lee, and Brian M. Balgley. "Proteome Analysis of Microdissected Formalin-fixed and Paraffin-embedded Tissue Specimens." Journal of Histochemistry & Cytochemistry 55, no. 7 (March 19, 2007): 763–72. http://dx.doi.org/10.1369/jhc.7a7177.2007.

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Targeted proteomics research, based on the enrichment of disease-relevant proteins from isolated cell populations selected from high-quality tissue specimens, offers great potential for the identification of diagnostic, prognostic, and predictive biological markers for use in the clinical setting and during preclinical testing and clinical trials, as well as for the discovery and validation of new protein drug targets. Formalin-fixed and paraffin-embedded (FFPE) tissue collections, with attached clinical and outcome information, are invaluable resources for conducting retrospective protein biomarker investigations and performing translational studies of cancer and other diseases. Combined capillary isoelectric focusing/nano-reversed-phase liquid chromatography separations equipped with nano-electrospray ionization-tandem mass spectrometry are employed for the studies of proteins extracted from microdissected FFPE glioblastoma tissues using a heat-induced antigen retrieval (AR) technique. A total of 14,478 distinct peptides are identified, leading to the identification of 2733 non-redundant SwissProt protein entries. Eighty-three percent of identified FFPE tissue proteins overlap with those obtained from the pellet fraction of fresh-frozen tissue of the same patient. This large degree of protein overlapping is attributed to the application of detergent-based protein extraction in both the cell pellet preparation protocol and the AR technique.
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ŞEVİK, Murat. "The extraction of Peste Des Petits Ruminants Virus RNA from paraffin-embedded tissues using a modified extraction method." Journal of Advances in VetBio Science and Techniques 7, no. 2 (August 31, 2022): 202–9. http://dx.doi.org/10.31797/vetbio.1078235.

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Peste des petits ruminants (PPR) which is caused by small ruminant morbillivirus (PPRV) has an important economic impact on small ruminant farming due to high mortality rates, weight loss and restrictions on the export of small ruminants products. Molecular assays are commonly used in the diagnosis of the disease. Extraction of RNA from formalin-fixed paraffin-embedded (FFPE) tissues is challenging because of the RNA is often degraded by formalin fixation process. Although commercial kits have been developed for extraction of nucleic acids from FFPE tissues, they are expensive than other extraction kits. In this study, a modified extraction method was evaluated for detection of PPRV from FFPE tissues. A total of 20 FFPE tissue samples including 15 PPRV positive and 5 PPRV negative FFPE tissue samples were used. Two years ago, these selected FFPE tissue samples were analysed by nucleoprotein gene based one step real time RT-PCR method before they were fixed with formalin and embedded in paraffin. FFPE tissue samples were extracted using modified extraction method and were tested by fusion (F) gene based one step RT-PCR. PPRV specific RNA was detected in 12 FFPE tissue samples whereas 3 positive samples were found negative by one-step RT-PCR. Furthermore, 5 negative FFPE tissue samples were also found negative. Three false negative results were from samples with high real-time RT-PCR cycle threshold. Therefore, false negative results could be related with lower viral loads which might be lower than detection limit of the one-step RT-PCR. The results of the study show that modified extraction method could be used for RNA extraction from FFPE tissues which had been stored for 2 years.
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Sequeiros, Tamara, Marta García, Melania Montes, Mireia Oliván, Marina Rigau, Eva Colás, Inés de Torres, Juan Morote, Jaume Reventós, and Andreas Doll. "Molecular Markers for Prostate Cancer in Formalin-Fixed Paraffin-Embedded Tissues." BioMed Research International 2013 (2013): 1–15. http://dx.doi.org/10.1155/2013/283635.

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Prostate cancer (PCa) is the most frequently diagnosed type of cancer in developed countries. The decisive method of diagnosis is based on the results of biopsies, morphologically evaluated to determine the presence or absence of cancer. Although this approach leads to a confident diagnosis in most cases, it can be improved by using the molecular markers present in the tissue. Both miRNAs and proteins are considered excellent candidates for biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues, due to their stability over long periods of time. In the last few years, a concerted effort has been made to develop the necessary tools for their reliable measurement in these types of samples. Furthermore, the use of these kinds of markers may also help in establishing tumor grade and aggressiveness, as well as predicting the possible outcomes in each particular case for the different treatments available. This would aid clinicians in the decision-making process. In this review, we attempt to summarize and discuss the potential use of microRNA and protein profiles in FFPE tissue samples as markers to better predict PCa diagnosis, progression, and response to therapy.
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Chung, Joon-Yong, Till Braunschweig, Reginald Williams, Natalie Guerrero, Karl M. Hoffmann, Mijung Kwon, Young K. Song, Steven K. Libutti, and Stephen M. Hewitt. "Factors in Tissue Handling and Processing That Impact RNA Obtained From Formalin-fixed, Paraffin-embedded Tissue." Journal of Histochemistry & Cytochemistry 56, no. 11 (July 21, 2008): 1033–42. http://dx.doi.org/10.1369/jhc.2008.951863.

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Formalin-fixed, paraffin-embedded (FFPE) tissue is the most common specimen available for molecular assays on tissue after diagnostic histopathological examination. RNA from FFPE tissue suffers from strand breakage and cross-linking. Despite excellent extraction methods, RNA quality from FFPE material remains variable. To address the RNA quality factors within FFPE tissues, we studied RNA quality, isolating individual elements of the tissue fixation and processing including length of fixation in formalin and the type of buffer incorporated in the fixative. We examined the impact of the length of the tissue processing cycle as well. The optimal fixation period of 12-24 hr in phosphate-buffered formalin resulted in better-quality RNA. Longer tissue processing times were associated with higher quality RNA. We determined that the middle region of gene suffers less damage by these processes as shown by real-time quantitative RT-PCR. These data provide key information for the development of methods of analysis of gene expression in archival FFPE tissues and contribute to the establishment of objective standards for the processing and handling of tissue in surgical pathology. This manuscript contains online supplemental material at www.jhc.org . Please visit this article online to view these materials.
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Nucci, Ricardo, Wilson Jacob-Filho, Alexandre Busse, Laura Maifrino, and Romeu de Souza. "Anatomopathological Assessment of the Diaphragm in Formalin-Fixed, Paraffin-Embedded Sections." Journal of Morphological Sciences 35, no. 03 (September 2018): 173–76. http://dx.doi.org/10.1055/s-0038-1673611.

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Introduction The analysis of frozen muscle biopsies has become a routine method in the evaluation of muscle structure in health and disease. However, the technique for frozen muscle specimens is not widely available in countries with limited medical facilities. The present study aimed to elucidate a reproducible formalin-fixed and paraffin-embedded (FFPE) method for this type of analysis in postmortem muscles. Methods Diaphragm muscle was obtained within 1 hour of sudden death. Diaphragm strips were washed in saline solution, fixed in 10% formalin, frozen at 4°C in a refrigerator, and stored for 24 hours. Then, the tissue samples were processed into paraffin-embedded blocks. Transversal sections were cut from each paraffin block and stained with hematoxylin and eosin, Picrosirius red, Verhoeff-Van Gieson, and Congo red for the qualitative analysis. Results Our analysis indicated a well-preserved muscle. Conclusion In summary, we demonstrate a simple technique for a reproducible FFPE method in postmortem muscle tissues.
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He, Helen, Yu Yang, Zhongmin Xiang, Lunyin Yu, Jouhara Chouitar, Jie Yu, Natalie Roy D’Amore, et al. "A Sensitive IHC Method for Monitoring Autophagy-Specific Markers in Human Tumor Xenografts." Journal of Biomarkers 2016 (May 10, 2016): 1–11. http://dx.doi.org/10.1155/2016/1274603.

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Objective. Use of tyramide signal amplification (TSA) to detect autophagy biomarkers in formalin fixed and paraffin embedded (FFPE) xenograft tissue. Materials and Methods. Autophagy marker regulation was studied in xenograft tissues using Amp HQ IHC and standard IHC methods. Results. The data demonstrate the feasibility of using high sensitivity TSA IHC assays to measure low abundant autophagy markers in FFPE xenograft tissue.
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Dissertations / Theses on the topic "Formalin-fixed, paraffin-embedded tissues- FFPE"

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Matilda, Rentoft. "The use of formalin fixed paraffin embedded tissue and global gene expression profiling for increased understanding of squamous cell carcinoma of the tongue." Doctoral thesis, Umeå universitet, Patologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-54005.

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Head and neck cancer is the 6th most common malignancy worldwide, with tumours of the tongue being one of the most prevalent sites. Despite advances in surgery and radiotherapy, the five-year survival has not changed during the last decades and remains at approximately 50%. Identification of novel biomarkers for more personalized treatment is important for increasing survival in these patients. One of the most commonly used methods in the search for new biomarkers is microarray analysis. A substantial limitation with this technique is the requirement for fresh frozen samples from which high quality RNA can be extracted. This becomes particularly problematic when attempting to discover differences associated with individual sub-types or rare cancers. Recent developments, including the DASL microarray platform, have provided the possibility of analysing RNA of poorer quality from formalin fixed paraffin embedded (FFPE) samples. FFPE is the standard way of preserving tissue from patients and millions of samples are stored around the world. In this thesis we have evaluated the use of FFPE samples and global gene expression profiling for increasing basic knowledge in a subgroup of oral cancer patients with tumours of the tongue. As confirmation of microarray results using qPCR is of outmost importance for conclusive data evaluation, we first aimed at finding a housekeeping gene stably expressed across malignant and non-malignant FFPE oral tissue. TUBA6, which belongs to the tubulin family was detected as being the most stable out of eight possible genes and was thus used for qPCR normalization throughout the following studies. We have performed three separate microarray experiments. Initially only a focused DASL array covering 502 cancer related genes was available and we used it to analyze a smaller cohort of patients and controls (n=36). A similar cohort (n=29) was also analyzed for expression of 836 micoRNAs. In 2009 a whole genome DASL array was launched, covering over 20,000 genes, and all tongue tumour samples available between 1997 and 2010 (n=87) were analysed using this array. Similar to other research groups we observed very high replicate reproducibility using both DASL arrays. When using the microRNA array and the whole genome DASL array an effect of sample quality on the detected expression level of individual genes was noticed. While the expression of some genes severely decreased with a decrease in sample quality others were not changed. This will impair normalization, leading to a residual non-biological variation within the data. Based on our findings we have presented some recommendations for minimizing the effect of sample quality and maximizing the level of biologically relevant information obtained from these experiments, e.g. ensuring that samples in groups to be compared are of the same quality range. For the microRNA data we also introduced an additional normalization step to the standard normalizations. We could show that lists of differentially expressed genes generated when taking these precautions were enriched for genes involved in cancer related processes and contained for tongue carcinoma previously identified changes. A number of differentially expressed genes, novel for tongue carcinoma, were also confirmed in high quality fresh frozen samples, including BCL2A1 (apoptosis), CXCL10 (immune response), SLC2A6 (energy transport) and miR-424 (angiogenesis). In conclusion microarrays can be used to analyze FFPE samples but should be performed with care. Standard normalization methods will not remove the variation introduced by samples being of different quality, leading to spurious results. Taking a few precautions, however, led to the identification of differentially expressed genes relevant in tumour development and maintenance. The recommendations we make can facilitate design of future studies using FFPE samples. The genes we identified as being differentially expressed in tumour tissue now need to be further evaluated for their potential as biomarkers in tongue carcinoma.
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Rossouw, Sophia Catherine. "Optimisation of proteomics techniques for archival tumour blocks of a South African cohort of colorectal cancer." University of Western Cape, 2020. http://hdl.handle.net/11394/8036.

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Philosophiae Doctor - PhD
Tumour-specific protein markers are usually present at elevated concentrations in patient biopsy tissue; therefore tumour tissue is an ideal biological material for studying cancer proteomics and biomarker discovery studies. To understand and elucidate cancer pathogenesis and its mechanisms at the molecular level, the collection and characterisation of a large number of individual patient tissue cohorts are required. Since most pathology institutes routinely preserve biopsy tissues by standardised methods of formalin fixation and paraffin embedment, these archived, FFPE tissues are important collections of pathology material, often accompanied by important metadata, such as patient medical history and treatments. FFPE tissue blocks are conveniently stored under ambient conditions for decades, while retaining cellular morphology due to the modifications induced by formalin.
2022
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Djidja, M.-C., S. Francese, Paul M. Loadman, Chris W. Sutton, P. Scriven, E. Claude, M. F. Snel, J. Franck, M. Salzet, and M. R. Clench. "Detergent addition to trypsin digest and Ion Mobility Separation prior to MS/MS improves peptide yield and Protein Identification for in situ Proteomic Investigation of Frozen and FFPE Adenocarcinoma tissue sections." Wiley, 2009. http://hdl.handle.net/10454/4565.

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The identification of proteins involved in tumour progression or which permit enhanced or novel therapeutic targeting is essential for cancer research. Direct MALDI analysis of tissue sections is rapidly demonstrating its potential for protein imaging and profiling in the investigation of a range of disease states including cancer. MALDI-mass spectrometry imaging (MALDI-MSI) has been used here for direct visualisation and in situ characterisation of proteins in breast tumour tissue section samples. Frozen MCF7 breast tumour xenograft and human formalin-fixed paraffin-embedded breast cancer tissue sections were used. An improved protocol for on-tissue trypsin digestion is described incorporating the use of a detergent, which increases the yield of tryptic peptides for both fresh frozen and formalin-fixed paraffin-embedded tumour tissue sections. A novel approach combining MALDI-MSI and ion mobility separation MALDI-tandem mass spectrometry imaging for improving the detection of low-abundance proteins that are difficult to detect by direct MALDI-MSI analysis is described. In situ protein identification was carried out directly from the tissue section by MALDI-MSI. Numerous protein signals were detected and some proteins including histone H3, H4 and Grp75 that were abundant in the tumour region were identified
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Clift, Sarah J. "Standardization and validation of an immunoperoxidase test for African horsesickness virus using formalin-fixed, paraffin-embedded tissues." Diss., University of Pretoria, 2009. http://hdl.handle.net/2263/24626.

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The aim of this study was to standardize and validate an immunohistochemical test for the routine diagnosis of African horsesickness in horses. Hamblin developed the primary anti- African horsesickness virus serum that I used and the avidin-biotin complex detection system was employed. During the standardization process I demonstrate that lung, heart and spleen samples are the most reliable. I also show that it is not necessary to take multiple samples per organ, because the AHSV-positive signal is generally widespread throughout the lung and heart, in particular. In order to validate the technique, samples from 118 negative and 128 positive horse cases, including all nine known serotypes, were immunostained. All of the positive cases were confirmed by means of virus isolation. Negative horse samples were obtained from countries where African horsesickness does not occur. None of the negative cases stained positive and all the positive cases were correctly identified. Therefore, there was 100 % concordance between immunohisto chemistry (when applied to formalin-fixed, paraffin-embedded heart and/or lung and/or spleen tissues from positive horse cases that had been archived for less than 10 years) and virus isolation results. Heart and lung had consistently more positive signal than spleen. The Hamblin antiserum did not cross-react with closely-related orbiviruses (specifically equine encephalosis virus and bluetongue virus) in selected horse and sheep tissues, respectively. Characteristic positive staining was observed in lung, heart and spleen samples from two dogs that died of African horsesickness. Positive signal was not affected by long-term storage in formaldehyde (up to 365 days). Also, specific positive staining could be detected in heart and/or lung and/or spleen samples in more than 95 % of positive horses where tissue blocks had been stored for between 10 and 83 years. The principal target cells in the horse and dog cases were microvascular endothelial cells, intravascular monocyte-macrophages and, to a lesser extent, interstitial macrophages in lung, spleen and liver, in particular. Positive staining is intracytoplasmic with a bead/dot and/or granular character. Beads, dots or granules may occur singly or in clusters. Occasionally, linear deposits of positive signal delineate segments of capillary vessels. The veterinary pathologist must look for characteristic positive signal in target cells, because, occasionally, certain bacteria (Rhodococcus equi and Helicobacter sp.) cross-react with the Hamblin antiserum. Clearly, the test is highly sensitive, specific and robust, sufficiently so for the routine diagnosis of African horsesickness virus.
Dissertation (MSc)--University of Pretoria, 2008.
Paraclinical Sciences
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Clift, Sarah Jane. "Standardization and validation of an immunoperoxidase test for African horsesickness virus using formalin-fixed, paraffin-embedded tissues." Pretoria : [s.n.], 2008. http://upetd.up.ac.za/thesis/available/etd-05132009-173308/.

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Viljoen, Rabia. "Optimisation of sample preparation for DNA extraction from formalin fixed paraffin embedded tissues of unresolved sudden unexpected death cases." Master's thesis, Faculty of Health Sciences, 2021. http://hdl.handle.net/11427/33072.

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A retrospective case review revealed an increase in sudden unexpected death (SUD) admittance at Salt River Mortuary (SRM) between 2014 and 2018, and that 40 % of SUD occurred in young individuals between the ages of 1 and 40 years old (SUDY). Despite extensive investigations, the cause of death remained undetermined in 26 % of SUDY cases. These dormant cases may benefit from retrospective post-mortem molecular autopsies for investigation into genetic causes of death. Often, formalin fixed paraffin embedded tissues (FFPETs) are the only archival sources of DNA available for retrospective analyses. This study aimed to optimise DNA recovery from FFPETs for potential use in molecular autopsies of unresolved SUDY cases. To this end, DNA was extracted from FFPET sections using the QIAamp® DNA FFPE tissue kit; the thickness and number of sections were varied. DNA was assessed using spectrophotometry, real-time PCR and digital capillary electrophoresis. Results showed that finer sectioning (1-µm thick as compared to 3-µm and 5-µm thick), improved DNA concentrations, purities and DNA fragment lengths. Increasing the number of 1-µm thick sections from 30 to 100, significantly improved DNA yield. DNA was not significantly more degraded for FFPETs stored for up to three years, which holds promise in the effectiveness of the technique for aged samples. The DNA extraction method developed in this study yielded a median of 320 ng (287 ng - 698 ng) of DNA with 55 % of DNA fragments being at least 400 bp in size. These results are especially informative for downstream molecular analyses, indicating that genotyping or sequencing assays need to be designed to target amplicons less than 400 bp in size. The degraded nature of the FFPET samples also suggests that massively parallel sequencing might be suited for downstream molecular analysis for determining cause of death in unresolved SUDY cases.
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Hutamo, Kutlwano Aggrineth. "Typing of Mycobacterium bovis in formalin-fixed, paraffin-embedded tissues from selected wildlife species in the Kruger National Park, South Africa." Diss., University of Pretoria, 2012. http://hdl.handle.net/2263/29674.

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Mycobaterium bovis is the causative agent of bovine tuberculosis (BTB) and it is a member of the Mycobacterium tuberculosis complex (MTBC). This bacterium has a wide host range of which, cattle is considered as the maintenance host. Humans, goats, wildlife, cats, dogs and lions are also susceptible to the bacterium and are considered putative spillover hosts as infection is not confined in these hosts. Mycobacterium bovis is prevalent in developing countries especially in farmed animals. This presents a problem since BTB is a zoonosis. People living in close contact with infected cattle or those who drink unpasteurized milk are at risk of infection. About 10% of cases of human tuberculosis are thought to be caused by M. bovis. In some instances, wildlife provides a reservoir for the pathogen and transmits it to cattle in farms and poses further risk to humans at the wildlife/livestock/human interface. Certain countries like the United Kingdom where BTB was previously eradicated are experiencing substantial increase in BTB infection. This is thought to be a result of wildlife reservoirs that infect farmed animals, especially cattle. Such reservoirs make eradication of the disease extremely difficult and require programmes to be put in place to control spread of the disease. This makes M. bovis a pathogen of economic importance since the programmes may be costly. In addition, wildlife that is infected cannot be exported and this further affects the economy negatively. In order to control the spread of the pathogen, it is essential to determine the source of infection. However, it is difficult to determine the source or to track the spread of BTB especially in wildlife where animals have unrestricted movement. The inability to conduct epidemiological studies of BTB may be a result of the lack of molecular typing methods that allow bacteria to be identified to strain level rapidly and fairly simpler than culture, thus providing much needed information about the pathogen. In recent years, typing of M. bovis isolates to strain level has been made possible by the development of PCR-based technologies such as IS6110 typing and spoligotyping. These technologies were however, found to be unsuitable for differentiating certain species in the MTBC. Newer technologies based on the variable number of tandem repeats (VNTRs) in organisms have been developed and allow for the differentiation of members in the MTBC, which have a high level of genome homology. These technologies include multiple-locus variable number tandem repeat analysis (MLVA) and mycobacterial interspersed repetitive unit (MIRU)-VNTR analysis. It was also discovered that mycobacteria have genomic regions of difference (RD) that could be used to identify the different species of bacteria in the MTBC. Retrospective studies may play a key role in tracing the source of diseases and following the pattern of transmission. However, in most instances, no fresh samples are available for such studies. For this reason, formalin-fixed paraffin-embedded (FFPE) tissue from wildlife in the Kruger National Park (KNP) was used for conducting a retrospective study aimed at determining the epidemiology of M. bovis in the KNP. However, amplification of DNA derived from FFPE tissue for PCR based techniques has been found to be a difficult exercise and not many standard protocols have been developed and validated for the use of such DNA. In this study, different methods of extraction were used to obtain DNA from FFPE tissue since it is difficult to obtain high quality DNA from such tissue, which is degraded. Formaldehyde, the main component of formalin which is used to fix tissue samples, causes degradation and cross-linking of DNA. In addition, previous studies are inconsistent with regards to the best method to use when extracting DNA from FFPE tissue. Three PCR-based techniques were used to type or identify the isolates in order to standardize a protocol for use in typing isolates from FFPE tissue. These techniques included analysis of the RDs, VNTR based methods i.e. MLVA and MIRU-VNTR and spoligotyping. Since there are many factors that influence the quality of FFPE tissue, samples confirmed BTB positive by VNTR analysis, spoligotyping and IS6110 analysis were used in order to optimize a PCR for FFPE tissue. Furthermore, in order to serve as control samples for spoligotyping and analysis of the RDs, DNA obtained from fresh tissue was also used in the study. Despite the various methods used to extract and to type DNA, the DNA from FFPE tissue provided unspecific results that did not allow for an informative retrospective study of M. bovis. This may be due to the fact that the DNA used had a high degree of degradation from prolonged fixation in formalin. Although M. bovis could not be typed in FFPE tissues, it could be identified by analysis of the regions of difference, more specifically the RD9 region. Amplification of RD9 is thus recommended for use in retrospective studies for diagnostic purposes, especially in cases where highly degraded DNA is used. This region (RD9) should however, only be used as a presumptive diagnosis since RD9 also identifies M. africanum, M. microti, M. pinnipedii, M. caprrae and M. bovis BCG. However, RD9 specifically excludes M. tuberculosis. In the SA context, particularly in the KNP, this allows for some sound inferences since the animals are likely to be infected with M. bovis as opposed to M. tuberculosis. This study highlighted statements in previous studies where it was stated that fixation of tissue in formalin should be done in such a way to reduce degradation of DNA in FFPE tissue in order to allow for its use in retrospective molecular studies which may be very insightful in determining the epidemiology of diseases that are difficult to track and/or control. Copyright
Dissertation (MSc)--University of Pretoria, 2012.
Veterinary Tropical Diseases
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Lüder, Ripoli Florenza [Verfasser]. "Comparison of fresh frozen vs. formalin-fixed, paraffin-embedded specimens and the expression profiling of 16 target genes in neoplastic and non-neoplastic canine mammary tissues using a multiplex branched-DNA assay / Florenza Lüder Ripoli." Hannover : Bibliothek der Tierärztlichen Hochschule Hannover, 2016. http://d-nb.info/1125394560/34.

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Kuo, Shanny Hsuan, and 郭. 軒. "Molecular Detection of Feline Coronaviruses in Formalin-Fixed and Paraffin-Embedded Tissue (FFPE) by nested RT-PCRs: a Diagnosis-Aiding Approach." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/dc943h.

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碩士
國立臺灣大學
分子暨比較病理生物學研究所
105
Feline infectious peritonitis (FIP), caused by feline coronavirus (FCoV), is a lethal disease in cats. The clinical signs are non-specific and antemortem diagnosis remains challenging and frustrating. Appling histopathology combined with immunohistochemical (IHC) staining is considered as the gold standard for FIP diagnosis. However, the sensitivity of the IHC method depends much on the numbers of intralesional antigen-bearing cells. Due to the limitations of small sampling sizes as well as the equivocal IHC staining pattern in some specimens, formalin-fixed and paraffin-embedded tissue (FFPE) biopsies frequently submitted for histopathological examination for FIP are the most challenging specimens for pathologists. It has been demonstrated that the consensus PCR targeting 3’UTR alone is non-specific for diagnosis of FIP in fresh tissues. Moreover, two recently described mutations, the substitution of methionine (M) to leucine (L) amino acid mutation at position 1058 (M1058L) and the substitution of serine (S) to alanine (A) amino acid mutation at position 1060 (S1060A) in spike (S) gene, which together can distinguish feline infectious peritonitis virus (FIPV) from feline enteric coronavirus (FECV) in >95% of serotype I FCoV-infected cases in freshly-collected specimens, have suggested a potential diagnostic value. The aim of this study was to compare the uses of a consensus nested RT-PCR (nRT-PCR) targeting 3’UTR and a nRT-PCR targeting the two mutations in S gene in aiding the diagnosis of FIP in FFPE tissues. After evaluation of the RNA quality in FFPE tissues by a RT-PCR targeting the housekeeping gene of feline GAPDH, a total of 38 histopathologically and immunohistochemically confirmed FIP cases and 22 non-FIP cases were used as the source of RNA and examined nRT-PCRs. We have successfully extracted RNA and amplified FCoV genes in 31/38 (82%) FIP cases using consensus nRT-PCR, whereas 17/38 (42%) FIP cases were detected using the S-specific nRT-PCR. Following subsequent sequencing, 16 out of 17 serotype 1 cases had one of the two mutations (M1058L and S1060A) in the S gene. None of the FFPF tissues from these non-FIP cats were positive by both methods. We have demonstrated that in combined with histopathology and IHC staining, both consensus nRT-PCR and S-specific nRT-PCR were capable of detecting viral RNA from FFPE samples where IHC signals were equivocal and possibly misinterpreted as negativity. Both methods serve as a useful tool in supporting FIP diagnosis and for the retrospective study of FIP in archival FFPE tissues.
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Zhang, XIAO. "EVALUATION OF RNA QUALITY FROM FORMALIN FIXED AND PARAFFIN EMBEDDED SAMPLES:APPLICATIONS AND LIMITATIONS." Thesis, 2008. http://hdl.handle.net/1974/1740.

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RNA molecules isolated from FFPE samples are highly fragmented and modified, and generally deemed unsuitable for downstream gene expression profiling. With the development of molecular biology, there has been growing interest in profiling archival FFPE samples. Successful profiling of transcripts from FFPE samples would greatly expand tissue sources for large scale gene expression studies; also it would pave the way for future applications on the type of tissue readily available in the clinical setting. So far, there is a lack of systemic studies evaluating the quality of RNA isolated from routinely processed FFPE samples, and it has remained difficult to assess how well FFPE-derived RNA mirrors the status of RNA isolated before fixation. In this project, the similarity of miRNA and mRNA profiles between matched frozen and FFPE lymphoid hyperplasia tissues (N=7 for miRNA comparison, N=4 for mRNA comparison) were evaluated. We found consistently good correlation (mean of Pearson coefficient=0.939, mean of Spearman coefficient=0.905, mean of Kendall tau=0.744) between matched frozen and FFPE-derived miRNA profiles, suggesting FFPE samples may retain miRNA expression information quite well. This has major positive implications for research using FFPE samples, as miRNA profiling becomes more prominent in bioprofiling studies. On the contrary, mRNA isolated from FFPE samples showed less correlation (Spearman coefficient less than 0.75) with its frozen counterpart on the Agilent microarray platform. With a post extraction heat treatment aimed at reversing base modifications and cross linking structures, obvious global mRNA quality improvement was observed in cases where samples appeared to be heavily cross linked, but was less effective and even detrimental in cases where cross linking was less prominent. This research suggests that the extent of cross linking may be critical in terms of determining whether a particular FFPE tissue will become a useful source of mRNA for global profiling studies
Thesis (Master, Pathology & Molecular Medicine) -- Queen's University, 2008-09-26 10:49:50.044
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Books on the topic "Formalin-fixed, paraffin-embedded tissues- FFPE"

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Al-Mulla, Fahd, ed. Formalin-Fixed Paraffin-Embedded Tissues. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-055-3.

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Formalin-fixed paraffin-embedded tissues: Methods and protocols. New York: Humana Press, 2011.

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Formalin-Fixed Paraffin-Embedded Tissues: Methods and Protocols. Humana Press, 2016.

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Book chapters on the topic "Formalin-fixed, paraffin-embedded tissues- FFPE"

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Bonin, Serena, Patricia J. T. A. Groenen, Iris Halbwedl, and Helmut H. Popper. "DNA Extraction from Formalin-Fixed Paraffin-Embedded (FFPE) Tissues." In Guidelines for Molecular Analysis in Archive Tissues, 33–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-17890-0_7.

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Howe, Karen. "Extraction of miRNAs from Formalin-Fixed Paraffin-Embedded (FFPE) Tissues." In Methods in Molecular Biology, 17–24. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6524-3_3.

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Longuespée, Rémi, Dominique Baiwir, Gabriel Mazzucchelli, Nicolas Smargiasso, and Edwin De Pauw. "Laser Microdissection-Based Microproteomics of Formalin-Fixed and Paraffin-Embedded (FFPE) Tissues." In Methods in Molecular Biology, 19–31. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7558-7_2.

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Piqueras, Marta, Manish Mani Subramaniam, Samuel Navarro, Nina Gale, and Rosa Noguera. "Fluorescence In Situ Hybridization (FISH) on Formalin-Fixed Paraffin-Embedded (FFPE) Tissue Sections." In Guidelines for Molecular Analysis in Archive Tissues, 225–30. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-17890-0_34.

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Tran, Diem, Mark Daniels, Ben Colson, Dikran Aivazian, Antonio Boccia, Ingrid Joseph, Steffan Ho, Steve French, Alex Buko, and Jing Wei. "Sample Preparation of Formalin-Fixed Paraffin-Embedded (FFPE) Tissue for Proteomic Analyses." In Sample Preparation in Biological Mass Spectrometry, 159–70. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-0828-0_10.

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Azimzadeh, Omid, Michael J. Atkinson, and Soile Tapio. "Quantitative Proteomic Analysis Using Formalin-Fixed, Paraffin-Embedded (FFPE) Human Cardiac Tissue." In Methods in Molecular Biology, 525–33. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1186-9_33.

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Azimzadeh, Omid, Michael J. Atkinson, and Soile Tapio. "Qualitative and Quantitative Proteomic Analysis of Formalin-Fixed Paraffin-Embedded (FFPE) Tissue." In Methods in Molecular Biology, 109–15. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2550-6_10.

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Bonin, Serena, Patricia J. T. A. Groenen, Iris Halbwedl, and Helmut H. Popper. "DNA Extraction from Formalin-Fixed Paraffin-Embedded Tissues (FFPE) (from Small Fragments of Tissues or Microdissected Cells)." In Guidelines for Molecular Analysis in Archive Tissues, 37–39. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-17890-0_8.

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Gomes, Bruno Costa, Bruno Santos, José Rueff, and António Sebastião Rodrigues. "Methods for Studying MicroRNA Expression and Their Targets in Formalin-Fixed, Paraffin-Embedded (FFPE) Breast Cancer Tissues." In Methods in Molecular Biology, 189–205. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3347-1_11.

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Dowling, Paul. "DIGE Saturation Labeling for Scarce Amounts of Protein from Formalin-Fixed Paraffin-Embedded (FFPE) Tissue." In Methods in Molecular Biology, 113–18. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2831-7_9.

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Conference papers on the topic "Formalin-fixed, paraffin-embedded tissues- FFPE"

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Galindo, Hector, Luisa Solis, Junya Fujimoto, Nana E. Hanson, Christina McDowell, Erick Riquelme, XiMing Tang, et al. "Abstract 3195: Formalin-fixed and paraffin-embedded (FFPE) DNA recovery for high-throughput genotyping of lung cancer tissues." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-3195.

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Reinholz, Monica M., Debrah M. Thompson, Ihab Botros, Matt Rounseville, and Patrick C. Roche. "Abstract 1383: NGS-based measurement of gene expression of 2560 oncology-related biomarkers in formalin-fixed, paraffin-embedded (FFPE) tissues." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-1383.

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Palescandolo, Emanuele, Robert Jones, Alina Raza, Ashwini Sunkavalli, Priscilla K. Brastianos, Matthew Ducar, Christina Go, et al. "Abstract 3178: Can DNA from archived formalin-fixed paraffin embedded (FFPE) cancer tissues be used for somatic mutation analysis in next generation sequencing." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-3178.

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Englert, D., D. Wilson, and S. Laken. "Amplification of mRNA from Formalin-Fixed Paraffin-Embedded (FFPE) Breast Cancer Tissues without 3' Bias and Multiplex Expression Analysis on Flow-Through Microarrays." In Abstracts: Thirty-Second Annual CTRC‐AACR San Antonio Breast Cancer Symposium‐‐ Dec 10‐13, 2009; San Antonio, TX. American Association for Cancer Research, 2009. http://dx.doi.org/10.1158/0008-5472.sabcs-09-3052.

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Gu, Jian. "Abstract 4127: Expression profiling of paired formalin-fixed, paraffin-embedded (FFPE) and fresh-frozen tissue samples on Ion Torrent PGMTM." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-4127.

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Smiley, Sheila, Celia Marginean, and Bryan Lo. "Abstract A40: Gene expression profiling of pancreatic cancer precursors directly from formalin fixed paraffin embedded (FFPE) tissue without nucleic acid extraction." In Abstracts: AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; May 12-15, 2016; Orlando, FL. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.panca16-a40.

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Thobe, Megan N., Suzane L. Um, Victoria L. Peek, Darryl W. Ballard, Bruce W. Konicek, Kelly M. Credille, Philip J. Ebert, Gregory P. Donoho, and S. Betty Yan. "Abstract 2087: Detection of KRAS mutations in circulating tumor cells (CTCs) and in formalin-fixed, paraffin-embedded (FFPE) tissue using castPCR method." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-2087.

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Baumbach, L., J. Yan, M. Ahearn, C. Gomez, M. Jorda, T. Halsey, A. Mejias, et al. "Gene Expression Profiling of Formalin-Fixed, Pariffin-Embedded (FFPE) Tissues from Triple-Negative (TN) Breast Cancer (BC) Patients." In Abstracts: Thirty-Second Annual CTRC‐AACR San Antonio Breast Cancer Symposium‐‐ Dec 10‐13, 2009; San Antonio, TX. American Association for Cancer Research, 2009. http://dx.doi.org/10.1158/0008-5472.sabcs-09-6125.

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Niland, Erin, Audrey D. McGuire, Mary L. Cox, and George E. Sandusky. "Abstract 3203: High quality DNA obtained with an automated DNA Extraction method with 15 to 40 year old formalin fixed paraffin embedded (FFPE) blocks from normal and cancer tissues." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-3203.

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Rusbuldt, Joshua James, Tanesha Cash-Mason, Shaozhou Tian, Alison VanSchoiack, Yan Liang, Chandra Rao, and Denis Smirnov. "Abstract 4691: Evaluation of the NanoString’s Digital Spatial Profiling (DSP) technology in formalin-fixed paraffin embedded (FFPE) cell line mixtures, PBMCs and non-small cell lung cancer (NSCLC) tissues." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-4691.

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