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Relevant bibliographies by topics / FFPE tissues

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Academic literature on the topic 'FFPE tissues'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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Journal articles on the topic "FFPE tissues"

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Pinto-Ribeiro, Ines, Rui M. Ferreira, Joana Pereira-Marques, Vanessa Pinto, Guilherme Macedo, Fátima Carneiro, and Ceu Figueiredo. "Evaluation of the Use of Formalin-Fixed and Paraffin-Embedded Archive Gastric Tissues for Microbiota Characterization Using Next-Generation Sequencing." International Journal of Molecular Sciences 21, no. 3 (February 7, 2020): 1096. http://dx.doi.org/10.3390/ijms21031096.

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Large numbers of well-characterized clinical samples are fundamental to establish relevant associations between the microbiota and disease. Formalin-fixed and paraffin-embedded (FFPE) tissues are routinely used and are widely available clinical materials. Since current approaches to study the microbiota are based on next-generation sequencing (NGS) targeting the bacterial 16S rRNA gene, our aim was to evaluate the feasibility of FFPE gastric tissues for NGS-based microbiota characterization. Analysis of sequencing data revealed the presence of bacteria in the paraffin control. After the subtraction of the operational taxonomic units (OTUs) present in the paraffin control to the FFPE tissue sample dataset, we evaluated the microbiota profiles between paired FFPE and frozen gastric tissues, and between different times of archiving. Compared with frozen gastric tissues, we detected a lower number of OTUs in the microbiota of paired FFPE tissues, regardless of the time of archiving. No major differences in microbial diversity were identified, but taxonomic variation in the relative abundance of phyla and orders was observed between the two preservation methods. This variation was also evident in each case and throughout the times of FFPE archiving. The use of FFPE tissues for NGS-based microbiota characterization should be considered carefully, as biases can be introduced by the embedding process and the time of tissue archiving.

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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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Asmann, Yan W., Vivekananda Sarangi, Bruce W. Eckloff, Julie M. Cunningham, Samantha J. McDonough, Yeon K. Lee, Eric D. Wieben, et al. "Comparison Of Single Nucleotide Mutations (SNVs) and Copy Number Variants (CNVs) Detection In Formalin Fixed Paraffin Embedded (FFPE) and Paired Frozen Tumor Tissues Using Target Capture and Sequencing Approach." Blood 122, no. 21 (November 15, 2013): 1784. http://dx.doi.org/10.1182/blood.v122.21.1784.1784.

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Abstract Background Next Generation sequencing (NGS) is a powerful tool to identify somatic mutations associated with tumor onset and drug response. While it is well suited for high quality fresh/frozen samples, NGS is not proven for FFPE tissue which is the most common type of clinical specimen. Since the nucleic acids can be readily extracted from FFPE samples for a variety of genomic analyses, a comparative mutational analysis of paired frozen and FFPE tissues is urgently needed. Our long term goal is to establish a lab protocol to detect mutations in FFPE tumors using a targeted capture and sequencing approach for genes of interest. This pilot study focuses on the comparison of FFPE and frozen samples to test the validity of using FFPE tissues in such application. Methods Gene Selection: 128 genes associated with known pathogenic mutations in lymphoma Sample Selection: 9 diffuse large B-cell lymphoma (DLBCL) cases with FFPE, frozen and germline samples, as well as 10 frozen normal lymphatic tissues as references for CNV detections Capture Probe Design: We targeted coding exons and UTR, as well as the evolutionarily conserved intronic regions. The capture probes were designed using the Agilent eArray tool. The titling density of the probes was set to 3 probes overlapping with every base in the target region to improve the capture efficiency in FFPE samples. The least stringent masking of the repeat regions was allowed to include regions with small repeats that are shorter than the length of the sequencing reads (100-bp). In addition, boosting parameters were picked to set various levels of probe replication in different regions in order to minimize the local coverage differences (e.g. between regions of different GC contents) Sequencing and Bioinformatics: The target capture and sequencing were performed by the Mayo Clinic Medical Genome Facility. The reads were mapped to Human Reference Genome Build 37 using Novalign, and SNVs were called using GATK. The CNVs were identified using an in-house developed algorithm, patternCNV. Results The designed probes covered 99.65937% of the target regions. We generated 2.2-6.7 Gbp of reads per sample, 57.4-71.5% of which were on target. This equalled an average coverage of 2100-6700 folds which is 10-30 times higher than the minimal coverage recommended by Agilent. Due to this high coverage, we observed duplicate reads that accounted for 7.7-73.5% of the total reads. When we analysed the data with and without the duplicated reads, the concordance of the called SNVs was between 84-93% out of 207-249 mutated positions per trio-sample. There were 7.8-8.9% and 1.1-2.2% unique SNVs per sample by excluding or including duplicate reads, respectively. The dis-concordances were mostly missed calls, where a SNV was observed in only 1 or 2 of the trio samples. The missed calls from frozen samples ranged from 0-10.4% compared to 1.4-10.4% from the FFPE tissues, with 0.88-2.4% more SNVs missed in FFPE. Further analyses showed that all of the missing calls came from the lack of or low coverage of the corresponding positions. There were also differences of the called SNVs between the trio samples. However, this was extremely rare. Only 2 out of the 9 trio samples at a total of 3 positions had disagreements in called SNVs between FFPE and frozen tissues, all due to the allelic imbalance where the percentage of reads supporting the alternative alleles were below 20%. Therefore, this dis-concordance can be removed by back-filling of the read-level information for each position. Unfortunately only 11.9-47.4% of the CNVs called in frozen tissues were identified in FFPE samples, due to the widely various coverage in FFPE samples. The consequent large noises of the log ratio values between the FFPEs and normal references significantly reduced the sensitivity for CNV calling. Conclusions This pilot study compared the performance of SNV and CNV detection in FFPE and paired frozen tissues using a target capture and sequencing approach. With a capture probe design strategized to benefit FFPE samples, we observed SNV detection rates in FFPE that were only slightly lower (0.88-2.4%) than those of frozen tissues due to poor coverage of some positions in FFPE samples. With a proper back-filling step, there was no dis-concordance of the called SNVs between FFPE and frozen samples. However, CNV detections in FFPE were more problematic due to the un-predictable regional coverage in FFPE samples. Disclosures: No relevant conflicts of interest to declare.

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Norgan, Andrew P., Lynne M. Sloan, and Bobbi S. Pritt. "Detection of Naegleria fowleri, Acanthamoeba spp, and Balamuthia mandrillaris in Formalin-Fixed, Paraffin-Embedded Tissues by Real-Time Multiplex Polymerase Chain Reaction." American Journal of Clinical Pathology 152, no. 6 (August 15, 2019): 799–807. http://dx.doi.org/10.1093/ajcp/aqz103.

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Abstract Objectives Pathogenic free-living amebae (FLAs) cause skin, ocular, and central nervous system (CNS) infections with significant morbidity and mortality. Diagnosis of FLA infections by pathologic examination of tissue sections can be aided using molecular assays. This study investigated the performance characteristics of a multiplex real-time polymerase chain reaction (PCR) assay (FLA-PCR) for detection and differentiation of FLAs in clinical specimens. Methods FLA-PCR was performed on 39 human specimens comprising one cutaneous, 14 corneal, and 24 CNS formalin-fixed, paraffin-embedded (FFPE) tissues with a histopathologic diagnosis of FLA infection and four CNS FFPE tissues with inflammation but no evidence of FLAs. In addition, clinical specificity and assay limit of detection were determined. Results FLA detection sensitivities ranged from 79% to 84% in FFPE tissues. No cross-reactivity was observed. Conclusions While sensitivity is limited, FLA-PCR assay may serve as a useful adjunct for detection or confirmation of FLA infections in FFPE tissues.

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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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Ghebeh, Hazem, Fatmah A. Mansour, Dilek Colak, Akram A. Alfuraydi, Amal A. Al-Thubiti, Dorota Monies, Monther Al-Alwan, Taher Al-Tweigeri, and Asma Tulbah. "Higher PD-L1 Immunohistochemical Detection Signal in Frozen Compared to Matched Paraffin-Embedded Formalin-Fixed Tissues." Antibodies 10, no. 3 (June 22, 2021): 24. http://dx.doi.org/10.3390/antib10030024.

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Purpose: Response to anti-PD-L1/PD-1 immunotherapy correlates with PD-L1 expression in breast cancer. However, the prevalence of PD-L1 positive breast cancer is variable, which could be due to differences in the population/cohort of patients tested or the preservation/detection technology used. To investigate this variability, we examined the effect of two tissue preservation methods on PD-L1 immunohistochemical detection in breast cancer. Methods: We compared PD-L1 expression in patient-matched frozen (FR) and formalin-fixed paraffin-embedded (FFPE) tissues of breast cancer patients. PD-L1 expression was assessed using tumor proportion score (TPS, simply PD-L1 score), and case positivity was determined with PD-L1 score ≥5. Results: In FFPE tissues, PD-L1 was positive in 7–10% of tested patients, depending on the antibody used. In patient-matched FR tissues, the same antibodies showed positive PD-L1 expression in 20–30% of cases. The impact of the antibody tested on the rate of PD-L1 positivity (% of PDL1 positive cases) was minor, as evident in the near perfect concordance between PD-L1 score obtained using the different antibodies whether tested in FR or FFPE tissues. However, there was a systematic drop by an average of 13–20% in the PD-L1 score obtained in FFPE tissues compared to their patient-matched FR tissues. Conclusions: In the tested patient-matched cohort, there was consistently a higher PD-L1 score in FR than FFPE tissues, regardless of the antibody used, demonstrating a significant effect on PD-L1 detection due to the preservation method. These findings should inspire further work to improve the sensitivity of PD-L1 detection and possibly search for more sensitive antibodies in FFPE tissues.

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Amemiya, Kei, Xiankun Zeng, Jeremy J. Bearss, Christopher K. Cote, Carl Soffler, Robert C. Bernhards, Jennifer L. Dankmeyer, et al. "Laser Scanning Confocal Microscopy Was Used to Validate the Presence of Burkholderia pseudomallei or B. mallei in Formalin-Fixed Paraffin Embedded Tissues." Tropical Medicine and Infectious Disease 5, no. 2 (April 29, 2020): 65. http://dx.doi.org/10.3390/tropicalmed5020065.

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Burkholderia pseudomallei and B. mallei are Gram-negative, facultative intracellular bacteria that cause melioidosis and glanders, respectively. Currently, there are no vaccines for these two diseases. Animal models have been developed to evaluate vaccines and therapeutics. Tissues from infected animals, however, must be fixed in formalin and embedded in paraffin (FFPE) before analysis. A brownish staining material in infected tissues that represents the exopolysaccharide of the pathogen was seen by bright field microscopy but not the actual microorganism. Because of these results, FFPE tissue was examined by laser scanning confocal microscopy (LSCM) in an attempt to see the microorganism. Archival FFPE tissues were examined from ten mice, and five nonhuman primates after exposure to B. pseudomallei or B. mallei by LSCM. Additionally, a historical spleen biopsy from a human suspected of exposure to B. mallei was examined. B. pseudomallei was seen in many of the infected tissues from mice. Four out of five nonhuman primates were positive for the pathogen. In the human sample, B. mallei was seen in pyogranulomas in the spleen biopsy. Thus, the presence of the pathogen was validated by LSCM in murine, nonhuman primate, and human FFPE tissues.

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Bao, Jian R., Richard B. Clark, Ronald N. Master, Kileen L. Shier, and Lynn L. Eklund. "Acid-fast bacterium detection and identification from paraffin-embedded tissues using a PCR-pyrosequencing method." Journal of Clinical Pathology 71, no. 2 (July 22, 2017): 148–53. http://dx.doi.org/10.1136/jclinpath-2016-204128.

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AimsAcid-fast bacterium (AFB) identification from formalin-fixed paraffin-embedded (FFPE) tissues is challenging and may not be readily available to the clinical laboratory. A method to detect and identify AFB from FFPE tissues using PCR and pyrosequencing (PCR-Seq) was developed and evaluated.MethodsThe method was validated using spiked cell-clotted paraffin blocks before use with patients’ specimens. DNA was extracted from tissue sections, and a 16S rRNA gene fragment was amplified and a signature sequence was produced on a PyroMark ID system. Sequences were aligned to established databases for AFB identification. Additional tissue sections were stained and examined for AFB.ResultsBoth sensitivity and specificity were 100% on spiked cell-clotted blocks without cross-reactivity with non-AFB. Of 302 FFPE tissues from patients, 116 (38%) were AFB-stain positive; 83 (72%) of these had AFB identified. The 21 AFB identified included Mycobacterium tuberculosis complex (14 cases), Mycobacterium leprae (3), Mycobacterium genavense (2), Mycobacterium marinum-ulcerans group (3) and 17 other AFB (61). Thirteen cases were AFB-stain indeterminate and 4 were positive by the PCR-Seq method. Of the AFB stain-negative cases, 167 were negative and 6 were positive by PCR-Seq.ConclusionsThe PCR-Seq method provided specific identification of various AFB species or complexes from FFPE tissues.

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Janecka-Widła, Anna, Agnieszka Adamczyk, Kaja Majchrzyk, Anna Cichocka, and Joanna Niemiec. "Qproteome FFPE Tissue Kit is not suitable for protein analysis using Agilent 2100 Bioanalyzer." Diagnostyka Laboratoryjna 54, no. 3 (September 20, 2018): 145–50. http://dx.doi.org/10.5604/01.3001.0013.7699.

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Introduction: The chip-based protein separation using Agilent 2100 Bioanalyzer is a promising tool for proteomic analysis. However, it has not been defined if the above-mentioned device is suitable for analysis of formalin-fixed paraffin-embedded (FFPE) proteins extracts.<br>The aim of the study: Therefore we performed the analysis aimed at testing if extracts from FFPE tissues are suitable for proteins detection using Agilent 2100 Bioanalyzer.<br>Material and methods: FFPE tissues and cell cultures were used for experiments. Proteins were extracted from them using Qproteome FFPE Tissue Kit and RIPA buffer, respectively. For protein analysis Bioanalyzer Instrument, Western Blot and immunohistochemistry (IHC) were applied.<br>Results: In FFPE extracts, using Bioanalyzer we failed to detect β-actin. However, Western Blot analysis proved β-actin presence in them. One of possible explanations of this phenomenon might be lack of antibody-antigen interaction during immunoprecipitation preceding Bioanalyzer analysis. We suspected that, Extraction Buffer (from Qproteome FFPE Tissue Kit) or β-mercaptoethanol (both present in FFPE protein extracts) might be responsible for the above-mentioned blockade. Therefore, we applied IHC with detection of CD34 because, CD34 staining is robust against small methodological variations and this marker is always present in tumor tissue sections. Anti-CD34 antibody was diluted in Tris saline buffer with Extraction Buffer, β-mercaptoethanol or without. We did not observe CD34 immunopositivity only in the presence of Extraction Buffer.<br>Conclusion: Qproteome FFPE Tissue Kit is not suitable for protein analysis using Agilent 2100 Bioanalyzer, because the Extraction Buffer from the kit prevents an interaction between antibody and antigen during immunoprecipitation procedure.

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Hafy, Zen, Veny Larasati, Riana Sari Puspita, Novizar S, Haekal M, Rafdi A, and Sentani R. "Hubungan Lama Penyimpanan Sampel Arsip Jaringan Dalam Blok Parafin Terfiksasi Formalindengan Kualitas Hasil Ekstraksidna Mitokondria Jaringan." SRIWIJAYA JOURNAL OF MEDICINE 1, no. 3 (October 31, 2018): 157–62. http://dx.doi.org/10.32539/sjm.v1i3.31.

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Formalin-fixed paraffin-embedded (FFPE) archival tissue presents a readily available resource in molecular study nowadays. The quality of nucleid acid, especially mitoconhdrial DNA (mtDNA) extracted from FFPE tissue could be affected by the storage time. Thus, this study investigated if the FFPE tissue’s storage time had an effect on the quality of the extracted mtDNA at Department of Pathology RSUP Dr. Mohammad Hoesin Palembang. DNA was extracted from 16 randomly selected archival FFPE tissues in Laboratory of Pathology Anatomy, RSUP dr. Mohammad Hoesin Palembang. The samples were grouped based on their storage time (less than 1 year and 1 to 5 yrs.’ old). The isolated DNA from each group was amplified using PCR with two primer pairs specifically designto amplify mtDNA of 320 bp and 142bp length, respectively. The PCR products were visualized by electrophoresismethod. None of the samples from both groups could be amplified witht the 320bp primers. However, the PCR result of the 149 bp primers showed positive for all of the samples from each study group. The study indicated that the storage time does not affect the quality of mtDNA isolated from the FFPE samples archived in Department of Pathology RSUP Dr. Mohammad Hoesin Palembang. Furthermore, the study showed that the mtDNA extracted from FFPE tissue has been degraded, therefore, the samples are not suitable for genetic studies require a long mtDNA amplicon.

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Dissertations / Theses on the topic "FFPE tissues"

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Potluri, Keerti. "Improving DNA quality using FFPE tissues for Array Comparative Genomic Hybridization to find Single Nucleotide Polymorphisms (SNPs) in Melanoma." Wright State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=wright1438267267.

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Zhivagui, Maria. "Genome-wide modeling of mutation spectra of human cancer-risk agents using experimental systems." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSE1278/document.

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Les génomes du cancer présentent une mosaïque de types de mutations. Trente signatures mutationnelles ont été identifiées à partir d'un grand nombre de tumeurs humaines primaires. Déchiffrer l'origine de ces signatures mutationnelles pourrait aider à identifier les causes du cancer humain. Environ 40% des signatures décrites sont d'origine inconnue, soulignant la nécessité de modèles expérimentaux contrôlés pour étudier l'origine de ces signatures. Au cours de mon travail de doctorat, j'ai caractérisé et utilisé des modèles in vitro et in vivo d'exposition aux cancérogènes, caractériser les signatures mutationnelles au niveau de génome entier de plusieurs composés cancérogènes pour lesquels le spectre de mutations n'était pas connu ou controversé. Tout d'abord, les conditions de cytotoxicités et genotoxicités pour chaque composé ont été établies et la formation d'adduits d'ADN a été évaluée. Suite au séquençage du gène TP53, on a effectué un séquençage au niveau du génome des clones MEF immortalisés dérivés de l'exposition à l'acrylamide, au glycidamide et à l'ochratoxine A. Le travail suggère une nouvelle signature mutationnelle unique pour l'acrylamide et médiée par son métabolite actif, le glycidamide. En fait, le motif des mutations de glycidamide, correspondant au profil de sa signature mutationnelle, a récapitulé les types de mutations attendus en fonction de l'analyse des adduits d'ADN. En outre, une analyse intégrée utilisant des modèles in vitro et in vivo suggère un manque de mutagénicité directe pour l'OTA avec une contribution potentielle d'un mode d'action lié à la production des radicaux libres à la signature mutationnelle OTA dans les MEF. Cette stratégie expérimentale simple et puissante peut faciliter l'interprétation des empreintes de mutations identifiées dans les tumeurs humaines, élucider l'étiologie du cancer et finalement soutenir la classification des cancers du CIRC en fournissant des preuves mécanistes
Cancer genomes harbour a mosaic of mutation patterns from which thirty mutational signatures have been identified, each attributable to a particular known or yet undetermined causal process. Deciphering the origins of these global mutational signatures in full could help identify the causes of human cancer, especially for about 40% of those signatures identified thus far that remain without a known etiological factor. Thus, well-controlled experimental exposure models can be used to assign particular mutational signatures to various mutagenic factors.During the time frame of my PhD work, I characterized and employed innovative in vitro and in vivo models of carcinogen exposure, namely, primary Hupki MEF cells, HepaRG and lymphoblastoid cell lines as well as rodent tumors. The cytotoxic and genotoxic conditions for each tested exposure compound were established and DNA adduct formation was assessed in select cases. Following a pre-screen by TP53 gene sequencing, genome-wide sequencing of immortalized Hupki MEF clones derived from exposure to acrylamide, glycidamide and ochratoxin A was performed, alongside whole genome sequencing of ochratoxin A induced rat renal tumors. The results reveal a novel mutational signature of acrylamide mediated by its active metabolite, glycidamide, a pattern that can be explained by the parallel analysis of individual glycidamide-DNA adducts. In addition, an integrative mutation analysis using in vitro and in vivo models suggests a lack of direct mutagenicity for OTA and possible indirect effects due to the ROS-mediated mode-of-action in MEF cells. The presented robust experimental strategy can facilitate the interpretation of mutation fingerprints identified in human tumors, thereby elucidating cancer etiology, elucidating the relationship between mutagenesis and carcinogenesis and ultimately providing mechanistic evidence for IARC’s carcinogen classification

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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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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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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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no
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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Smolina, Margarita. "Breast cancer cell lines grown in a three-dimensional culture model: a step towards tissue-like phenotypes as assessed by FTIR imaging." Doctoral thesis, Universite Libre de Bruxelles, 2018. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/267686.

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Despite the possible common histopathological features at diagnosis, cancer cells present within breast carcinomas are highly heterogeneous in their molecular signatures. This heterogeneity is responsible for disparate clinical behaviors, treatment responses and long-term outcomes in breast cancer patients. Although the few histopathological markers can partially describe the diversity of cells found in tumor tissue sections, the full molecular characterization of individual cancer cells is currently impossible in routine clinical practice. In this respect, Fourier transform infrared (FTIR) microspectroscopic imaging of histological sections allows obtaining, for each pixel of tissue images, hundreds of independent potential markers, which makes this technique a particularly powerful tool to distinguish cell types and subtypes. As a complement to the conventional clinicopathological evaluation, this spectroscopic approach has the potential to directly reveal molecular descriptors that should allow identifying different clonal lineages found within a single tumor and therefore provide knowledge relevant to diagnosis, prognosis and treatment personalization. Yet, interpretation of infrared (IR) spectra acquired on tissue sections requires a well-established calibration, which is currently missing. Conventionally, mammary epithelial cells are studied in vitro as adherent two-dimensional (2D) monolayers, which lead to the alteration of cell-microenvironmental interplay and consequently to the loss of tissue structure and function. A number of key in vivo-like interactions may be re-established with the use of three-dimensional (3D) laminin-rich extracellular matrix (lrECM)-based culture systems. The aim of this thesis is to investigate by FTIR imaging the influence of the in vitro growth environment (2D culture versus 3D lrECM culture and 3D monoculture versus 3D co-culture with fibroblasts) on a series of thirteen well-characterized human breast cancer cell lines and to determine culture conditions generating spectral phenotypes that are closer to the ones observed in malignant breast tissues. The reference cell lines cultured in a physiologically relevant basement membrane model and having undergone formalin fixation, paraffin embedding (FFPE), a routine treatment used to preserve clinical tissue specimens, could contribute to the construction of a spectral database. The latter could be ultimately employed as a valuable tool to interpret IR spectra of cells present in tumor tissue sections, particularly through the recognition of unique spectral markers.To achieve the goal, we developed and optimized, in a first step, the preparation of samples derived from traditional 2D and 3D lrECM cell cultures in order to preserve their morphological and molecular relevance for FTIR microspectroscopic analysis. We then highlighted the importance of the influence of the growth environment on the cellular phenotype by comparing spectra of 2D- and 3D-cultured breast cancer cell lines between them. A particular focus was placed to establish a correlation between FTIR spectral data and publicly available microarray-based gene expression patterns of the whole series of breast cancer cell lines grown in 2D and 3D lrECM cultures. Our results revealed that, although based on completely different principles, gene expression profiling and FTIR spectroscopy are similarly sensitive to both the cell line identity and the phenotypes induced by cell culture conditions. We also identified by FTIR imaging changes in the chemical content occurring in the microenvironment surrounding cell spheroids grown in 3D lrECM culture model. Finally, we illustrated the impact of the in vivo-like microenvironment on the IR spectra of breast cancer cell lines grown in 3D lrECM co-culture with fibroblasts and compared them with spectra of cell lines grown in 3D lrECM monoculture. Unsupervised statistical data analyses reported that cells grown in 3D co-cultures produce spectral phenotypes similar to the ones observed in FFPE tumor tissue sections from breast carcinoma patients. Altogether, our results suggest that FFPE samples prepared from 3D lrECM cultures of breast cancer cell lines and studied by FTIR microspectroscopic imaging provide reliable information that could be integrated in the setting up of a recognition model aiming to identify and interpret specific spectral signatures of cells present in breast tumor tissue sections.
Le cancer du sein est une maladie très hétérogène, tant au niveau clinique que biologique. Cette hétérogénéité rend impossible la caractérisation moléculaire complète des cellules cancéreuses individuelles dans la pratique clinique courante. Dans ce contexte, l’imagerie infrarouge à transformée de Fourier (FTIR) des coupes tissulaires permet d'obtenir pour chaque pixel d'une image de tissu des centaines de marqueurs potentiels indépendants, ce qui pourrait faire de cette technique un outil particulièrement puissant pour identifier des différents types et sous-types cellulaires. L'interprétation des spectres infrarouges (IR) enregistrés à partir des coupes histologiques nécessite cependant une calibration qui fait actuellement défaut. Cette calibration pourrait être obtenue à partir de lignées cellulaires tumorales bien caractérisées. Traditionnellement, les cellules épithéliales mammaires sont étudiées in vitro sous forme de monocouches adhérentes bidimensionnelles (2D), ce qui conduit à l'altération de la communication entre les cellules et leur environnement et, par conséquent, à la perte de l’architecture et de la fonction du tissu épithélial. Un certain nombre d'interactions physiologiques clés peuvent être rétablies en utilisant des systèmes de culture tridimensionnelle (3D) dans une matrice extracellulaire riche en laminine (lrECM). L'objectif de cette thèse consiste à étudier par imagerie FTIR l'influence du microenvironnement (via une comparaison entre les cultures 2D et 3D lrECM ou les cultures 3D lrECM en présence ou en l’absence de fibroblastes) sur une série de treize lignées de cellules tumorales mammaires humaines bien caractérisées et à déterminer les conditions de culture générant des phénotypes spectraux qui se rapprochent le plus de ceux observés dans les tissus tumoraux. Au cours de ce travail, nous avons mis au point la culture des lignées cellulaires dans un modèle 3D lrECM ainsi qu’une méthodologie de préparation des échantillons offrant la possibilité de les comparer de manière pertinente avec les cellules cancéreuses présentes dans les coupes histologiques. De même, nous avons étudié par imagerie FTIR les effets du microenvironnement sur les lignées de cellules tumorales et inversement. Pour les lignées investiguées, le passage d’une culture 2D à une culture 3D lrECM s’accompagne, en effet, de modifications du spectre IR étroitement corrélées aux modifications du transcriptome. Les marqueurs spectraux indiquent également que l’environnement 3D génère un phénotype cellulaire proche de celui trouvé dans les coupes histologiques. De manière intéressante, cette proximité est d’autant plus renforcée en présence de fibroblastes dans le milieu de culture.
Doctorat en Sciences agronomiques et ingénierie biologique
info:eu-repo/semantics/nonPublished

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Huang, Wei-Jyun, and 黃暐竣. "Differential expressions of genes related to stromal remodeling and epithelial-mesenchymal transformation of FFPE tissues from different human breast lesions." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/37136572207875536350.

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碩士
國立中興大學
動物科學系所
101
Formalin fixed paraffin embedded (FFPE) is commonly applied for long-term preservation of the morphology of biological samples, but the process of fixation has been demonstrated damaging the chemical structures of cellular components including nucleic acids. Recent studies have suggested a feasibility of RT-PCR in estimating gene expressions of FFPE tissues using PCR primers encoding amplicon size less than 100 bp. Matrix metalloproteinases (MMP) and tissue inhibitors of metalloproteinase (TIMP) synergistically control stromal remodeling and are up-regulated in various diseases. Epithelial-mesenchymal transition (EMT) has also been demonstrated accompanying the advancement of many diseases, including fibrosis and cancer. Transforming growth factor-β (TGF-β) induces EMT and stromal remodeling partially via p38 MAPK signal pathway. The purpose of this study was conducted using RT-PCR to estimate expressions of MMP, TIMP and EMT markers of different breast lesion FFPE tissues. Breast lesion FFPE tissues collected from 2009 to 2011 were supplied by National Taiwan University Hospital Hsin-Chu Branch which include 10 cases of each ductal carcinoma in situ (DCIS), invasive ductal carcinoma (IDC), fibroadenoma (Fa), fibrocystic disease (Fc), and mastitis (Ma) diagnosed by the Department of Pathology. Genes measured by RT-PCR comprise MMP-2, MMP-9, MMP-14, TIMP-2, p38 MAPK, TGF-β, E-cadherin, N-cadherin, vimentin, ZO-1 and β-catenin. Sequence and specificity of PCR products were confirmed before PCR primers were applied to every FFPE tissues. Total mRNA were extracted from FFPE tissues before conducting the optimized RT-PCR procedure. RT-PCR products were quantified for the specified size and standardised with GAPDH before statistical comparison among different lesions. Results showed that among malignant breast tumors, expressions of TIMP-2, vimentin and p38 MAPK were significantly higher in IDC than DCIS (P < 0.05), while TGF-β was significantly higher in DCIS than those of IDC (P < 0.05). Comparisons between malignant and benign breast tumors suggested that expressions of MMP-2, TIMP-2 and TGF-β were significantly higher in DCIS plus IDC than those of Fa (P < 0.05). Comparisons between breast tumors and non-tumor breast tissues showed that the expressions of MMP-2, MMP-9, MMP-14, TGF-β, p38 MAPK, β-catenin, vimentin, E-cadherin and ZO-1were significantly higher in DCIS plus IDC plus Fa than those of Fc plus Ma (P < 0.05). Comparisons between the two non-tumor breast tissues showed that the expressions of TIMP-2 and E-cadherin were significantly higher in Ma than those of Fc (P < 0.01), while the expression of ZO-1 was in reverse trend (P < 0.05). The current results were based on not sufficient sample sizes and some tissues were extremes. Further results of morphology examination and correlation analyses would be helpful for elucidating possible mechanisms underlain the differential gene expression. Conclusions drawn based the current results are, using non-tumor breast tissues as contrasts, it is likely that TGF-β might be an important trigger of the metastases of breast tumors into invasive and malignancy, probably via p38 MAPK pathways. Furthermore, vimentin is the best malignant breast tumor index among all studied mesenchymal cell markers, so as TIMP-2 comparing to MMP.

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"Highly Multiplexed Single Cell in situ Protein Analysis with Cleavable Fluorescent Probes." Doctoral diss., 2019. http://hdl.handle.net/2286/R.I.53605.

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abstract: Measurements of different molecular species from single cells have the potential to reveal cell-to-cell variations, which are precluded by population-based measurements. An increasing percentage of researches have been focused on proteins, for its central roles in biological processes. Immunofluorescence (IF) has been a well-established protein analysis platform. To gain comprehensive insights into cell biology and diagnostic pathology, a crucial direction would be to increase the multiplexity of current single cell protein analysis technologies. An azide-based chemical cleavable linker has been introduced to design and synthesis novel fluorescent probes. These probes allow cyclic immunofluorescence staining which leads to the feasibility of highly multiplexed single cell in situ protein profiling. These highly multiplexed imaging-based platforms have the potential to quantify more than 100 protein targets in cultured cells and more than 50 protein targets in single cells in tissues. This approach has been successfully applied in formalin-fixed paraffin-embedded (FFPE) brain tissues. Multiplexed protein expression level results reveal neuronal heterogeneity in the human hippocampus.
Dissertation/Thesis
Doctoral Dissertation Chemistry 2019

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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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Votavová, Hana. "Odlišení primárně mediastinálního a difuzního velkobuněčného B-lymfomu s využitím metody real-time kvantitativní polymerázové řetězové reakce." Doctoral thesis, 2011. http://www.nusl.cz/ntk/nusl-299441.

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Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma. It is a molecular and prognostic heterogeneous disease. Three main genetic subtypes are called germinal center-like DLBCL (GC-like DLBCL), non-germinal center-like DLBCL (nonGC-like DLBCL) and primary mediastinal B-cell lymphoma (PMBL). These subtypes can be reliably distinguished only with usage of gene expression profiling (GEP). The GEP method can be applied only when fresh frozen tissue is available. The method is technically difficult and expensive. Thus, it is not used routinely. Since the DLBCL subtypes differ in prognosis, it is extremely important to be able to distinguish them. The presented thesis is focused on distinguishing of PMBL diagnosis in the group of DLBCL. Easily stored formalin-fixed, paraffin-embedded tissue (FFPE) and gene expression analysis using real-time quantitative polymerase chain reaction (RTqPCR) are used. In the first step, PMBL and DLBCL cases were distinguished with an internationally accepted clinical-pathological method. The agreement between clinical-pathological diagnosis and GEP is only 76%. In the presented text a genetic algorithm for PMBL/DLBCL distinguishing is suggested. It uses three carefully chosen genes and their expression is measured with RTqPCR. Both, the...

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Book chapters on the topic "FFPE tissues"

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Glavač, Damjan, and Ermanno Nardon. "Microsatellite Instability (MSI) Detection in DNA from FFPE Tissues." In Guidelines for Molecular Analysis in Archive Tissues, 155–69. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-17890-0_28.

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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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Bosso, Mira, and Fahd Al-Mulla. "Whole Genome Amplification of DNA Extracted from FFPE Tissues." In Methods in Molecular Biology, 161–80. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-055-3_11.

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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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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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Dallol, Ashraf, Waleed Al-Ali, Amina Al-Shaibani, and Fahd Al-Mulla. "Analysis of DNA Methylation in FFPE Tissues Using the MethyLight Technology." In Methods in Molecular Biology, 191–204. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-055-3_13.

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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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With, Catherine M., David L. Evers, and Jeffrey T. Mason. "Regulatory and Ethical Issues on the Utilization of FFPE Tissues in Research." In Methods in Molecular Biology, 1–21. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-055-3_1.

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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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Nardon, Ermanno. "Quantitative Methylation Status Assessment in DNA from FFPE Tissues with Bisulfite Modification and Real-Time Quantitative MSP." In Guidelines for Molecular Analysis in Archive Tissues, 193–200. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-17890-0_31.

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Conference papers on the topic "FFPE tissues"

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Consugar, Mark, Leonardo Arbiza, Kristin Butcher, Siyuan Chen, Hutson Chilton, Richard Gantt, Yehudit Hasin-Brumshtein, et al. "Abstract 3544: High performance multiplexed targeted enrichment sequencing from FFPE 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.am2019-3544.

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Consugar, Mark, Leonardo Arbiza, Kristin Butcher, Siyuan Chen, Hutson Chilton, Richard Gantt, Yehudit Hasin-Brumshtein, et al. "Abstract 3544: High performance multiplexed targeted enrichment sequencing from FFPE 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.sabcs18-3544.

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Huw, Ling-Yuh, Rajesh Patel, Carol O'Brien, Ling Fu, Rajiv Raja, Lukas Amler, Garret Hampton, and Mark Lackner. "Abstract 3505: Development of robust copy number assays for tumor FFPE tissues." 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.am2013-3505.

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Burr, Tom, Rick Dixon, Andy Green, Ian Ellis, and Cliff Murray. "Abstract 2953: Evaluating gene expression in FFPE breast cancer tissues using DASL®." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-2953.

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Mistry, Sejal, Gajalakshmi Dakshinamoorthy, Jessica Yuan, Pieter Noordam, Joseph Kim, Won-Mean Lee, and Julia Kennedy-Darling. "Abstract 387: Analysis of FFPE human tumor tissues using CODEX with signal amplification." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-387.

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Nikulina, Nadezhda, Oliver Braubach, Sayantani Basak, Maria Elena Gallina, Won-Mean Lee, Joseph Kim, Cassandra Hempel, et al. "Abstract 1654: Highly multiplexed analysis of FFPE breast tissues using the codex technology." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-1654.

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Font-Tello, Alba, Nikolas Kesten, Yingtian Xie, Len Taing, Joaquim Bellmunt, Myles Brown, Paloma Cejas, and Henry Long. "Abstract 3662: FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-3662.

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Schuster, Claudia, Falk Hlubek, Katharina Malinowsky, Sibylle Liebmann, Daniela Berg, Claudia Wolff, Simone Reu, et al. "Abstract 4875: Combining immunohistochemistry and proteomics for improved antibody validation in complex FFPE tissues." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-4875.

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Filges, Stefan, Daniel Andersson, Helena Kristiansson, Christoffer Vannas, Gustav Johansson, Junrui Li, Tony E. Godfrey, Max Levin, Barbro Linderholm, and Anders Ståhlberg. "Abstract A23: Ultrasensitive mutation detection in FFPE tissues and circulating tumor DNA using SiMSen-Seq." In Abstracts: AACR Special Conference on Advances in Liquid Biopsies; January 13-16, 2020; Miami, FL. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1557-3265.liqbiop20-a23.

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Zheng, Yi, Pallavi Thuse, Linying Liu, Edward C. Stack, Michael Campisano, Kent Johnson, Darryn Unfricht, Nara Narayanan, Clifford Hoyt, and Milind Rajopadhye. "Abstract 2238: Understanding immune phenotypes and their spatial relationships to breast adenocarcinoma in 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.am2016-2238.

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