scholarly journals Detection of cytogenomic abnormalities by OncoScan microarray assay for products of conception from formalin-fixed paraffin-embedded and fresh fetal tissues

2021 ◽  
Author(s):  
Jiadi Wen ◽  
Brittany Grommisch ◽  
Autumn DiAdamo ◽  
Hongyan Chai ◽  
Sok Meng Evelyn Ng ◽  
...  
Keyword(s):  
Diagnostic Yield ◽  
False Negative ◽  
Microarray Assay ◽  
Fragmented Dna ◽  
Formalin Fixed Paraffin ◽  
Products Of Conception ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Molecular Inversion Probes ◽  
Formalin Fixed

Abstract Background The OncoScan microarray assay (OMA) using highly multiplexed molecular inversion probes for single nucleotide polymorphism (SNP) loci enabled the detection of cytogenomic abnormalities of chromosomal imbalances and pathogenic copy number variants (pCNV). The small size of molecular inversion probes is optimal for SNP genotyping of fragmented DNA from fixed tissues. This retrospective study evaluated the clinical utility of OMA as a uniform platform to detect cytogenomic abnormalities for pregnancy loss from fresh and fixed tissues of products of conception (POC). Results Fresh specimens of POC were routinely subjected to cell culture and then analyzed by karyotyping. POC specimens with a normal karyotype (NK) or culture failure (CF) and from formalin-fixed paraffin-embedded (FFPE) tissues were subjected to DNA extraction for OMA. The abnormality detection rate (ADR) by OMA on 94 cases of POC-NK, 38 cases of POC-CF, and 35 cases of POC-FFPE tissues were 2% (2/94), 26% (10/38), and 57% (20/35), respectively. The detected cytogenomic abnormalities of aneuploidies, triploidies and pCNV accounted for 50%, 40% and 10% in POC-CF and 85%, 10% and 5% in POC-FFPE, respectively. False negative result from cultured maternal cells and maternal cell contamination (MCC) were each detected in one case. OMA on two cases with unbalanced structural chromosome abnormalities further defined genomic imbalances and breakpoints. Conclusion OMA on POC-CF and POC-FFPE showed a high diagnostic yield of cytogenomic abnormalities. This approach circumvented the obstacles of CF from fresh specimens and fragmented DNA from fixed tissues and provided a reliable and effective platform for detecting cytogenomic abnormalities and monitoring true fetal result from MCC.

scholarly journals Detection of cytogenomic abnormalities by OncoScan microarray assay for products of conception from formalin-fixed paraffin-embedded and fresh fetal tissues

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jiadi Wen ◽  
Brittany Grommisch ◽  
Autumn DiAdamo ◽  
Hongyan Chai ◽  
Sok Meng Evelyn Ng ◽  
...  
Keyword(s):  
False Negative ◽  
Microarray Assay ◽  
Maternal Cell ◽  
Fragmented Dna ◽  
Formalin Fixed Paraffin ◽  
Products Of Conception ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Molecular Inversion Probes ◽  
Formalin Fixed

Abstract Background The OncoScan microarray assay (OMA) using highly multiplexed molecular inversion probes for single nucleotide polymorphism (SNP) loci enabled the detection of cytogenomic abnormalities of chromosomal imbalances and pathogenic copy number variants (pCNV). The small size of molecular inversion probes is optimal for SNP genotyping of fragmented DNA from fixed tissues. This retrospective study evaluated the clinical utility of OMA as a uniform platform to detect cytogenomic abnormalities for pregnancy loss from fresh and fixed tissues of products of conception (POC). Results Fresh specimens of POC were routinely subjected to cell culture and then analyzed by karyotyping. POC specimens with a normal karyotype (NK) or culture failure (CF) and from formalin-fixed paraffin-embedded (FFPE) tissues were subjected to DNA extraction for OMA. The abnormality detection rate (ADR) by OMA on 94 cases of POC-NK, 38 cases of POC-CF, and 35 cases of POC-FFPE tissues were 2% (2/94), 26% (10/38), and 57% (20/35), respectively. The detected cytogenomic abnormalities of aneuploidies, triploidies and pCNV accounted for 50%, 40% and 10% in POC-CF and 85%, 10% and 5% in POC-FFPE, respectively. False negative result from cultured maternal cells and maternal cell contamination were each detected in one case. OMA on two cases with unbalanced structural chromosome abnormalities further defined genomic imbalances and breakpoints. Conclusion OMA on POC-CF and POC-FFPE showed a high diagnostic yield of cytogenomic abnormalities. This approach circumvented the obstacles of CF from fresh specimens and fragmented DNA from fixed tissues and provided a reliable and effective platform for detecting cytogenomic abnormalities and monitoring true fetal result from maternal cell contamination.

scholarly journals Characterization of epididymal and testicular histologic lesions and use of immunohistochemistry and PCR on formalin-fixed tissues to detect Brucella canis in male dogs

2021 ◽  
pp. 104063872098688
Author(s):  
Andrea M. Camargo-Castañeda ◽  
Lauren W. Stranahan ◽  
John F. Edwards ◽  
Daniel G. Garcia-Gonzalez ◽  
Leonardo Roa ◽  
...  
Keyword(s):  
Accurate Diagnosis ◽  
Testicular Atrophy ◽  
Detection Techniques ◽  
Formalin Fixed Paraffin ◽  
Brucella Canis ◽  
Formalin Fixed Paraffin Embedded ◽  
Variable Sensitivity ◽  
Ffpe Tissues ◽  
Formalin Fixed

In male dogs, Brucella canis frequently causes epididymitis, ultimately resulting in testicular atrophy and infertility. Although B. canis predominantly affects the epididymis, the misleading term “orchitis” is still commonly used by clinicians. Of additional concern, diagnosis in dogs remains challenging because of variable sensitivity and specificity of serologic assays and fluctuations in bacteremia levels in infected dogs, reducing the sensitivity of blood culture. We describe here the histologic lesions in the scrotal contents of 8 dogs suspected of being infected with B. canis and clinically diagnosed with orchitis. We explored the possibility of using immunohistochemistry (IHC) and real-time PCR (rtPCR) in formalin-fixed, paraffin-embedded (FFPE) tissues to detect the presence of B. canis. Epididymitis of variable chronicity was identified in all 8 dogs, with only 3 also exhibiting orchitis. Using rtPCR, the presence of B. canis was identified in 4 of 8 dogs, with 3 of these 4 dogs also positive by IHC. These results suggest that rtPCR and IHC are promising techniques that can be used in FFPE tissues to detect B. canis when other detection techniques are unavailable. Additionally, accurate recognition of epididymitis rather than orchitis in suspect cases could aid in accurate diagnosis.

Sarcoma Subgrouping by Detection of Fusion Transcripts Using NanoString nCounter Technology

2018 ◽  
Vol 22 (3) ◽  
pp. 205-213 ◽  
Author(s):  
Javal Sheth ◽  
Anthony Arnoldo ◽  
Yunan Zhong ◽  
Paula Marrano ◽  
Carlos Pereira ◽  
...  
Keyword(s):  
Rt Pcr ◽  
Fusion Transcripts ◽  
Pediatric Sarcoma ◽  
Formalin Fixed Paraffin ◽  
Pediatric Sarcomas ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Nanostring Technology ◽  
Future Work ◽  
Formalin Fixed

Background NanoString technology is an innovative barcode-based system that requires less tissue than traditional techniques and can test for multiple fusion transcripts in a single reaction. The objective of this study was to determine the utility of NanoString technology in the detection of sarcoma-specific fusion transcripts in pediatric sarcomas. Design Probe pairs for the most common pediatric sarcoma fusion transcripts were designed for the assay. The NanoString assay was used to test 22 specific fusion transcripts in 45 sarcoma samples that had exhibited one of these fusion genes previously by reverse transcription polymerase chain reaction (RT-PCR). A mixture of frozen (n = 18), formalin-fixed, paraffin-embedded (FFPE) tissue (n = 23), and rapid extract template (n = 4) were used for testing. Results Each of the 22 transcripts tested was detected in at least one of the 45 tumor samples. The results of the NanoString assay were 100% concordant with the previous RT-PCR results for the tumor samples, and the technique was successful using both FFPE and rapid extract method. Conclusion Multiplexed interrogation for sarcoma-specific fusion transcripts using NanoString technology is a reliable approach for molecular diagnosis of pediatric sarcomas and works well with FFPE tissues. Future work will involve validating additional sarcoma fusion transcripts as well as determining the optimal workflow for diagnostic purposes.

scholarly journals Molecular Markers for Prostate Cancer in Formalin-Fixed Paraffin-Embedded Tissues

2013 ◽  
Vol 2013 ◽  
pp. 1-15 ◽  
Author(s):  
Tamara Sequeiros ◽  
Marta García ◽  
Melania Montes ◽  
Mireia Oliván ◽  
Marina Rigau ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Molecular Markers ◽  
Tumor Grade ◽  
Developed Countries ◽  
Response To Therapy ◽  
Tissue Samples ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Formalin Fixed

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.

scholarly journals Clostridium perfringens–Associated Necrotic Enteritis-Like Disease in Coconut Lorikeets (Trichoglossus haematodus)

2020 ◽  
pp. 030098582097178
Author(s):  
Llorenç Grau-Roma ◽  
Mauricio Navarro ◽  
Sohvi Blatter ◽  
Christian Wenker ◽  
Sonja Kittl ◽  
...  
Keyword(s):  
Clostridium Perfringens ◽  
Toxin Gene ◽  
Necrotic Enteritis ◽  
Gene Encoding ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Polymerase Chain ◽  
Beta Toxin ◽  
Formalin Fixed

Several outbreaks of necrotic enteritis-like disease in lorikeets, from which Clostridium perfringens was consistently isolated, are described. All lorikeets had acute, segmental, or multifocal fibrinonecrotizing inflammatory lesions in the small and/or the large intestine, with intralesional gram-positive rods. The gene encoding C. perfringens alpha toxin was detected by PCR (polymerase chain reaction) on formalin-fixed, paraffin-embedded (FFPE) tissues in 20 out of 24 affected lorikeets (83%), but it was not amplified from samples of any of 10 control lorikeets ( P < .0001). The second most prevalent C. perfringens toxin gene detected was the beta toxin gene, which was found in FFPE from 7 out of 24 affected lorikeets (29%). The other toxin genes were detected inconsistently and in a relatively low number of samples. These cases seem to be associated with C. perfringens, although the specific type involved could not be determined.

scholarly journals Molecular identification of Coccidioides immitis in formalin-fixed, paraffin-embedded (FFPE) tissues from a Colombian patient

2015 ◽  
Vol 53 (5) ◽  
pp. 520-527 ◽  
Author(s):  
Cristina E. Canteros ◽  
Alejandro Vélez H. ◽  
Adriana I. Toranzo ◽  
Roberto Suárez-Alvarez ◽  
Ángela Tobón O. ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Coccidioides Immitis ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Formalin Fixed

Accurate Classification of Diffuse Large B Cell Lymphoma Into Germinal Center and Activated B Cell Subtypes Using a Nuclease Protection Assay On Formalin Fixed Paraffin Embedded Tissue: A Study From the Lymphoma and Leukemia Molecular Profiling Project.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 620-620
Author(s):  
Lisa M. Rimsza ◽  
George Wright ◽  
Mark Schwartz ◽  
Wing C. Chan ◽  
Elaine S Jaffe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Clinical Trial ◽  
B Cell ◽  
High Throughput ◽  
Germinal Center ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Formalin Fixed

Abstract Abstract 620 Classification of DLBCL into cell-of-origin (COO) subtypes based on gene expression profiles has well-established prognostic value. These subtypes, termed Germinal Center B cell (GCB) and Activated B cell (ABC) also have different genetic alterations and over-expression of different pathways that may serve as therapeutic targets. Thus, accurate classification is essential for analysis of clinical trial results and planning new trials using targeted agents. The gold standard for COO classification uses gene expression profiling (GEP) of snap frozen tissues, and a Bayesian predictor algorithm utilizing the expression levels of 14 key genes (G. Wright et al PNAS 2003). An immunohistochemistry (IHC) classification scheme by C. Hans et al (Blood 2004), based on 3 antibodies, is widely used as a substitute for GEP classification, however does not completely correlate with GEP. We recently described a qNPA assay (ArrayPlateR, High ThroughPut Genomics, Tucson, AZ) with excellent correlation between frozen and formalin fixed paraffin embedded (FFPE) tissues (R. Roberts et al, Lab Invest 2007). In this study, we investigated whether this technique could be used for accurate classification of COO using FFPE tissues. We expanded the previous gene probe repertoire of the DLBCL-ArrayPlateR assay to include the 14 genes (represented by 17 probe sets) most pertinent to COO classification. 52 cases of R-CHOP treated DLBCL that had undergone GEP using the Affymetrix U133 Plus 2.0 microarray and had matching FFPE blocks were analyzed with qNPA in duplicate. The genes included CD10, LRMP, CCND2, ITPKB, PIM1, IL16, IRF4, FUT8, BCL6, PTPN1, LM02, CD39, MYBL1, IGHM. Results were evaluated using the previously published algorithm with a leave-one-out cross validation scheme to classify cases into GCB or ABC subtypes. These results were compared to COO classification based on frozen tissue GEP profiles. All 14 genes in all 52 cases were successfully analyzed with no missing data points. For each case, a probability statistic was generated indicating the likelihood that the classification using qNPA was accurate. Of the 54 cases, 25 were GCB, 27 were ABC and 4 were unclassifiable by GEP. Of the GCB cases, 23/25 (92%) were classified correctly by qNPA with a confidence cut-off of >0.9 and 25/25 (100%) classified correctly with a confidence cut-off of >0.8. Of the ABC cases, 25/27 (93%) were correctly classified as ABC using qNPA with a confidence cut-off of >0.9 and 27/27 (100%) classified correctly with a confidence cut-off of >0.8. In summary, the qNPA technique accurately categorized DLBCL into GCB and ABC subtypes, as defined by GEP. There were no technical difficulties with any of the pathological materials although they were collected retrospectively from a variety of institutions and countries with different fixation methods. This approach represents a substantial improvement over previously published IHC methods and is applicable to FFPE tissues, therefore overcoming the need for snap frozen materials. This technically robust classification method has potential to have a significant impact on future DLBCL research and clinical trial development. Disclosures: Rimsza: High Throughput Genomics: HTG provided the assays at no charge to Dr. Rimsza's lab. Schwartz:High Throughput Genomics: Employment. Gascoyne:Roche Canada: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding.

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