scholarly journals Genomic aberrations in myeloid sarcoma without blood or bone marrow involvement: Characterization of formalin-fixed paraffin-embedded samples by chromosomal microarrays

2014 ◽  
Vol 38 (9) ◽  
pp. 1091-1096 ◽  
Author(s):  
M. Kamran Mirza ◽  
Madina Sukhanova ◽  
Friedrich Stölzel ◽  
Kenan Onel ◽  
Richard A. Larson ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Bone Marrow Involvement ◽  
Myeloid Sarcoma ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Genomic Aberrations ◽  
Formalin Fixed ◽  
Chromosomal Microarrays

scholarly journals BRAFV600E-Positive Precursors As Molecular Markers of Bone Marrow Involvement in Pediatric Langerhans Cell Histiocytosis

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 3588-3588
Author(s):  
Ko Kudo ◽  
Rika Kanezaki ◽  
Akie Kobayashi ◽  
Tomohiko Sato ◽  
Takuya Kamio ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Somatic Mutations ◽  
Bone Marrow Involvement ◽  
Braf V600e ◽  
Sensitive Assay ◽  
System Disease ◽  
Multiple Organs ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

Introduction: The BRAF mutation V600E, the most common somatic mutation in Langerhans cell histiocytosis (LCH), has been reported in approximately 50% of LCH patients and is associated with certain high-risk clinical features. Precursors harboring this mutation can differentiate into Langerhans cells resulting in infiltrates in multiple organs under inflammatory conditions. However, BRAF status in the bone marrow of pediatric LCH patients is unclear. The present study examined somatic mutations in paired tumor and bone marrow samples, using a highly sensitive assay involving next-generation targeted sequencing and droplet digital polymerase chain reaction (PCR) for pediatric LCH patients. Methods: Between 1996 and 2019, in total of 17 Japanese pediatric patients with LCH were enrolled. The male/female ratio was 7/11. Ages of onset of LCH were median 13 months (range 5-193 months). At diagnosis of LCH, 2 patients were positive for risk organ involvement, 15 were negative. We retrospectively performed mutational analyses of 17 LCH cases using formalin-fixed paraffin-embedded LCH tumor specimens to provide templates for PCR-based targeted amplicon sequencing with customized primers to detect mutations in exons 12 and 15 in BRAF, and exons 2 and 3 in MAP2K1. Thereafter, we identified somatic mutations in the 17 paired bone marrow samples via droplet digital allele-specific PCR, targeting BRAF V600E and BRAF exon 12 in-frame deletion 496-500 (Ex12 in-del). Results: We detected BRAF V600E in 11 of 17 tumor samples (65%) and the BRAF Ex 12 in-del in 3 of 17 tumors (18%). We identified BRAF V600E in bone marrow samples in 10 of the 11 cases (90%) with the mutation in the tumor at low variant allele frequency (median 0.25%, range 0.14-7.0%). BRAF Ex 12 in-del was not detected in the bone marrow. Cases with detectable bone marrow involvement included eight patients with multi-system disease affecting multiple organs, one patient with multi-focal bone disease, and one patient with single-system disease. Clinical phenotypes including relapse did not correlate with BRAF V600E upon detection in the bone marrow. Conclusion: We established the sensitive assay based on PCR-based targeted NGS for detecting somatic mutations in LCH even accessible for formalin-fixed, paraffin-embedded clinical specimens. Bone marrow involvement is frequently detectable at the molecular level in pediatric LCH with the BRAF V600E mutation. A prospective study is warranted to evaluate the clinical impact of mutational burden in bone marrow. Disclosures Kudo: Unum Therapeutics: Patents & Royalties. Imai:Juno Therapeutics: Patents & Royalties.

Clinical Utility of the Detection of Genomic Aberrations in Formalin-Fixed Paraffin-Embedded Myeloid Sarcoma Samples

2013 ◽  
Vol 206 (5) ◽  
pp. 214-215
Author(s):  
Madina Sukhanova ◽  
Kamran M. Mirza ◽  
Zejuan Li ◽  
Friedrich Stolzel ◽  
Kenan Onel ◽  
...  
Keyword(s):  
Clinical Utility ◽  
Myeloid Sarcoma ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Genomic Aberrations ◽  
Formalin Fixed

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.

scholarly journals PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results

2020 ◽  
pp. mcp.TIR120.002216
Author(s):  
Daniel J. Geiszler ◽  
Andy T. Kong ◽  
Dmitry M Avtonomov ◽  
Fengchao Yu ◽  
Felipe da Veiga Leprevost ◽  
...  
Keyword(s):  
Shotgun Proteomics ◽  
Chemical Modifications ◽  
Bioinformatics Tool ◽  
Site Specific ◽  
Search Results ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Small Set ◽  
Formalin Fixed

Open searching has proven to be an effective strategy for identifying both known and unknown modifications in shotgun proteomics experiments. Rather than being limited to a small set of user-specified modifications, open searches identify peptides with any mass shift that may correspond to a single modification or a combination of several modifications. Here we present PTM-Shepherd, a bioinformatics tool that automates characterization of PTM profiles detected in open searches based on attributes such as amino acid localization, fragmentation spectra similarity, retention time shifts, and relative modification rates. PTM-Shepherd can also perform multi-experiment comparisons for studying changes in modification profiles, e.g. in data generated in different laboratories or under different conditions. We demonstrate how PTM-Shepherd improves the analysis of data from formalin-fixed paraffin-embedded samples, detects extreme underalkylation of cysteine in some datasets, discovers an artefactual modification introduced during peptide synthesis, and uncovers site-specific biases in sample preparation artifacts in a multi-center proteomics profiling study.

Enumeration and Immunologic Characterization of Basophils in Normal Bone Marrow and Patients with Myeloproliferative Disorders.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4754-4754
Author(s):  
Hermine Agis ◽  
Maria T. Krauth ◽  
Leonhard Muellauer ◽  
Lawrence B. Schwartz ◽  
Hans P. Horny ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Chronic Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Histidine Decarboxylase ◽  
Chronic Phase ◽  
Myeloproliferative Disorders ◽  
Staining Procedure ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded

Abstract Basophils are highly specialized granulocytes that express a unique profile of antigens and increase in myeloproliferative disorders. In chronic myeloid leukemia (CML), basophilia is an independent prognostic variable. So far, however, no reliable immunohistochemical approach for routine-detection and enumeration of bone marrow (bm) basophils has become available. To overcome this disadvantage, we have applied the anti-basophil antibody 2D7 on formalin-fixed, paraffin-embedded sections of normal bm and bm from patients (pts) with chronic myeloid leukemia (CML; chronic phase, n=21; accelerated phase, n=9), other myeloproliferative disorders (idiopathic myelofibrosis [IMF], n=3; polycythemia vera [PV], n=7; essential thrombocythemia [ET], n=7), and normal / reactive bm (n=32). As assessed by serial section-staining of bm specimens, the 2D7 antibody was found to be a basophil-specific immunohistochemical reagent. In serial bm sections, 2D7+ basophils co-expressed histidine decarboxylase, CD15, and CD43, but did not express B- or T-cell restricted antigens corresponding to the phenotype of normal blood basophils. Bm basophils were found to increase in number in pts with CML and other myeloproliferative disorders compared to normal bm (median 2D7+ cells/mm2 bm: normal bm: 7; CML: 46; IMF: 26; PV: 21; ET: 21, p<.05). The highest numbers of bm basophils were recorded in pts with accelerated phase CML (111 2D7+ cells/mm2). Together, we have established a useful immunohistochemical staining procedure for basophil detection in normal bm and pts with myeloid neoplasms. This approach should enable the quantification of basophils in these pts and the monitoring of bm basophil counts during follow up examinations and anti-leukemic therapies.

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