miRNA Profiling of Hungarian Regressive Wilms’ Tumor Formalin-Fixed Paraffin-Embedded (FFPE) Samples by Quantitative Real-Time Polymerase Chain Reaction (RT-PCR)

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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Detection of Corynebacterium kroppenstedtii in Granulomatous Lobular Mastitis Using Real-Time Polymerase Chain Reaction and Sanger Sequencing on Formalin-Fixed, Paraffin-Embedded Tissues

Archives of Pathology & Laboratory Medicine ◽

10.5858/arpa.2021-0061-oa ◽

2021 ◽

Author(s):

Hamza Tariq ◽

Preethi D. Menon ◽

Hongxin Fan ◽

Kumari V. Vadlamudi ◽

Sri Lakshmi Pandeswara ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Real Time ◽

Sanger Sequencing ◽

Breast Abscess ◽

Chain Reaction ◽

Radiographic Findings ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

Polymerase Chain ◽

Formalin Fixed

Context.— Associations between granulomatous lobular mastitis (GLM) and Corynebacterium kroppenstedtii have been reported since 2002, but large scale studies to assess the actual prevalence of this bacterium in GLM have not been performed. Objective.— To assess the prevalence of C kroppenstedtii in GLM using real-time polymerase chain reaction and Sanger sequencing. Design.— We analyzed formalin-fixed, paraffin-embedded tissues from 67 cases of GLM by sequential DNA amplification and sequencing to assess the rate of C kroppenstedtii detection in GLM. A retrospective analysis including patient demographics, history of pregnancy and lactation, clinical signs and symptoms, radiographic findings, histologic pattern, Gram stain results, and microbial cultures was performed on 67 cases of GLM. In addition, 10 cases of nongranulomatous breast abscess were included as controls. Results.— C kroppenstedtii 16S rRNA SYBR real-time polymerase chain reaction was positive on formalin-fixed, paraffin-embedded tissues from 46 of 67 (68.7%) GLM cases, while all control cases were negative. Among the positive cases, the majority showed features of cystic neutrophilic granulomatous mastitis. Conclusions.— C kroppenstedtii was highly prevalent in GLM cases and was not found to be associated with nongranulomatous breast abscess in our study (P < .001).

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Laboratory-Developed L1 Sequencing and Type-Specific, Real-Time Polymerase Chain Reaction for the Detection and Typing of Human Papillomaviruses in Formalin-Fixed, Paraffin-Embedded Tissues

Archives of Pathology & Laboratory Medicine ◽

10.5858/arpa.2011-0392-oa ◽

2013 ◽

Vol 137 (1) ◽

pp. 50-54 ◽

Cited By ~ 6

Author(s):

Anne Mills ◽

Rajeev Balasubramaniam ◽

Teri A. Longacre ◽

Christina S. Kong ◽

Benjamin A. Pinsky

Keyword(s):

Polymerase Chain Reaction ◽

High Risk ◽

Real Time ◽

Clinical Laboratory ◽

Low Risk ◽

Chain Reaction ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

Polymerase Chain ◽

Formalin Fixed

Context.—The detection and typing of high-risk and low-risk human papillomavirus (HPV) in archival formalin-fixed, paraffin-embedded tissues by nucleic acid amplification testing is an important adjunct to immunohistochemical staining in evaluation of squamous cell proliferations of the oropharynx, larynx, and anal canal. Objective.—To evaluate semiautomated, xylene-free extraction from formalin-fixed, paraffin-embedded tissues combined with laboratory-developed HPV L1 sequencing and type-specific HPV 6, 11, 16, and 18 real-time polymerase chain reaction for identification and typing of HPV in the clinical laboratory. Design.—We evaluated the adequacy of extraction using β-globin amplification and compared L1 sequencing and real-time polymerase chain reaction methods for typing accuracy using 68 formalin-fixed, paraffin-embedded tissues, including 56 anorectal biopsy or surgical resection specimens and 12 laryngeal papilloma specimens from patients with recurrent respiratory papillomatosis. Results.—Adequate DNA was obtained from 68 of 68 specimens analyzed and all were HPV positive. In 47 cases where L1 sequencing demonstrated that the predominant HPV type was 6, 11, 16, or 18, type-specific, real-time polymerase chain reaction provided concordant results. Sequencing revealed additional low-risk (HPV 40) and high-risk HPV types (HPV 31, 33, 56, and 58) in anorectal specimens, whereas HPV 6 or 11 were the types found in laryngeal papillomas. Conclusion.—Both L1 sequencing and type-specific, real-time polymerase chain reaction are suitable methods for routine HPV testing of formalin-fixed, paraffin-embedded tissues in a clinical laboratory setting.

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