Browsing by Author "Sen, Joyashree D."

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    qPCR is a sensitive and rapid method for detection of cytomegaloviral DNA in formalin-fixed, paraffin-embedded biopsy tissue
    (MyJoVE Corporation, 2014-07-09) McCoy, Morgan H.; Post, Kristin; Sen, Joyashree D.; Chang, Hsim Y.; Zhao, Zijin; Fan, Rong; Chen, Shaoxiong; Leland, Diane; Cheng, Liang; Lin, Jingmei; Department of Pathology and Laboratory Medicine, IU School of Medicine
    It is crucial to identify cytomegalovirus (CMV) infection in the gastrointestinal (GI) tract of immunosuppressed patients, given their greater risk for developing severe infection. Many laboratory methods for the detection of CMV infection have been developed, including serology, viral culture, and molecular methods. Often, these methods reflect systemic involvement with CMV and do not specifically identify local tissue involvement. Therefore, detection of CMV infection in the GI tract is frequently done by traditional histology of biopsy tissue. Hematoxylin and eosin (H&E) staining in conjunction with immunohistochemistry (IHC) have remained the mainstays of examining these biopsies. H&E and IHC sometimes result in atypical (equivocal) staining patterns, making interpretation difficult. It was shown that quantitative polymerase chain reaction (qPCR) for CMV can successfully be performed on formalin-fixed, paraffin-embedded (FFPE) biopsy tissue for very high sensitivity and specificity. The goal of this protocol is to demonstrate how to perform qPCR testing for the detection of CMV in FFPE biopsy tissue in a clinical laboratory setting. This method is likely to be of great benefit for patients in cases of equivocal staining for CMV in GI biopsies.
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    Utilization of Cell-Transfer Technique for Molecular Testing on H&E-stained Sections- A Viable Option for Small Biopsies that Lack Tumor Tissues in Paraffin Block
    (2016-12) Wu, Howard H.; Jovonovich, Stephen M.; Randolph, Melissa; Post, Kristin M.; Sen, Joyashree D.; Curless, Kendra; Cheng, Liang; Department of Pathology and Laboratory Medicine, School of Medicine
    Context.— In some instances the standard method of doing molecular testing from formalin-fixed, paraffin-embedded block is not possible because of limited tissue. Tumor cell–enriched cell-transfer technique has been proven useful for performing immunocytochemistry and molecular testing on cytologic smears. Objective.— To establish the cell-transfer technique as a viable option for isolating tumor cells from hematoxylin-eosin (H&E)–stained slides. Design.— Molecular testing was performed by using the cell-transfer technique on 97 archived H&E-stained slides from a variety of different tumors. Results were compared to the conventional method of molecular testing. Results.— Polymerase chain reaction–based molecular testing via the cell-transfer technique was successfully performed on 82 of 97 samples (85%). This included 39 of 47 cases for EGFR, 10 of 11 cases for BRAF, and 33 of 39 cases for KRAS mutations. Eighty-one of 82 cell-transfer technique samples (99%) showed agreement with previous standard method results, including 4 mutations and 35 wild-type alleles for EGFR, 4 mutations and 6 wild-type alleles for BRAF, and 11 mutations and 21 wild-type alleles for KRAS. There was only 1 discrepancy: a cell-transfer technique with a false-negative >KRAS result (wild type versus G12C). Conclusions.— Molecular testing performed on H&E-stained sections via cell-transfer technique is useful when tissue from cell blocks and small surgical biopsy samples is exhausted and the only available material for testing is on H&E-stained slides.