Dataset Information

Overcoming the Challenges of High Quality RNA Extraction from Core Needle Biopsy.

ABSTRACT: The use of gene expression profiling (GEP) in cancer management is rising, as GEP can be used for disease classification and diagnosis, tailoring treatment to underlying genetic determinants of pharmacological response, monitoring of therapy response, and prognosis. However, the reliability of GEP heavily depends on the input of RNA in sufficient quantity and quality. This highlights the need for standard procedures to ensure best practices for RNA extraction from often small tumor biopsies with variable tissue handling. We optimized an RNA extraction protocol from fresh-frozen (FF) core needle biopsies (CNB) from breast cancer patients and from formalin-fixed paraffin-embedded (FFPE) tissue when FF CNB did not yield sufficient RNA. Methods to avoid ribonucleases andto homogenize or to deparaffinize tissues and the impact of tissue composition on RNA extraction were studied. Additionally, RNA's compatibility with the nanoString nCounter® technology was studied. This technology platform enables GEP using small RNA fragments. After optimization of the protocol, RNA of high quality and sufficient quantity was obtained from FF CNB in 92% of samples. For the remaining 8% of cases, FFPE material prepared by the pathology department was used for RNA extraction. Both resulting RNA end products are compatible with the nanoString nCounter® technology.

SUBMITTER: Locy H

PROVIDER: S-EPMC8143498 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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Overcoming the Challenges of High Quality RNA Extraction from Core Needle Biopsy.

Locy Hanne H Correa Rohann J M RJM Autaers Dorien D Schiettecatte Ann A Jonckheere Jan J Waelput Wim W Cras Louise L Brock Stefanie S Verhulst Stefaan S Kwan Keith K Vanhoeij Marian M Thielemans Kris K Breckpot Karine K

Biomolecules 20210422 5

The use of gene expression profiling (GEP) in cancer management is rising, as GEP can be used for disease classification and diagnosis, tailoring treatment to underlying genetic determinants of pharmacological response, monitoring of therapy response, and prognosis. However, the reliability of GEP heavily depends on the input of RNA in sufficient quantity and quality. This highlights the need for standard procedures to ensure best practices for RNA extraction from often small tumor biopsies with ...[more]

PMID: 33922016

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Project description:Accurate pathologic diagnosis and molecular classification of breast mass biopsy tissue is important for determining individualized therapy for (neo)adjuvant systemic therapies for invasive breast cancer. The CassiII rotational core biopsy system is a novel biopsy technique with a guide needle and a "stick-freeze" technology. The comprehensive assessments including the concordance rates of diagnosis and biomarker status between CassiII and core needle biopsy were evaluated in this study. Estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), and Ki67 were analyzed through immunohistochemistry. In total, 655 patients with breast cancer who underwent surgery after biopsy at Sir Run Run Shaw Hospital between January 2019 to December 2021 were evaluated. The concordance rates (CRs) of malignant surgical specimens with CassiII needle biopsy was significantly high compared with core needle biopsy. Moreover, CassiII needle biopsy had about 20% improvement in sensitivity and about 5% improvement in positive predictive value compared to Core needle biopsy. The characteristics including age and tumor size were identified the risk factors for pathological inconsistencies with core needle biopsies. However, CassiII needle biopsy was associated with tumor diameter only. The CRs of ER, PgR, HER2, and Ki67 using Cassi needle were 98.08% (kappa, 0.941; p<.001), 90.77% (kappa, 0.812; p<.001), 69.62% (kappa, 0.482; p<.001), and 86.92% (kappa, 0.552; p<.001), respectively. Post-biopsy complications with CassiII needle biopsy were also collected. The complications of CassiII needle biopsy including chest stuffiness, pain and subcutaneous ecchymosis are not rare. The underlying mechanism of subcutaneous congestion or hematoma after CassiII needle biopsy might be the larger needle diameter and the effect of temperature on coagulation function. In summary, CassiII needle biopsy is age-independent and has a better accuracy than CNB for distinguishing carcinoma in situ and invasive carcinoma.

Project description:ObjectiveTo evaluate the feasibility and diagnostic performance of ultrasound (US)-guided fine-needle aspiration cytology and core-needle biopsy (US-FNAC/CNB) for the diagnosis of laryngo-hypopharyngeal masses.Materials and methodsThis was a single-center prospective case series. From January 2018 to June 2019, we initially enrolled 40 patients with highly suspicious laryngo-hypopharyngeal masses on laryngoscopic examinations. Of these, 28 patients with the mass involving or abutting the pre-epiglottic, paraglottic, pyriform sinus, and/or subglottic regions were finally included. These patients underwent US examinations with/without subsequent US-FNAC/CNB under local anesthesia for evaluation of the laryngo-hypopharyngeal mass.ResultsOf the 28 patients who underwent US examinations, a laryngo-hypopharyngeal mass was identified in 26 patients (92.9%). US-FNAC/CNB was performed successfully in 25 of these patients (96.2%), while the procedure failed to target the mass in 1 patient (3.8%). The performance of US caused minor subclinical hematoma in 2 patients (7.7%), but no major complications occurred. US-FNAC/CNB yielded conclusive results in 24 (96.0%) out of the 25 patients with a successful procedure, including 23 patients with squamous cell carcinoma (SCC) and 1 patient with a benign mass. In one patient with atypical cells in US-FNAC, additional direct laryngoscopic biopsy (DLB) was required to confirm SCC. Among the 26 patients who received US-FNAC/CNB, the time from first visit to pathological diagnosis was 7.8 days. For 24 patients finally diagnosed with SCC, the time from first visit to the initiation of treatment was 25.2 days. The mean costs associated with US-FNAC/CNB was $272 under the Korean National Health Insurance Service System.ConclusionUS-FNAC/CNB for a laryngo-hypopharyngeal mass is technically feasible in selected patients, providing good diagnostic performance. This technique could be used as a first-line diagnostic modality by adopting appropriate indications to avoid general anesthesia and DLB-related complications.

Dataset Information

Overcoming the Challenges of High Quality RNA Extraction from Core Needle Biopsy.

Publications

Overcoming the Challenges of High Quality RNA Extraction from Core Needle Biopsy.

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