Jonas J Heymann, Cristiana M Pineda, Christine N Booth, Elizabeth Jenkins, Joshua R Menke, Sara E Monaco, Ritu Nayar, Michiya Nishino, Sinchita Roy-Chowdhuri, Roberto Ruiz-Cordero, Donna K Russell, Anjali Saqi, Kaitlin E Sundling, Michael J Thrall, Vanda F Torous, Christopher J VandenBussche, Paul A VanderLaan, M Lisa Zhang, Momin T Siddiqui
{"title":"Tools, techniques, and challenges in preparing cytology specimens for ancillary studies: results of the ASC Optimizing Cytology and Small Biopsy Specimen Processing for Ancillary Studies task force survey.","authors":"Jonas J Heymann, Cristiana M Pineda, Christine N Booth, Elizabeth Jenkins, Joshua R Menke, Sara E Monaco, Ritu Nayar, Michiya Nishino, Sinchita Roy-Chowdhuri, Roberto Ruiz-Cordero, Donna K Russell, Anjali Saqi, Kaitlin E Sundling, Michael J Thrall, Vanda F Torous, Christopher J VandenBussche, Paul A VanderLaan, M Lisa Zhang, Momin T Siddiqui","doi":"10.1016/j.jasc.2024.10.001","DOIUrl":"10.1016/j.jasc.2024.10.001","url":null,"abstract":"<p><strong>Introduction: </strong>Ancillary testing on cytopathology and other small biopsy specimens is crucial for diagnosis and provides critical information to clinicians. Testing is dependent on preanalytic factors and would benefit from standardization of specimen collection protocols across laboratories. To assess institutional practices and areas of need for evidence-based standards, we surveyed current practices across cytopathology laboratories.</p><p><strong>Materials and methods: </strong>A twelve-question electronic survey was distributed to American Society of Cytopathology (ASC) members through email, social media, and the ASC from January 8, 2024 to March 1, 2024. Survey responses were tabulated.</p><p><strong>Results: </strong>Of 294 respondents, 257 (87%) completed at least 10/12 questions. Formalin-fixed, paraffin-embedded cell blocks (CBs) are utilized for immunohistochemistry, molecular testing, and in situ hybridization by 89%, 84%, and 71% of respondents, respectively. For fine needle aspirations, no collection medium is utilized by a majority of respondents. In contrast, 61% utilize no collection medium for fluids; 64% predominantly utilize liquid-based preservatives for other exfoliative specimens. For CB preparation, 58% of respondents use coagulating agent; 67% use no fixative before formalin. The two most significant factors limiting clinical utility of ancillary testing in cytology specimens are low cellularity and lack of validation (49% and 23% of respondents, respectively).</p><p><strong>Conclusions: </strong>There is wide variation in current practices among laboratories, reflecting lack of consensus. Although laboratories utilize different collection media for different specimen types, for CB utilization, current survey results are similar to those reported previously. ASC has convened a task force to facilitate specimen standardization and minimize variability among preanalytic factors.</p>","PeriodicalId":38262,"journal":{"name":"Journal of the American Society of Cytopathology","volume":" ","pages":"55-63"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Michael J Thrall, Erin McCarthy, Jeffrey K Mito, Jianyu Rao
{"title":"Triage options for positive high-risk HPV results from HPV-based cervical cancer screening: a review of the potential alternatives to Papanicolaou test cytology.","authors":"Michael J Thrall, Erin McCarthy, Jeffrey K Mito, Jianyu Rao","doi":"10.1016/j.jasc.2024.09.003","DOIUrl":"10.1016/j.jasc.2024.09.003","url":null,"abstract":"<p><p>The American Cancer Society has recommended high-risk human papillomavirus (HPV) testing as the primary screening method for cervical cancer since 2020. Up to this point, the transition from Pap test cytology-based screening or co-testing with cytology and HPV testing has been slow and limited. However, more health systems in the United States are in the process of implementing this change. The transition to HPV-based screening requires a triage strategy for positive results. Genotyping to specifically detect HPV types 16 and 18 in conjunction with reflex cytology for the remaining high-risk HPV genotypes has been the recommended method. Testing options including Dual Stain for p16/Ki-67 and extended HPV genotyping are currently being incorporated into treatment algorithms as alternatives. Methylation testing is another promising method extensively investigated around the world. This review, performed by members of the Clinical Practice Committee of the American Society of Cytopathology, examines the rationale behind the switch away from reliance on Pap test cytology in the cervical cancer screening algorithm and the opportunities and problems associated with the most promising alternative approaches. Published studies that give insight into the performance characteristics of these newer tests are reviewed. At the present time, Pap test cytology remains a viable triage option for positive HPV screening results, but alternative tests have significant appeal and should be considered in tandem with the decision to offer primary HPV screening.</p>","PeriodicalId":38262,"journal":{"name":"Journal of the American Society of Cytopathology","volume":" ","pages":"11-22"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142476887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Olisaemeka Chukwudebe, Elizabeth Lynch, Manish Vira, Louis Vaickus, Anam Khan, Rubina Shaheen Cocker
{"title":"A review of the performance of urinary cytology with a focus on atypia, upper tract and updates on novel ancillary testing.","authors":"Olisaemeka Chukwudebe, Elizabeth Lynch, Manish Vira, Louis Vaickus, Anam Khan, Rubina Shaheen Cocker","doi":"10.1016/j.jasc.2024.09.001","DOIUrl":"10.1016/j.jasc.2024.09.001","url":null,"abstract":"<p><p>The Paris System for Reporting Urine Cytology (TPS) is remarkable for its high predictive value in the detection of high-grade urothelial carcinoma, especially of the bladder. However, universal compliance with TPS-recommended threshold for atypical call rates (15%) and TPS performance in the rarer upper tract urothelial carcinomas (UTUC) are challenging. UTUC diagnosis is compounded by instrumentation artifacts, degenerative changes superimposed on an ambiguous cytology, difficult-to-access location, lack of specific standardized criteria, and a limited number of UTUC-focused studies. We reviewed TPS-applied studies published since 2022, noting up to 50%, exceeding the suggested 15% threshold for atypia. Our examination of ancillary tests for UTUC explored novel approaches including DNA methylation analysis, the detection of overexpressed tumor-linked messenger RNAs, and immunohistochemistry on markers such as CK17. Preliminary evidence from our review suggests that ancillary tests display superior performance over cytology, including in voided samples and low-grade urothelial carcinoma. Importantly, voided samples obviate the risks of ureterorenoscopy. Finally, we explored the future opportunities offered by artificial intelligence and machine learning for a more objective application of TPS criteria on urine samples.</p>","PeriodicalId":38262,"journal":{"name":"Journal of the American Society of Cytopathology","volume":" ","pages":"23-35"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142591957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Susanne K Jeffus, Chien Chen, Taha Keskin, Nicole Massoll, Soheila Korourian, Felicia Allard
{"title":"Entrustable professional activities for cytopathology fellowship.","authors":"Susanne K Jeffus, Chien Chen, Taha Keskin, Nicole Massoll, Soheila Korourian, Felicia Allard","doi":"10.1016/j.jasc.2024.10.003","DOIUrl":"10.1016/j.jasc.2024.10.003","url":null,"abstract":"<p><p>Entrustable professional activities (EPAs) are an educational tool in the framework of competency-based medical education. EPAs are a relatively new concept in pathology. No studies to date exist on the utilization of EPAs during cytopathology fellowship training. This article reviews the recent literature on this topic and shares our institutional experience with the implementation of an EPA for fine needle aspirations and rapid on-site evaluations. While EPAs allow for tracking the competence of the cytopathology fellow toward independent practice for fine needle aspirations and rapid on-site evaluations, the required amount of documentation may represent a potential barrier for the widespread adoption of this new tool.</p>","PeriodicalId":38262,"journal":{"name":"Journal of the American Society of Cytopathology","volume":" ","pages":"5-10"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142682902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sana Ahuja, Adil Aziz Khan, Charanjeet Ahluwalia, Sunil Ranga
{"title":"Application of the WHO reporting system for soft tissue cytopathology with assessment of risk of malignancy: a retrospective study.","authors":"Sana Ahuja, Adil Aziz Khan, Charanjeet Ahluwalia, Sunil Ranga","doi":"10.1016/j.jasc.2024.09.004","DOIUrl":"10.1016/j.jasc.2024.09.004","url":null,"abstract":"<p><strong>Introduction: </strong>Soft tissue tumors are complex neoplasms requiring accurate diagnosis, often through fine needle aspiration (FNA). The World Health Organization (WHO) classification system aims to standardize cytopathological diagnoses and assess the risk of malignancy (ROM) for these tumors.</p><p><strong>Materials and methods: </strong>This retrospective study reviewed cytological specimens from January 2022 to June 2023. Samples were categorized using the WHO classification into 6 categories: nondiagnostic, benign, atypical, soft tissue neoplasm of uncertain malignant potential, suspicious for malignancy (SFM), and malignant. Histopathological correlation was performed, and ROM, sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy were calculated.</p><p><strong>Results: </strong>A total of 203 samples were analyzed: 62.5% benign, 13.8% SFM, and 9.9% malignant. ROMs were 33.3% (nondiagnostic), 1.2% (benign), 40% (atypical), 25% (soft tissue neoplasm of uncertain malignant potential), 80% (SFM), and 100% (malignant). Histopathological correlation was available for 117 cases. Sensitivity and diagnostic accuracy were highest (77.3% and 93.9%) when SFM and malignant categories were combined as positive for malignancy. Specificity was highest (100%) when only malignant cases were considered positive. The interobserver agreement was moderate (Cohen's kappa 0.45).</p><p><strong>Conclusions: </strong>The WHO classification system for soft tissue cytopathology improves diagnostic accuracy and standardizes reporting. It effectively categorizes soft tissue tumors and guides clinical management, though further refinement is needed for broader applicability.</p>","PeriodicalId":38262,"journal":{"name":"Journal of the American Society of Cytopathology","volume":" ","pages":"44-54"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142476886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Cytology fine-needle aspiration and surgical pathology core needle biopsy reporting: blurred lines or battle lines?","authors":"Paul A VanderLaan","doi":"10.1016/j.jasc.2024.10.002","DOIUrl":"10.1016/j.jasc.2024.10.002","url":null,"abstract":"","PeriodicalId":38262,"journal":{"name":"Journal of the American Society of Cytopathology","volume":" ","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142629994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"FNA diagnosis of secondary malignancies in the parotid gland: over 20 years of experience from a single institute.","authors":"Aditya M Bhatt, Hector Mesa, Shaoxiong Chen, Brent Molden, Tieying Hou","doi":"10.1016/j.jasc.2024.08.131","DOIUrl":"10.1016/j.jasc.2024.08.131","url":null,"abstract":"<p><strong>Introduction: </strong>Metastatic solid tumors account for a significant portion of malignancies in the parotid gland. Fine-needle aspiration (FNA) is a primary tool to diagnose these tumors.</p><p><strong>Materials and methods: </strong>We retrospectively reviewed 134 FNA cases of metastatic solid tumors affecting the parotid gland, spanning from 2000 to 2023 at our institute. We summarized the medical histories, cytology diagnoses, correlations with surgical resections, clinical treatments, and follow-up outcomes.</p><p><strong>Results: </strong>The patient cohort included 107 male and 27 female patients, with a median age of 71 years (range: 4-96 years). Eighty-five percent of metastases (113 of 134) originated from head and neck (H&N) malignancies, comprising 66% from cutaneous source and 19% from mucosal sites. The most frequent primary sites outside the H&N were lung (4%), kidney (2%), and non-H&N skin (2%). Sixty-eight percent of metastases (92 of 134) were squamous cell carcinoma (SqCC) including 61% conventional type and 7% human papillomavirus-related SqCC. Melanoma is the second most common metastatic malignancy (28 of 134, 21%). The median time from primary diagnosis to metastasis was 10 months (range: 0 to 132 months). During clinical follow-up, 59 (44%) patients died from the disease in a median follow-up of 10 months (range: 2 to 56 months).</p><p><strong>Conclusions: </strong>This study represents one of the largest series of secondary malignancies in the parotid gland collected from a single institution. Most of these tumors are metastases from H&N malignancies, with cutaneous SqCC being the most prevalent primary site and histology. Accurate diagnosis relies heavily on clinical history, morphologic evaluation, and ancillary studies.</p>","PeriodicalId":38262,"journal":{"name":"Journal of the American Society of Cytopathology","volume":" ","pages":"36-43"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11695149/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142355877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tianye Liu, Swikrity Upadhyay Baskota, Abel Gonzalez
{"title":"Endoscopic ultrasound-guided fine-needle aspiration and fine-needle biopsy in the diagnosis of gastrointestinal lymphomas.","authors":"Tianye Liu, Swikrity Upadhyay Baskota, Abel Gonzalez","doi":"10.1016/j.jasc.2024.12.002","DOIUrl":"https://doi.org/10.1016/j.jasc.2024.12.002","url":null,"abstract":"<p><strong>Introduction: </strong>The role of endoscopic ultrasound-guided fine-needle aspiration and fine-needle biopsy (EUS-FNA/B) in the clinical management of gastrointestinal lymphoma has not been extensively studied. This study investigates the use of EUS-FNA/B in the diagnosis of first-time and recurrent gastrointestinal lymphomas at a large academic institution.</p><p><strong>Materials and methods: </strong>A total of 40 patients who had final diagnosis of lymphoma according to the World Health Organization (WHO) classification of tumors of hematopoietic lymphoid tissues who underwent EUS-FNA/B were included in the study. Cases with concurrent forceps mucosal biopsies or lost to clinical follow-up were excluded. The diagnostic accuracy and clinical use of EUS-FNA/B was investigated by comparing EUS-FNA/B diagnosis with the final diagnosis.</p><p><strong>Results: </strong>EUS-FNA/B diagnoses were concordant with the final WHO diagnosis for as high as 72.5% of the cases. Of the remaining 27.5%, 17.5% had enough cytologic features for lymphoma diagnosis with incomplete phenotyping, while the remaining 10.0% showed features suspicious for lymphoma. Cell block and flow cytometry quality significantly affected diagnostic accuracy. Number of passes between 1 and 5 yielded better diagnostic accuracy than 6 or more passes during FNA; however, no difference was identified during procedures that used FNB alone or combined with FNA. There is no significant difference in onsite adequacy diagnostic performance of EUS-FNA performed by cytopathologists or cytotechnologists.</p><p><strong>Conclusions: </strong>EUS-FNA/B with concurrent ancillary studies such as immunocytochemistry in cell block and flow cytometry can be helpful in efficient first and recurrent diagnoses of gastrointestinal lymphomas.</p>","PeriodicalId":38262,"journal":{"name":"Journal of the American Society of Cytopathology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142898810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Primary tumor characteristics and immunohistochemical profile of renal cell carcinoma in serous fluid cytology.","authors":"Mason Marshall, Sigfred Lajara, Gabriela Quiroga-Garza, Dimitrios Korentzelos, Maedeh Mohebnasab, Samer Khader","doi":"10.1016/j.jasc.2024.11.002","DOIUrl":"https://doi.org/10.1016/j.jasc.2024.11.002","url":null,"abstract":"<p><strong>Introduction: </strong>Renal cell carcinoma (RCC) involves serosal surfaces in 2%-3% of cases, and thus few papers describe serous fluid cytology (SFC) involvement by RCC. This diagnosis is challenging, given its rarity, nondescript cytomorphologic features and infrequent expression of widely used epithelial markers MOC31 and BerEP4. We describe our institutional experience with RCC in SFC specimens.</p><p><strong>Methods: </strong>Our institutional laboratory information system was queried for SFC specimens from patients with RCC between 2013 and 2023. Cases signed out as \"Suspicious for Malignant Cells\" and \"Positive for Malignant Cells\" were included. Patient demographics, immunohistochemical results, primary tumor characteristics, and molecular data were recorded.</p><p><strong>Results: </strong>Sixty-one cases, 50 pleural, and 11 peritoneal fluid specimens were identified. Fifty (50) were signed out as positive for malignancy and 11 were signed out as suspicious for malignancy. MOC31 and BerEP4 were positive in 59% and 55% of cases, respectively. PAX-8, CA9, CD10, and RCC were positive in 85%, 82%, 73%, and 29% of cases, respectively. Primary tumor histologic subtypes included 39 clear cell, 6 papillary, 1 chromophobe, and 15 were not further subclassified. Fifty-nine percent (59%) of cases had a nuclear grade of 4%, and 37% had sarcomatoid or rhabdoid differentiation. Seventy-one percent (71%) of cases had stage 3 or 4 disease.</p><p><strong>Conclusions: </strong>RCC metastases to serosal surfaces are more likely to be seen in patients with higher disease stage, high nuclear grade, and sarcomatoid or rhabdoid differentiation. MOC31 and BerEP4 performed poorly in this setting. We recommend the addition of cytokeratins, PAX-8, CD10, and CA-9 to confirm metastatic involvement.</p>","PeriodicalId":38262,"journal":{"name":"Journal of the American Society of Cytopathology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142847959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gloria H Sura, Kevin Tran, Alexander J Trevarton, Michal Marczyk, Chunxiao Fu, Lili Du, Jiaxin Qu, Rosanna Lau, Amy Tasto, Rebekah E Gould, Agata Tinnirello, Bruno V Sinn, Lajos Pusztai, Christos Hatzis, W Fraser Symmans
{"title":"Comparative analysis of Ficoll-Hypaque and CytoLyt techniques for blood removal in breast cancer malignant effusions: effects on RNA quality and sequencing outcomes.","authors":"Gloria H Sura, Kevin Tran, Alexander J Trevarton, Michal Marczyk, Chunxiao Fu, Lili Du, Jiaxin Qu, Rosanna Lau, Amy Tasto, Rebekah E Gould, Agata Tinnirello, Bruno V Sinn, Lajos Pusztai, Christos Hatzis, W Fraser Symmans","doi":"10.1016/j.jasc.2024.11.001","DOIUrl":"https://doi.org/10.1016/j.jasc.2024.11.001","url":null,"abstract":"<p><strong>Introduction: </strong>To optimize RNA sequencing (RNA-seq) outcomes, we investigated preanalytical variables in malignant effusions containing metastatic breast cancer. We compared 2 processing methods-Ficoll-Hypaque density gradient enrichment and CytoLyt hemolysis-focusing on their effects on RNA quality, transcript abundance, and variant detection from cytospin slides, relative to fresh-frozen samples. Additionally, we compared read-based and Unique Molecular Identifier (UMI)-based library preparation methods.</p><p><strong>Materials and methods: </strong>Thirteen malignant effusion specimens from metastatic breast cancer were processed using both the Ficoll-Hypaque and Cytolyt methods. RNA was extracted from fresh-frozen samples stored in RNA preservative and from cytospin slides fixed in Carnoy's solution. RNA quality was evaluated using RNA integrity number (RIN) and the percentage of fragments >200 bases (DV200). Sequencing was conducted with both read- and UMI-based methods.</p><p><strong>Results: </strong>Purified RNA was more fragmented by the Cytolyt method (mean RIN: 3.56, DV200: 78.97%), compared to the Ficoll-Hypaque method (mean RIN: 6.29, DV200: 88.08%). Sequencing data had high concordance correlation coefficient (CCC) for measurements of gene expression, whether from Cytolyt or Ficoll-Hypaque treated samples, and whether using the UMI- or read-based sequencing methods (read-based mean CCC: 0.967 from Cytolyt versus 0.974 from Ficoll-Hypaque, UMI-based mean CCC: 0.972 from Cytolyt versus 0.977 from Ficoll-Hypaque).</p><p><strong>Conclusions: </strong>Despite the increased RNA fragmentation with the Cytolyt, RNA-seq data quality was comparable across Cytolyt and Ficoll-Hypaque methods. Both clearing methods are viable for short-read RNA-seq analysis, with read and UMI-based approaches performing similarly.</p>","PeriodicalId":38262,"journal":{"name":"Journal of the American Society of Cytopathology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142819681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}