ArticleArchives of pathology & laboratory medicine2016
Optimizing Workflows and Processing of Cytologic Samples for Comprehensive Analysis by Next-Generation Sequencing: Memorial Sloan Kettering Cancer Center Experience.
Article in Archives of pathology & laboratory medicine, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
25 citing papers in PubMed.
- Molecular profiling of breast cancer pleural effusions using cytology specimens: Impact of sample source and cytological features on next-generation sequencing performance.Cancer cytopathology · 2026Article
- Exploring alternatives to tumor tissue for BRCA1/2 next-generation sequencing testing in high-grade serous ovarian cancer: A 34-case series of malignant ascites.Cancer cytopathology · 2026Article
- Ultrarapid BRAF mutation detection on supernatant cell-free DNA obtained by FNA: An accurate and expedient method for BRAF assessment in aggressive thyroid carcinomas.Cancer cytopathology · 2026Article
- Urinary Biomarkers Objectively Measure Minimal Residual Disease in Non-Muscle-Invasive Bladder Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Maximizing the clinical utility and performance of cytology samples for comprehensive genetic profiling.Nature communications · 2025Article
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- Feasibility and tissue concordance of genomic sequencing of urinary cytology in upper tract urothelial carcinoma.Urologic oncology · 2023Article
- The basics of commonly used molecular techniques for diagnosis, and application of molecular testing in cytology.Diagnostic cytopathology · 2023Review
- Percutaneous Image-Guided Biopsy for a Comprehensive Hybridization Capture-Based Next-Generation Sequencing in Primary Lung Cancer: Safety, Efficacy, and Predictors of Outcome.JTO clinical and research reports · 2022Article
- Evaluation of Cytologic Sample Preparations for Compatibility With Nucleic Acid Analysis.American journal of clinical pathology · 2022Article
- Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing.Nature biotechnology · 2021Article
- Comparison of PD-L1, EGFR, ALK, and ROS1 Status Between Surgical Samples and Cytological Samples in Non-Small Cell Lung Carcinoma.Balkan medical journal · 2021Article
- Rapid EGFR Mutation Detection Using the Idylla Platform: Single-Institution Experience of 1200 Cases Analyzed by an In-House Developed Pipeline and Comparison with Concurrent Next-Generation Sequencing Results.The Journal of molecular diagnostics : JMD · 2021Article
- Cell-blocks and other ancillary studies (including molecular genetic tests and proteomics).CytoJournal · 2021Review
- UltrarapidJTO clinical and research reports · 2020Article
- Next-generation sequencing analysis of endometrial screening liquid-based cytology specimens: a comparative study to tissue specimens.BMC medical genomics · 2020Article
- Consistent RNA sequencing contamination in GTEx and other data sets.Nature communications · 2020Article
- Invited review-next-generation sequencing: a modern tool in cytopathology.Virchows Archiv : an international journal of pathology · 2019Review
- Comparison of endoscopic ultrasound tissue acquisition methods for genomic analysis of pancreatic cancer.Journal of gastroenterology and hepatology · 2019Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
The value and suitability of cytology specimens for molecular diagnosis has been demonstrated by numerous studies. In practice, however, the success rates vary widely across institutions depending on the disease setting, institutional practices of acquisition, handling/processing, and testing methodologies. As the number of clinically relevant biomarkers continues to increase, more laboratories are turning to next-generation sequencing platforms for testing. Although amplicon-based next-generation sequencing assays, interrogating a limited genomic territory, can be performed with minimal input material, broader-based next-generation sequencing assays have higher DNA input requirements that may not be met if the small tissue samples are not acquired and handled appropriately. We briefly describe some of the process changes we have instituted in our laboratories when handling cytologic material to maximize the tissue available for broad hybrid-capture-based next-generation sequencing assays. Among the key changes established were the consolidation and preservation of previously discarded supernatant material in cytologic samples, the introduction of mineral oil for deparaffinization of cell blocks, and adjustments in the molecular laboratory process and bioinformatics pipelines. We emphasize that even minimal changes can have broad implications for test performance, highlighting the importance of a cohesive group-based approach among clinical, cytopathology, surgical pathology, molecular, and bioinformatics teams.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.