| Literature DB >> 33792981 |
Pasquale Pisapia1, Francesco Pepe1, Roberta Sgariglia1, Mariantonia Nacchio1, Gianluca Russo1, Floriana Conticelli1, Ilaria Girolami2, Albino Eccher3, Claudio Bellevicine1, Elena Vigliar1, Umberto Malapelle1, Giancarlo Troncone1.
Abstract
The application of next generation sequencing (NGS) technology to cytological samples has significantly modified molecular cytopathology practice. Cytological samples represent a valid source of high-quality DNA for NGS analysis, especially for predicting patients' response to targeted treatments and for refining the risk of malignancy in indeterminate cytological diagnoses. However, several pre-analytical factors may influence the reliability of NGS clinical analysis. Here, we briefly review the challenges of NGS in cytology practice, focusing on those pre-analytical factors that may negatively affect NGS success rates and routine diagnostic applications. Finally, we address the future directions of the field.Entities:
Keywords: FNA; biomarkers; cytopathology; molecular cytopathology; next generation sequencing
Mesh:
Year: 2021 PMID: 33792981 PMCID: PMC8451925 DOI: 10.1111/cyt.12974
Source DB: PubMed Journal: Cytopathology ISSN: 0956-5507 Impact factor: 2.073
Different cytological preparations: Pros and cons
| Preparation | Pros | Cons |
|---|---|---|
| Direct smear |
High‐quality nucleic acids Possibility to perform ROSE, useful to triage the aspirated material |
Necessity of careful additional validation steps for any given molecular approach Unique and unrepeatable |
| CB |
Possibility to perform ancillary studies without the need of additional validation Ensure the preservation of diagnostic slides |
Low quality nucleic acids due to formalin fixation Impossibility to perform ROSE |
| LBC |
Avoid inadequate administration of the aspirated material by untrained physicians Aspirated material can be rapidly collected and preserved in alcohol‐based media |
Impossibility to perform ROSE Variable yield and quality of nucleic acids depending on the fixative adopted |
| Supernatant |
High yield and quality of nucleic acids Ensure the preservation of diagnostic material Enabling molecular analyses even when cytological slides are inadequate or insufficient |
Impossibility to perform ROSE Impossibility to perform morphological evaluation |
Abbreviations: CB, cell block; LBC, liquid‐based cytology; ROSE, rapid on‐site evaluation.
Principal pre‐analytical factors that may affect next generation sequencing analysis on cytological samples and clinical applications
| Pre‐analytical factors |
Fixation modalities Sample preparation Staining Assessment of neoplastic cell content Type of adopted slide Extraction techniques |
| Clinical applications |
Diagnosis Refine the risk of malignancy Therapy |
Summary of the studies that adopted next generation sequencing on cytological samples
| Platform | Panel | Sample type | Number of analysed samples | Adequate sample rate | Clinical application | Reference |
|---|---|---|---|---|---|---|
| Ion S5 System™ (Thermo Fisher Scientifics) | Custom Panel (7 genes) | Direct smear, Cell block | 180 | 91.1% | Therapy |
|
| Ion PGM™ (Thermo Fisher Scientifics) | NextDaySeq Lung panel (7 genes) | Cell block | 16 | 93.8% | Therapy |
|
| Ion PGM™ (Thermo Fisher Scientifics) | Oncomine DNA panel for Solid Tumors and Fusion Transcripts (26 genes) | Direct smear | 8 |
92.0% (RNA‐based) 100.0 (DNA‐based) | Therapy |
|
| HiSeq 2000 (Illumina) | WU‐CaMP27 panel (27 genes) | Direct smear | 5 | 100.0% | Therapy |
|
| Ion PGM™ (Thermo Fisher Scientifics) | Ion AmpliSeq Cancer Hotspot Panel (50 genes) | Liquid‐based cytology | 49 | 77.5% | Therapy |
|
| Ion PGM™ (Thermo Fisher Scientifics) | Ion AmpliSeq Cancer Hotspot Panel (50 genes) | Direct smear | 37 | 91.8% | Refine the risk of malignancy |
|
| Ion PGM™ (Thermo Fisher Scientifics) | Ion AmpliSeq Cancer Hotspot Panel (50 genes) | Direct smear, Cell block | 34 | 85.2% | Refine the risk of malignancy |
|
| Ion Torrent PGM or Ion Proton (Thermo Fisher Scientifics) | ThyroSeq v2.1 panel (56 genes) | Supernatant | 465 | 100.0% | Refine the risk of malignancy |
|
| Ion Proton (Thermo Fisher Scientifics) | ThyroSeq v3 panel (112 genes) | Supernatant | 175 | 100.0% | Refine the risk of malignancy |
|
| Next‐Seq500 (Illumina) | AmpliSeq Comprehensive Panelv3 (161 genes) | Supernatant | 33 | 97.0% | Diagnosis |
|
| iSeq platform (Illumina) | AmpliSeq for Illumina Cancer Hotspot Panel v2 (50 genes) | Direct smear | 32 | 100.0% | Refine the risk of malignancy |
|
| Ion S5 System™ (Thermo Fisher Scientifics) | ‘Oncomine BRCA Research Assay (2 genes) | Direct smear | 11 | 100.0% | Therapy |
|
| Ion Proton (Thermo Fisher Scientifics) | Ion AmpliSeq Cancer Hotspot Panel v2 (50 genes) | Supernatant, Cell block | 35 | 100.0% | Diagnosis, Refine the risk of malignancy, Therapy |
|
| Ion PGM™ (Thermo Fisher Scientifics) | Solid Tumor Focus Assay (69 genes) | Supernatant | 30 | 100.0% | Therapy |
|
| Ion Proton (Thermo Fisher Scientifics) | Ion AmpliSeq Cancer Hotspot Panel v2 (50 genes) | Supernatant | 116 | 89.7% | Therapy |
|
| NextSeq (Illumina); digital droplet PCR | IAseq Targeted ActionableSolid Tumor Panel (20 genes) | Supernatant | 17 | 100.0% | Therapy |
|
| Ion Proton (Thermo Fisher Scientifics) | Ion AmpliSeq Cancer Hotspot Panel v2 (50 genes) | Supernatant | 156 | 83.0% | Refine the risk of malignancy |
|