Preanalytic Variables and Tissue Stewardship for Reliable Next-Generation Sequencing (NGS) Clinical Analysis Paolo A. Ascierto, Carlo Bifulco, Giuseppe.

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Presentation transcript:

Preanalytic Variables and Tissue Stewardship for Reliable Next-Generation Sequencing (NGS) Clinical Analysis Paolo A. Ascierto, Carlo Bifulco, Giuseppe Palmieri, Solange Peters, Nikoletta Sidiropoulos The Journal of Molecular Diagnostics Volume 21, Issue 5, Pages 756-767 (September 2019) DOI: 10.1016/j.jmoldx.2019.05.004 Copyright © 2019 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Key stages for biomarker determination. Biomarker diagnostics involve genomic, transcriptomic, and protein assays. Each diagnostic has specific requirements in specimen preparation, molecular isolation, management, and material yield, as well as analytical normalization. CNV, copy number variant; dMMR, mismatch repair deficiency; IHC, immunohistochemistry; indels, insertions/deletions; MSI, microsatellite instability; NGS, next-generation sequencing; PD-L1, programmed death ligand 1; SNV, single nucleotide variant; SV, structural variant; TMB, tumor mutational burden. The Journal of Molecular Diagnostics 2019 21, 756-767DOI: (10.1016/j.jmoldx.2019.05.004) Copyright © 2019 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Typical tissue journey. Tissue biopsy, together with imaging techniques, contributes to accurate diagnosis. Tissue sampling may involve tissue resection or less invasive techniques, including core needle biopsy, fine-needle aspiration, exfoliative cytology, or liquid biopsy. Specimens are processed by fixation or ultralow-temperature freezing. Preserved specimens are used for morphologic assessment and ancillary diagnostic analysis (examples included). The latter may include molecular analyses, inclusive of next-generation sequencing, that require the isolation of respective molecular profiles. Key personnel are responsible for each stage of the tissue journey but should all be mindful of the considerations and requirements of the end point analyses as well as the fact that a single tissue specimen may be used for different diagnostic assays. dMMR, mismatch repair deficiency; FACS, fluorescence-activated cell sorting; FFPE, formalin-fixed, paraffin-embedded; FISH, fluorescence in situ hybridization; IHC, immunohistochemistry; ISH, in situ hybridization; MSI, microsatellite instability; PD-L1, programmed death ligand 1; RNA-seq, RNA sequencing; RT-qPCR, quantitative RT-PCR; WES, whole-exome sequencing; WGS, whole-genome sequencing. The Journal of Molecular Diagnostics 2019 21, 756-767DOI: (10.1016/j.jmoldx.2019.05.004) Copyright © 2019 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions