Landscape of approaches for streamlining pre-analytical and early analytical variables for solid tumor next-generation sequencing: A Genomics Organization for Academic Laboratories consortium report.

The scope of pre-analytical and early analytical methods used in clinical molecular laboratories can have vast effects on the quality and turnaround time for solid tumor next-generation sequencing assays. To learn more about various approaches, a survey of 24 academic laboratories within the Genomics Organization for Academic Laboratories consortium was administered, focusing on pre-analytical and early analytical issues in next-generation sequencing clinical assays that may affect patient care. The survey revealed the landscape of clinical laboratory practices for use of cytopathology smears, block selection, histology practices and protocols, sample transport, slide imaging, sample adequacy assessment, tumor cell enrichment, and deparaffinization methods. Most laboratories reported that they either accepted cytopathology smears for next-generation sequencing testing or had a plan to accept them soon. All laboratories surveyed performed micro- or macro-dissection on unstained formalin-fixed, paraffin-embedded slides for tumor cell enrichment. Several laboratories reported sectioning blocks within the molecular laboratory. While most respondents used an organic solvent for deparaffinization, several laboratories used mineral oil as an alternative. The approaches of other laboratories reported here are expected to be an impactful resource to address pre-analytical issues that may improve assay quality and turnaround time.