Objectives	To describe the role of genomic alterations in the pathogenesis of various neoplasms and to differentiate various types of genomic alterations and their impact in carcinogenesis and management of the disease To be able to acquire a basic technical knowledge of various genomic tests, used in patients with cancer and their specimen requirements
Key Concepts	Demonstrate an understanding of molecular biology (eg, properties of nucleic acid, structure of chromosome, DNA repair process, epigenetic changes, and omics) and basic pathways and signalling networks Recognise genomic findings that impact classification, prognostication and the treatment of various neoplasms Recognise that the role of genomic findings in classification of most neoplasms is in combination with morphologic and immunophenotypic findings Classify tiers of genomic variants, based on the available clinical evidence Give examples of various publicly available databases for annotation of variants Distinguish various types of pathogenic variants, including point mutations, rearrangements, and copy number alterations Demonstrate an understanding of the difference between an oncogene and a tumour suppressor and types of variants, considered pathogenic in each group (activating mutations versus truncating mutations) Explain how specimens are managed and how pre-analytical variables (eg, fixation, decalcification, contamination) may affect the performance of a molecular assay Define adequacy of tumour tissue sample for downstream molecular assays Evaluate critically new genomic technologies considering the downstream costs secondary to genomic analysis for the laboratory and the patient, including the costs associated with new technologies Evaluate basic tests characteristics, such as analytical sensitivity and specificity, and distinguish them from clinical sensitivity and specificity Determine the advantage and limitation of the clinical diagnostic test modalities, including cytogenetics, flow cytometry, immunohistochemistry (IHC), fluorescence in situ hybridisation (FISH), reverse transcriptase polymerase chain reaction (RT-PCR), Sanger sequencing, next-generation sequencing (NGS), and gene expression panels Recognise internal and external quality control parameters of a molecular assay Recognise that within NGS there is a conceptual distinction between panel sequencing, exome sequencing and genome-wide sequencing Recognise that there are different types of assays that can be used in a laboratory, namely regulatory-approved assays, laboratory-developed assays with internal evidence for analytical validity and purely research assays Interpret guidelines/recommendation to refer to for biomarker evaluation
Skills	Demonstrate the ability to: Define genome, exome, metabolome and proteome Select the appropriate molecular test based on patients' needs Distinguish various genomic alterations (eg, point mutations, rearrangements, copy number alterations) and their pathogenicity as it relates to specific type of gene and neoplasm Select appropriate molecular tests based on tumour histology Recognise the circumstances when germline testing and genetic counselling is required and the appropriate tests Identify whether an assay requires DNA, RNA, or protein and how that impacts tissue requirements Predict the analytical sensitivity of an assay and suitability for minimal residual disease testing Recognise the scope and limitation of an assay (eg, single analyte, versus targeted multiple analyte panel, versus genome-wide assay) Interpret molecular pathology reports in conjunction with active discussion with pathologists and clinical geneticists whenever needed Report and contextualise a clinical case within a molecular tumour board