Teaching learning objectives for 2017/18 HTML Teaching – Learning Objectives 2017 / 2018 Next Generation Sequencing - Lee Murphy Learning Outcomes: Importance of understanding sample provenance from sample collection through to sequencing Overview of current sequencing platforms available on the Western General Campus and elsewhere in Edinburgh Importance of choosing the correct sequencing platform based on platform specifications and project requirements. An understanding of different sequencing protocols and how each sequencing platform works. An oversight of future genomic technologies Translating your Research - Helen Nickerson Recognise the importance of translating MRC-funded research towards health and economic impact Understand the different ways research may be translated Understand the purpose and nature of intellectual property Develop a basic understanding of processes involved in translating research output towards novel diagnostic or therapeutic techniques Develop a basic understanding of the pathways and support available to translate research Research Best Practice - Helen Nickerson, Kerri Miller Recognise our responsibility to the University and research funders in the way we conduct our research Understand the need for proper research ethics Understand the systems used by the University and MRC to track research impact Understand what Open Access publication means and how this can be achieved through University support Understand the importance of proper data management and how to plan for this Disease Mechanisms 1- Toby Hurd Understand the basic biology of primary cilia with respect to structure and function Appreciate the growing role of cilia in human disease with a focus on the kidney and eye Understand the genetics of cilia-associated disease Utilisation of web-based tools and cell biology to identify disease-causing genes Disease Mechanisms 2 - Alex Von Kreigsheim How the mass spectrometer works Analysing mass spectrometry data Protein complexes regulating cell signalling Design and execution of interaction proteomic experiments. Disease Mechansims 3 – Genome editing technologies in basic research: from historical perspectives to state of the art - Andrew Wood Understand the principles of genome editing and the key discoveries that led to its development. Design simple gene disruption and gene correction experiments using Cas9. Understand current strategies for Cas9-based high throughput functional genetic screens, including the use of deep sequencing approaches for quantitative analyses. Identify limitations of current technologies, and discuss how current and future challenges will be met. Imaging at the IGMM Part 1 - Ann Wheeler & Team Principles of Optics Understanding of the technologies available in the Imaging facility Basic understanding of image analysis and resources we have Practical experience of Mesoscopy and Fluorescent microscopy Practical experience of Confocal microscopy Quantitative Skills 7 – Imaging at the IGMM Part 2 Getting more from your data, an introduction to image informatics and automation (*) Understanding of the image informatics resources available at the IGMM The necessity of automation in processing of image data Accepted standards for image analysis in the Biomedical research field Introduction to Scripting, Batch processing and Machine learning software Generation of a basic data analysis pipeline for automated analysis Quantitative Skills 8 – Super Resolution Imaging - Ann Wheeler Super-resolution microscopy, a Nobel pursuit in interdisciplinary research What defines the resolution limit and the implications of this General introduction to standard super-resolution modalities What is ESRIC and what can it do for my PhD? Use and application of SIM and STORM in IGMM research. Emerging technologies for nanoscale imaging. Biomedical Genomics 1 - Alison Meynert To gain an understanding of the computational challenges involved in extracting meaningful information from raw whole genome sequencing (WGS) data. To understand potential pitfalls and commonly used algorithms used to align WGS to a reference genome assembly. To understand the strategies and algorithms commonly used to predict the presence and functional significance of genetic variants detected in aligned WGS data. Biomedical Genomics 2 - Chris Ponting Become familiar with the logic and challenges underlying the identification of causative variants. Identify the importance of traits relevant to different tissues and cell types. Discuss the potential and opportunities of CRISPR/Cas9 technology to discover causative variants. Discuss the importance of experimental design and hypothesis testing in identifying causative variants. Learn to integrate results from different experiments to select variants of interest. Biomedical Genomics 4 - Chris Haley The basis of quantitative genetic variation Heritability and its estimation The threshold model of disease Linkage disequilibrium and association tests. Biomedical Genomics 7 - Susan Farrington GWAS identification of expression Quantitative trait loci/ differential expression and links with anatomy/ physiology. Genome Regulation 1 - Duncan Sproul, Bob Hill Familiarity with the regulation of tissue-specific gene expression by enhancers. Understanding of the diversity of the enhancer landscape (eg super enhancers and enhancer archipeligos). Understanding of the importance of transcription factors in gene regulation. Knowledge of the types of interactions that can occur between transcription factors and epigenetic marks (eg pioneer factors). Genome Regulation 4 - Javier Caceres 1] Introduction to general mechanisms of post-transcriptional regulation of gene expression 2] RNA biology methods Transcriptomic approaches RNA-seq analysis of Alternative splicing CLIP (UV cross-linking immunoprecipitation) Structural approaches (SHAPE) Ribosomal profiling RNAi screens 3] RNA quality control mechanisms Major focus on the Nonsense-mediated decay (NMD) pathway Genome Regulation 6 - Wendy Bickmore Understand the technical limitations of methods for studying higher-order chromatin organisation and the importance of orthologonal methods Appreciate the distinction between correlation and causation, and think about experimental methods that can distinguish cause from consequence Understand the importance of tissue-specific gene control by distant cis-regulatory elements (enhancers), their exquisite cell-specificity and the technical challenges that this poses. Have an appreciation of the importance of genetic variation in cis-regulatory elements for human disease. Interdisciplinary Interactions 1 – Drug Discovery - Asier Unciti-Broceta Differences between small molecule drugs and biotherapeutics Basis of drug design Understanding the challenges associated with the development of new drugs Interdisciplinary Interactions 3 – Next Generation Sequencing in Clinical Practice, Mary Porteous Compare and contrast the requirements on data obtained in a research setting versus a diagnostic setting. Outline a structured approach to the interpretation of a variant of uncertain significance in a diagnostic laboratory. Appreciate some of the ethical and counselling issues involved in genetic diagnosis. This article was published on 2024-09-23
HTML Teaching – Learning Objectives 2017 / 2018 Next Generation Sequencing - Lee Murphy Learning Outcomes: Importance of understanding sample provenance from sample collection through to sequencing Overview of current sequencing platforms available on the Western General Campus and elsewhere in Edinburgh Importance of choosing the correct sequencing platform based on platform specifications and project requirements. An understanding of different sequencing protocols and how each sequencing platform works. An oversight of future genomic technologies Translating your Research - Helen Nickerson Recognise the importance of translating MRC-funded research towards health and economic impact Understand the different ways research may be translated Understand the purpose and nature of intellectual property Develop a basic understanding of processes involved in translating research output towards novel diagnostic or therapeutic techniques Develop a basic understanding of the pathways and support available to translate research Research Best Practice - Helen Nickerson, Kerri Miller Recognise our responsibility to the University and research funders in the way we conduct our research Understand the need for proper research ethics Understand the systems used by the University and MRC to track research impact Understand what Open Access publication means and how this can be achieved through University support Understand the importance of proper data management and how to plan for this Disease Mechanisms 1- Toby Hurd Understand the basic biology of primary cilia with respect to structure and function Appreciate the growing role of cilia in human disease with a focus on the kidney and eye Understand the genetics of cilia-associated disease Utilisation of web-based tools and cell biology to identify disease-causing genes Disease Mechanisms 2 - Alex Von Kreigsheim How the mass spectrometer works Analysing mass spectrometry data Protein complexes regulating cell signalling Design and execution of interaction proteomic experiments. Disease Mechansims 3 – Genome editing technologies in basic research: from historical perspectives to state of the art - Andrew Wood Understand the principles of genome editing and the key discoveries that led to its development. Design simple gene disruption and gene correction experiments using Cas9. Understand current strategies for Cas9-based high throughput functional genetic screens, including the use of deep sequencing approaches for quantitative analyses. Identify limitations of current technologies, and discuss how current and future challenges will be met. Imaging at the IGMM Part 1 - Ann Wheeler & Team Principles of Optics Understanding of the technologies available in the Imaging facility Basic understanding of image analysis and resources we have Practical experience of Mesoscopy and Fluorescent microscopy Practical experience of Confocal microscopy Quantitative Skills 7 – Imaging at the IGMM Part 2 Getting more from your data, an introduction to image informatics and automation (*) Understanding of the image informatics resources available at the IGMM The necessity of automation in processing of image data Accepted standards for image analysis in the Biomedical research field Introduction to Scripting, Batch processing and Machine learning software Generation of a basic data analysis pipeline for automated analysis Quantitative Skills 8 – Super Resolution Imaging - Ann Wheeler Super-resolution microscopy, a Nobel pursuit in interdisciplinary research What defines the resolution limit and the implications of this General introduction to standard super-resolution modalities What is ESRIC and what can it do for my PhD? Use and application of SIM and STORM in IGMM research. Emerging technologies for nanoscale imaging. Biomedical Genomics 1 - Alison Meynert To gain an understanding of the computational challenges involved in extracting meaningful information from raw whole genome sequencing (WGS) data. To understand potential pitfalls and commonly used algorithms used to align WGS to a reference genome assembly. To understand the strategies and algorithms commonly used to predict the presence and functional significance of genetic variants detected in aligned WGS data. Biomedical Genomics 2 - Chris Ponting Become familiar with the logic and challenges underlying the identification of causative variants. Identify the importance of traits relevant to different tissues and cell types. Discuss the potential and opportunities of CRISPR/Cas9 technology to discover causative variants. Discuss the importance of experimental design and hypothesis testing in identifying causative variants. Learn to integrate results from different experiments to select variants of interest. Biomedical Genomics 4 - Chris Haley The basis of quantitative genetic variation Heritability and its estimation The threshold model of disease Linkage disequilibrium and association tests. Biomedical Genomics 7 - Susan Farrington GWAS identification of expression Quantitative trait loci/ differential expression and links with anatomy/ physiology. Genome Regulation 1 - Duncan Sproul, Bob Hill Familiarity with the regulation of tissue-specific gene expression by enhancers. Understanding of the diversity of the enhancer landscape (eg super enhancers and enhancer archipeligos). Understanding of the importance of transcription factors in gene regulation. Knowledge of the types of interactions that can occur between transcription factors and epigenetic marks (eg pioneer factors). Genome Regulation 4 - Javier Caceres 1] Introduction to general mechanisms of post-transcriptional regulation of gene expression 2] RNA biology methods Transcriptomic approaches RNA-seq analysis of Alternative splicing CLIP (UV cross-linking immunoprecipitation) Structural approaches (SHAPE) Ribosomal profiling RNAi screens 3] RNA quality control mechanisms Major focus on the Nonsense-mediated decay (NMD) pathway Genome Regulation 6 - Wendy Bickmore Understand the technical limitations of methods for studying higher-order chromatin organisation and the importance of orthologonal methods Appreciate the distinction between correlation and causation, and think about experimental methods that can distinguish cause from consequence Understand the importance of tissue-specific gene control by distant cis-regulatory elements (enhancers), their exquisite cell-specificity and the technical challenges that this poses. Have an appreciation of the importance of genetic variation in cis-regulatory elements for human disease. Interdisciplinary Interactions 1 – Drug Discovery - Asier Unciti-Broceta Differences between small molecule drugs and biotherapeutics Basis of drug design Understanding the challenges associated with the development of new drugs Interdisciplinary Interactions 3 – Next Generation Sequencing in Clinical Practice, Mary Porteous Compare and contrast the requirements on data obtained in a research setting versus a diagnostic setting. Outline a structured approach to the interpretation of a variant of uncertain significance in a diagnostic laboratory. Appreciate some of the ethical and counselling issues involved in genetic diagnosis.
