Genomic Medicine MSc/PGDip/PGCert

• Bioinformatics, Interpretation and Data Quality Assurance in Genome Analysis (15 credits)

  The module will cover the fundamental principles of informatics and the impact of bioinformatics on clinical genomics. Students will be expected to be able to find and use major genomic and genetic data resources, use software packages and analysis tools for big data and undertake literature searches to critically assess, annotate and interpret findings from sequence data and genetic variants. Theoretical sessions will be coupled with practical exercises involving the analysis and annotation of predefined data sets.

  This module will equip the student with the essential skills to analyse genomic data, applying professional best practice guidelines. Upon completion of this module students will be able to understand how bioinformatics is used to analyse, interpret and report genomic data in a clinical context.

  Students will also be equipped to utilise the 100,000 Genomes Project data set if relevant for their research project.

  *No prior knowledge in programming is required for this module.

• Fundamentals of Human Genetics and Genomics (15 credits)

  This module will cover the structure and variations in the human genomics, including fundamental principles of genetics and genomics. Students undertaking this module will review the architecture of the human genome and the functional units embedded in it. Students will also cover aspects of gene regulation and chromatin structure and consider the importance of the epigenome in these processes.

  In addition, this module will cover DNA sequence variation and structural variation, how this sort of variation is normal but that sometimes it can be associated with disease. Classic chromosomal abnormalities will be described and the mechanisms that lead to them explained. Students will learn about monogenic and multifactorial genetic disorders and how gene mapping and sequencing can be used to identify causal and contributory variants.

  In essence, this module covers what the genome is, what abnormalities can arise and how they arise, as well as how they can be detected.

• Omics Techniques and Technologies - Their Application to Genomic Medicine (15 credits)

  This module explores current genomics techniques used for DNA sequencing (e.g. targeted approaches, whole exome and whole genome sequencing) and RNA sequencing, using highly parallel methodologies, together with current technologies routinely used to investigate genomic variation in the clinical setting.

  This module will introduce the bioinformatics approaches required for the analysis of genomic data. The module will also cover the use of array-based methodologies and RNA sequencing in estimating levels of protein expression, micro RNAs and long non–coding RNAs.

  An introduction to metabolomics and proteomics, which are important for the functional interpretation of genomic data and discovery of disease biomarkers will also be included. Students will also learn about the strategies employed to evaluate pathogenicity of variants for clinical reporting.

• Research project (30 credits)

  This is an ideal option for students taking the MSc part-time and working at the same time.

  Students will be undertaking original research and writing it up in the style of a journal review. They will need to use language, style and formatting of the scientific literature that they have read when it comes to writing up.

  The project can be carried out in any appropriate research university or hospital department or industry environment with joint supervision, i.e., supervisors from both the hosting department and the course.

• Research project (60 credits)

  Students will use both the theoretical knowledge they will acquire throughout the taught part of the course and the analytical skills they will develop in order to tackle a research question by themselves. Undertaking of the research project will involve formulating the question, acquiring and analysing the data and finally presenting and discussing the results.

  The project can be carried out in the hosting NHS laboratory, research department and industry under joint supervision i.e. tutors from both the hosting department and the programme.

  Research projects should be presented in the format of a paper for publication (additional figures and tables can be presented as supplementary material).

• Application of Genomics in Infectious Disease (15 credits)

  The teaching sessions of this module will cover the basics of pathogen genome biology, methods for whole genome sequencing (WGS) applied to pathogens and bioinformatic analysis of pathogen genomes. Numerous examples will demonstrate the relevance of infectious disease genomics to key topics such as antimicrobial resistance, diagnostics, vaccine design, disease surveillance, host susceptibility to infection, public health epidemiology and clinical management of patients.

  The application of WGS and implications of pathogen genomics from a perspective of healthcare pathways and public health for its future impact will be the key focus for your study. The sessions will be interspersed with a series of case studies and research papers for self-directed study, taken from a limited reading list comprising exemplar organisms from the recent literature.

  The sessions explore and present multiple examples of pathogens and genomics: TB drug therapy, Pseudomonas aeruginosa and E. coli outbreaks, Staphylococcus aureus and MRSA, STI diagnostics and resistance, HIV, influenza and the COVID-19 pandemic, pneumococcal and meningococcal vaccine design and surveillance.

  Together the sessions, self-directed learning and associated resources form the defined knowledge base for the module. The literature and other reading materials provide the students with the basis for extended self-study and as a foundation for the module’s summative assessments.

• Genomics of Common and Rare Inherited Diseases (15 credits)

  This module uses exemplars of both common and rare diseases from across the entire healthcare spectrum to demonstrate the clinical utility of genomic data in the healthcare setting.

  The module examples give an insight into how advances in genomic technologies and integration of genomic data into clinical pathways are impacting on the management of patients from the prenatal setting, through paediatrics and into adult medicine and cancer.

  The module will explore the clinical presentation and genetic architecture of disease, as well as the diagnostic and therapeutic implications of genomic data for a myriad of common and rare inherited conditions using expertise from across SGH/GSTT/SGUL/KCL. We will explore traditional and current approaches used to identify genetic predisposition to common and rare inherited diseases, focusing on the latter, within the context of clinical diagnostics.

  We will learn how to select patients with unmet diagnostic needs that will benefit from exome or whole genome sequencing, and some of the complexities involved in the interpretation of genomic data in the clinical context. We will also discuss the Genomics England, genomics medicine services and data infrastructure.

• Molecular Pathology of Cancer and Application in Cancer Diagnosis, Screening and Treatment (15 credits)

  The module will guide the students from a basic introduction in cancer biology, to comparing molecular and pathological information applied in the diagnosis, classification, treatment of cancer.

  We will look at immuno-oncology, early detection, and predisposition of cancer, and the use of molecular data and diagnostics in clinical trials. In addition, we will introduce basic machine learning methodologies and different molecular technologies of tumour tissue in the context of target identification, and biomarker development to capture their clinical relevance.

• Pharmacogenomics and Stratified Healthcare (15 credits)

  The module will provide an overview of the techniques and analytical strategies used in pharmacogenetics and pharmacogenomics and explore some of the challenges and limitations in this field. Moreover, the module will use examples of known, validated pharmacogenetics and pharmacogenomic tests, relevant to the use of drug treatments.

• Advanced Bioinformatics (15 credits)

  This module builds upon and extends the module “Bioinformatics, interpretation and data quality assurance in genome analysis ” and further explores state of the art bioinformatics pipelines for genetic data in a clinical context, suitable for studying genetic variants underlying Mendelian diseases, cancer genetics, and RNA expression data using Galaxy, and also introduces the student to basic Bioinformatic data skills using the command line, R/RStudio and Bioconductor.

  The student will learn about the landscape of tools for read mapping and variant calling and how they are suitable for different types of genetic data and analysis. Lectures will be combined with hands on computer workshops/tutorials, where students can practice designing their own bioinformatics pipelines in the Galaxy environment.

  They will work with real gene expression, rare disease and cancer genomics datasets. The course will also provide a primer for working with large genetic datasets using command line tools, scripting bioinformatics pipelines and using R/RStudio and Bioconductor to analyses and explore and visualise NGS and other ‘Omics data.

  *Students aiming to do the Advanced Bioinformatics module will have to complete the Bioinformatics module first. No prior knowledge in programming is required for either module. You will learn R-coding in the Advanced Bioinformatics module and, although you might find it challenging at first, your module leads will provide you with plenty of support and guidance.

  Students doing the Advanced Bioinformatics module will need to download free VPN software and set up a VPN connection to be able to access our cloud computing facilities in advance. You can find a guide about how to do this on macOS, Linux or Microsoft Windows and the VPN configuration file.

• Genomics of Cardiovascular Disorders (15 credits)

  This module explores the burden of cardiovascular disease and the underlying contribution of genetics to these diseases. Students will receive refresher sessions focused on cardiac function as well as being introduced to the key diagnostic tools used in cardiology.

  They will learn about the major arrhythmias and cardiomyopathies which can lead to premature and sudden death. By studying genetic causes of lipid disorders students will understand the impact of rare and common genetic variants on the risk of coronary heart disease. The contribution of "big data" and the development of gene panel tests will be discussed to demonstrate some of the benefits that genomic medicine can offer to this group of diseases.

  Students will hear about the role and challenges of genetic counselling in inherited cardiac conditions.

• Ethical, Legal and Social Issues in Applied Genomics (15 credits)

  Students will be provided with a platform of ethical understanding from which to consider issues of confidentiality, privacy and disclosure, autonomy, welfare, informed consent and justice. Upon this platform, students will consider the impact of genomic technologies on individual lives and public discourse.

  The social implications of the availability of genetic testing and screening will be considered, especially in the context of reproductive technologies. Finally, students will be provided with a discussion of legal issues surrounding the use of genetic information as well as the use of genetic data for research, diagnostic and therapeutic purposes.

• Fetal Genomics (15 credits)

  There have been rapid advancements in genomics technologies and their increasing application in prenatal medicine. In today's modern age, where litigation rates in obstetrics and fetal medicine are increasingly high, the need for accurate diagnosis, interpretation, and transparent communication of genomic results has never been more pressing.

  This climate demands practitioners are adept in employing the latest technologies and conveying complex genetic information clearly and compassionately to patients.

  The fetal genomics module aims to bridge this critical gap, providing the necessary training and insights to support precise diagnostics, risk assessments, and patient-centric communication, thereby reducing the potential for legal complications and enhancing trust within the patient-provider relationship.

  This module ensures that students are proficient with the latest techniques and are attuned to the societal, legal, and ethical aspects of prenatal genetic testing.

  The module reflects the need for a multidisciplinary approach in genomics medicine, paving the way for more informed decisions and personalised care in maternal and child health.

• Genomics of Neurological Disorders (15 credits)

  This module explores the contribution of genomics to neurological disorders. Students will receive refresher sessions focussed on neuroanatomy and the development of the neurological system followed by an introduction to the key diagnostic tools used in neurology.

  They will learn about the major neurological disorder categories which have a high genetic contribution. The module will explore the value of the multidisciplinary team in phenotyping, interpretation of results, management and family communication.

• Introduction to Counselling Skills in Genomics (15 credits)

  This module will provide students with an introduction to general communication skills and specific counselling skills used in genomic medicine. Students undertaking this module will be taught how to communicate and provide appropriate support to individuals and their families.

  Development of counselling skills will be achieved via theoretical and practical sessions through the use of role play within an academic setting. Students will understand the importance of a family history and communication of pathogenic and/or uncertain results.

This award can be tailored to suit your career goals and interests.

If you would like to discuss the module options available, please contact the Admissions Tutor Dr George Wardley for more information.

• Bioinformatics, Interpretation and Data Quality Assurance in Genome Analysis (15 credits)

  The module will cover the fundamental principles of informatics and the impact of bioinformatics on clinical genomics. Students will be expected to be able to find and use major genomic and genetic data resources, use software packages and analysis tools for big data and undertake literature searches to critically assess, annotate and interpret findings from sequence data and genetic variants. Theoretical sessions will be coupled with practical exercises involving the analysis and annotation of predefined data sets.

  This module will equip the student with the essential skills to analyse genomic data, applying professional best practice guidelines. Upon completion of this module students will be able to understand how bioinformatics is used to analyse, interpret and report genomic data in a clinical context.

  Students will also be equipped to utilise the 100,000 Genomes Project data set if relevant for their research project.

  *No prior knowledge in programming is required for this module.

• Fundamentals of Human Genetics and Genomics (15 credits)

  This module will cover the structure and variations in the human genomics, including fundamental principles of genetics and genomics. Students undertaking this module will review the architecture of the human genome and the functional units embedded in it. Students will also cover aspects of gene regulation and chromatin structure and consider the importance of the epigenome in these processes.

  In addition, this module will cover DNA sequence variation and structural variation, how this sort of variation is normal but that sometimes it can be associated with disease. Classic chromosomal abnormalities will be described and the mechanisms that lead to them explained. Students will learn about monogenic and multifactorial genetic disorders and how gene mapping and sequencing can be used to identify causal and contributory variants.

  In essence, this module covers what the genome is, what abnormalities can arise and how they arise, as well as how they can be detected.

• Molecular Pathology of Cancer and Application in Cancer Diagnosis, Screening and Treatment (15 credits)

  The module will guide the students from a basic introduction in cancer biology, to comparing molecular and pathological information applied in the diagnosis, classification, treatment of cancer.

  We will look at immuno-oncology, early detection, and predisposition of cancer, and the use of molecular data and diagnostics in clinical trials. In addition, we will introduce basic machine learning methodologies and different molecular technologies of tumour tissue in the context of target identification, and biomarker development to capture their clinical relevance.

• Omics Techniques and Technologies - Their Application to Genomic Medicine (15 credits)

  This module explores current genomics techniques used for DNA sequencing (e.g. targeted approaches, whole exome and whole genome sequencing) and RNA sequencing, using highly parallel methodologies, together with current technologies routinely used to investigate genomic variation in the clinical setting.

  This module will introduce the bioinformatics approaches required for the analysis of genomic data. The module will also cover the use of array-based methodologies and RNA sequencing in estimating levels of protein expression, micro RNAs and long non–coding RNAs.

  An introduction to metabolomics and proteomics, which are important for the functional interpretation of genomic data and discovery of disease biomarkers will also be included. Students will also learn about the strategies employed to evaluate pathogenicity of variants for clinical reporting.

• Pharmacogenomics and Stratified Healthcare (15 credits)

  The module will provide an overview of the techniques and analytical strategies used in pharmacogenetics and pharmacogenomics and explore some of the challenges and limitations in this field. Moreover, the module will use examples of known, validated pharmacogenetics and pharmacogenomic tests, relevant to the use of drug treatments.

• Application of Genomics in Infectious Disease (15 credits)

  The teaching sessions of this module will cover the basics of pathogen genome biology, methods for whole genome sequencing (WGS) applied to pathogens and bioinformatic analysis of pathogen genomes. Numerous examples will demonstrate the relevance of infectious disease genomics to key topics such as antimicrobial resistance, diagnostics, vaccine design, disease surveillance, host susceptibility to infection, public health epidemiology and clinical management of patients.

  The application of WGS and implications of pathogen genomics from a perspective of healthcare pathways and public health for its future impact will be the key focus for your study. The sessions will be interspersed with a series of case studies and research papers for self-directed study, taken from a limited reading list comprising exemplar organisms from the recent literature.

  The sessions explore and present multiple examples of pathogens and genomics: TB drug therapy, Pseudomonas aeruginosa and E. coli outbreaks, Staphylococcus aureus and MRSA, STI diagnostics and resistance, HIV, influenza and the COVID-19 pandemic, pneumococcal and meningococcal vaccine design and surveillance.

  Together the sessions, self-directed learning and associated resources form the defined knowledge base for the module. The literature and other reading materials provide the students with the basis for extended self-study and as a foundation for the module’s summative assessments.

• Genomics of Cardiovascular Disorders (15 credits)

  This module explores the burden of cardiovascular disease and the underlying contribution of genetics to these diseases. Students will receive refresher sessions focused on cardiac function as well as being introduced to the key diagnostic tools used in cardiology.

  They will learn about the major arrhythmias and cardiomyopathies which can lead to premature and sudden death. By studying genetic causes of lipid disorders students will understand the impact of rare and common genetic variants on the risk of coronary heart disease. The contribution of "big data" and the development of gene panel tests will be discussed to demonstrate some of the benefits that genomic medicine can offer to this group of diseases.

  Students will hear about the role and challenges of genetic counselling in inherited cardiac conditions.

• Fetal Genomics (15 credits)

  There have been rapid advancements in genomics technologies and their increasing application in prenatal medicine. In today's modern age, where litigation rates in obstetrics and fetal medicine are increasingly high, the need for accurate diagnosis, interpretation, and transparent communication of genomic results has never been more pressing.

  This climate demands practitioners are adept in employing the latest technologies and conveying complex genetic information clearly and compassionately to patients.

  The fetal genomics module aims to bridge this critical gap, providing the necessary training and insights to support precise diagnostics, risk assessments, and patient-centric communication, thereby reducing the potential for legal complications and enhancing trust within the patient-provider relationship.

  This module ensures that students are proficient with the latest techniques and are attuned to the societal, legal, and ethical aspects of prenatal genetic testing.

  The module reflects the need for a multidisciplinary approach in genomics medicine, paving the way for more informed decisions and personalised care in maternal and child health.

• Ethical, Legal and Social Issues in Applied Genomics (15 credits)

  Students will be provided with a platform of ethical understanding from which to consider issues of confidentiality, privacy and disclosure, autonomy, welfare, informed consent and justice. Upon this platform, students will consider the impact of genomic technologies on individual lives and public discourse.

  The social implications of the availability of genetic testing and screening will be considered, especially in the context of reproductive technologies. Finally, students will be provided with a discussion of legal issues surrounding the use of genetic information as well as the use of genetic data for research, diagnostic and therapeutic purposes.

• Genomics of Common and Rare Inherited Diseases (15 credits)

  This module uses exemplars of both common and rare diseases from across the entire healthcare spectrum to demonstrate the clinical utility of genomic data in the healthcare setting.

  The module examples give an insight into how advances in genomic technologies and integration of genomic data into clinical pathways are impacting on the management of patients from the prenatal setting, through paediatrics and into adult medicine and cancer.

  The module will explore the clinical presentation and genetic architecture of disease, as well as the diagnostic and therapeutic implications of genomic data for a myriad of common and rare inherited conditions using expertise from across SGH/GSTT/SGUL/KCL. We will explore traditional and current approaches used to identify genetic predisposition to common and rare inherited diseases, focusing on the latter, within the context of clinical diagnostics.

  We will learn how to select patients with unmet diagnostic needs that will benefit from exome or whole genome sequencing, and some of the complexities involved in the interpretation of genomic data in the clinical context. We will also discuss the Genomics England, genomics medicine services and data infrastructure.

• Genomics of Neurological Disorders (15 credits)

  This module explores the contribution of genomics to neurological disorders. Students will receive refresher sessions focussed on neuroanatomy and the development of the neurological system followed by an introduction to the key diagnostic tools used in neurology.

  They will learn about the major neurological disorder categories which have a high genetic contribution. The module will explore the value of the multidisciplinary team in phenotyping, interpretation of results, management and family communication.

• Fundamentals of Human Genetics and Genomics (15 credits)

  This module will cover the structure and variations in the human genomics, including fundamental principles of genetics and genomics. Students undertaking this module will review the architecture of the human genome and the functional units embedded in it. Students will also cover aspects of gene regulation and chromatin structure and consider the importance of the epigenome in these processes.

  In addition, this module will cover DNA sequence variation and structural variation, how this sort of variation is normal but that sometimes it can be associated with disease. Classic chromosomal abnormalities will be described and the mechanisms that lead to them explained. Students will learn about monogenic and multifactorial genetic disorders and how gene mapping and sequencing can be used to identify causal and contributory variants.

  In essence, this module covers what the genome is, what abnormalities can arise and how they arise, as well as how they can be detected.

• Genomics of Common and Rare Inherited Diseases (15 credits)

  This module uses exemplars of both common and rare diseases from across the entire healthcare spectrum to demonstrate the clinical utility of genomic data in the healthcare setting.

  The module examples give an insight into how advances in genomic technologies and integration of genomic data into clinical pathways are impacting on the management of patients from the prenatal setting, through paediatrics and into adult medicine and cancer.

  The module will explore the clinical presentation and genetic architecture of disease, as well as the diagnostic and therapeutic implications of genomic data for a myriad of common and rare inherited conditions using expertise from across SGH/GSTT/SGUL/KCL. We will explore traditional and current approaches used to identify genetic predisposition to common and rare inherited diseases, focusing on the latter, within the context of clinical diagnostics.

  We will learn how to select patients with unmet diagnostic needs that will benefit from exome or whole genome sequencing, and some of the complexities involved in the interpretation of genomic data in the clinical context. We will also discuss the Genomics England, genomics medicine services and data infrastructure.

• Introduction to Counselling Skills in Genomics (15 credits)

  This module will provide students with an introduction to general communication skills and specific counselling skills used in genomic medicine. Students undertaking this module will be taught how to communicate and provide appropriate support to individuals and their families.

  Development of counselling skills will be achieved via theoretical and practical sessions through the use of role play within an academic setting. Students will understand the importance of a family history and communication of pathogenic and/or uncertain results.

• Ethical, Legal and Social Issues in Applied Genomics (15 credits)

  Students will be provided with a platform of ethical understanding from which to consider issues of confidentiality, privacy and disclosure, autonomy, welfare, informed consent and justice. Upon this platform, students will consider the impact of genomic technologies on individual lives and public discourse.

  The social implications of the availability of genetic testing and screening will be considered, especially in the context of reproductive technologies. Finally, students will be provided with a discussion of legal issues surrounding the use of genetic information as well as the use of genetic data for research, diagnostic and therapeutic purposes.

• Application of Genomics in Infectious Disease (15 credits)

  The teaching sessions of this module will cover the basics of pathogen genome biology, methods for whole genome sequencing (WGS) applied to pathogens and bioinformatic analysis of pathogen genomes. Numerous examples will demonstrate the relevance of infectious disease genomics to key topics such as antimicrobial resistance, diagnostics, vaccine design, disease surveillance, host susceptibility to infection, public health epidemiology and clinical management of patients.

  The application of WGS and implications of pathogen genomics from a perspective of healthcare pathways and public health for its future impact will be the key focus for your study. The sessions will be interspersed with a series of case studies and research papers for self-directed study, taken from a limited reading list comprising exemplar organisms from the recent literature.

  The sessions explore and present multiple examples of pathogens and genomics: TB drug therapy, Pseudomonas aeruginosa and E. coli outbreaks, Staphylococcus aureus and MRSA, STI diagnostics and resistance, HIV, influenza and the COVID-19 pandemic, pneumococcal and meningococcal vaccine design and surveillance.

  Together the sessions, self-directed learning and associated resources form the defined knowledge base for the module. The literature and other reading materials provide the students with the basis for extended self-study and as a foundation for the module’s summative assessments.

• Bioinformatics, Interpretation and Data Quality Assurance in Genome Analysis (15 credits)

  The module will cover the fundamental principles of informatics and the impact of bioinformatics on clinical genomics. Students will be expected to be able to find and use major genomic and genetic data resources, use software packages and analysis tools for big data and undertake literature searches to critically assess, annotate and interpret findings from sequence data and genetic variants. Theoretical sessions will be coupled with practical exercises involving the analysis and annotation of predefined data sets.

  This module will equip the student with the essential skills to analyse genomic data, applying professional best practice guidelines. Upon completion of this module students will be able to understand how bioinformatics is used to analyse, interpret and report genomic data in a clinical context.

  Students will also be equipped to utilise the 100,000 Genomes Project data set if relevant for their research project.

  *No prior knowledge in programming is required for this module.

• Genomics of Cardiovascular Disorders (15 credits)

  This module explores the burden of cardiovascular disease and the underlying contribution of genetics to these diseases. Students will receive refresher sessions focused on cardiac function as well as being introduced to the key diagnostic tools used in cardiology.

  They will learn about the major arrhythmias and cardiomyopathies which can lead to premature and sudden death. By studying genetic causes of lipid disorders students will understand the impact of rare and common genetic variants on the risk of coronary heart disease. The contribution of "big data" and the development of gene panel tests will be discussed to demonstrate some of the benefits that genomic medicine can offer to this group of diseases.

  Students will hear about the role and challenges of genetic counselling in inherited cardiac conditions.

• Fetal Genomics (15 credits)

  There have been rapid advancements in genomics technologies and their increasing application in prenatal medicine. In today's modern age, where litigation rates in obstetrics and fetal medicine are increasingly high, the need for accurate diagnosis, interpretation, and transparent communication of genomic results has never been more pressing.

  This climate demands practitioners are adept in employing the latest technologies and conveying complex genetic information clearly and compassionately to patients.

  The fetal genomics module aims to bridge this critical gap, providing the necessary training and insights to support precise diagnostics, risk assessments, and patient-centric communication, thereby reducing the potential for legal complications and enhancing trust within the patient-provider relationship.

  This module ensures that students are proficient with the latest techniques and are attuned to the societal, legal, and ethical aspects of prenatal genetic testing.

  The module reflects the need for a multidisciplinary approach in genomics medicine, paving the way for more informed decisions and personalised care in maternal and child health.

• Genomics of Neurological Disorders (15 credits)

  This module explores the contribution of genomics to neurological disorders. Students will receive refresher sessions focussed on neuroanatomy and the development of the neurological system followed by an introduction to the key diagnostic tools used in neurology.

  They will learn about the major neurological disorder categories which have a high genetic contribution. The module will explore the value of the multidisciplinary team in phenotyping, interpretation of results, management and family communication.

• Molecular Pathology of Cancer and Application in Cancer Diagnosis, Screening and Treatment (15 credits)

  The module will guide the students from a basic introduction in cancer biology, to comparing molecular and pathological information applied in the diagnosis, classification, treatment of cancer.

  We will look at immuno-oncology, early detection, and predisposition of cancer, and the use of molecular data and diagnostics in clinical trials. In addition, we will introduce basic machine learning methodologies and different molecular technologies of tumour tissue in the context of target identification, and biomarker development to capture their clinical relevance.

• Omics Techniques and Technologies - Their Application to Genomic Medicine (15 credits)

  This module explores current genomics techniques used for DNA sequencing (e.g. targeted approaches, whole exome and whole genome sequencing) and RNA sequencing, using highly parallel methodologies, together with current technologies routinely used to investigate genomic variation in the clinical setting.

  This module will introduce the bioinformatics approaches required for the analysis of genomic data. The module will also cover the use of array-based methodologies and RNA sequencing in estimating levels of protein expression, micro RNAs and long non–coding RNAs.

  An introduction to metabolomics and proteomics, which are important for the functional interpretation of genomic data and discovery of disease biomarkers will also be included. Students will also learn about the strategies employed to evaluate pathogenicity of variants for clinical reporting.

• Pharmacogenomics and Stratified Healthcare (15 credits)

  The module will provide an overview of the techniques and analytical strategies used in pharmacogenetics and pharmacogenomics and explore some of the challenges and limitations in this field. Moreover, the module will use examples of known, validated pharmacogenetics and pharmacogenomic tests, relevant to the use of drug treatments.

• Omics Techniques and Technologies - Their Application to Genomic Medicine (15 credits)

  This module explores current genomics techniques used for DNA sequencing (e.g. targeted approaches, whole exome and whole genome sequencing) and RNA sequencing, using highly parallel methodologies, together with current technologies routinely used to investigate genomic variation in the clinical setting.

  This module will introduce the bioinformatics approaches required for the analysis of genomic data. The module will also cover the use of array-based methodologies and RNA sequencing in estimating levels of protein expression, micro RNAs and long non–coding RNAs.

  An introduction to metabolomics and proteomics, which are important for the functional interpretation of genomic data and discovery of disease biomarkers will also be included. Students will also learn about the strategies employed to evaluate pathogenicity of variants for clinical reporting.

• Introduction to Counselling Skills in Genomics (15 credits)

  This module will provide students with an introduction to general communication skills and specific counselling skills used in genomic medicine. Students undertaking this module will be taught how to communicate and provide appropriate support to individuals and their families.

  Development of counselling skills will be achieved via theoretical and practical sessions through the use of role play within an academic setting. Students will understand the importance of a family history and communication of pathogenic and/or uncertain results.

• Application of Genomics in Infectious Disease (15 credits)

  The teaching sessions of this module will cover the basics of pathogen genome biology, methods for whole genome sequencing (WGS) applied to pathogens and bioinformatic analysis of pathogen genomes. Numerous examples will demonstrate the relevance of infectious disease genomics to key topics such as antimicrobial resistance, diagnostics, vaccine design, disease surveillance, host susceptibility to infection, public health epidemiology and clinical management of patients.

  The application of WGS and implications of pathogen genomics from a perspective of healthcare pathways and public health for its future impact will be the key focus for your study. The sessions will be interspersed with a series of case studies and research papers for self-directed study, taken from a limited reading list comprising exemplar organisms from the recent literature.

  The sessions explore and present multiple examples of pathogens and genomics: TB drug therapy, Pseudomonas aeruginosa and E. coli outbreaks, Staphylococcus aureus and MRSA, STI diagnostics and resistance, HIV, influenza and the COVID-19 pandemic, pneumococcal and meningococcal vaccine design and surveillance.

  Together the sessions, self-directed learning and associated resources form the defined knowledge base for the module. The literature and other reading materials provide the students with the basis for extended self-study and as a foundation for the module’s summative assessments.

• Genomics of Cardiovascular Disorders (15 credits)

  This module explores the burden of cardiovascular disease and the underlying contribution of genetics to these diseases. Students will receive refresher sessions focused on cardiac function as well as being introduced to the key diagnostic tools used in cardiology.

  They will learn about the major arrhythmias and cardiomyopathies which can lead to premature and sudden death. By studying genetic causes of lipid disorders students will understand the impact of rare and common genetic variants on the risk of coronary heart disease. The contribution of "big data" and the development of gene panel tests will be discussed to demonstrate some of the benefits that genomic medicine can offer to this group of diseases.

  Students will hear about the role and challenges of genetic counselling in inherited cardiac conditions.

• Genomics of Common and Rare Inherited Diseases (15 credits)

  This module uses exemplars of both common and rare diseases from across the entire healthcare spectrum to demonstrate the clinical utility of genomic data in the healthcare setting.

  The module examples give an insight into how advances in genomic technologies and integration of genomic data into clinical pathways are impacting on the management of patients from the prenatal setting, through paediatrics and into adult medicine and cancer.

  The module will explore the clinical presentation and genetic architecture of disease, as well as the diagnostic and therapeutic implications of genomic data for a myriad of common and rare inherited conditions using expertise from across SGH/GSTT/SGUL/KCL. We will explore traditional and current approaches used to identify genetic predisposition to common and rare inherited diseases, focusing on the latter, within the context of clinical diagnostics.

  We will learn how to select patients with unmet diagnostic needs that will benefit from exome or whole genome sequencing, and some of the complexities involved in the interpretation of genomic data in the clinical context. We will also discuss the Genomics England, genomics medicine services and data infrastructure.

• Advanced Bioinformatics (15 credits)

  This module builds upon and extends the module “Bioinformatics, interpretation and data quality assurance in genome analysis ” and further explores state of the art bioinformatics pipelines for genetic data in a clinical context, suitable for studying genetic variants underlying Mendelian diseases, cancer genetics, and RNA expression data using Galaxy, and also introduces the student to basic Bioinformatic data skills using the command line, R/RStudio and Bioconductor.

  The student will learn about the landscape of tools for read mapping and variant calling and how they are suitable for different types of genetic data and analysis. Lectures will be combined with hands on computer workshops/tutorials, where students can practice designing their own bioinformatics pipelines in the Galaxy environment.

  They will work with real gene expression, rare disease and cancer genomics datasets. The course will also provide a primer for working with large genetic datasets using command line tools, scripting bioinformatics pipelines and using R/RStudio and Bioconductor to analyses and explore and visualise NGS and other ‘Omics data.

  *Students aiming to do the Advanced Bioinformatics module will have to complete the Bioinformatics module first. No prior knowledge in programming is required for either module. You will learn R-coding in the Advanced Bioinformatics module and, although you might find it challenging at first, your module leads will provide you with plenty of support and guidance.

  Students doing the Advanced Bioinformatics module will need to download free VPN software and set up a VPN connection to be able to access our cloud computing facilities in advance. You can find a guide about how to do this on macOS, Linux or Microsoft Windows and the VPN configuration file.

• Fetal Genomics (15 credits)

  There have been rapid advancements in genomics technologies and their increasing application in prenatal medicine. In today's modern age, where litigation rates in obstetrics and fetal medicine are increasingly high, the need for accurate diagnosis, interpretation, and transparent communication of genomic results has never been more pressing.

  This climate demands practitioners are adept in employing the latest technologies and conveying complex genetic information clearly and compassionately to patients.

  The fetal genomics module aims to bridge this critical gap, providing the necessary training and insights to support precise diagnostics, risk assessments, and patient-centric communication, thereby reducing the potential for legal complications and enhancing trust within the patient-provider relationship.

  This module ensures that students are proficient with the latest techniques and are attuned to the societal, legal, and ethical aspects of prenatal genetic testing.

  The module reflects the need for a multidisciplinary approach in genomics medicine, paving the way for more informed decisions and personalised care in maternal and child health.

• Genomics of Neurological Disorders (15 credits)

  This module explores the contribution of genomics to neurological disorders. Students will receive refresher sessions focussed on neuroanatomy and the development of the neurological system followed by an introduction to the key diagnostic tools used in neurology.

  They will learn about the major neurological disorder categories which have a high genetic contribution. The module will explore the value of the multidisciplinary team in phenotyping, interpretation of results, management and family communication.

• Molecular Pathology of Cancer and Application in Cancer Diagnosis, Screening and Treatment (15 credits)

  The module will guide the students from a basic introduction in cancer biology, to comparing molecular and pathological information applied in the diagnosis, classification, treatment of cancer.

  We will look at immuno-oncology, early detection, and predisposition of cancer, and the use of molecular data and diagnostics in clinical trials. In addition, we will introduce basic machine learning methodologies and different molecular technologies of tumour tissue in the context of target identification, and biomarker development to capture their clinical relevance.

• Pharmacogenomics and Stratified Healthcare (15 credits)

  The module will provide an overview of the techniques and analytical strategies used in pharmacogenetics and pharmacogenomics and explore some of the challenges and limitations in this field. Moreover, the module will use examples of known, validated pharmacogenetics and pharmacogenomic tests, relevant to the use of drug treatments.

• Advanced Bioinformatics (15 credits)

  This module builds upon and extends the module “Bioinformatics, interpretation and data quality assurance in genome analysis ” and further explores state of the art bioinformatics pipelines for genetic data in a clinical context, suitable for studying genetic variants underlying Mendelian diseases, cancer genetics, and RNA expression data using Galaxy, and also introduces the student to basic Bioinformatic data skills using the command line, R/RStudio and Bioconductor.

  The student will learn about the landscape of tools for read mapping and variant calling and how they are suitable for different types of genetic data and analysis. Lectures will be combined with hands on computer workshops/tutorials, where students can practice designing their own bioinformatics pipelines in the Galaxy environment.

  They will work with real gene expression, rare disease and cancer genomics datasets. The course will also provide a primer for working with large genetic datasets using command line tools, scripting bioinformatics pipelines and using R/RStudio and Bioconductor to analyses and explore and visualise NGS and other ‘Omics data.

  *Students aiming to do the Advanced Bioinformatics module will have to complete the Bioinformatics module first. No prior knowledge in programming is required for either module. You will learn R-coding in the Advanced Bioinformatics module and, although you might find it challenging at first, your module leads will provide you with plenty of support and guidance.

  Students doing the Advanced Bioinformatics module will need to download free VPN software and set up a VPN connection to be able to access our cloud computing facilities in advance. You can find a guide about how to do this on macOS, Linux or Microsoft Windows and the VPN configuration file.

• Bioinformatics, Interpretation and Data Quality Assurance in Genome Analysis (15 credits)

  The module will cover the fundamental principles of informatics and the impact of bioinformatics on clinical genomics. Students will be expected to be able to find and use major genomic and genetic data resources, use software packages and analysis tools for big data and undertake literature searches to critically assess, annotate and interpret findings from sequence data and genetic variants. Theoretical sessions will be coupled with practical exercises involving the analysis and annotation of predefined data sets.

  This module will equip the student with the essential skills to analyse genomic data, applying professional best practice guidelines. Upon completion of this module students will be able to understand how bioinformatics is used to analyse, interpret and report genomic data in a clinical context.

  Students will also be equipped to utilise the 100,000 Genomes Project data set if relevant for their research project.

  *No prior knowledge in programming is required for this module.

• Application of Genomics in Infectious Disease (15 credits)

  The teaching sessions of this module will cover the basics of pathogen genome biology, methods for whole genome sequencing (WGS) applied to pathogens and bioinformatic analysis of pathogen genomes. Numerous examples will demonstrate the relevance of infectious disease genomics to key topics such as antimicrobial resistance, diagnostics, vaccine design, disease surveillance, host susceptibility to infection, public health epidemiology and clinical management of patients.

  The application of WGS and implications of pathogen genomics from a perspective of healthcare pathways and public health for its future impact will be the key focus for your study. The sessions will be interspersed with a series of case studies and research papers for self-directed study, taken from a limited reading list comprising exemplar organisms from the recent literature.

  The sessions explore and present multiple examples of pathogens and genomics: TB drug therapy, Pseudomonas aeruginosa and E. coli outbreaks, Staphylococcus aureus and MRSA, STI diagnostics and resistance, HIV, influenza and the COVID-19 pandemic, pneumococcal and meningococcal vaccine design and surveillance.

  Together the sessions, self-directed learning and associated resources form the defined knowledge base for the module. The literature and other reading materials provide the students with the basis for extended self-study and as a foundation for the module’s summative assessments.

• Fetal Genomics (15 credits)

  There have been rapid advancements in genomics technologies and their increasing application in prenatal medicine. In today's modern age, where litigation rates in obstetrics and fetal medicine are increasingly high, the need for accurate diagnosis, interpretation, and transparent communication of genomic results has never been more pressing.

  This climate demands practitioners are adept in employing the latest technologies and conveying complex genetic information clearly and compassionately to patients.

  The fetal genomics module aims to bridge this critical gap, providing the necessary training and insights to support precise diagnostics, risk assessments, and patient-centric communication, thereby reducing the potential for legal complications and enhancing trust within the patient-provider relationship.

  This module ensures that students are proficient with the latest techniques and are attuned to the societal, legal, and ethical aspects of prenatal genetic testing.

  The module reflects the need for a multidisciplinary approach in genomics medicine, paving the way for more informed decisions and personalised care in maternal and child health.

• Genomics of Cardiovascular Disorders (15 credits)

  This module explores the burden of cardiovascular disease and the underlying contribution of genetics to these diseases. Students will receive refresher sessions focused on cardiac function as well as being introduced to the key diagnostic tools used in cardiology.

  They will learn about the major arrhythmias and cardiomyopathies which can lead to premature and sudden death. By studying genetic causes of lipid disorders students will understand the impact of rare and common genetic variants on the risk of coronary heart disease. The contribution of "big data" and the development of gene panel tests will be discussed to demonstrate some of the benefits that genomic medicine can offer to this group of diseases.

  Students will hear about the role and challenges of genetic counselling in inherited cardiac conditions.

• Genomics of Common and Rare Inherited Diseases (15 credits)

  This module uses exemplars of both common and rare diseases from across the entire healthcare spectrum to demonstrate the clinical utility of genomic data in the healthcare setting.

  The module examples give an insight into how advances in genomic technologies and integration of genomic data into clinical pathways are impacting on the management of patients from the prenatal setting, through paediatrics and into adult medicine and cancer.

  The module will explore the clinical presentation and genetic architecture of disease, as well as the diagnostic and therapeutic implications of genomic data for a myriad of common and rare inherited conditions using expertise from across SGH/GSTT/SGUL/KCL. We will explore traditional and current approaches used to identify genetic predisposition to common and rare inherited diseases, focusing on the latter, within the context of clinical diagnostics.

  We will learn how to select patients with unmet diagnostic needs that will benefit from exome or whole genome sequencing, and some of the complexities involved in the interpretation of genomic data in the clinical context. We will also discuss the Genomics England, genomics medicine services and data infrastructure.

• Genomics of Neurological Disorders (15 credits)

  This module explores the contribution of genomics to neurological disorders. Students will receive refresher sessions focussed on neuroanatomy and the development of the neurological system followed by an introduction to the key diagnostic tools used in neurology.

  They will learn about the major neurological disorder categories which have a high genetic contribution. The module will explore the value of the multidisciplinary team in phenotyping, interpretation of results, management and family communication.