Overview

This module will explore how information from the transcriptome, metabolome and proteome can be applied to the interpretation of genomic information. This will include: the basis of genotyping and detection of genetic variation; and the strategies employed for evaluating pathogenicity of variants for clinical reporting. Students will be taught; the methodologies employed for whole exome and whole genome sequencing; the methodologies to assess the transcriptome; methodologies to assess the metabolome and proteome. The module will also demonstrate the importance of metabolomics and proteomics for the functional interpretation of genomic data and discovery of disease biomarkers.

Topics will be presented via lectures, seminars, study groups work-based learning and tutorials. The syllabus will include topics such as: • The basis of genotyping and detection of genetic variation. • Whole exome and whole genome sequencing, including library preparation methods, sequencing chemistries and platforms • Genomic testing strategies as: gene focused, multiple genes, or whole genome or exome, and for detection of sequence, copy number or rearrangements • An overview of the methodologies to assess the transcriptome, including RNA expression profiling and sequencing
• A brief introduction into the methodologies employed to assess the metabolome and proteome. • How information from the transcriptome, metabolome and proteome can be applied to the interpretation of genomic information. • Approaches to the evaluation of pathogenicity of variants in the context of an NHS clinical report.

Assessment Strategy

-threshold -Pass (C- to C+) (range 50-59%)Primary criteriaA pass level demonstrates knowledge and comprehension of key areas & principles, with understanding of the main elements of the subject area, although gaps and weaknesses in the argument are evident. No real evidence of background study and wider reading is evident. Answers are focussed on questions but also with some irrelevant material and weaknesses in structure & argument. Answers have several factual/computational errors. Lack of originality and interpretation. No links between topics are described. Limited problem solving skills. Some weaknesses in presentation accuracy & delivery.Secondary CriteriaC+ Good within the class - Exceeds expectations for some primary criteria - Strong factual knowledge with some weaknesses in understanding - Ideas/arguments are limited but are well presentedC Mid-level - Matches all primary criteria - Moderate factual knowledge with some weaknesses in understanding - Ideas/arguments are limited presented with weaknesses in logic/presentationC- Meets requirements of class - Matches most but not all primary criteria - Moderate factual knowledge with several weaknesses in understanding - Ideas/arguments are limited presented with weaknesses in logic/presentation

-good -Merit (B- to B+) (range 60-69%)Primary criteriaGood students demonstrate strong knowledge & understanding of most but not all of the subject area. Limited evidence of background study. The answers are focussed with good structure. Arguments are presented coherently, mostly free of factual/computational errors. Some limited original interpretation. Well know links between topics are described. Problems are addressed by existing methods/approaches. Good presentation with accurate communicationSecondary CriteriaB+ Good - Exceeds expectations for most primary criteria - Command of subject but with gaps in knowledge - Some ideas/arguments originalB Mid-level - Meets all primary criteria - Strong factual knowledge and understanding - Ideas/arguments are well presented by few are originalB- Meets requirements of class - Meets most but not all primary criteria - Strong factual knowledge with minor weaknesses in understanding - Most but not all ideas/arguments are well presented and few are original

-excellent -Distinction (A- to A) (range 70-100%)Primary criteriaComprehensive knowledge & detailed understanding. Clear evidence of extensive background study & originality. Highly focussed, relevant and well structured answers. Arguments logically presented and defended with evidence and examples. Excellent presentation skills with very accurate communication.Secondary CriteriaA Outstanding - Exceeds expectations for most primary criteria - Complete command of subject and other relevant areas - Ideas/arguments are highly originalA+ Excellent - Exceeds expectations for some primary criteria - Complete command of subject - Ideas/arguments are highly originalA Good - Meets all primary criteria - Command of subject but with minor gaps in knowledge areas - Ideas/arguments are mostly originalA- Meets requirements of Class - Meets most but not all primary criteria - Complete command of subject but with some gaps in knowledge - Ideas/arguments are mostly original

Learning Outcomes

• Critically interpret functional applications of genomic, transcriptome, metabolome and proteome data in pathogenicity and disease biomarker discovery 

• Demonstrate subject expertise and understanding of methodologies and technologies employed in whole exome and genome library preparation, and transcriptome, metabolome, proteome assessment and analysis

• Evaluate the pathogenicity of variants in the context of clinical reporting