Module MSE-4089:
Molecular Diagnostics

Run by School of Medical Sciences

20 Credits or 10 ECTS Credits

Semester 2

Organiser: Dr David Pryce

The Molecular Diagnostics module is designed to provide the opportunity for students to expand their theoretical knowledge and understanding of molecular genetics and immunoassays into practical laboratory applications, utilised in clinical prognosis and monitoring of Chronic Myeloid Leukaemia patients and in academic research, in detection of novel protein biomarkers. The module will enable students to develop both conceptual understanding and practical experience in molecular diagnostics, performed within the clinic, in biomedical sciences and in research.

The module is delivered over two weeks. In the first week students will spend 2 and half laboratory days preforming an RQ-PCR prognostic test, to determine the level of BCR-ABL transcripts present in peripheral blood derived from a chronic myeloid leukaemia patient, undergoing standard tyrosine kinase therapy. Two days will then be used to develop proficiency in using the BioRad CFX manager qPCR analysis software to perform data quantification and report productions, to level expected of a certified BCR-ABL monitoring laboratory. European Leukaemia Network

In the second week students will spend 3 laboratory days preforming an immunoprecipitation experiments, to detect 'novel' protein antigenic biomarkers present in peripheral blood derived from a chronic myeloid leukaemia patient, undergoing standard tyrosine kinase therapy. Two days will then be used to develop proficiency in utilising the BioRad ImageLab analysis software to perform quantitative multiplex westernblot analysis to a level required to produce publication quality data.

Students will employ a number of molecular laboratory techniques; including plasmid extraction, purification, qualitative and quantitative analyse using fluorometer estimation, agarose gel electrophoresis and RQ-PCR analysis of cDNA. Protein work will include standardised extraction of total proteins from human cells, utilising RIPA buffer, estimation of protein concentration using BCA - standard curve analysis, immunoprecipitation utilising protein G magnetic bead technology, SDS-PAGE protein separation and multiplex fluorescent western blotting.

excellent

Distinction (A- to A**) (range 70-100%)

Primary criteria

Comprehensive 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 Criteria

A* Outstanding

• Exceeds expectations for most primary criteria
• Complete command of subject and other relevant areas
• Ideas/arguments are highly original

A+ Excellent

• Exceeds expectations for some primary criteria
• Complete command of subject
• Ideas/arguments are highly original

A Good

• Meets all primary criteria
• Command of subject but with minor gaps in knowledge areas
• Ideas/arguments are mostly original

A- 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

good

Merit (B- to B+) (range 60-69%)

Primary criteria

Good students demonstrate strong knowledge & understanding of most but not all of the subject area. Limited evidence of background study. The answer is 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 communication

Secondary Criteria

B+ Good

• Exceeds expectations for most primary criteria
• Command of subject but with gaps in knowledge
• Some ideas/arguments original

B Mid-level

• Meets all primary criteria
• Strong factual knowledge and understanding
• Ideas/arguments are well presented by few are original

B- 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

threshold

Pass (C- to C+) (range 50-59%)

Primary criteria

A threshold student demonstrates knowledge of key areas & principles, and understands the main elements of the subject area, although gaps and weaknesses in the argument are evident. No evidence of background study and wider reading. Answer focussed on question but also with some irrelevant material and weaknesses in structure & argument. Answers have several factual/computational errors. No original interpretation. No links between topics are described. Limited problem solving skills. Some weaknesses in presentation accuracy & delivery.

Secondary Criteria

C+ 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 presented

C Mid-level

• Matches all primary criteria
• Moderate factual knowledge with some weaknesses in understanding
• Ideas/arguments are limited presented with weaknesses in logic/presentation

C- 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

1. Critically discuss molecular diagnostic data in the context of medical research

2. Correctly interpret, accurately and ethically report laboratory-derived molecular diagnostic and/or prognostic results

3. Identify and appropriately employ bioinformatic applications to generate, interpret and analyse molecular diagnostic data

4. Demonstrate in-depth knowledge and understanding of the principles and current limitations of molecular diagnostic applications and data

5. Demonstrate appropriate good laboratory practices and technical skills for accurate and precise generation of molecular diagnostic data

Type	Name	Description	Weight
INDIVIDUAL PRESENTATION	Clinical Report Presentation	Students will prepare a deliver a Powerpoint presentation, during a presentation day to be held during the end of semester 2 examination period. The presentation and presenter should deliver - A standardised 'clinical monitoring report' that presents the determination of the normalised copy number of BCR-ABL transcripts present in cells derived from a Chronic Myeloid Leukaemia patient who is undergoing Tyrosine Kinase inhibitor (TKI) therapy regime A prognosis and discussion of potential treatment options for the patient, based on the patients RQ-PCR data results and current TKI therapy regime Detailed guidance is available via the module Evernote site	40
REPORT	Research Paper	The practical report will be written as a Research paper formatted for submission to the peer-reviewed scientific journal Cell. It is estimated 30 hours of notional effort time is required in preparation for the report assessment The Practical Report should be as concise as possible and written in a style that is accessible to the broad, scientific readership. The abstract (summary) should be no more than 150 words (±10%), a Word count must be presented. Highlights (4 points maximum) and In Brief section, of no more than 4 sentences. The total word count for the rest of the report should be approximately 3000 words, excluding bibliography/references. A word count must be presented at the beginning of the main report Further guidance is available on the module Evernote site Essential information will be recorded using the Panopto system.	60

		Hours
Workshop	1 x 3hr Computer based tuition on utilisation of CFX manager qPCR analysis software and identification of ‘best' qPCR data sets 1 x 3hr Computer based tuition on creation of qPCR calibration standard curves and bar graphs, statistical analysis and '% normalised copy number' for clinical reporting of BCR-ABL transcript levels 1 x 3hr Computer based tuition on use of BioRad Imagelab software for semi-quantitive fluorescent blot analysis and figure production	9
Laboratory	Two consecutive weeks of laboratory-based experiment practical work week one laboratory work, Monday and Tuesday 9:30-5:00, Wednesday 9:30-13:00, week two laboratory work, Monday and Tuesday 9:30-5:00, Wednesday 9:30-13:00 Results and analysis will be updated throughout laboratory stages, utilising cloud based electronic laboratory book. Panopto recordings of analysis and workshop sessions will be employed, as and when necessary.	32
Private study	Self-directed study to develop in-depth knowledge and understanding and preparation of assessments	159

• Literacy - Proficiency in reading and writing through a variety of media
• Numeracy - Proficiency in using numbers at appropriate levels of accuracy
• Computer Literacy - Proficiency in using a varied range of computer software
• Self-Management - Able to work unsupervised in an efficient, punctual and structured manner. To examine the outcomes of tasks and events, and judge levels of quality and importance
• Exploring - Able to investigate, research and consider alternatives
• Information retrieval - Able to access different and multiple sources of information
• Inter-personal - Able to question, actively listen, examine given answers and interact sensitevely with others
• Critical analysis & Problem Solving - Able to deconstruct and analyse problems or complex situations. To find solutions to problems through analyses and exploration of all possibilities using appropriate methods, rescources and creativity.
• Safety-Consciousness - Having an awareness of your immediate environment, and confidence in adhering to health and safety regulations
• Presentation - Able to clearly present information and explanations to an audience. Through the written or oral mode of communication accurately and concisely.
• Teamwork - Able to constructively cooperate with others on a common task, and/or be part of a day-to-day working team
• Mentoring - Able to support, help, guide, inspire and/or coach others
• Caring - Showing concern for others; caring for children, people with disabilities and/or the elderly
• Management - Able to utilise, coordinate and control resources (human, physical and/or financial)
• Argument - Able to put forward, debate and justify an opinion or a course of action, with an individual or in a wider group setting
• Self-awareness & Reflectivity - Having an awareness of your own strengths, weaknesses, aims and objectives. Able to regularly review, evaluate and reflect upon the performance of yourself and others
• Leadership - Able to lead and manage, develop action plans and objectives, offer guidance and direction to others, and cope with the related pressures such authority can result in

• Ability to plasmid DNA from bacteria and perform serial dilution to achieve specific plasmid copy number concentrations
• Ability to extract, analyse and quantify RNA from chronic myeloid leukaemia (CML) cell lines, grown in standard and tyrosine kinase supplemented culture conditions
• Ability to perform RQ-PCR BCR-ABL transcript monitoring, to certified European Leukaemia Network laboratory standards.
• Proficiency in utilising BioRad CFX manager software to perform RQ-PCR data analysis and produce publication quality data.
• Ability to extract and quantify protein from CML cells lines
• Ability to preform magnetic bead technology immunoprecipitation, SDS-PAGE protein separation and multiplex fluorescent western blotting to detect specific proteins.
• Proficiency in utilising BioRad ImageLab analysis to perform quantitative multiplex western blot analysis to a level required to produce publication quality data.

Resource implications for students

All resources needed to complete this module are provided. Computers can be accessed in multiple locations across the university. All teaching materials will be available on Blackboard. Completed assignments will be uploaded onto Turnitin through Blackboard. A limited number of the recommended textbooks can be found within the library.

Talis Reading list

http://readinglists.bangor.ac.uk/modules/mse-4089.html