1. GENETICS & BIOINFORMATICS GENETICS & BIOINFORMATICS SARAH DOWSON: CLINICAL SCIENTIST STP GRADUATE (2015)

2. WHAT IS GENETICS? What do we do  We receive, test, analyse and report patient samples for various genetic diseases  We perform a huge range of tests – PCR/DNA sequencing/FISH/Array…  We provide fully interpreted genetic reports to the referring doctors and advise on further testing options Some examples of testing we do  BRCA testing for people with family history of breast cancer – can make informed surgical decisions to reduce risk  Neonatal blood spot screening for Cystic Fibrosis – early detection and management of babies affected  Follow up testing from the 100,000 genomes project  Many many more

3. STRUCTURE OF PROGRAM Training course is 3 years long 1 st year is rotations (3 out of Biochemistry, Immunology, Haematology, Reproductive science, Histopathology or Cytopathology) 2 nd and 3 rd year specialist Masters runs alongside  Either block release or distance learning Elective (4-6 weeks) can be done anytime during 2/3 year but typically done towards the end second year ~5 month research project usually done end 2 nd /beginning 3 rd year (to comply with university requirements)

4. MSc QUALIFICATION Funded three year academic study to parallel work based rotations / placements Underpins the experimental learning being undertaken in the workplace Distance learning vs. block release

5. WORK BASED TRAINING - competencies Basic day-to-day role is to fulfil competency/learning outcome list by performing tasks related to the role of a clinical scientist (examples to follow) Competencies broken down into different modules:  Genetics of Learning Disability  Genetics of Infertility and Sexual Differentiation  Genetics of Cancer (Inherited and Acquired)  Genetics of Neuromuscular Disease  Genetics of Population Screening Professional practice competencies run alongside the specialism competencies and are common to all trainees  These are things you should generally cover whilst completing your training

6. WORK BASED TRAINING - assessments Continued assessment using the different methods:  DOPS – i.e. perform analysis on a patient sample referred for learning disability, perform DNA extraction techniques, write fully interpretive reports for patients referred for a neuromuscular disorder  CBD – two in relation to each module i.e. for a CBD in the Cancer genetics module write a case on an interesting BRCA screening and one on an unusual HNPCC referral  OCE – slightly harder in a laboratory based specialism as very limited patient contact i.e. ‘take a patient history’ features in all modules – using a volunteer take a history in the context of the module Reflective practice is encouraged through the ‘Reflective Diary’ section of OLAT

7. Day-Day Activities Receive samples into the lab and select and assign correct tests in the computer system The samples booked in you then process in the lab carrying out the relevant procedures The analysis is then performed on these patients and results recorded All patients analysed you would then write the reports for …

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9. BIOINFORMATICS (GENOMICS) Information kindly provided by Matt Garner (Cambridge 3 rd year STP in Bioinformatics) What is bioinformatics: Computationally analyze, visualize, catalogue and interpret large biological data sets related to the genome sequences.

10. BIOINFORMATICS ROTATION

11. 1 ST YEAR ROTATION BREAK DOWN Introduction to Clinical Bioinformatics and Genetics: application of bioinformatics tools to aid gene annotation/variant interpretation Computing for Clinical Scientists: database design/implementation ICT in the Clinical Environment: software development, networking, data backup Health Informatics: tools and considerations (lots of information governance) for handling large sensitive data sets

12. SPECIALISM BREAKDOWN Programming: Design/code/document/evaluate a small bioinformatics application Advanced Clinical Bioinformatics: Variant annotation Applied Next Generation Sequencing: NGS data QC, analysis and interpretation IT for Advanced Clinical Bioinformatics Applications: Design/develop/test/deploy an automated bioinformatics workflow Whole Systems Molecular Medicine: Mathematical modelling of gene networks to drive testing strategies

13. ACADEMIC COMPONENT Content of academic component matches work based content closely for the first and second years Third year geared towards building awareness of the direction things may be going in the future, and introductions to tools/resources we may find useful The academic component is delivered in block release at Manchester (except 2 weeks in Liverpool during year 1 to cover medical physics). Assessment is by evaluation of group work generated during problem based learning sessions, and coursework given following each block to be completed when we return to host depts. There are also exams for year 1 modules, but not for years 2-3. Research project selection also varies considerably between labs – some get a lot of choice of subject, others get a project assigned

14. TYPICAL DAY-TO-DAY ROLE Seems to be a lot of variation between labs The most common tasks in the work based component (after rotations) include:  Developing software tools for the lab to use  Evaluating/validating new software from external sources  Assisting clinical scientists with understanding bioinformatics data/results  Running the pipeline (usually not developing it)  Code review  Training others  Writing SOPs

15. EXAMPLE COMPETENCIES

16. GENERAL POINTS There are many tasks which are limited to one/few labs, and the even common tasks are not common to all labs, so it’s really dependent on where you are. The role is not well defined yet, probably because it is relatively new, and due to the diversity between different labs in terms of NGS adoption and existing bioinformatics expertise. There are very few, if any people already in post who know much of the stuff you need to learn. As a result, a large proportion of time is spent doing self directed learning of skills, i.e. learning Python, databases, Linux, shell, version control, good software development practices etc. There’s little training specifically in Genetics, but you obviously need to understand the biology to interpret the data, so there’s a lot to learn that’s not explicit within the curriculum, but necessary to know to be useful.

17. GENERAL POINTS The STP is hard work! – its not a 9-5 job, there is lots of work outside of normal hours It must be driven by you the trainee You may not get the location you want and this is something you have to consider It is very competitive It is nothing at all like research and the opportunities for research are minimal and depend on where you are based Depending on the specialism and where you are based, peoples knowledge of the course may still not be great; you may end up training the trainers

18. QUESTIONS?