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FRCPath genomics 2022 > session 7: lab management > Flashcards

session 7: lab management Flashcards

1
Q

what is a contingency plan?

A

A management process that analyses specific potential events or emerging situations that might threaten society. These plans establish arrangements in advance to enable timely, effective, and appropriate responses to such events and situations

eg. Brexit, COVID, NICE guidelines change

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2
Q

what are the 3 steps to create a contingency plan?

A
  1. assess the risks
  2. create contingency plan (what is the risk? who is in charge? document communications, update SOPs)
  3. maintain contingency plan
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3
Q

give examples of scenarios where a contingency plan may be needed for a genomics lab?

A
  • flood, severe weather, illness, hazardous spill, terrorism, theft, loss of equipment, loss of IT, covid, Brexit
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4
Q

what local mitigating actions would you take to minimise risk to genomics delivery for contingency plan? Eg. For covid

A
  • document changes to services in quality management system
  • minute meetings where decisions to staff and services are made (UKAS requirement)
  • consult with service users
  • how you would deal with sudden increase in numbers as clinics return
    -keep staff well: social distancing at work (move desks, screens, mental health support), regular cleaning, handwash stations, face mask supplies
  • work out minimum staffing required at all bands
  • validate alternative suppliers/reagents which are less likely to be effected
  • share equipment with other labs
  • allow flexible working for childcare
  • NHSE - distribute resources centrally
  • flexible rotas, prioritise urgent samples
  • redeploy staff to urgent tests eg. prenatal
  • virtual clinics
  • cross-team working
  • consider evening/weekend work
  • arrange to divert samples if necessary
  • virtual MDT meetings
  • arrange business contingency planning meetings
  • ask for feedback from staff
  • ensure staff have necessary competencies - may require training
  • raise any issues of concern on the local risk register for Trust-level awareness
  • stop services with low staffing and least critical
  • reduce NGS runs to accommodate lower staffing
  • automation where possible
    obtain bank staff, locums, retired staff
  • one way systems in lab
  • communicate to service-users that buccal not allowed and to switch to bloods
  • order consumables in good time, increase orders to ensure well-stocked
  • use alternative local/national equipment and discuss if maintenance can be performed in-house
  • engage with IT to highlight resources required - laptops, headsets, Teams support
  • signpost staff to health and wellbeing support
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5
Q

how does the covid pandemic affect genomics labs?

A

NEGATIVES
- staff sickness and leave for isolation/childcare
- anxiety and stress
- mental health/lonliness
- furlough for staff who cannot work on site and have no work to do at home
- tensions around mask-wearing and PPE
- inequality between scientists at home and lab staff
- WFH demand, information governance, ICT, chair and desk suitability, paperless workflows, ICT support - VPN and remote access
- resources - consumables and reagents
- lack of availability of engineers
- license availability like mutation surveyor key
- engagement in remote meeting
- individual performances difficult to monitor
- lack of team ethos/social aspect
- Brexit supply chain compounding issue
- sample reductions - but may have sudden influx and urgent patients may present late or more accutely
- disruption to UKAS inspection, EQA and conferences
- infectious samples - need risk assessments

POSITIVES
- boost to genomics profile due to covid genomics consortium
- increased profile of key workers and public acknowledgement of healthcare scientists
- lower cost conferences
- breathing space to catch up on backlogs
- new skills for volunteers in covid labs
- Pharmacogenomic drugs approved for 1st line therapy instead of chemo

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6
Q

what are national level covid pandemic impacts?

A
  • increased knowledge of COVID and RNA-based vaccines in the public domain
  • increased understanding of genetics of SARS-coV-2 virus
  • creation of COVID-19 genomics UK consortium for WGS of covid
  • delays to major developments eg. WGS
  • delays to GLH reorganising
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7
Q

what are the key points involved in major incident planning?

A
  • business continuity plan
  • workforce planning
  • redeployment
  • communication with service users and staff
  • Datix - record incidents
  • prioritise urgent samples
  • risk assessments and document decisions in quality management system
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8
Q

what is included in a business continuity plan?

A
  • outlines minimum levels of service achieved during a major incident eg. prenatal, outsource testing
  • estimated timeframe of disruption
  • defines risk and how they may affect service eg. fire, IT disruption, staffing
  • recovery plan
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9
Q

which referrals should be prioritised when there is a major incident?

A
  • urgent cancer diagnoses, to inform therapy or MRD monitoring, chimerism testing for SC ttransplant monitoring, prenatal diagnosis, pregnant carrier testing, rapid exome for NICU/PICU, NBS, therapy-informed testing eg. BRCA, neonatal diabetes
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10
Q

what does recovery plan from pandemic involve?

A
  • audits of sample numbers TATs
  • new ways of working
  • feedback from staff
  • restore TATs
  • restore UKAS, accreditation, training
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11
Q

what are the advantages of genomic test directory?

A
  • equity of access
  • up to date with most appropriate technology for best diagnosis and clinical outcome
  • standardised testing
  • introduce new tests in-line with research and evidence
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12
Q

what is the purpose of panel app?

A

expert review and consensus on which genes related to clinical indication
- manually curated
- repository for gene panels in the NHSE Genomic Medicine Service and mapped to the test directory
- addition of new genes, STRs and CNVs as evidence emerges

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13
Q

what factors need to be considered when introducing a new test?

A
  • is there a clinical need? prevalence, severity, expected samples and workload, is the service provided elsewhere?
  • is there clinical demand? who is requesting and who would refer, would it be a screen or diagnosis?
  • is there clinical utility - is there a treatment? would it diagnose a new disease? is there low penetrance, environmental effects, would there be predictive or prenatal testing, would it improve health?
  • is it legal/ethical? incidental findings, prenatal testing, predictive testing, data access and storage, paternity testing, sexing
  • technical testing strategy - test type, no of genes, hot spots, alternative tests (pre-screen IHC, biochemical, methylation), accuracy, reliability, sensitivity, specificity, false negs and positives, IQC, uncertainty of measurement, intermediate outcomes (premutations, mosaicism), incidental findings, sample types,
  • how would new test impact on practice - workload, staffing, time to set up (validation, equipment)
  • will new test replace an old one? increased TAT? less DNA? national guidelines and EQA, positive and neg controls, confirmation with another test?
  • budget - consumables, equipment, staff, competitive price, funding, maintenance costs, business case required,
  • skills and training - workload, external training available? support for troubleshooting, new starters needed - consider annual leave and sickness, IT and bioinformatics, health and safety, COSHH RIDDOR, SOPs
    -equipment & lab- new equipment? can current equipment be used? automation? can equipment be used for other tests? is there space?
  • population factors - incidence, regional or national, variable expressivity, penetrance, carrier frequency, ethnicity-specific, as age, gender, or co-morbidities may affect the accuracy
  • background work - research clinical, molecular, inheritance, acceptance criteria, guidelines, clinicans are aware, assay, reagents, equipment and positive controls
  • validation - SOPs, screen known samples, Test samples in parallel using old/new method, demonstrate repeatability, accuracy robustness, examination, vertical & horizontal audit, review sample figures of expected vs observed, EQA scheme, follow ISO
  • implement service - authorise SOP, ensure staff trained, design worksheets and info folders, report templates, provide info, BPGs, user-satisfaction surveys

ACCE framework (Analytical validity, Clinical validity, Clinical utility, and ethical legal and social implications) should be used as part of the evaluation process.

  • request feedback from users and act on feedack to optimise service
  • ongoing verification - review of trends in process by audit, report, prioritise and resolve errors,
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14
Q

what is UKAS Accreditation to Standard ISO 15189?

A
    • Globally recognised standard specific for medical laboratories
  • focus on patient care and safety
  • sets out standards for quality management systems
  • demonstrates quality and reliability of the diagnostic services.
  • full assessment every 4 years with surveillance annually in-between- expected to improve quality in-between and address non-conformance
  • clinical assessors review docs, witness procedures and interview staff
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15
Q

what is a quality management system?

A

Collection of process focussed on meeting service requirements and improvements
ensures tests/service are fit for purpose
Quality of results- compliance with specification
Compliance to ISO15189 requirement for quality and competence

  • be subject to annual review and continual improvement
  • monitors effectiveness to safeguard organisations and public
  • management of QMS carried out using Q-pulse - Allows for management of document control, audits, incident reporting and equipment maintenance
  • need quality policy and manual and quality manager
  • continual improvement
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16
Q

what areas should be covered in a quality management system?

A
  • roles and responsibilities
  • document control
  • EQA
  • non conformance and preventative/corrective measures
    • Resolution of complaints
  • risk assessment
  • audit
  • management review and actions
  • training, competency, PPRs,
  • validation and verification, documentation and measurement of uncertainty
  • IQC
    • Lab equipment, reagents and consumables, including safety, maintenance and repair and record keeping
  • Pre-examination process; request forms, information for users, sample collection and sample reception
  • Post- examination processes – review, reporting and release of results
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17
Q

what is clinical governance?

A

A system through which organisations are accountable for continually improving the quality of their services and safeguarding high standards of care by creating an environment in which excellence in clinical care will flourish

  • Three key attributes:
    1. Recognisably high standards of care.
    2. Transparent responsibility and accountability for those standards.
    3. Constant dynamic of improvement.

achieved through trust boards and BSGM.

18
Q

what are the components of clinical governance?

A

Clinical audit - review of clinical performance, refining clinical practice as a result and the measurement of performance against agreed standard. EQA is a component of this.

Clinical effectiveness - how well does the intervention work?

Education and training - CPD

Risk management - considered and balanced

Openness - open to public scrutiny

Research and development - review literature and develop guidelines and put into practice

Clinical information and information technology - use info to improve patient care

Patient and public involvement - patient centered

Staffing and staff management

19
Q

what is risk management?

A

risk = “the potential that a chosen action, inaction or activity will lead to an undesirable outcome”.

Risk management is about minimising these risks by:

  • Identifying what can and does go wrong during care
  • Understanding the factors that influence this
  • Learning lessons from any adverse events
  • Ensuring action is taken to prevent recurrence
  • Putting systems in place to reduce risks
  • Clinical incidents reported
20
Q

give examples of risk management in a genetics lab?

A

• Manual handling training
- COSHH assessments
- • Prevention of infection - PPE. risk assessments and SOPs in place
- Adverse Incident Reporting - Patterns and trends should be analysed and changes made to policies and procedures and/or feedback provided to staff where appropriate > put action plan in place
- • There is a legal requirement, under the Reporting of Injuries, Diseases and Dangerous Occurrences Regulations (RIDDOR) 1995, for some incidents to be reported to the Health and Safety Executive (HSE),

21
Q

what is a lab audit?

A

A laboratory audit is an assessment performed to demonstrate that the laboratory’s operations are according to regulatory standards and accreditation regulations, such as ISO 15189. It also detects any deviation in their processes that could affect the quality system.

can be external eg. UKAS or NEQAS or internal. ensure that examination processes are being conducted to agreed procedures and correctly performed. It is a system of comparing reality with requirements. Enables improvement of QMS.

horizontal = • Examines one part of a process applied to more than one item
vertical = • Examines more than one part of a process on one item.
Examination = witnessing of a laboratory procedure as it is performed to ensure compliance with the SOP

22
Q

what is a clinical audit?

A

a quality improvement process that seeks to improve patient care and outcomes through systematic review of care against explicit criteria

23
Q

what is IQC?

A

activities undertaken to detect, reduce and correct deficiencies in a laboratory’s internal analytical process which gives confidence that the test if performing well

24
Q

what is verification?
what is validation

A

verification = ‘Confirmation, through the provision of objective evidence, that specified requirements have been fulfilled’ (doing test correctly)’

If a suitable performance specification is available, it is necessary to check that the new test meets this specification within the laboratory (verification).

Verification is also appropriate when a new test is introduced that uses a well-established method within the lab.

validation = ‘Confirmation, through the provision of objective evidence, that the requirements for a specific intended use or application have been fulfilled’ (doing correct test)

Validation is required when there is no suitable performance specification available and the performance characteristics of the test need to be defined.

25
Q

what is the ACCE framework?

A

Analytical validity = The testing method and details of the validation process; sensitivity and specificity, reliability and re-producibility, based on the labs data from performing the test to date

Clinical validity = how consistently and accurately the test detects or predicts the intermediate or final outcomes of interest PPV and sensitivity

Clinical utility = how likely the test is to significantly improve patient outcomes. does new test remove need for invasive/expensive tests? DO the results influence lifestyle choice? predictive - can the result predict future risk? does the result reduce need for testing family members?

Ethical, legal & social implications of genetic testing

26
Q

what is EQA?

A

“A system of objectively assessing the laboratory performance by an outside agency. EQA is a system whereby a set of reagents and techniques are assessed by an external source and the results of the testing laboratory are compared with those of an approved reference laboratory. The main objective of external quality assessment is to establish inter-laboratory compatibility” (WHO 1981)

27
Q

what is an incidental finding? what are the 3 categories?

A

An incidental finding (IF) can be defined as a finding that has potential health or reproductive importance for an individual but it beyond the primary aim of study.

1) actionable - therapy or prevention
2) clinically relevant but not actionable - eg. carrier status for AR condition
3) VUS - may affect a gene that is relevant to the indication for testing or may be incidental in an unrelated gene

28
Q

what is the difference between a secondary finding and an incidental finding?

A

Secondary findings are purposely analyzed as part of the test, but unrelated to the primary testing indication. Incidental findings are detected unexpectedly during the analysis, and also unrelated to the primary testing indication eg. revealing non-paternity

29
Q

what are the considerations for reporting IFs?

A

• Is it clinically relevant
• Is the disease or risk clearly proven
• Would reporting the finding lead to a better clinical outcome (e.g. are treatments available)
• Has the patient given informed consented for this test
• Patient autonomy- Is there an option for the patient to opt-out for receiving feedback from incidental findings
• Would withholding the information open the department to litigation
• Is it ethical to withhold the information

30
Q

when might incidental carrier findings be reported?

A
  • high carrier status and carrier screening available
  • may provide opportunity for reproductive counselling eg. CF
  • If there is clinical concern of a recessive disorder
  • clinical features consistent with the patient’s reason for referral
31
Q

give examples of IFs that could be reported?

A
  • pre-symptomatic conditions to facilitate early access to medical care eg. diabetes, cancer
  • deletions of known TSGs eg. FAP - . Regular surveillance and prophylactic surgery
  • BRCA mutation in prenatal array - implications for mother
  • fetus carrier of x-linked disorder - risk to future pregnancies
  • MECP2 deletion in control probe in DMD MLPA kit
    -identification of Klinefelter (XXY) males during routine fragile X testing

prenatal CNV guidelines has list of reportable and non-reportable CNVs was included.

32
Q

what is the difference between a screen and a test?

A

The primary purpose of screening tests is to detect early disease or risk factors for disease in large numbers of apparently healthy individuals.
The purpose of a diagnostic test is to establish the presence (or absence) of disease as a basis for treatment decisions in symptomatic or screen positive individuals (confirmatory test).

33
Q

what is specificity?

A

proportion of those without the condition who return a negative screen result. True negative.

high specificity means the screen has as few false positives as possible

34
Q

what is sensitivity?

A

the proportion of those with the condition who have a positive screen result; also known as detection rate. True positive

35
Q

what is clinical utility?

A

The clinical utility of a genetic test is based on the health benefits related to the interventions offered to individuals with positive test results.

36
Q

is sensitivity or specificity more important for a screen? and a test?

A

screen = high sensitivity
test = high specificity. More weight given to accuracy and precision

The more sensitive a test, the less likely an individual with a negative test will have the disease and thus the greater the negative predictive value. The more specific the test, the less likely an individual with a positive test will be free from disease and the greater the positive predictive value.

37
Q

how can you decrease a lab’s budget?

A

1) Genetics/molecular pathology laboratory service integration
- cross-training staff, sharing equipment/consumables cost, shared LIMS systems that can cross-talk with other systems

2) Reduction of staff costs (80% of budget) - cross-training staff, recruit lower band workers and release time from higher bands, Replacing retiring/leaving staff at a lower pay-scale band, • Not employing staff for maternity leave cover, reduce staff hours, redundancy, automate wet lab, automate dry lab with bioinformatics. risk of loss of expertise compromises quality.

3) Reduction of non-staff costs - alternative cheaper consumables, longer term orders, collaborate to order in batch, reduce repair contracts, stop offering specific tests, replace with cheaper testing kits, do in-house instead of sendaway, funding for research, batch testing, optimise testing to reduce failure-rates, cut out stationary, WFH, switch energy suppliers.

4) increase income - charge more for private testing, research grants,

staff cost the most so reduce this area first.
• Changes to a service have to be cost neutral, unless you are prepared to write a business plan. If there is a change in price for a service, users must be informed and have the opportunity to move elsewhere
- often better to rent than to buy outright

38
Q

what is the difference between cost and price

A

Cost is what it actually costs the department to perform a test in terms of consumables, however price is what the department charges, which includes staff time, maintenance etc.

39
Q

what is the main piece of legislation which affects the management of health and safety across all sectors

A

health and safety at work act 1974

40
Q

when should a risk assessment be done?how is it done?

A
  • implementing new chemicals or equipment
  • a change to policy

• Identify the hazards
• Decide who might be harmed and how
• Evaluate the risks and decide on precautions
• Record your findings and implement them
• Review your assessment and update if necessary

41
Q

what is the role of the quality manager

A
  • ensures adherence to lab quality manual.
42
Q

what is a quality manual?

A
  • defines your lab QMS to establish and maintain continuity of activity. Sets out organisation structure and clear roles and responsibilities of staff.
  • management report which contains yearly quality objectives including your lab vision/strategic intent (outline future direction) and how that will be operationalised against time frame. Achievement of objectives of your strategy needs to be monitored/reviewed/reflected on in following report

FRCPath genomics 2022 (10 decks)

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