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FRCPath Genomics > 09 - Quality > Flashcards

09 - Quality Flashcards

1
Q

What is the basic steps of an Audit

A

1) Set Standards
2) Measure current practice
3) Compare results of current practice Vs standards set
4) reflect, plan and implement change
5) re-audit

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2
Q

why audit?

A

1 - demonstrate quality of service to users
2 - identify areas for change
3 - improve quality
4 -assist with implementation of policies + guidelines
5 - monitor consistency of performance
6 - measure actual performance Vs benchmark

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3
Q

what are the 4 types of audit?

A

1) Clinical
systematic review of care against explicit criteria

2) Verticle
exams all parts of a process on a single item (i.e. a sample - from booking in, to extraction, to testing, reporting etc)

3) horizontal
looks at a single process - multiple items

4) examination
witness a procedure being performed - is it done in accordance to SOP

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4
Q

What are the 5 key aspects of a Quality Management System

A

1) People, training and experience
2) Equipment and facilities
3) Reviewing and checking
4) Processes
5) Documents and records

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5
Q

What may be considered under the QMS People, training and experience category?

A
  • job descriptions
  • staff profiles
  • records of staff training (competency docs)
  • CPD
  • staff reviews (PDRs)
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6
Q

What may be considered under the QMS Equipment and facilities category?

A
  • equipment lists
  • maintenance records
  • calibration
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7
Q

What may be considered under the QMS Reviewing and checking category?

A
  • descriptions of set standards

- records of update

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8
Q

What may be considered under the QMS Processes category?

A
  • SOP
  • COSSH
  • risk assessment
  • BPG
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9
Q

What may be considered under the QMS Documents and records category?

A
  • lists of secure controlled documents
  • meeting minutes
  • distribution lists
  • contacts
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10
Q

What approaches can be taken to met ‘Quality improvement’ in a diagnostic lab

A
  • Internal audits (non-compliance found and corrective actions put in place)
  • Set quality objectives
  • User Surveys
  • Use of error log / adverse incident recording system
  • complaint policy
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11
Q

What approaches can be taken to met ‘Quality maintenance’ in a diagnostic lab

A
  • Assigned quality manager / team
  • regular assessment of Key Performance Indicators (KPIs)
  • staff training
  • assessment through external quality schemes
  • appropriate laboratory management structure
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12
Q

what is the key ISO standard for diagnostic lab

A

ISO15189

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13
Q

What are the 8 sections CPA / UKAS assess based upon ISO15189

A 
1 - Organisation and QMS
2 - Personnel
3 - Premise and environment
4 - Equipment (inc. IT)
5 - Pre-examination process
6 - Examination process
7 - post-examination process
8 - Evaluation & quality assurance
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14
Q

What can be assessed by an EQA

A

1 - technical performance (DNA quantification)
2 - Analytical (detection of abnormality)
3 - Interpretative (variant classification)

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15
Q

What is UKAS

A
  • UKAS is the UK accreditation Service
  • Sole national accreditation body recognised by the government
  • genetic labs are expected to comply with ISO15189
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16
Q

Can you provide an example of an EQA scheme

A

GenQA

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17
Q

what are the 5 steps UKAS follows

A 
1 - Pre-assessment
2 - Assessment (on site visit)
3 - Post-assessment
4 - Surveillence Report
5 - Re-assessment
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18
Q

Name the most common framework used to evaluate the performance of a genetic test (was previously used by UKGTN)

A

ACCE:

A - Analytical Validity
C - Clinical Validity
C - Clinical Utility
E - ethical, legal and social implications

19
Q

What is Analytical Validity

A
  • need to consider how accurate and reliable the test measures genotype of interest
  • sensitivity
  • specificity
  • repeatability
20
Q

What is Clinical Validity

A
  • how consistently / accurately the test detects/predicts the immediate/final outcome of interest:
  • positive predictive value - the probability of having / developing a disorder with a positive test result
  • negative predictive value - the probability of NOT having / NOT developing a disorder following a negative test result.

i.e. if 50 mutations are currently known to cause disease - if test all 50 and get negative result = highly unlikely to develop disorder. BUT if only offer test for 1 / 50 mutations and get a negative result, its a bit of a futile test

21
Q

what is Clinical Utility

A
  • how likely will a test significantly improve a patients life (i.e. why test?). Reasons could be:

> Diagnosis (would a diagnosis change management / prevent another more invasive test?)

> Prognosis and Management - would result benefit prognosis/managment

> Pre-symptomatic testing - do results open upon accurate future predictive testing

> Genetic Risk assessment - will as result reduce the need for clinical investigation in other family members

22
Q

What can the ACCE framework help with

A

Implementing a new diagnosis test

23
Q

What is the main difference between a Verification and a Validation

A

Is a suitable performance specification available?

If yes = Verifiation
If No = validation

24
Q

Provide an example of a Verification

A
  • Introduction of a new test which has been CE marked.
  • Introduction of CF-EU2 kit from commercial company.
  • Kit has specified protocol to adhere to and performance (mutations detected, sensitivity and specificity) is all documented.
  • verification is required to confirm that kit complies with its own set standards (i.e. the mutations it should detect, are detected)
25
Q

Provide an example of a Validation

A

Introducing a new in-house developed assay.

  • expected standards need to be set and tested to prove that assay can adhere to this. I.e. an assay may be required to detect an SNV at a v. low level (1%) - need to test and prove this can be achieved, reliably
26
Q

When introducing a new service into a lab, there are many considerations. List all considerations

A

1 - Is there a clinical NEED for service
2 - Is there a clinical DEMAND for service
3 - is there a clinical UTILITY for service
4 - what are the legal / ethical considerations
5 - what is the technical testing strategy
6 - What is the impact upon current working practices
7 - Will the new service replace an old one
8 - Need to consider BUDGET
9 - Need to consider STAFF TRAINING + EDUCATION
10 - Need to consider EQUIPMENT
11 - Need to consider POPULATION FACTORS

THEN

12 - Research. Conduct testing
13 - Validation
14 - implementation
15 - Ongoing Verification

27
Q

what are the key components of Clinical Governance

A 
1 - Clinical Audit
2 - Clinical effectiveness
3 - Education and training
4 - RISK MANAGEMENT
5 - Openness
6 - Research and development
7 - Clinical Information (inc. IG, IT)
8 - Public and Patient Engagement
28
Q

What is a Screen?

A
  • process of identifying apparantly healthy individuals at increased risk of disease / condition
  • can improve life through early risk identification
  • but does NOT provide a diagnostic value
  • targets populations rather than those at risk
  • key:
  • low risk result does NOT exclude a positive result
  • high risk result does NOT mean a positive result
29
Q

A validation / verification process should include:

A

> description of process and its intended use
aims and objective
defined acceptance criteria
details of evaluation process (methodology)
record of evidence
review

30
Q

During a validation / verification what criteria can be assessed?

A

> Trueness - quantitative tests (how close is result to true value)
Sensitivity - % positive results correctly identified
Specificity - % negative results correctly identified
Accuracy
Precision - degree in which replicate measurements differ
Robustness - reliability of test which variable change
repeatability - closeness of agreement of results obtained using same samples and test conditions
reproducibility - closeness of agreement of results obtained when using same sample but different conditions

31
Q

So for QUANTITATIVE tests - what are the key criteria to assess

A

> trueness
precision
limits of detection

32
Q

So for CATEGORICAL tests - what are the key criteria to assess. (where a quantitative signal is placed within a category - i.s. HD)

A

> Accuracy
Trueness
Precision
Limits of Detection

33
Q

So for QUALITATIVE tests - what are the key criteria to assess

A

> sensitivity
specificity
accuracy
limits of detection

34
Q

An incidental finding can be defined as…..

A

a finding that has potential health or reproductive importance for an individual, discoed in the course of conducting a particular study, but is beyond the aims of that study

35
Q

Incidental findings fall into 1 of 3 categories, what are they?

A

1) Actionable
2) Clinically Relevant (non actionable)
3) Uncertain significance

36
Q

What is an ACTIONABLE incidental finding

A

One in which a known therapy or preventative measure exists which can significantly benefit health of the individual

37
Q

what is a CLINICALLY RELEVANT incident finding

A

Has a relevance clinically, but is non actionable. The classic example is detection of carrier status in an AR disorder where carrier screening is available (e.g. CF)

38
Q

What should you consider when deciding whether or not to report an incidental finding?

A

> Is it clinically relevant?
Is it actionable?
would reporting it lead to a significant health benefit to the patient
would withholding the information open the department up to litigation?
is it ethical to withhold the information?

39
Q

can you provide an example of an incidental finding detected during karyotype investigations? Would you report it?

A

Patient is undergoing cytogenetic investigations in relation to leukaemia and a balanced germline chromosome rearrangement (unlikely to be relevant to their leukaemia) has been detected.
This would be reported as potential impact on reproductive options for the patient and risks or an unbalanced offspring in the future.

40
Q

A pathogenic CNV has been detected by array/NGS in an Autosomal Recessive Gene. Should you report?

A

> if the AR disorder is relevant to the patients presenting phenotype - yes report.
if the AR disorder is unrelated to patient’s presenting phenotype, do NOT report.
one caveat, is detection of pathogenic CNV in AR gene where there is carrier screening available.

41
Q

Should you report a CNV detected in a gene associated with late-onset disease?

A

Yes report

42
Q

Should you report a CNV detected in a gene associated with susceptibility to cancer

A

yes report

43
Q

what guidance is available to determine if a IF should be detected?

A

> Currently no ACGS guidance
ACMG produced guidelines on report incidental findings in 2017, provide a list of genes in which pathogenic variants detected, should be reported.
Most of these genes are cancer susceptibility genes, or involved in cardiac conditions.
ESHG have similar recommendations to ACMG

FRCPath Genomics (12 decks)

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