Part 2 Flashcards
What can drive the addition of a new test into a lab?
Request from clinician
Change to meet BP/NICE Guidelines
Change to meet needs of lab - more efficient, cost effective, access to new equip
What 4 broad factors should you consider when setting up a new test?
Clinical and Genetic
Population
Technical
Other - staffing, space, cost etc
Setting up a new test - clinical factors - what are the 3 main categories for clinical purpose of new test?
1) To reduce morbidity or mortality
2) To provide information to the care of patient/family
3) To assist family in reproductive decision making
What clinical information can a test provide for the care of a patient/family?
Diagnosis, treatment options, prognosis, management
What reproductive information can a test provide for a family?
Carrier testing, prenatal testing, pregnancy management, PND, NIPD/NIPT, accurate risk scores
In what ways can a result of a test aid clinical care and outcome for a patient?
Direct impact on treatment options
Confirmed diagnosis - end of diagnostic odyssey
Family implications - cascade testing, parental samples etc
What genetic knowledge is needed to set up test?
Gene(s) involved, mode of inheritance, mutation spectrum, penetrance, ethnic differences, pseudogenes, penetrance, populations to target
How might the genetics of a disorder dictate the use of a particular assay?
Pseudogenes - eg CAH
Triplet disorders - eg FRAX, HD
Mosaic disorders - eg Pallister Killian
CNV vs SNV vs both
What population factors should be considered when implementing a new test?
Disease Prevalence
Ethnicity of test population
Clinical and social infrastructure to support genetic findings
What equipment/reagent implications should be considered when setting up a new test?
New vs existing equipment
New - cost, including service contract, space and future applications
Existing - impact on other tests in lab
Sharing with another lab
COSHH, storage, calibration, acceptance of use
What IT infrastructure might be needed when setting up a new test?
Analysis software
Data output and storage
Level of bioinformatics required
Additional info in existing LIMS - eg workflows etc
What sample considerations must be taken if implementing a new test?
Easy to get DNA/cells from Stability of cfDNA if applicable Transport requirements Sample type Existing pathways for sample - eg if sample routinely fixed for pathology and therefore unsuitable for culture etc
What staffing requirements need to be considered when setting up a new test?
Is a new vacancy required? Business case
Training for existing staff? Who to provide
Impact on other services if new staff not brought in
Staff competency records
How might the cost of a new test be covered?
Business case Grant - eg Innovate UK Commissioned by Trust Private partnership - placing of equipment in lab/reagent rental etc Partnership with charity - eg Jnetics
What miscellaneous factors should be considered when setting up a new test?
Existing/new BPGs Space - equipment/storage/processing, new staff Future proof as knowingly possible? MDT working needed? Does TAT fit clinical need? Legal implications Health economics
How might you carry out a cost analysis on the implementation of a new test?
Calculate cost per patient and validation
How does cost of test compare to sending away?
Should include equipment, reagents, staffing, IT
What factors could affect cost effectiveness of test
Batch vs single processing
Numbers received - balance of batch vs TAT
Economies of scale - higher numbers processed can incur savings on reagents
Numbers of controls needed per run - eg MLPA
What documentation is needed when setting up a new test?
SOP - include details of acceptance/rejection criteria, disease, genes, test purpose, limitations, unusual scenarios, test analysis and reporting procedure COSHH and risk assessments Staffing competency documentation Validation Documentation Accreditation documentation
What is a Business Plan?
Statement of strategic objectives and an outline for how these objectives will be met. Supports proposals for new service development, new staff, new equipment or a capital project
What is a budget?
Estimate of income, costs and cash flows over a specified period. Should reflect objectives in business plan and other events forecast to happen
What 6 basic questions might we consider when writing a business plan?
1) What do we want to do? 2) What have we done in the past? 3) What must we do well to succeed? 4) What can we already do? 5) What might we do next? 6) What should we do?
What 6 areas should be considered when writing a business plan?
1) Expectations of Trust/key stakeholders 2) Analysis of current and past performance 3) Identification of key success factors 4) Strengths and weaknesses of resources and capabilities 5) Opportunities and threats 6) Identification of range of options
How might you set the framework within national and local priorities in your business plan?
Undertake SWOT analysis
Identify need for change - target cohort, clinical utility, long term goals
How might you define the aims and objectives of your business plan?
SMART objectives
Identify benefit criteria - eg clinical quality, improved patient outcomes, staffing
Specify quantified targets
How might you carry out an option appraisal when writing a business plan?
Explore different deliver model options
Generate long list - brainstorm, consider different methods
Consider relative advantage, disadvantages and feasibility of each option
Engage with KEY STAKEHOLDERS
Costing exercise
How might you narrow a long list to a short list in a business plan?
Intended outcomes, expected workload and throughput, staffing consequences, implications for estates, impact on KPIs, impact on financial performance, impact on IT systems.
Identify total be costs of each option
Estimate capital costs, revenue costs, costs due to change in working practice, other one-off costs
Forecast for demand
Reimbursement
How might you structure a business plan?
Introduction Aims Option Appraisal Proposal Impact of proposal Risk analysis Conclusions and recommendations
What is SWOT analysis
Strengths
Weaknesses
Opportunities
Threats
Assessments of internal/external and helpful/harmful factors
What factors should be considered under strengths/weakness of SWOT analysis?
Human Resources - staff, target pop, service users
Physical resources - location, building, equipment
Financial - grants, funding agencies, other sources of income
Activities and processes - programs you run, systems you employ
Past experiences
What opportunities/threats should you consider in SWOT analysis?
Future trends in field/culture
Economy - local and national
Funding sources - foundations, donors, legislatures
Demographics - changes in race, age, gender, culture of those you serve
Physical environment
Legislation
Local, national or international events
What are SMART objectives?
Specific Measurable Attainable Relevant Time based
What tactics might you employ to execute strategy?
Plan to fill clinical need Costing Communication Promotion Launch dates Configuration of services Recruitment Training
How might you evaluate and manage an ongoing business plan?
Regular review and revision
Tracking of progress and performance - KPI audit
Regular course corrections
Add to quality objectives - regularly reviewed and evidence - ISO requirement
What is SBAR?
Situation
Background
Assessment
Recommendation
Tool for effective communication
What was NHSI’s vision for Pathology Services released in 2017?
29 hubs to be set up from existing services
Achieve £200m saving by 2021/21
Providers to be put into 1 of 29 proposed pathology hubs
What were some of RCPath’s concerns over Carter Report for Pathology Integration (2016)?
Activity and cost data flawed
Assumption that cheaper = better is flawed
Investing in Path Services leads to earlier diagnosis and better treatment - cheaper than cutting services
Potential for loss of skilled staff
Timetable unrealistic
What parallels can be drawn between Carter Report for Pathology services and Genetics Reconfiguration?
Hub and spoke models
Emphasis on cost-cutting rather than excellence
No staff engagement by NHSE before plan announced
Moving scientists away from Clinicians - reducing #’s of labs
What is QIPP?
Quality, Innovation, Productivity and Prevention
What are main focuses of QIPP?
Demand side - actions by COMMISSIONERS to reduce demand for provider’s services - avoiding duplication, preventing errors and stopping ineffective practices
What is predicted mismatch between funding and need identified in 2014 5YFV?
Nearly £30 billion a year by 2020/21
What efficiencies are needed in 5YFV to meet funding shortfall by April 2021?
2-3% per year - effectively a 10-15% real terms cost reduction target
What is CQUIN?
Commissioning for Quality and Innovation
What is aim of CQUIN?
Encourages care providers to share and continually improve how care is delivered
Transparency and overall improvement in healthcare
What is CIP?
Cost Improvement Programme
Describe a CIP
Scheme to increase efficiencies or reduce expenditure
What is the main difference between a CIP and a QIPP?
CIP is Trust’s responsibility
QIPP is commissioner’s responsibility
Name two other names for a CIP
Transformational change programme
Improvement programme
What are the 5 key factors in delivering sustainable CIPs?
1) Clear organisational purpose and vision
2) Involvement and buy-in from whole organisation
3) Organisation culture that seeks to improve safety, quality and pat experience
4) Strong governance arrangements, clear lines of accountability and clinical leadership
5) Realistic evidence-based CIP schemes
What are the 4 steps to delivering a CIP?
1) Identify potential CIPs
2) Assess potential impact on quality and cost
3) Approve plans
4) Assess actual impact on quality
What are 3 considerations when Identifiying a potential CIP?
Majority of CIPs should be based on change to current process
Neutral or positive impact on quality as well as reducing costs
CIPs should not put registration at risk by bringing quality below essential common standards
How would you assess potential impact on quality and cost of a CIP?
Categorised by potential impact on quality
Significant impact on quality should be subject and an assessment including:
Analysis of current processes
KPI benchmarking
Historical evidence
Detailed assessment of financial impact in line with current practice
How would you approve plans for a CIP?
Ensure clinicians understand and accept CIP - clinical ownership
Board assurance required that CIPs have been assessed for quality
Appropriate mechanism in place for capturing front-line staff concerns
What 3 mains areas can you consider for cutting lab costs?
1) staffing
2) non-staff
3) Income generation
What staffing considerations can you make during CIP?
Staffing traditionally 70-80% of lab costs
Natural wastage/ loss of vacant posts/reduce sickness
PRP/fixed term contract
Restructuring/streamlining
What non-staff costs can you consider in your CIP?
Methodology
Consumables
Equipment
Reduction of errors
Give examples of how we monitor performance?
Regular audit Use of controls EQA Monitoring KPIs Incident reporting User surveys Staff-related indicators
Give 4 types of audit
Horizontal
Vertical
Examination
Clinical
What are the 9 dimensions of the Healthcare Leadership Model
Inspiring shared purpose Leading with care Evaluating information Connecting our service Sharing the vision Engaging the team Holding to account Developing capability Influencing for results
What is the purpose of audit?
Demonstrate quality Identify areas for change Monitor consistency Improve quality Implementation Measure performance ISO Compliance
Where does uncertainty come from in measurement?
Instrument Item being measured Measurement process Imported uncertainties Operator skill Sampling issues The environment
What are the differences between Type A evaluations and Type B evaluations seen in UoM?
Type A - uncertainty measurements using statistics
Type B - uncertainty measurements from any other information
What types of information can inform Type B evaluations in UoM?
Past experience, calibration certificates, manufacturer information, published information or common sense
What is PESTLE?
Political Environmental Social Technological Legal Ethical
What is trend analysis in QMS?
Monitor performance of assays to highlight potential performance issues before the become errors
When an audit identifies non-conformance - what steps are undertaken?
Immediate/remedial action Root cause analysis Corrective action Preventative action Follow - up
What are the 3 stages of testing - defined for quality monitoring purposes?
Pre-analytical - receipt, booking in, DNA extraction etc
Analytical - testing, data analysis
Post-analytical - reporting, authorising, archiving
What 6 types of competence assessment are suggested by ISO15189?
Direct observation of routine work
Direct observation of equipment maintenance
Monitoring the recording and reporting of results
Review of work record
Assessment of problem solving schools
Examination of specially provided samples (eg EQA)c
What are some of the complications of diagnosis of rare paediatric disorders?
Range in path mechanisms Mosaicism Penetrance Variable expressivity Locus heterogeneity Phenotypic heterogeneity Genetic modifiers Environmental factors
What are disadvantages of large scale sequencing in diagnostics? (Eg CES, WES, WGS)
Specificity of findings to disorder decreases
Variants per patient increases
Data to store increases - logistics and security
Ethics - when is consent no longer ‘informed’?
Overdiagnosis
What are advantages of trio sequencing in diagnostics?
Rare benign familial variants filtered out
De novo findings easily captured
Phase of variants in recessive/imprinted disorders established by inheritance
In family of unaffected parents - trio gives tenfold reduction in candidate variants and 50% increase in diagnostic yield
What is a MAF?
Minor allele frequency - Measurements of how often the less common allele occurs at a given polymorphic locus.
What is the start codon usually?
Methionine ATG
Name 6 indications for paediatric WES
Neurodevelopmental disorder Congenital abnormalities Abnormal growth parameters Dysmorphic features Behavioural problems Disorder of considerable impact with significant evidence for underlying genetic cause
What is pleiotropy?
The phenomenon whereby variants in a single gene may cause multiple phenotypic expressions or disorders.
What is transcriptomics?
A global approach for looking at gene expression patterns
What is epigenomics?
A global approach for looking at the complete collection of epigenetic marks, such as DNA methylation and histone modifications, and other molecules that can transmit epigenetic information, such as noncoding RNAs, that exist in a cell at any given point in time.
What is metabolomics?
A global approach using quantitative analytical methods to look at the entire metabolic content of a cell or organism at a given time.
What 4 methods are there for CNV detection using NGS?
- Read depth/count – relies on depth of coverage correlating to relative copy number which is not always the case particularly where enrichment methods are used which introduce bias
- Paired-end – Uses the distance between the two pairs of reads to calculate whether the insert is significantly different from expected/average.
- Split reads – uses paired end reads where one of the pairs is unmapped or partially mapped, suggesting a breakpoint location.
- De novo assembly – genome is assembled from WGS data without the use of a reference genome. Computationally complex and slow.
What is proteomics?
A global approach for looking at the complete collection of proteins in a cell or tissue at a given time.
What are the 5 main areas laid out in the UK Strategy for Rare Disease?
Empowering those affected by rare disease Identifying and preventing rare disease Diagnosis and rare disease Coordination of care The role of research
Give 3 reasons why a mutation in a drug receptor gene could affect a patient’s response to the drug
Ineffective drug binding
Altered receptor expression
Impaired binding to effector
Name 3 examples of pharmacogenomics drugs
Warfarin
Abacavir
Thiopurines
What considerations can be made for Warfarin dosing wrt genotyping?
CYP2C9 - Variants *2 and *3 require lower Warfarin dose due to slowed metabolism
VKORC1 A haplotype require lower Warfarin as a result of decreased expression of mRNA
What genetic considerations should be made when dosing Abacavir for HIV?
Approx 5% patients experience immune-mediated hypersensitivity and need to stop Abacavir immediately.
Carry *57:01 variant in HLA-B gene
What genetic considerations should be made before prescribing Thiopurines?
Patients with low TPMT activity are at risk of Thiopurine induced toxicity - drug is partly metabolised by TMPT.
TMPT*2, *3A and *3C
What are the complications of looking for pharmacogenomic variations as incidental findings in WGS/WES?
How can variants be stored in patient medical record to be available at appropriate time?
Variant knowledge changes over time - how often is patient’s data reviewed to look for new clinically relevant alterations?
Large number of genes to screen for - how to handle VUS without over-burdening diagnostic team?
What are the benefits to patients of using genetic testing in drug prescription?
Fewer adverse events, quicker pathway onto correct dose of correct drug, reduced stress of repeated clinic appointments and time spent getting onto right drug/dose, more faith in doctor/system, can reduce risk of overdose/addiction
What are the benefits of genetic testing prior to drug administration to doctors/big pharmas?
Cost effective (?), fewer appointments wasted, patient well sooner, target drug to right population, more knowledge will support drug development in future
How can the cost-effectiveness of genetic testing prior to drug administration be determined?
Balance testing and cost of alternative drug against cost of adverse events on original drug
ICER - Incremental cost effectiveness ration: Difference in cost/Difference in effect
Benefits typically measured in Quality Adjusted Life Year
Suggest 5 uses for ctDNA
Prognosis determination Monitoring for treatment efficacy Selection of treatment Tumour size/disease burden Detection in asymptomatic individuals
What are limitations of using ctDNA analysis as population screen in asymptomatic individuals?
Low PPV
Fast growing cancers may be missed in first test and then detected too late
Very slow growing cancers which may remain indolent for many years could be detected - worried well
Blood brain barrier can stop ctDNA from brain tumours reaching plasma - false negatives
What are potential outcomes from population screening for ctDNA?
True positive
True negative
False positive - leading to unnecessary testing/treatment
False negative - false reassurance, miss opportunity for treatment
Equivocal result - what to do then??
What could cause a false positive result from population screening for ctDNA?
Mutation not cancer related
Pre-cancerous/indolent disease
Test not absolutely specific
What could cause false negative result from population screening for ctDNA?
Not enough ctDNA in plasma
Blood brain barrier preventing brain tumour DNA entering plasma
Rare mutation not screened for
What secondary findings are 100k feeding back on?
CF carrier status Bowel Cancer susceptibility Breast Cancer susceptibility Ovarian Cancer susceptibility Monogenic Familial Hypercholesterolaemia
Why are large structural rearrangements more common in BRCA1 than BRCA2?
High abundance of Alu repeats in BRCA1
What is possible role of BRCA2 and what supports this theory?
Highest expression in late G1 phase and remains elevated in S Phase indicating a role in DNA synthesis
Which 2 mutations in BRCA1 make up 98% of Ash J BRCA1 mutns?
c. 68_69delAG
c. 5266dupC
Discuss testing strategies for BRCA1/2 mutns
Sequence analysis of all genes - NGS
Targeted analysis for certain ethnic groups
Dosage analysis
Tumour DNA can be examined for LOH
- Co-segregation complicated by phenocopies and incomplete penetrance
What are some of the ethical considerations of BRCA1/2 Predictive testing
Need genetic counselling - age on onset highly variable
Treatment may be mastectomy or increased screening - need to be sure about pathogenicity
Prenatal testing and testing of minors not usually offered
Mutn carrier may not disclose mutn to other family members - then they can’t access testing
Individual might not want testing but other family members might inadvertently determine their result
What treatments are available if BRCA1/2 mutn found?
Prophylactic mastectomy/oophrectomy
Chemoprevention - Tamoxifen
PARP inhibitors - induce apoptosis of cancer cells
Give some examples of cancer predisposition syndromes
Li-Fraumeni Syndrome - TP53 Peutz-Jeghers - STK11 Cowden Syndrome - PTEN NF1 - NF1 Nijmegen Breakage Syndrome - NBN Hereditary diffuse gastric cancer and/or lobar BC - CDH1
What 4 genes are associated with Lynch Syndrome?
MLH1 - greater tenancy to GI ca
MSH2 - Greater variety of cancers
MSH6 - Reduced age-related penetrance
PMS2 - Reduced age-related penetrance
What cancer spectrum do you see with Lynch?
Colorectal cancer, Endometrial cancers, Small intestine cancers (MSH2, MLH1), Breast cancer, Hepatobiliary tract and pancreatic cancer (MSH2, MLH1), Gastric cancer (MSH2, MLH1), Ovarian non-serous cancer (MSH2, MLH1), Renal pelvis and ureter carcinoma (MSH2, MSH6), bladder carcinoma (MSH2,MSH6), sebaceous gland carcinoma, prostate cancer (MSH2)
Germline mutn spectrum of Lynch Syndrome
80-90% MLH1 and MSH2
7-10% MSH6
10Mb inversion of 2p - disrupts MSH2
Describe Lynch Syndrome testing
Stepwise
1 - Molecular MSI testing +/- IHC for 4 MMR proteins - remember sporadic show MSI too
2 - Molgen testing of tumour for methylation and/or somatic BRAF mutns
3 - MMR gene testing to identify germline mutn assoc with LS
February 2017 NICE Guidelines for Lynch
Offer testing to all with CRC - using IHC for MMR proteins or MSI testing
- If MLH1 IHC abnormal - use sequential BRAF V600E and MLH1 promotor hypermethylation to differentiate Lynch and sporadic
- If MSH2, MSH6 or PMS2 IHC abnormal - confirm Lynch by germline testing
- If BRAF V600E -be, do MLH1 promotor hypermethylation
- If MLH1 promotor hypermethylation -ve, confirm Lynch by germline testing
Name some MMR genes and their key roles
MSH2-MSH6 - complex preferentially repairs single base mismatch or mononucleotide repeats
MSH2-MSH3 - complex preferentially recognises larger loop our errors such as dinucleotide repeats
MSH2 and MLH1 are the obligate constituents of their respective pairs
What gene is associated with Familial Adenopolyposis Syndrome?
APC - component of want signalling pathway
AD
10% cases de novo
Describe FAP
Development of 100’s->1000’s of polyps during 2nd decade of life (as early as 7) -> eventually cause rectal bleeding or anaemia, almost 100% risk of CRC if untreated. Colectomy advised when >20-30 polyps
Colonoscopies begin aged 10-12 years
Attenuated FAP due to certain mutns in APC
Which 3 genes are responsible for 70-95% of path variants in FH?
APOB
LDLR
PCSK9
List 6 genes associated with FH
LDLR PCSK9 APOB LDLRAP APOE STAP1
What 4 genes form the ABL-class rearrangements in ALL?
ABL1, ABL2, PDGFR and CSF1R
What must an ALL testing strategy cover?
Ploidy shifts - HeH, HoL, NH iAMP21 KMT2A Rearrangements ETV6-RUNX1 BCR-ABL1, TCF3-HLF, TCF3-PBX1 ABL-Like rearrangements Copy number alterations
What methods could you use for ALL testing strategy?
NGS - Single test capable of detecting all but validation req’d
SNP Arrays and FISH
Karyotype and FISH
What methods could you use to confirm CNVs following NGS?
Long Range PCR FISH Arrays Digital droplet PCR Bespoke MLPAs In house dosage assays
WRT Information Governance - What is HORUS?
Holding data securely and confidentially Obtaining it fairly and efficiently Recording it accurately and reliably Using it effectively and ethically Sharing is appropriately and lawfully
What are some of the laws and guidelines governing IG?
Data Protection Act Freedom of Information Act IS017799 (Standards for IT) Confidentiality NHS Code of Practice Records Management NHS code of practice GDPR
What are the 7 Caldicott Principles?
- Justify purpose of using information
- Don’t use confidential data unless necessary
- Use minimum personal data possible
- Access to personal info should be on need-to-know basis
- Everyone should be aware of their responsibilities
- Comply with the law
- Duty to share can be as important as duty to protect confidentiality
What are the 4 p’s of Stratified Medicine?
Predict
Prevent
Precise
Personalised
What will sarcoma strategy be?
WGS from end of June/beginning of July
21 day TAT
Fresh tissue
Urgent FISH still done in hubs
What five considerations are then when designing and implementing a Screening programme?
- The Condition
- The Test
- The Intervention
- The Screening Programme
- Implementation Criteria
Screening Programme: What considerations about the Condition should be made?
Important health problem - freq or severity
Cost-effective interventions should have been implemented
If mutn carriers identified as part of screen, implications should be known, including psychological
Screening programme: What do you need to understand wrt defining the important health problem?
Epidemiology, incidence, prevalence, natural history, development from latent -> declared disease, robust evidence about assoc between risk/disease marker and serious/treatable disease
Screening Programme: What considerations should be made with respect to the Test being considered for a screening programme?
- Simple, safe, validated
- Distribution of results known and cut-off levels agreed
- Acceptable to target population
- Agreed policy on further diagnostic intervention
- If only screening for specific mutations - list should be regularly reviewed
Screening Programme: What considerations about the Intervention should be made?
There should be effective intervention - evidence that pre-symptomatic intervention leads to better outcome, if benefit to family members is good but not sole consideration, agreed policies on who to screen, who to offer intervention to and what intervention to offer
Screening Programme: What considerations should be made to the programme itself?
Evidence that programme is effective at reducing morbidity/mortality, if for informed consent there must be robust evidence that risk is accurately measured.
Must be clinically, socially and ethically acceptable.
Benefit should outweigh harm
Economically viable
Screening Programme: What potential harms could there be?
Over diagnosis Over treatment False positives False negatives Uncertain findings Complications
Screening Programmes: What implementation criteria should be considered prior to screening programme introduction?
Clinical management should be optimised
All other options for managing condition should have been considered
Plan for managing and monitoring in place with agreed QA Standards
Staffing and facilities
Info available for participants for informed-consent
Public pressure for widening criteria etc should be anticipated and scientifically justifiable
Name 5 categories of Additional Findings from the 100k
Bowel cancer, breast and ovarian cancer, other cancer, FH and carrier status
Which bowel cancer predisposition genes will be reported as additional findings in the 100k?
Adult only: MLH1, MSH2, MSH6, MUTYH
Adult and child: APC
Which breast and ovarian cancer genes will be reported back as additional findings in the 100k project?
BRCA1 and BRCA2 - adult only
Which other cancer predisposition genes will be reported back as additional findings from the 100k GP?
Adult and child: VHL, MEN1, RET
Which FH genes will be reported back as additional findings from the 100k GP?
Adult and child: LDLR, APOB, PCSK9
What are the benefits of an early diagnosis from PICU/NICU Rapid Exome?
Faster care plan, reduced testing odyssey, reduced anxiety, earlier prognosis, better recurrence risks sooner
What are some criteria you should consider for acceptance criteria for PICU/NICU Rapid exomes?
Trio approach, suspected mono genic cause, diagnosis alter clinical management, single gene test not available/practical (highly heterogeneous disorder), small panel not practical, imminent demise not likely
What considerations should you make when setting up a rapid exome service?
Clear gene/HPO link (phenotype key here), engaged MDT, clearly agreed analysis plan (triage?stepwise?), lab workflow clearly laid out (how would an urgent sample suddenly turning up affect use of NGS machines for eg?), validation of findings, robust and validated decision tools
What pretest considerations are there for Prenatal Exomes?
Inclusion criteria Test design Phenotyping Trio analysis Pretest Counselling TATs
What reporting considerations are there for fetal exomes?
Known disease gene Uncertain gene/disease association Fetal Incidental findings Parental incidental findings Misattributed parentage Consanguinity
What post test considerations are there for fetal exomes?
Post-test counselling
Management of pregnancy with/without diagnosis
Chance of upgrading/downgrading classification
What cost considerations are there for fetal exomes?
Cost effectiveness not known
Savings may be made by avoiding sequential testing, improved management plans, early intervention, palliative care plans
Additional tests may be needed post-genomic diagnosis
What pretest counselling considerations are there for Prenatal Exomes?
What can test detect? What can’t test detect? Incidental findings Exclusion list Consent - opt-in or opt-out
What complications are there for TATs with Fetal Exomes?
May have had to wait until 20 week scan for abnormal findings, then have to wait for invasive test and likely also have exclusion test such as array with its own 14 day TAT
Need to get result to family in time for prenatal decision making
What Fetal Incidental findings should/shouldn’t be reported from Fetal Exome?
Highly penetrant path/likely path variants in genes known to cause moderate to severe childhood disorders should be reported
Variants without a known fetal/childhood phenotype should not be reported
Carrier status should not be reported
What are Neutrophin Receptor Tyrosine Kinases?
NTRK1, NTRK2, NTRK3
Genes encode TRKA, TRKB, TRKC
TRK inhibition provides prime example of histology-independent activity of targeted therapy in molecularly defined subset of cancers
Name 3 cancer types where somatic NTRK mutations have been identified
Colorectal, lung cancers (NSCLC, large cell neuro-endocrine carcinoma), Melanoma, AML
Name 2 cancers where activating splice variants of NTRK1 have been identified
Neuroblastoma, AML
Describe NTRK Fusions
Inter/intrachromosomal rearrangements form hybrid genes - 3’ sequence of NTRK1, 2 or 3 that includes kinase domain are juxtaposed to 5’ sequence of different gene
Chimaeric oncoprotein characterised by ligand-independent constitutive activation of the TRK kinase
What are 2 different classes of NTRK groups?
1) Rare cancer types highly enriched for NTRK fusions (approx 90%)
2) Other cancers types where fusion found at much lower frequency (typically 1%)
Name 2 TRK Inhibitor Therapies
Larotrectinib
Entrectinib
