william cross [email protected] nhs diagnostics: healthcare science genetics
TRANSCRIPT
William [email protected]
Agenda1) Introduction to healthcare science in the
NHS
2) Genetic Disorders: Aneuploidy diagnosis using Karyotyping
3) Karyotyping Workshop
4) Genetic Disorders: Aneuploidy diagnosis using QF PCR (finger printing)
5) QF PCR workshop
6) Answers and Questions
William [email protected]
Working as a Healthcare Scientist
• Around 50 scientific disciplines covering patient care and research in the NHS.
• Occupy 5% of the total NHS workforce (55,000 staff).
• Many job roles within each discipline; Clinical Scientists, Scientist Practitioners, Biomedical Scientists, Support Workers.
William [email protected]
Healthcare Genetics• Aims to give patients better quality of life using
knowledge of genetics and diagnostic tests. • NHS genetic services are based in UK hospitals,
but can also have separate clinical centres.• Co-ordinated by the UKGTN a subsidiary group
of the department of health.• Our local laboratory is BGL at Southmead
Hospital and our clinical centre is at St.Michaels hospital.
William [email protected]
What does Bristol Genetics Laboratory do day to day?
• Receives patient referrals from GPs, Hospital wards and other specialist services such as Paediatrics and Oncology centres.
• Arrange appropriate tests to be carried out based on the patients needs/symptoms.
• Analyse results and write reports for Doctors and Specialists to interpret.
• Offer specialist advice to all healthcare professionals.
William [email protected]
Testing Workflow
Doctor examines patient
Blood sample sent to BGL DNA extracted from
blood sample
Genetic analysis performedGenetic analysis performed
Report written
Report sent to Doctor
William [email protected]
Types of Genetic TestingNHS genetic services cover many areas of patient healthcare.
• Diagnostics - When a patient has symptoms of a disorder
• Predictive - When a family member has a disorder• Cancer work - diagnosis of cancer types• Prenatal diagnosis - diagnosing from abnormal
foetal scans• Neonatal screening - screening newborn infants
William [email protected]
Southmead ‘Super’ Hospital http://www.superhospitalforbristol.nhs.uk/
William [email protected]
See NHS Careers/Jobs websites for further details of scientific careers in the NHS:
http://www.nhscareers.nhs.uk/
http://www.jobs.nhs.uk/
William [email protected]
Genetic Disorders: Overview• Mutations within the genes of an individual can
cause genetic disorders.• Can be ‘new’ to a family (de-novo mutation) or
inherited.• Mutations come in many types from whole
genome duplications (triploidy), to a single nucleotide change (point mutation).
• Mutations can be detected by a variety of techniques: PCR, sequencing, Southern blotting, Real-time PCR, MLPA.
William [email protected]
Aneuploidy Mutations • Aneuploidy is the condition of having an abnormal
number of chromosomes (karyotype).• Can be a chromosome number reduction or increase
(monosomy / trisomy) • Often caused by faults in the cell division of the gametes
(meiotic non-disjunction)Chromosome 21 pair in a dividing gamete
Normal division Abnormal division
William [email protected]
Aneuploidy disordersEdwards syndrome.• Chromosome 18 trisomy (2nd most
common autosomal trisomy, 1:7900).• High mortality rate; life expectancy is a few
days from birth and less than 1 in 10 live to the first year of life.
• Many clinical features, which can be observed from 1st trimester scan and after birth.
William [email protected]
Edwards Syndrome
•Congenital heart defects
•Growth retardation
•Dysmorphic features (see diagram)
•Facial clefts
•Spina bifida
•Sever developmental delay
William [email protected]
Aneuploidy disordersPatau syndrome• Chromosome 13 trisomy.
• High mortality rate; median life expectancy is 2.5 days after birth.
• Rare; 1:9500.
• Many clinical features, which can be observed from 1st trimester scan and after birth.
William [email protected]
Patau Syndrome
•Growth retardation
•Cardiac malformations
•Kidney malformations
•Cultis aplaisa (scalp defects)
•Omphalocele
William [email protected]
Aneuploidy disordersDown syndrome
• Chromsome 21 trisomy (most common autosomal trisomy).
• 1:1000 births
• Life expectancy around 60 years.
• Well established clinical features that can be determined through scans or at birth.
William [email protected]
Down Syndrome
•Delayed milestones
•Mean intelligence quota (IQ) in children and young adults is 45-48
•Cardiac defects
•Neonatal hypotonia
•Dysmorphic features
William [email protected]
Aneuploidy Mutations• Can be detected by karyotyping.• Karyotyping involves culturing patient cells
then spreading on a microscope slide and staining (G-banding).
• Cells in Metaphase of the cell cycle are viewed under a microscope and specialist software image captures chromosomes for analysis.
• A karyotype is produced that enables the chromosomes to be counted and analysed.
William [email protected]
Karyotype Example
Female Patient
Increasing Size
Chromosome numbers
Pairs look nearly identical
William [email protected]
Workshop Examples• Each group will be given four anonymous
prenatal/infant karyotypes with accompanying referral forms.
• Read referral forms for each foetus/infant examine the karyotype and record your answers in the spaces provided.
• Keep your results for later.
• Please ask questions if unsure.
William [email protected]
QF PCR OverviewWhy is QF PCR required?• Enables high throughput chromosome screening
for most common abnormalities (chromosomes 13, 18 and 21).
• Increases scientific evidence for abnormal cases.
• Allows a cursory result to be obtained far quicker than karyotyping. Very useful in prenatal cases where there are time constraints.
William [email protected]
PCR: A Quick Overview
• Used to amplify specific DNA strands for molecular analysis. The ‘main’ technique of genetics.
• Well established technique with many variations e.g. QF PCR, TP PCR, RT PCR.
• Utilizes thermostable enzymes (Taq polymerase) and thermocyclers.
• Primers can be designed to target most regions in the human genome.
William [email protected]
PCR Reaction
Target Loci30 sec @ 95ºc
Exponential amplification
45 sec @ 55ºc
Primers
William [email protected]
Visualizing PCR ProductsGel Electrophoresis• PCR products added to gel well.• Gel contains Ethidium bromide that
‘stains’ DNA as it migrates.• Electrical current applied to the gel.• DNA migrates to positive electrode.• After a predetermined run time
DNA can be seen in the gel under a UV light.
• Enables fragments to be sized; larger fragments towards the top of the gel (smaller fragments run quicker).
M-veSamples
Large to small fragments
William [email protected]
Visualising: Sizing Products
Molecular weight ladder allows known size fragments to be seen
Sample bands line up with known size standard band (250bp) as ladder has fragments 50bp apart.
Product sizes can be calculated from the size standard and quantity can also be estimated from band intensity.
Large to small fragments
William [email protected]
Multiplex PCR• A method of amplifying more than one
PCR target simultaneously.• Very useful when designing assays for
specific tasks performed routinely e.g. CF mutation screens.
• Attention has to be paid to expected PCR product sizes when designing multiplex assays. As overlaps can be difficult to interpret.
William [email protected]
Multiplex Example
• There are 5 products in this PCR reaction.
• Each product is a distinctly different size otherwise overlap wouldn’t be seen.
M 1 2 3 4 5
Why do you think patient 3 has only 4 product bands?
Large to small fragments
William [email protected]
PCR With Variable Number Tandem Repeats
• VNTRs are found throughout the human genome in various untranslated regions (UTRs).
• They represent regions of DNA where a nucleotide repeat occurs e.g (GCGCGC)n or (CGGTCGGTCGGT)n
• VNTRs have varying repeat units thus different alleles present in the general population, e.g 20-30 repeat units of GC.
• A person can be heterozygous for the number of repeats in a given loci so will produce two different sized PCR products.
William [email protected]
PCR With Variable Number Tandem Repeats: Example
M 1 2
Patient 1 is Homozygous for a tandem repeat on chromosome 13.
His/Her genotype therefore is 45/45 repeats, meaning each allele of this loci in both the patients chromosome 13s are 45 repeats long; the same size on a gel.
Patient 2 is Heterozygous for this VNTR on chromosome 13 so has two bands.
His/Her genotype therefore is 45/50 repeats, meaning the patients chromosomes have different alleles at this loci. This is very common.
Large to small fragments
William [email protected]
Why Are VNTR Useful?• Since most people are heterozygous for
some VNTR alleles, this can be used to distinguish between each chromosome within an individual (fingerprinting).
• This also allows the amount of each chromosome to be compared thus PCR can be used to test for Aneuploidy by examining the band intensities on a gel.
William [email protected]
Aneuploidy Gel Example
• This gel displays 4 patients, 2 heterozygous and 2 homozygous.
• Patient 1 has two bands with equal intensity.
• Patient 2 has double the intensity on the upper (48 repeat) band.
Why?
45/30 48/30 51/51 51/51 M
Ratios represent patients genotypes
1 2 3 4
48 repeat allele
30 repeat allele
William [email protected]
Aneuploidy Gel ExamplePatient 2 has a trisomy at this loci that is
detectable by the VNTR
Since VNTR lengths are different in most people, this patient has inherited two different versions from his/her parents.
Hence there is twice as much 48 repeat allele than 30.
48 repeat alleles
30 repeat allele
William [email protected]
Problems With Gel ElectrophoresisInterpretation can be subjective• Bands not always clear.• Intensity can be subjective so
quantification not very reliable.• Bands made brighter the longer the
fragments are run through the gel.• Gel bed electrophoresis is still used but
other techniques are more common.
William [email protected]
Modern Detection Methods: QF PCR
• Stands for Quantitative Fluorescence PCR.• Replaces a flat bed gel with a capillary gel inside
a genetic analysis machine.• The principles are exactly the same as gel beds,
except no Ethidium bromide is needed to stain DNA.
• A detector within the machine can measure DNA levels as electrophoresis is performed.
• Superior quantification over viewing band intensities.
William [email protected]
Capillary Electrophoresis
Beckman Coulter CEQ 8000
Gel Bed Version
Capillary Versions
45/50 repeats
45/45 repeats
Ladder in red
William [email protected]
Electropherograms in Detail
Red peaks always indicate sizing ladder
Numbers on the ‘x’ axis represent fragment size
Patient peaks are any colour other than red
Fragment sizes are shown at the top of peaks
This kind of analysis is made far easier with genetic analysers!
Numbers on the ‘y’ axis represent amount of PCR product
William [email protected]
Workshop ExamplesEach group is given electropherograms corresponding to each patient karyotyped earlier.
These are QF PCR sex chromosome, 13, 18 and 21 Aneuploidy tests.
See if these results match your assessments from earlier.
Please ask for help if unsure.
William [email protected]
Workshop ResultsPatient A: Normal male foetus
William [email protected]
Workshop ResultsPatient B: Trisomy 18 (Edwards syndrome) foetus
William [email protected]
Workshop ResultsPatient C: Turners syndrome infant
William [email protected]
Workshop ResultsPatient D: Translocation 1:22. Undetectable from QF PCR
result, may be balanced and display no pathogenicity
QF PCR looks normal
William [email protected]
Thank you for listening.I hope this workshop was helpful.Good luck with your final exams.
Questions welcomed