Session 5: Population screening Flashcards
define allele frequency?
the proportion of a given allele among all alleles at a give locus- usually given a s a percentage
What is an association study?
See statistical method for determining the co-occurrence of a phenotype with a genotype
- if there is an association an allele will be found with a specific phenotype in a population more often then predicted by chance
independent of linkage
what is a linkage study?
linkage atypically looks at a few families with the same trait and multiple affected
Uses micro satellites to narrow down candidate region that is associated with the trait and can be used to study variants with large effect
what is genetic linkage?
tendency of 2 genes that are located in close proximity to be inherited together. The further apart 2 genes the more chance there will be a recombination event between them preventing them being inherited together
what is epistasis?
Interaction between non-allelic genes that influence phenotype
- modifier genes
- one gene modifies the expression of another
what is fitness?
ability for a population to survive and reproduce in a particular environment
what is gene flow?
flow of genetic info between different population of the same specie by mating and migration
what is gene pool?
full range of alleles within an breeding population
what is genetic drift?
change in allele frequency in a population over generation due to chance i.e. not driven by selective pressure
- can result in loss of certain alleles
- more common in small populations
what is genetic load?
the difference between the fitness of an average genotype in a population and the fitness of some reference genotype (the best present in popul or optimal genotype)
what is genotype freq?
frequency of a specific genotype in a population
what is a GWAS study?
Studies looking at associations between alleles throughout the genome and phenotypes.
study lost of unaffected and affected control
use SNPs for high resolution coverage
They are effective in detecting common alleles that contribute to the inherited component of common multifactorial diseases. Typically, the alleles identified by this approach have modest effect sizes that cannot fully account for disease susceptibility.
define haplotype?
combination of linked alleles on a chromosome- can be used to track inheritance of an unknown genetic trait
what is the Hardy-Weinberg law?
according to H-W allele freq will remain constant in a population if there is no evolutionary influence i.e. no sex selection, genetic drift, genetic flow, no mutation
used to asses risk for individuals with genetic disease
what is linkage disequilibirum?
the co-occurrence of 2 alleles in a population more often then predicted by chance
An association can only be found between alleles and disease if the disease is in LD with a marker allele.
LD is often expressed as D. If D=0 there is no association between alleles and, in this case, the distribution of alleles in the population is as expected (randomly distributed) and dependent on the allelic frequency.
define species?
group of organisms that can reproduce with each other to produce fertile offspring
what is the LOD score
“logarithm of the odds”
- log of the odds
stat used in the analysis of linkage
LOD= 3 indicates that 2 loci are statistically linked
A LOD score of 3 indicates that the odds that the loci are linked are 1,000 times greater than the odds that they are not
what is a map unit (µu)?
measure of genetic distance between 2 genes
crorresponds to recombination freq of 1% or 1 centimorgan (CM)
what is the minor and major allele freq?
frequency of the most and least common alleles of a given locus
what is a morgan unit?
unit used to express the ditance between 2 genes based on the likelihood of recombination between them- more distantly located genes with have a grreater chance of recmobination
1M = recombination possibility of 100%
1 dM (deciMorgan)- recombination value of 10&
1 cM - recombination value of 1%
what is the mutation rate?
number of mutation per biological unit e.g. per round of division, per gamete
what is the odds ratio?
odds of having the disease and disease allele divided by
the odds of having the disease without the risk allele
in pop study basically cases with genotype over controls with genotype and the higher the OR the greater the risk associated with the disease allele
what is penetrance?
proportion of individuals with a specific allele that express the associated genetic trait
what is the relative risk?
estimated probability of having the disease when the patient carries the risk allele in an association study
what was the Myriad Vs Association of molecular pathology case of 2013?
Land mark case between Myriad genetics and the association of molecular pathology
Myriad was one of the first US companies to offer DTC (Direct-to-consumer) testing and held a patent for BRCA1/2 testing. Until the case against the AMP in which the US supreme court ruled that natural DNA is not patentable
what is a screening test? (who does it test and aims)
screening tests asymptomatic/presymptomatic people in the population at risk of a disease
aims to identify disease before the patient develops symptoms and provide early intervention for improved health outcomes- reduced mortality and/or morbidity
what types of population screening are there?
- mass- newborn screening
- targeted- lung disease in coal miners
- opportunist- BP at routine GP appointment
- pro-active- cervical screening in women >25yrs
what is genetic screening?
for early detection (pre-symptomatic) or esclusion of a genetic disease, genetic predispostion to a disease or if an individual carries a variant that may result in disease in their offspring
different to population screening as a targeted to specific populations e.g. CF testing in ovum/sperm donors
what are the WHO criteria for offering a screening programme for a specific condition?
Condition
- must pose a significant health burden either due to its severity or prevalence (or both)
- natural history and epidemiology must be known
Test
- safe, simple, effective, precise and validated
- distribution of results must be known and cut-offs determined for positive and negative results
- acceptable to the population
Treatment
- must be an effective treatment available with evidence that early intervention improves outcomes
- agreed policy and pathway for follow-up of +ve result determined and optimised before testing offered
Programme
- benefits outweigh harm
- cheaper then only treating patients when they become symptomatic
- improving current treatment pathways should be considered first
what is sensitivity, specificity, PPV and NPV
positive/negative predictive value (PPV/NPV)
sensitivity= % true positives detected by the test
specificity= % true negative
PPV = TP/TP+FN
NPV= TN/TN+FP
sensitivity is prioritised if there is
- an efective treatment
- confirmatory diagnostic test
- communicable disease
PPV can be improved by increasing the prevalence of the disease in the population being screened either by pre-screening or only screening a selected population
what are the advantages of screening?
less radical treatment required
reduced costs and resources
-ve result can provide reassurance
what are the disadvantages of screening?
false -ve may give fale reassurance
false +ve may result in unecessary treatment, anxiety and testing
longer morbidity if prognosis is unaltered
what is the current state of newborn screening in the UK and EU?
currently no active screening programmes but it has been variable approved pending implementation or undergoing pilot schemes across the EU
In the UK in 2019 the UK national screening committee refused to add SMA to the NBS programme at this point because of too little info on:
reliability of test
evidence of nusernisen in asymptomatic children
acceptability and pathways for families following a positive result
- Pilot scheme ongoing in UK
what is the UK national screening committee?
set up in 1993 and responsible for screening policies and procedures in the UK
- ensure that introduction of new screening programmes is acceptable and scientifically backed
- review existing screening programmes and pathways to ensure they are
ESHG and ACMG have also published screening recommendations
what is the newborn screening programme?
bloodspot test offered to all neonates on day 5
- guthrie card test
9 conditions where early intervention is beneficial, there are effective treatment and the tests are reliable, sensitive and specific
CF
Phenyketonuria (PKU)
medium chain acyl coA dehydrogenase deficiency (MCCAD)
Sickle cell
congenital hypothyroidism
maple syrup urine disease
isovaeric acidemia
glutaric aciduria type 1
homocysteinuria
what is the FASP programme?
Fetal anomlay screening programme
Fetal anomlay screening programme
- detailed USS scan at ~ 20weeks gestation
- aims to identify chromosomal abn that are associated with fetal anomaly
- 1+ USS abn or NT>3.5mm = offered invasive testing (PCR and array- now includes trio WES)
what is the down syndrome screening programme?
biochemical screening to ID pregnancies at increased risk of T21 who can be offered invasive testing (>1 in 150)
combined screen 11-13+6 weeks
NT, BhCG, Mat age, PAPP-A = age asjusted risk bask on MOM
quadruple score - 14-20wks
less good for T14 and 18
BhCG, unconjugated estriol, a-fetoprotein and inhibin
what is preconception screening?
preconception screening involves screening a couple for their risk of having offspring affected by a recessive disorder. Best if carried out before couple gets pregnant as there are more options available e.g. PGD, in practice its often only carried out during pregnancy
carrier screening is available for
- CF in Australia and Italy
- SMA in US
- B-thallasemia in Cyprus, Turkey, Sardinia. In Cyprus testing is a requirement for getting a marriage licence as the carrier freq is so high the number of affected individuals would cripple the health service
what is expanded carrier testing?
panels covering common AR diseases- mainly available privately.
tend to only test for the most common mutations so individuals need appropriate counselling and the residual risk should be given
what are the findings and requirement of the ESHG and ACMG on expanded carrier testing?
- aim is to enable autonomous decision making
- need clear information available if there is reduced penetrance or variable expressivity
- provide residual risk figures
what expanded carrier testing is available in the UK?
not routinely available in the UK however testing is targeted to specific groups for example AKJ can be tested for 30 diseases with high prevalence
carrier testing also offered if there is a family history or 1 member of a couple is a known carrier
what are the potential benefits or limitations of population genetic screening for breast cancer?
study suggested that screening women with no family history may be cost effective due to earlier diagnosis
however ESHG states cost cannot be the only justification for population screening
- reduced penetrance
- other factors- diet, lifestyle also v relevant
- low penetrance of breast cancer variants in general pop without family history
- potential physical and psychological harm to patients- may have unnecessary surgery or chemoprevention and the lack of effective strategy for ovarian cancer may increase anxiety with no benefit
what are the 4 key ethical priniciples in medicine?
- autonomy- pateint has the autonomy and choicde
- beneficence- highest priority is th welfare of the patient and minimising harm to them
- non-maleficence- prevent and minimise harm to the patient
- justice- equity of access and patients should be treated fairly
what is the importance of non-directive counselling in genetics?
-Genetic information may affect the entire family.
-Genetic discoveries may be predictors of future adverse effects on an individual/family.
-Genetic information and choices made may affect future generations.
what are the key ethical issues surrounding preconception/prenatal screening?
reproductive autonomy- individuals have the right to make informed decisions therefore need informed consent but counselling should be non-directive
what are the potential benefits of population genetic screening (ESHG 2013)?
- pre-symptomatioc detection where there are options for prevention, early treatment
detection of carrier status will allow people to make informed reproductive decisions
improved reproductive decision making and autonomy
what are the potential issues with prenatal
- ethical issues surrounding consent- NBS or prenatal testing may ID carrier status which will affect that individuals reproductive decisions and they have not consented for so removes their right to autonomous decision making
- may result in anxiety if information cannot be used to make positive choices e.g. variant of variable penetrance
- compliance: offered by medical professional so individuals may feel obliged to have the test
- may be undue pressure on an individual (family, religious, partner) to make certain reproductive decisions
- disclosure of information- results for one family member may have implications for relative who have not consented to testing.
- need to ensure the information is not misused by insurers or employers
what are the potential issues of preconception testing? (6)
- may result in -ve stigma against people with the condition and could be considered a form of eugenics
- chosing not to have a child with a genetic condition could devalue those people that have it
- pressure on parents to not have a child with a condition or judged if they do for placing extra burden on health service
- fewer people born with the condition may reduce the funding for services and treatment of people with the condition
- most conditions have a residual risk even after carrier testing
how can the potential issues of preconception carrier testing be overcome (ESHG/ACMG)
- test for common variants rather than whole gene to prevent detection of VUS
- provide clear information on penetrance and onset of conditions in pre-test counselling
- screening programmes must also have well defined pathways for affected individuals to ensure they are not receiving fewer services
- sufficient support should be given to couples chosing to terminate or continue a pregnancy so they have the choice to do either
- voluntary participation, equity of access and assess the benefit in terms of improved reproductive decision making rather than a reduce birth rate of affected individuals
what are the future directions in genetic screening?
increased used of NGS- WES and WGS
what are the future directions in genetic screening? ctDNA
NGS is being applied to cell free tumour DNA obtained from blood samples- this could enable non-invasive screening on a population scale.
Benefits= earlier diagnosis and treatment should result in better outcomes and decreased disease burden
limitations= technical, test sensitivity, false positive and cost
what are the future directions in genetic screening? cffDNA
cffDNA is being used for NIPD for some single gene disorders and NIPT is in the process of being rolled out as an NHS test following review by the national screening committee and NHS england and the RAPID study
what are the future directions in genetic screening? WGS/WES
ACMG has recommened that IFs in a specific genes and encourage labs to actively look for variants in a list of 59 reportable genes including genes associated with breast cancer, lynch syndrome, Marfan syndrome and cardiomyopathy
this is a cost effective method but requires informed counselling and does not provide equity of access
what are the future directions in genetic screening? preconception carrier screening- benefits and thoughts
offered commercially currently - so access not equitsable as based on abilit to afford testing, widespread adoption could follow
likelihood a non-consanguineous couple having a child with a AR affected offspring is low and primary goal of increasing reproductive autonomy is hard to quantify so herd to justify the cost effectiveness ads a publicly funded service
further research such as a pilot study in the netherlands which is offering the service through GPs will provide more information on the potential benefits of such a national programme
what is newborn screening?
screening offered to all noenates on day 5 of life using a heel prick bloodspot on a gutrhie card
first developed for phneylketonuria in 1969 and is now pone of the largest screening programmes with >800,000 newborns screened in the UK each year
should we screen for more diseases?
There is pressure to screen for more conditions and the public is generally accepting of screening however new programmes need to be carefully evaluated before being introduced?
what issues have there been with prostrate cancer and neuroblastoma screening?
prostate cancer screening can result in unnecessary surgery with side effects of incontinence and impotence as PSA is a poor marker for disease that will develop into cancer so unnecessary treatments carried out
neuroblastoma screening was suspended in 2004 because although superficially 90% of those screened survived compared to 50% not screened there was no decrease in mortality therefore it may be that the screen is identifying patients that will never progress to severe disease of is failing to detect patients who will develop serious disease
hard to remove screening once introduced as patients who have had the screen and been positive and survived may attribute this to the screen even if thee is no evidence to support their belief
how does screening differ to diagnostic testing?
test asymptomatic/ pre-symptomatic individuals
not diagnostic and may need a confirmatory test
what are the features of down syndrome?
LD, DD
risk of early onset alzheimers
VSD or other congenital heart defect
facial dysmorphism
hearing, opthalmic, muscoskeletal, GI and thryoir features
increased risk of leukemia
what are the MoM for DS screening?
multiple of the median (MoM)
DS risk from serum makers and age is calculated bydetermining how different a womens results are from the ref pop mean of unaffected population at the same gestational age
serum marker conc for pateint/ serum marker mean for normal pop
used in a bayes calcuation to adjust the prior risk based on maternal age
what factors can affect DS screening serum markes
need to adjust for the following
- weight (increased weight can dilute markers)
- IVF
- smoking
- ethnicity
- accuracy of dating (gestational age)
what are the justifications for DS screening?
- significant LD and risk of severe congenital abn e.g. cardiac defects
- likely to require ongoing support and be a cost to society (health and social care) and unlikely to contribute to the economy
- most women who undergo screening and have a positive result chose to terminate indicating support from the population
- screening can provide earlier diagnosis (than 20 week FASP allowing earlier less invasive termination)
- even if people don’t chose to terminate the knowledge of the result provides time to adjust, and access support services
what are the issues with DS screening?
- poor understanding of risk in the general population and low risk screen does not mean no chance of T21
- fale +ves could result in pregnancy loss from invasive
- women may feel obliged to have screen, then invasive and terminate as offered by medical professionals
- high rate of natural pregnancy loss in T21 so this may result in unnecessary decisions and anxiety for a pregnancy that would be naturally lost anyway
- perception that if screening is available a life with T21 is less valid- people that chose to continue pregnancies may feel they are a burden on sociability and less valid
what is the aim of the newborn screening programme?
aims is to provide treatment to newborn ASAP to reduce/prevent potential severe phenotype
when should patients be contacted by if there is a positive screening result?
2 weeks for PKU
3 weeks for CHT and MCADD
4 weeks for CF
6 weeks for SCD
what are the WHO criteria for a screening test?
- Significant health issue (severe or common)
- know the natural history of the disease and have defined cut off of affected or not. Assumption is all cases will progress to the most severe form
- effective treatment available and evidence that early intervention is beneficial
- known incidence in target pop e.g. UK
- test with high PPV and sensitivity and specificity available that is acceptable and suitable to screening (ethical, safe, simple)
- cost effective
what are the 9 conditions tested for in NBS- which are genetic and which are metabolic?
genetic
- sickle cell disease
- CF
- congenital hypothyroidism
- phenylketonuria
inborn errors of metablism
MCADD medium chain acyl-coA dehydrogenase
Isovaleric acidemia
glutaric acidemia type 1
maple syrup urine disease
homocystinuria
predominantly treated by long term dietary management to prevent toxic build up of causative metabolite- due to deficiency in metabolism and toxic build-up
what is the phenotype in PKU?
results in severe MR
growth failure, poor skin pigmentation, microcephaly, seizures, global developmental delay and severe intellectual impairment.
what is the cause of PKU
AR genetic disease due to mutation in the DAH gene
phenyalanine dehydrogenase which converts phenylalanine to tyrosine resulting in a toxic build-up especially in the brain
how is PKU tested for?
NBS detects increased phenylalanine in the blood by tandem MS
How is PKU treated?
patients are put on a low phenylalanine diet which significatly reduces the risk of neurologic handicap but if diagnosed too late there may be no benefit as damage has already been done
what are the feature of congenital hypothyroidism
failure to thrive and don’r grow properly
physical and mental handicap
neonates may have a protuding tongue, jaundice, feeding difficulties and low hairline
The Hardy–Weinberg principle relies on a number of assumptions:
The Hardy–Weinberg principle relies on a number of assumptions:
(1) random mating (i.e, population structure is absent and matings occur in proportion to genotype frequencies),
(2) the absence of natural selection,
(3) a very large population size (i.e., genetic drift is negligible),
(4) no gene flow or migration,
(5) no mutation, and
(6) the locus is autosomal.
When these assumptions are violated, departures from Hardy–Weinberg proportions can result.
what causes congenital hypothyroidism?
primary- agenesis or dysgenesis of the thyroid gland
secondary- deficient levels of TSH
genetically heterogeneous and associated win mutations in multiple gene - e.g. thyroid transcription factors
how is congenital hypothryoidism treated?
thyroxine supplementation
How CH screened for?
increased level of TSH- produced as abn thyrpid gland is not responding
what are the features of MCADD?
deficiency in fat metabolism and can result in death
what causes MCADD?
AR mutations in ADADM = build up medium chain fatty acids (C8) which the body can’t efficiently uses for gluconeogenesis resulting in low energy availability especially for the brain
How is MCADD screened for?
tandem mass spec for levels of medium chain FA C8 compared to C10
what is the treatment for MCADD?
dietry intervention- regularly eat to prevent need for gluconeogenesis
