Session 5: Population screening Flashcards

Question

what was the Myriad Vs Association of molecular pathology case of 2013?

Answer 1

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

Answer 2

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

Answer 3

1. mass- newborn screening 2. targeted- lung disease in coal miners 3. opportunist- BP at routine GP appointment 4. pro-active- cervical screening in women >25yrs

Answer 4

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

Answer 5

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

Answer 6

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

Answer 7

less radical treatment required reduced costs and resources -ve result can provide reassurance

Answer 8

false -ve may give fale reassurance false +ve may result in unecessary treatment, anxiety and testing longer morbidity if prognosis is unaltered

Answer 9

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

Answer 10

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

Answer 11

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

Answer 12

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)

Answer 13

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

Answer 14

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

Answer 15

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

Answer 16

- aim is to enable autonomous decision making - need clear information available if there is reduced penetrance or variable expressivity - provide residual risk figures

Answer 17

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

Answer 18

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

Answer 19

1. autonomy- pateint has the autonomy and choicde 2. beneficence- highest priority is th welfare of the patient and minimising harm to them 3. non-maleficence- prevent and minimise harm to the patient 4. justice- equity of access and patients should be treated fairly

Answer 20

-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.

Answer 21

reproductive autonomy- individuals have the right to make informed decisions therefore need informed consent but counselling should be non-directive

Answer 22

- 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

Answer 23

- 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

Answer 24

1. may result in -ve stigma against people with the condition and could be considered a form of eugenics 2. chosing not to have a child with a genetic condition could devalue those people that have it 3. pressure on parents to not have a child with a condition or judged if they do for placing extra burden on health service 4. fewer people born with the condition may reduce the funding for services and treatment of people with the condition 5. most conditions have a residual risk even after carrier testing

Answer 25

- 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

Answer 26

increased used of NGS- WES and WGS

Answer 27

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

Answer 28

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

Answer 29

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

Answer 30

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

Answer 31

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

Answer 32

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?

Answer 33

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

Answer 34

test asymptomatic/ pre-symptomatic individuals not diagnostic and may need a confirmatory test

Answer 35

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

Answer 36

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

Answer 37

need to adjust for the following - weight (increased weight can dilute markers) - IVF - smoking - ethnicity - accuracy of dating (gestational age)

Answer 38

- 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

Answer 39

- 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

Answer 40

aims is to provide treatment to newborn ASAP to reduce/prevent potential severe phenotype

Answer 41

2 weeks for PKU 3 weeks for CHT and MCADD 4 weeks for CF 6 weeks for SCD

Answer 42

- 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

Answer 43

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

Answer 44

results in severe MR growth failure, poor skin pigmentation, microcephaly, seizures, global developmental delay and severe intellectual impairment.

Answer 45

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

Answer 46

NBS detects increased phenylalanine in the blood by tandem MS

Answer 47

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

Answer 48

failure to thrive and don'r grow properly physical and mental handicap neonates may have a protuding tongue, jaundice, feeding difficulties and low hairline

Answer 49

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.

Answer 50

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

Answer 51

thyroxine supplementation

Answer 52

increased level of TSH- produced as abn thyrpid gland is not responding

Answer 53

deficiency in fat metabolism and can result in death

Answer 54

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

Answer 55

tandem mass spec for levels of medium chain FA C8 compared to C10

Answer 56

dietry intervention- regularly eat to prevent need for gluconeogenesis

Answer 57

AR disease with het advantage so has high carrier freq in regions of world affected by malaria e.g. Africa in hom form RBCs are sickle shaped and cannot flexibly bend to fit through small capillaries resulting in damage to blood vessels and organs, chronic pain ans infection

Answer 58

by seperating HB protein by isoelctric focusing or high performance liquid chromatography- abn Hb protein will have a different mass charge ration (IEF) or elution time (HPLC) genetic testing can also be carried out for to allow family testing other clinically significant heamoglobinopathies are also screened for

Answer 59

mutation in the CFTR gene

Answer 60

uses combination of genetic testing and IRT -IRT has a poor PPV on its onwn and is raised imediately after birth in all so need to wait till day 5 to test - genetic testing alone with a panel would identify a high number of carriers which should be avioded in prenatal testing 1. test for IRT - if raised test, re assay then for 4 most common CF mutations - CF confirmed - no more testing - carrier- test with full CF panel and may need to IRT again if still not second mut detected - no mutation - IRT again

Answer 61

mutlisystem disorder affecting - GI tract - fertility - BAVD - respiratory tract- recurrent infections, disseminated bronchiecstasis - failure to thrive - pancreatitis

Answer 62

early intervention with high energy diet, medicine and physiotherapy does not cure but improves symptoms and outcomes

Answer 63

urine smells of maple syrup vomiting lethargy progressive neurologic deterioration due to defect in keto acid dehydrogenase resulting in build up of leucine, iso-leucine and valine

Answer 64

tandem mass spec for leucine. iso-leucine and valine

Answer 65

low protein diet to prevent build up of amino acid and thiamine early intervention prevents neurologic damage

Answer 66

AR didease due to mutation in cystathione b-synthase = catabolism of methionine and toxic accumulation of homocyteine results in skeletal abn and LD

Answer 67

tandem MS for undeviated MRM methionine

Answer 68

very low methionie diet and supplmetation - without treatment patients die before 30yrs

Answer 69

accumulation of glutyaric acid due to deficiency in glutaryl co-a dehydrogenase macrocephaly and metabolic and neurologic crisis

Answer 70

Tandem mass spec for glutaryl carnitine

Answer 71

low protein lysine restricted diet with carnitine supplementation

Answer 72

Tandem mass spec for isovalerylcarnitine confirmed by analysis of urine organic acids

Answer 73

defective catabolism of leucine results in toxic accumulation of isovaleric acid and its glycine and carnitine derivatives vomiting, metabolic crisis, failure to thrive, coma and even NND

Answer 74

long term dietary management

Answer 75

Due to defects in metabolic pathways classical symptoms are either due to an accumulation of a substrate which toxic to the body or a deficiency in a product generally AR or XLR

Answer 76

Multisystem disorder can present with: failure to thrive and wight loss vomiting and lethargy cytopenia heart failure immunodeficiency hypotonia NDD, seizure and stroke organomeglay

Answer 77

dietary restriction/management for disorders resulting from a toxic accumulation of products and supplementation for deficiency's

Answer 78

medium chain acyl-coA dehydrogenase deficiency homocystinuria glutaric acidemia isovaleric acidemia maple syrup urine disease phnyketonuria

Answer 79

traditionally tested for biochemically but this can be non specific e.g. czellweger syndrome can be cuased by multiple peroxisomal storage disorders biochemical testing may also require invasive testing e.g. liver biopsy for glycogen storage disorders so genetic testing is also carried out as this can: - be used to identify carriers and inform prenatal testing or reproductive descisions - can help indicate mutation specific therpay e.g. PTC read through - provide prognostic information - provide specific diagnosis

Answer 80

disorder of peroxisome biogenesis cause by multiple PEX gene and 3 different types

Answer 81

severe and can result in death < 1 yr- affects development, hearing, eyes and liver AR biochemical test is for very long chain fatty acids

Answer 82

ornithine transcarbamylase deficiency due to mutations in the OTC gene can test for decreased OTC enzyme deficiency

Answer 83

urea cycle is the primary mechanism for removing waste nitrogen from protein turn over and metabolising nitrogenous compounds deficiency result in hyperammonemia

Answer 84

Semi-lemli-Opitz syndrome due to a deficiency in 7DHC 7-dehydrocholesterol reductase

Answer 85

Pompe disease type II hypotonia, cardiomegaly, FTT, respiratory distress and hearing loss

Answer 86

deficiency in GAA enzyme acid gucosidase- essential for dregredation of glycogen to glucose in lysosomes and enzyme deficiency is biochemically diagnostic

Answer 87

IEM due to the toxic build up of material in cells due to enzyme deficiencies so lysosomes cannot perform their normal functions due to mutations in emzymes that act in the lysosomes or transporters

Answer 88

cellular membrane bound protein with an acidic content due to a H+ pump - usually function to digest materials and symptoms arise from the build up of partially degraded substances in the lysosomes

Answer 89

mucopolysacharidoses- build up of glycosaminoglycans oligosaccharidoses- build up of oligosaccharides sphingolipodoses- build up of sphingolipids

Answer 90

AR or XLR LOF mutations increased risk of neurodegenerative disorders in carries (alzheimers and parkinsons reported)

Answer 91

Being considered as there is a better outcome if treatment started early - screening offered in Israel for Tay sachs - taiwan tests for Pompe and Fabrys

Answer 92

disorder of lipid storage mutations in enzymes that break down sphingolipids - important for the CNS and form part of the myelin sheath

Answer 93

Fabrys- X linked Gaucher - AR Niemann Pick - AR

Answer 94

result in an accumulation of glycosaminoglycans which are very long chain fatty acids due to a deficiency in the enzymes required to break them down

Answer 95

affects skeletal muscle and cause neuronal dysfunction

Answer 96

MPS II Hunter syndrome MPS III San Fillipo syndrome MPS IV Morquio syndrome

Answer 97

glycogen storage disorders due to a deficiency in enzymes required to degrade olligosaccharides into gycoproteins and glycolipids

Answer 98

affects skeletal muscle and cause neuronal dysfunction

Answer 99

Pompe disease Battens disease (neuronal ceroid lipofuscinoses)

Answer 100

cause by pathogenic variants in the genes that encode the globin genes

Answer 101

HB alpha is encoded by HBA1 and HBA2 found on chr 16 in 2 4kb gene clusters have high sequence homology 1 HBB gene on 11p

Answer 102

fe containing O2 transport metalloprotein in the red blood cells of vertebrates

Answer 103

pathogenic variants result in reduced synthesis of the hB or an abnormal Hb structure. this causes disease in the thalassemias but resulting in a chain imbalance between HBA and HBB excess of a subunit rather than a lack of expression causes the clinical consequences in thalassemia

Answer 104

have a heterozygote advantage and protect against severe malaria in childhood therefore there are high levels in areas affected by Malaria e.g. Mediterranean (cyprus, turkey), middle East, Africa and Asia. there are also regionally specific disorders and therefore ethnic origin may point to a diagnosis

Answer 105

most common hemoglobinopathy due to mutation in one of the HBA genes (HBA1/2) defecit in a chain production results in an imbalance with B chain formation

Answer 106

deletion of 1 or both HBA genes accounts for 90%- most commonly sue to unequal corssing over betweeen the HBAS clusters on 2 chromosome 16's due to the high sequence homology remaining 10% are point mutations spread throughout the gene

Answer 107

the more copies of HBA that a missing the more severe the phenotype

Answer 108

type 1 have loss of 1 gene- symptomless carrier type 2- loss of 2 genes- asymptomatic but may have macrocytic anemia on examination type 3 - loss of 3 genes = affected with anemia, hemolysis and splenomegaly - may require blood transfusions - lack of HBA results in abn b-globin tetramers being formed type 4- loss of all 4 genes - severe and onset in utero, results in still birth of early NND - early diagnosis may enable blood transfusion in utero but likely to still have abn - associated with rec misc - fetal form as HBA is expressed in the fetus

Answer 109

due to a deficiency in B globin and there is a reduction in adult Hb in red blood cells expression begins at birth when fetal gamme globin declines so not associated with fetal onset as with HBA type 4

Answer 110

results in anemia and hepatosplenomegaly onset from 6 months and blood transfusions from 2 yrs most severe form can be treated with regular blood transfusion but risk of fe overload so also need to prescribe fe chelators to overcome this

Answer 111

mild to mod anemia generally normal life but may need occasional blood transfusions

Answer 112

due to imbalance in a and b chains so severity can be reduced with co-inheritance with A-thal - variants that sustain gamma globin levels also decrease severity

Answer 113

AR disorder due to mutations in HBS most commonly homozygosity ofr c.20A>T Glu7Val results in RBCs with an abnormal rigid 'sickle' shape- means they cant pass through small capillaries resulting in vascular occlusion = sickle crisis - bone and joint pain and necrosis - organ damage - anaemia - risk of infection - stroke

Answer 114

full blood count Hb pattern analysis using isolectric focusing, HLPC or capilliary electrophoresis DNA testing is used to confirm the mutation so carrier testing and prenatal diagnosis can be offered.

Answer 115

offers screening to all mothers as part of the antenatal care - if mother is a carrier the father is also offered testing - all pregnant women offered in high prevelance areas but in low prevelance areas only women identified as being at risk from a family origin questionnaire are tested - aim is to offer all women testing by 10 weeks gestation and to report result by 13 weeks to allow pregnancy decision making - involvement of genetic testing depends on the prev hem lab result and as a screening service is will not detect all possible deleterious outcomes.

Answer 116

blood transfusion with concurrent fe chelation BM transplant for severe cases but risk of GVHD research currently looking into using lentiviral vectors (as they can carry large transgenes and infect quiescent cells) for gene therapy. - phase 1 trials are ongoing for SCD gene therapies

Answer 117

due to an inability to from blood clots - result in excessive bleeding, oozing or re-initiation of bleeding, easy bruising. caused by a deficiency in platelets or clotting factors

Answer 118

VWF is a bleeding disorder caused by mutation in the VWF gene at 2p13

Answer 119

is essential for platelet depending homeostasis and carries factor VII (F8) protecting it from degredation to sites of vascular damage

Answer 120

Type 1 - partial quantitative deficiency in VWF - most mild disease and genetic testing is not generally indicated - AR or AD Type 2 is a qualitative deficiecy with high penetrance and can be AR or AD Type 3 is most severe and is a complete quantitative deficiency due to 2 null mutatnts - AR - genetic testing indicated and prenatal testing can be offered

Answer 121

it is a very large gene and there is a highly homologous PVWF psuedoegen

Answer 122

Due to a deficiency in F8 Xq28 XLR more common than hemophilia B 1 in 5000

Answer 123

severity is defined by the plasma activity of the F8 coagulation factor genetic testing first looks for a intron 22 or intron 1 inversion as this accounts for >50% of cases - intron 22 tested for by inverse PCR with primers designed to only produce a product when the inversion is present negative cases have further mutation screening by sequencing and MLPA

Answer 124

decrease in clotting activity = joint and muscle bleeds, easy bruising recurrent bleeding in joints causes synovitis leading cause of death in hemorrhage in the CNS female carried are generally asymptomatic but may show mild features due to skewed X intactivation. Homozygous females are rare but present with the same features as males

Answer 125

deficiency in F9 xq27 XLR less common than HA - 1 in 30,000

Answer 126

increased risk of venous or arteriol thrombosis thrombosis is a predisposition to from blood clots inappropriately

Answer 127

Factor V leiden thrombophilia Hereditaty antithrombin deficiency

Answer 128

Von Willebrand disease hemophilia A hemophilia B

Answer 129

thrombosis characterised by a poor anticoagulant response to activated protein C usually no thrombotic event until adult and some may never develop one

Answer 130

due to mutation in the Fv gene on 1q24 FV is a glycorpotein made in the liver. In response to injury it is activated and acts with other factors to from a complex which converts inactive prothombin to active thrombin = blood clots mutations result in 10x slower inactivation so there is excessive thrombin production and risk of abnormal clotting

Answer 131

AD disorder resulting in increased risk of blood clots typically DVT and pulmonary embolism

Answer 132

Maps heritable traits to their chromosomal location. - start by identifying genetic markers, commonly SNPs or STRs, on a section of a chromosome and then narrowing the region down until the gene or gene variant of interest is identified

Answer 133

1. Gene discovery 2. Family studies when the mutation is unknown- this assumes the locus i.e. the gene of the familial disease is known. - Method should use several informative microsatellite markers flanking the locus of interest to identify the high-risk haplotype. - Requires analysis of key family members to assign phase and the high-risk haplotype and informativity of markers. - Recombination may occur, which can make interpretation more difficult – Bayes calculations may be required.

Answer 134

* DMD – identify high-risk haplotype where no causative pathogenic variant has been identified but a clinical diagnosis of dystrophinopathy has been confirmed by muscle biopsy. * SMA – identify the high-risk haplotype where a homozygous SMN1 deletion has been identified in an affected child, but a parent carries two copies of SMN1 on one allele. * HD – indirect prenatal test * PGD- haplotype analysis allows the same design to be applied to multiple families regardless of the underlying mutation

Answer 135

* Suited to highly penetrant monogenic disorders with mendelian inheritance. * Requires large, multi-generational families. * Poor genetic resolution, centimorgan range. * Likelihood of linkage calculated as a LOD score.

Answer 136

The non-random association of alleles at two or more loci with a frequency greater than expected by chance. * Due to natural selection or chance. * Underpins association studies. An association can only be found between alleles and disease if the disease is in LD with a marker allele. * When a disease mutation arises on a founder chromosome and not much time has elapsed since the mutational event, the disease mutation will be in linkage disequilibrium with alleles from loci close to the gene. Thus, linkage disequilibrium can be a powerful tool for genetic mapping. * Loci in LD will often be genetically linked, but LD can occur even if loci are on different chromosomes.

Answer 137

* Recombination * gene conversion * selection * population structure * new mutation * genetic drift * gene flow- The greater the allele frequency differences between populations the greater the LD created when populations join. * population history

Answer 138

- LD is often expressed as D. If D=0 there is no association between alleles - D=1 is complete LD - Between 0 and 1 there is some linkage between the alleles

Answer 139

Over time recombination between loci will gradually reduce LD as alleles that were shared on an ancestral chromosome are separated. It can therefore be harder to find LD in older populations. Areas of the genome with lower recombination rate can maintain LD for longer.

Answer 140

Over time recombination between loci will gradually reduce LD as alleles that were shared on an ancestral chromosome are separated. It can therefore be harder to find LD in older populations. Areas of the genome with lower recombination rate can maintain LD for longer.

Answer 141

If there is a selective advantage to two alleles coexisting, LD between the alleles is more likely to be maintained whereas a negative selection can remove LD

Answer 142

- Inbreeding and non-random mating will alter the expected allele distributions. - Older populations have shorter regions of LD as more recombination’s have taken place

Answer 143

A high new mutation rate at a locus will make it hard to detect LD. Mutations will arise on different ancestral backgrounds, the phenotypic affect may be the same, but the underlying haplotypes will not.

Answer 144

The tendency of alleles that are closely located on a chromosome to be inherited together at meiosis.

Answer 145

* They occur frequently so can check short chromosome segments for disequilibrium- although only bi-allelic they are more common than STRs and can be detected via gentypeing chips allowing 100’s to be genotyped at once * They have a relatively low mutation rate so persist through the population * They are easy to genotype on a large scale * Phase must be assigned, this is generally done using family members. If not available computer algorithms can determine the most likely haplotype

Answer 146

- Need to identify many families with several affected generations- this is harder for late onset or diseases with a high mortality - Linkage studies are less helpful for complex traits, such as diabetes where multiple genes are important in disease causation

Answer 147

* Linkage analysis requires the scoring of meioses as recombinant or non-recombinant for the locus in question. * If this can be done (i.e. there aren’t too many homozygotes and enough variation) the locus is described as informative for linkage. * All results must be replicated to be credible. * Failure to replicate linkage does not necessarily disprove the hypothesis as linkages will often involve weak effects.

Answer 148

In Parametric linkage analysis a series of parameters need to be - Mode of inheritance (dominant/recessive/X-linked etc) - Gene frequencies - Penetrance – the most difficult to specify (beware phenocopies)

Answer 149

- Parametric linkage analysis is used for simple Mendelian disorders. - Not suitable for complex disease such as diabetes or schizophrenia (no idea of gene frequencies or penetrance of any susceptibility alleles or sometimes mode of inheritance).

Answer 150

Double crossovers can involve 2 or more chromatids, but if the region crossing over is close to the gene, a second event in the immediate vicinity is unlikely as the first event creates a phenomenon called interference, which restricts further crossing over.

Answer 151

- Log of the odds that 2 loci are linked - Used log as it makes the numbers easier to work with - Lod scores can be added across families

Answer 152

* Z= 3.0 is the threshold of significance for accepting linkage (with a 5% chance of falsely rejecting the null hypothesis). * Linkage can be rejected at values of Z

Answer 153

* Autozygosity mapping is a form of linkage analysis used in consanguineous families. * Autozygosity occurs when individuals are homozygous at a particular locus because the alleles are identical by descent (IBD)- inherited from a common ancestor.

Answer 154

Method of linkage analysis that does not require an inheritance model. Non-parametric methods are widely assumed to be more robust than parametric methods, but is complicated when combining data from families of different sizes

Answer 155

The region of the genome with the disease gene will be from a common ancestor by affected members of the family more frequently than would be expected by chance. This is identified by analysis for shared segments- this can be in any affected family members but affected sib-pairs are most commonly used.

Answer 156

1. Genotype large no, of SNPs/ STRs in sibs covering whole genome 2. Look for markers that do not follow mendelian ratios (1:2:1 ratios - e.g. sharing of one allele is >½ and sharing of 2 alleles is >¼ ) - if parents are available can determine if region is IBD or IBS 3. Using the combined data from all the families the IBD/IBS frequencies at each locus can be determined and each tested to see if it deviates from the null hypothesis of simple Mendelian segregation. Thus identifying over the whole dataset, loci where there is a significant excess of sib pairs that are IBD. 4. When regions of suggestive linkage are identified, the region will then usually be re-examined using more densely spaced markers in an independent data set.

Answer 157

Compare cases to controls to identify association (statistical relationship) between a particular allele/genotype and a genetic trait. Essentially cases and controls are genotyped and allele frequency differences are determined. If a SNP is more common in cases than controls it is said to be associated with the disease. It is not necessarily causative itself but marks a region of the genome which influences the risk of disease.

Answer 158

Association studies have fine genetic resolution in the kilo base range.

Answer 159

Investigate the entire genome. The approach is therefore said to be non-candidate-driven in contrast to gene-specific candidate-driven studies.

Answer 160

1. Chance. 2. False linkage due to linkage disequilibrium between marker being studies and the true disease-causing variant. 3. Bias in resulting from population stratification. Different genetic variants are known to occur with varying frequencies in different populations and ethnic groups, quite independent of the frequency of disease in these groups- confounding bias. Need to be aware that apparent association may just reflect shared population history 4. True association- the genetic variant is important in disease causation.

Answer 161

Linkage investigates the relationship between transmission of a haplotype/locus and the expression of a disease trait in families Association analysis investigates the relation between a specific allele and the disease/trait within population.

Answer 162

Gene-association studies can be used for * Can identify association in complex diseases e.g., diabetes and hypertension – in linkage unless you have a VERY large family you need to combine data from multiple families. For polygenic disorders it is highly unlikely that every family will have the same collection of underlying genetic factors and so linkage results will conflict. * Can be used to study rare diseases * Can be used to test for a specific marker in a particular gene (individual SNPs). * It can also be useful in investigating gene-gene or gene-environment interactions.

Answer 163

* Case and control participants are drawn from the same population. * Case participants are representative of all cases of the disease or limitations on diagnostic specificity and representativeness are clearly specified. * Genomic and epidemiologic data are collected similarly in cases and controls. * Differences in allele frequencies relate to the outcome of interest rather than differences in background population between cases and controls.

Answer 164

The power of a study is the ability of a design to pick up associations accurately.

Answer 165

- frequency of the risk allele in the population - relative risk conferred by the disease-associated allele - LD between genotyped marker and true risk allele - sample size and genetic heterogeneity of the sample population

Answer 166

Illumina HumanOmni5 Affymetrix Genome-Wide Human SNP array 6.0.

Answer 167

- Increasing the sample size and using carefully matched cases and controls - To increase the number of participants and prevent re-genotyping many studies combine previous data sets in meta-analysis. - To confirm associations a study can genotype further patients and controls for any those if interest that appear to have an association. This increases the power of thr study but is cheaper than fully genotyping more individuals and can help ID false positives.

Answer 168

When an association is detected, the significance is calculated using P. If P=0.05 this would represent a 5% chance of a false result.

Answer 169

The high number of SNPs genotyped for GWAS means the value is only considered significant if VERY low. For examples if the p-value was 0.05 then if 1,000,000 SNPs were genotyped you would expect 50,000 to be false results. This is too high therefore a P-value of less than 5x10-8 is used.

Answer 170

* cannot test causality just association * Prone to confounding variables – need a carefully matched case and control population * Expensive * Necessity for multiple testing correction makes statistical threshold for significance hard to reach. * Need large studies to have sufficient power to identify association for rare or low penetrance variants. * Missing heritability- most GWAS identify SNPs only conferring small effects- this has led to the belief that GWA studies were ultimately not worth the expenditure * Design efforts made to reduce false-positive results, may result in overlooking a true association.

Answer 171

The rapidly decreasing price of complete genome sequencing have also provided a realistic alternative to genotyping array-based GWA studies.

Answer 172

GWAS studies are laying the foundations for personalised medicine and a move from a one size fits all model to one that aims to customise strategies based on an individual’s genetics. Genome-wide association studies have successfully identified genetic variations that contribute to risk of type 2 diabetes, Parkinson's disease, heart disorders, obesity, Crohn's disease and prostate cancer.

Answer 173

diseases of the cardiac muscle not caused by coronary disease, high blood pressure or heart valves due to inherited or sporadic variants in cardiac muscle proteins phenotypic variability from asymptomatic to severe

Answer 174

AR, XLR, AD, mitochondrial > 40 genes TTN accounts for 1/3 inherited cases

Answer 175

dilated CM Hypertrophic CM Restricted HC

Answer 176

disorders of the hearts electricla system including tachycardia, bradycardia or arrythmia

Answer 177

Long QT syndrome- genes encoding potassium and sodium channels- e.g. KCNQ1 Brugada syndrome- SCN5A