Inheritance patterns and genetic diseases Flashcards

Question

Describe male Rett syndrome

Answer 1

~1% of males with severe MR - Males with MECP" variants are born with neonatal encephalopathy resulting in death before age two years - adult males with classical Rett are 47,XXY or mosaics and have the same phenotype as females or have less severe neurological maifestations but carry variants not seen in females with Rett- presumably to mild to cause disease in het state

Answer 2

Variant Rett is caused by variants in FOXG1 (Chromosome 14, distinguished by congenital microcephaly and corpus callosum abnormalities) and CDKL5 (X chromosome, distinguished by early onset seizures)

Answer 3

affects hair, skin, teeth, nail and CNS- nail dystrophy, and eye and dental abnormalities and born with a rash. males spontaneously miscarry in the first trimester or have some mosaicism Due to mutations if IKBKG high penetrance and variable severity

Answer 4

CFNS is a XLD disorder with affects females but not males. females have frontonasal dysplasia, craniofacial asymmetry and craniosynostosis, whereas males typically show only hypertelorism Caused by mutations in EFNB1- encodes a TM protein involved in bi-directional cell signalling females are affected as skewed X-inactivation leads to a population of mutant and non-mutant cells. This interface between the normal and mutant protein population is the cause for the phenotype in males. Therefore a mosaic male may also express an phenotype.

Answer 5

- can result in the expression of an XLR disorder - high skewing can affect the severity of XLD and there have been reports of asymptomatic carriers of Rett due to inactivation of the mutant allele

Answer 6

AR or AD as the PAR regions is found on both the X and Y chormosome

Answer 7

incidence 1/10,000 carrier freq ranges from 1/40 to 1/60 (1/50 in the UK) second most common AR disease in hr UK and the most common cause of infant deaths

Answer 8

SMA is caused by a mutation in the survival motor neuron (SMN) gene. SMA results in progressive muscular weakness due to loss of anterior horn neurons in the brain and spinal cord. The neurons are required to relay signals to proximal muscles from the brain for them to contract. muscle weakness is proximal to distal with inclusion of he intercostal muscles, the diaphragm is usually spared.

Answer 9

Progressive symmetrical muscle weakness of the proximal limbs and trunk - difficulty breathing due to inclusion of intercostal muscles - normal or above average IQ - facial weakness - fine muscle tremor in fingers - poor suck/swallowing - difficulty feeding

Answer 10

Athrogryposis mutliplex congential

Answer 11

SMA is due to mutations in SMN there are 2 copies of SMN located in tandem in a 500kb inverted dup in 5q13 - 5q13 is a has a highly complex structure containing many repetitive regions, pseudogenes, retro- transposable elements, deletions, inverted dups

Answer 12

In the normal population the majority of individuals have 1 copy of SMN1 on each chromosome. However approximately 4% of the population have 2 copies of SNM1 on a single chromosome - this can cause issues with carrier testing.

Answer 13

SMN protein is ubiquitously expressed in motro neurons of the spinal cord. it is though to be involved in RNAP transport in motor neurons. SMA is essental and loss of SMN1 and 2 is embryonic lethal

Answer 14

SMN1 is the native gene and is telomeric to the SMN2 pseudogene. Both genes are highly homologous and only differe byt few bases in thr 3' of the. The key difference is a C>T transition in SMN2 exon 7. This synonymous change disrupts a splice enhancer site at the intron6-exon7 border resulting in inefficient splicing and a shorter transcript lacking exon 7. This results in only ~10% of the full lengthtranscript being translated. In SMN1 90% of the full length transcript is translated.

Answer 15

loss of exon 7 causative of SMA- result in a decrease in the amount of SMN produced Homozygous deletion of at least exon 7 of SNM1 is responsible for ~95% of cases - approximately 2% of the deletions are de novo 4% are compound het for an SMN1 deletion and a pathogenic sequence variant 1% and homozygous for a pathogenic sequence variant

Answer 16

prenatal/congenital form AKA Werdnig Hoffman disease - onset at birth and life expectancy to ~6months - never sit unsupported - profound hypotnia, feeding difficulties and death from respiratory failure homozgous SMN1 del

Answer 17

severe/ actue SMA AKA Werdnig Hoffman disease onset at 0-6 months and die < 2 years from respiratory failure - never sit unsupported - frog leg posture - profound hypotnia, feeding difficulties and death from respiratory failure homozygous del

Answer 18

``` intermediate AKA Dubowitz disease - onset 6-18 months - death >2 years and 75% reach 25 - can sit but never stand or walk independently - profound hypotonia and muscle weakness postural hand tremor avg or >avg IQ ``` SMN gene conversion & SMN del

Answer 19

Kugelbury Walander disease - onset > 18 month and nearly normal life expectancy - can walk unsupported - may have hand tremor - phenotype similar to muscular dystophy 2 SMN2 gene conversions

Answer 20

Adult onset normal lifespan and reach all motor milestones have more copies of the SMN2 gene which acts a a disease modulator and compensates for the lack of SMN

Answer 21

SMN2 can modify the disease severity in a dose dependent manner. The more copies of SMN2 the less severe the pheno. - there has been a report an asymptomatic individual with homozygous SMN1 del but 5 copies of SMN2 BEWARE- correlations are imprecise so this is not used clinically to predict the course if the disease.

Answer 22

- there is an SMN2 point mutation that can result in the inclusion of exon 7 by creating a new splicing enhancer and thereby increasing the amount of full length transcript - plastin 3 shown to be upregulated in a family member with no SMA and an SMN1 del and same number of SMN2 copies as an affected family member.

Answer 23

As majority of cases have homozygous del the first line test is dosage analysis of at least SMN1 exon 7 - 95% sensitivity and 99% specificity only loos of SMN1 exon 7 is required to develop SMA as it is the clinically relevant transcript

Answer 24

dosage analysis will detect 95%, sequwncing will detect a further 4% only exons 7 & 8 are tested as they have SNPs whish allow distinction of SMN1 & 2 MRC holland MLPA kit available with probes targeted to SNPs in exon 7 and 8- can detect carriers, dels, dups and gene conversion Quantitative PCR uses flourescently labelled primers specific to the nt differences in ex 7 & 8. Products are separated by capillary electrophoresis and copy number determined by comparison to controls

Answer 25

4% of the popultaion carry 2 copies of SMN1 on a single chromosome. As doage does not provide positional information this can mask the presence of a deletion in the other allele and can't distinguish 2:0 from 1:1. - linkage analysis can help resolve carrier status in cases with a proband with a hom deletion and only 1 carrier parent identified - grandparents can be tested- if a parent id 2:0 the liklihood is there parents will be 1:0 and 2:0, but if the deletion in the proband is de novo the grandparents are liekely to be 1: as this is the most common in the population. Small risk of both grandparents being 2:0 but chance of this is vanishingly small. - de novo deletion occurs in 2% of cases so this should also be considered. Bayesian calculations can be used to determine the residual risk of being a carrier after a normal dosage result (considers chance of 2:0 and sequence variants) the finding of 2 copies if SMN1 significantly reduces the chance of being a carrier

Answer 26

May habour a pathognic SNV in the remaining SMN1 copy. Can carry out sequence analysis but this is complicated by the SMN2 psuedogene. - therefore allele specific long-range PCR and RNA seq technologies are required for specific analysis of the SMN1 gene - a multiplex PCR for the most common small intragenic mutations has been developed

Answer 27

Prental diagnosis by NIPD has been diagnosed as part of the NIPSIGEN project - this uses enrichment of highly heterozygous SNPs across the SMN1/2 region followed by massively parallel sequencing and analysis of relative haplotype dosage. . Maternal, paternal and proband DNA samples are also tested for haplotyping purposes.

Answer 28

linkage analysis can be used to detect the inheritance of the high risk allele. - this is useful in cases where a second mutation has not been identified but SMA has been diagnosed clinically to enable carrier and prenatal testing. - amplified MS markers flanking the region and needs DNA from proband to determine phase. Need to consider risk of a double recombination resulting in the high risk allele being associated with the low risk haplotype. - sensitive to MCC from 5% (lower than the 10% excluded by QF-PCR in most labs)

Answer 29

Nusinersen (AKA spiranza) is an 18mer anitsensne oligonucleotide which has been approved by NICE for treatment of molecularily confirmed SMA I,II and III. - treatment works by promoting the inclusion of the SMN2 exon 7 in SMN2 transcripts to increase the level of the full length transcript. does not need to cross BB as increasing SMN in the CNS is not reuired to rescue the preipheral muscle phenotype and rescue motor neurons andincreaase long term survival (study in mice)

Answer 30

gene conversion of SMN1 to SMN2 has been reported, stem cell or gene therapy may compensate for the lack of sufficient SMN. AAV9 can infect numerous cells and cross the BBB. In Mice has been shown to result in mice expressing the engineered WT gene and therefore an increase in SMN levels

Answer 31

Most patients diagnosed with SMA are already in the advanced stages with significant motor neuron degeneration having already taken place. no there is treatment available there is an argument for NBS as late treatment is less beneficial. Already included in NBS in the US and being considered in Belgian and Taiwan

Answer 32

truncating mutations are more severe and there is stronger selection against them in the 5' of the gene. missense mutations are less severe so may only be seen in male Rett

Answer 33

MECP2 is implicated in the transcription in neuronal cells e.g. regulated BDNF transcription - affects synaps plasticity and neuronal development

Answer 34

bi directional sequencing detect 85-90% of mutations. dosage analysis by MLPA can also be performed.

Answer 35

PCR of polymorphic CAG repeat in the 1st exon of the androgen receptor. DNA is digested by a methylation snsitive restirction enzyme to determine which CAG repeat length (and therefore which X) is silenced. Can be used to determine the degree of skewing by comparing the level of digestion of each allele.

Answer 36

In XLR females are generally not affected whereas in XLD females are affected. However the standard definitions of AR or AD do not capture the variable expressivity due to skewed x inactivation.

Answer 37

vertical transmission from mothers- 50% of sons will be affected and 50% of daughters will be carriers. Male transmission- all daughters will be carriers. there is no male-male transmission so no sons will be affected. pairing of an affected male with an affected female can give the false impression of male-male transmission.

Answer 38

skewed X-inactivation 45,X Inheritance of mutation from both parents UPD for X chromosome

Answer 39

SBMA is a late onset progressive neuromuscular disorder that results in muscular atrophy and distal to proximal muscle weakness and wasting onset is 30-50 yrs and require a wheelchair within 10yrs

Answer 40

caused by a CAGn polyglutamine expansion in the 1st exon of the AR gene. 35-37 repeats is variable penetrance 38+ repeats is full penetrance shows anticipation GOF , precise mechanism is unknown but it is thought to result from the CAG tract being cleaved into a polyglutmaine fragment which is retained in the nucleus where it forms nuclear inclusions. female carriers asymptomatic

Answer 41

AIS is caused by pathogenic LOF mutations in the AR gene. Encodes the androgen receptor which allows cells the respond to testosterone and is required for male sexual development characterised by female external genitalia and abnormal secondary sexual development at puberty mainly missense mutations and dela and dups are rare. Testosterone levels are normal or elevated

Answer 42

complete AIS- normal female external genitalia, raised as females. Associated with variants throughout the coding region partial AIS- Nearly normal female genitalia or ambiguous. Variants mainly in the steroid ir DNA binding domains Mild AIS- typically have male external genitalia and mutations in ex 5 or 7 or amino terminal domain

Answer 43

Due to mutations in the coagulation factors factor VIII (F8 in haem A) and factor IX (F9 in haem B). Mutations cause F8 and F9 to be ineffective in coagulation cascade. Clinically indistinguishable. diagnosed by a deficiency in clotting of the relevant factor complications arise from bleeding into joints, muscle, brain or other internal organs. female carriers are biochemically abnormal but clinically unaffected. 10% of females are symptomatic and at risk of bleeding F8- large gene. Intron 22 is the most common mutation. 1 in 6000 males F9- small gene, mainly SNVs and 1 in 30,000

Answer 44

Due to mutations in the IDS gene- this encodes the enzyme for the breakdown of mucopolysacharides. without this enzymes MPS build up resulting in tissue damage. variable severity, age of onset and rate of progression. In the severe disease there is CNS involvement and progressive airway and cardiac disease result in death. In the attenuated form the CNS is spared.

Answer 45

Most common muscular dystrophy - 1 in 3500 males penetrance is 100% in males and variable in females prevalence of BMD is 1 in 8000 and females rarely display phenotype

Answer 46

Mutations in the dystrophin gene can also result in X-linked cardiomyopathy. This presents as cardiac disease with no skeletal muscle involvement. due to a mutation in promote and 1st exon resulting in no dystrophin present in cardiac muscle. - skeletal muscle spared as it can use other promoters - onset is 20-25yrs in males was fast progress and death in a few years - in melanges onset is 40-50 yrs and is slower

Answer 47

- onset < 5yrs and delayed motor development - wheelchair bound by 12 years - progressive muscle weakness and muscle replaced by fat and fibrotic tissue - gower sign - legs and pelvis affected first - scoliosis may develop - 95% of males develop cardiomyopathy - dev delay present in 30-50% and coincides with later onset of symptoms (may be referred for array for LD and DMD discovered then) - mean age at death is 25yrs due to respiratory and cardiac insufficiency - creatine kinase levels are 10-100x normal

Answer 48

milder than DMD - 20% have dilated cardiomyopathy - may be lat learning to walk - muslce weakness onset from ~ 11yrs - lose ability to walk at 49-50 yrs - no LD - survive to middle - creatine kinase 5x normal

Answer 49

largest human gene with 79 exons- 2.4MB in size but only 3% is coding 7 tissue specific promoters including brain, cardiac an skeletal muscle

Answer 50

dystrophin is a rod shaped cytoskeletal protein which provide structural support dystroglycan complex (DGC) the DGC forms a critical link between the cytoskeleton and the ECM and stabilizes the sarcolemma during contraction and relaxation. loss of dsytrophin disrupts the link between the ECM and cytoskeleton which increase the fragility of the cell membrane and muscle becomes mechanically damaged during contraction. This also increases the permeability to Ca2+ which activate proteases which digest contractile proteins increased creatine kinase levels indicate muscle damage

Answer 51

In DMD dystrophin is virtually absent In BMD there is between 20% to normal levels (although abnormal protein is expressed)

Answer 52

No correlation between del/dup sizer and the severity of the phenotype. Majority of pathogenic variants are exon deletion (>1 exon) clustering in exons 2-20 (20%) and 45-55 (80%). duplications are clustered in these regions with opposite frequencies nonsense mutations are next most common mut in DMD followed by dups and indels. single exons deletions- do not routinely test asymptomatic patients therefore do not know the frequency of these in the normal population. If detected in a patient with phenotype it is considered to confirm the diagnosis but could be masking the true diagnosis

Answer 53

mutations that disrupt the reading frame result in a no functionla dystrophin due to NMD and asre associated with DMD in-frame dels and dups result in the expression of a partially functional protein and are associated with BMD the reading frame hypothesis holds true in 90% of cases therefore a diagnosis should be made on clinical assessment not the reported prediction.

Answer 54

- hypothesis is based on DNA not RNA. Due the RNA processing this should be tested to give a definitive diagnosis - in-frame deletions may result in DMD if they affect the protein binding domain - assumes that duplications are tandem- may be inverted or inserted elsewhere in the gene or genome - central-rod domain may be associated with no/mild symptoms - exon skipping could result in rescue of the reading frame or vice versa - exceptions to the reading frame rule are more common in BMD

Answer 55

- Mutations affecting the barin specific isoform as associated with later onset of muscle phnotype and LD (Dp140 and Dp71) - In BMD dels including the a.a. terminal are associated with early onset cardiomyopathy - central rod domain is associated with mil manifestions

Answer 56

XLR 2/3 of cases are inherited from a carrier mother and 1/3 are do novo - new mutation can occur in the oocyte, embryo post conception (mosaic) or be in the mothers germline (7-10% recurrence risk) when the at risk haplotype is known the recurrence risk is 8.6%. However testing my MLPA does not revel this (need linkage) therefore the recurrence risk for a mother of an affected who has not been found to be a carrier is 4.3% sibling of an affected is also at risk of being a carrier even if mother is not. If the sibling then tests negative for the family mutation there is no recurrence risk and her risk of an affected is reduced to that of the general population. DMD has a high recombination rate- 4x greater than would be predicted by its size alone

Answer 57

2-8% range from mild muscle weakness to an inability to walk. If cardiomopathy is included the incidence is 38%- therefore monitoring for cardiac involvement should be included in female carrier reports

Answer 58

- Normal CK levels rule out a diagnosis of DMD - elevated CK support s diagnosis but does not confirm it as can be raised for other reasons e.g. after muscle injury or heavy exercise - IHC - lack of staining for dystrophin confirms DMD and reduced BMD. requires invasive muscle biopsy so not commonly tested.

Answer 59

Dosage analysis (MLPA - 2 kits, can only use one if it will detect known mut in familial cases) will detect 72% - sequencing analysis for CNV negatuve cases - linkage analysis using microsatellites can be used for carrier testing and PND in cases where the pathogenic mutaion has not been detected but there is a confirmed clinical diagnosis in MLPA is a single exon del or dup is detected it should be confirmed by another method e.g. dosage pCR or sequencing across the breakpoint

Answer 60

if the mutation is not known and the poband is not available them most closley related at risk family member is tested as they have the highest risk of carrying the mutation (mother then sibling). If a mutation is not found it does not rule out that they are carriers just reduces the risk Even if the mutation is known there is still a recurrence risk in mothers if affected due to the possibility of germline mosaicism so PND is still offered

Answer 61

for all known carriers of mothers of affected. Only male pregnancies tested, NIPD for sex is becoming more common as can avoid the need for an invasive test in a female pregnancy

Answer 62

Preferably need a sample from the proband but if not available can use an unaffected male sibling for exclusion testing - 10% rate of recombination across the DMD gene - to reduce the risk of recombination markers spanning the whole gene are used not just flanking it. Still need to calculate the risk of a double recombination which could result in the mutation being present on the low risk allele - recombination risk is calculated from the average risk of a double recombination between markers and multiplying by the percentage of the coding region that is covered by the markers

Answer 63

- may be detected in a male referred for LD- explains pheno | - may be detected in females referred for LD- does not explain pheno byt result is reported for risk to family members

Answer 64

- Limb girdle dystrophy- clinically simillar but AR and AD inheritance - emery dreiffus muscular dystrophy- characterized by joint contractures and progressive muscle weakness _ SMA- poor muscle tone and neonatal hyopotonia - dilated cardiomyopathy- AR, AD and XLR

Answer 65

No cures, treatments aims to help the symptoms e.g. physiotherapy and steroids. Transplant in severe cases of DCM

Answer 66

Stop codon read through using amnioglycosides to result in some functional dystrophin being produced and can convert DMD to BMD pheno. 15% of DMD have a PTC. exon skipping by mopholino ASO interferes with splicing and can skip the alterd exon to restore the reading frame and give a BMD phenotype

Answer 67

Genes are described as HI when inactivation/loss of a single allele (leaving the second allele unaffected) produces a clinical phenotype. A gene is likely to be HI is all mutation types (missense, nonsense, deletion etc) result in the same phenotype. Show AD inheritance Note that genes on sex chromosomes cannot show haploinsufficiency.

Answer 68

Current theories focus on the specific function of the gene and the context of the gene’s function. - Genes encoding enzymes are rarely haploinsufficient - genes linked to srtuctural and regulatory function or are members of complexes or celullar signalling networks are more sensitive to changes in dosage.

Answer 69

imprinted genes highly expressed genes dosage sensitive genes

Answer 70

in imprinting only one of the 2 alleles of a gene is expressed in a parent of origin depending manner, therefore mutations in the expressed gene are dominant. e.g. UBE3A mutation causes AS

Answer 71

Highly expressed show HI as they need a very high amount of gene product and a single functional copy is insufficient in producing enough. e.g, Elastin- Loss of one copy has no effect in skin and lung (low levels of product required), but can cause supraventricular aortic stenosis because the aorta requires high expression levels.

Answer 72

Dosage sensitve genes include: - gene whose products are part of a quantitative signalling system depending on partial occupancy or competition for binding to DNA or receptor- gene products that compete to determine a metabolic swith - gene products that cooperate in interactions with stoichiometry. Includes many structural proteins In these situations the gene product is titrated against something in the cell, therefore relative not absolute levels are important. Genes whose products are essentially alone e.g. soluble involved in metabolism, rarely show dosage sensitivity

Answer 73

Some genes with AD inheritance also have a recessive form. e.g. Marfans syndrome. A phenotype cause by complete loss of one allele could also be caused by a 50% reduction in the activity of 2 alleles. Variation in penetrance & expression of both mono-allelic and bi-allelic mutant alleles highlights the fact that external factors are involved in such systems. These may include expression of other genes, environment, age, developmental status, ability of the individual to up-regulate expression of other genes or (in heterozygous individuals) the unaffected allele to compensate.

Answer 74

less likely to be found in segmentally duplicated regions which are prone to mutation (CNV) but NAHR. This suggests a selective pressure to maintain HI genes at their correct CN

Answer 75

hypertrophic cardiomyopathy (HCM) HNPP Aniridia

Answer 76

22q11.2 Di George syndrome | del5p Cri-du-chat syndrome

Answer 77

HI affects TSGs TP53 BRCA1 PTEN

Answer 78

Clinical features: - Left-ventricular hypertrophy (LVH) in the absence of predisposing cardiac/cardiovascular conditions. - Characteristic abnormal ECG. - highly variable and can include palpitation, progressive heart failure and heart congestions - Sudden cardiac death (often in early adulthood and associated with exertion, e.g. sport) is a major cause of mortality Onset varies from childhood to middle age, LVH occurs in ~1 in 500. Between half and three-quarters of these patients have an HCM mutation

Answer 79

70-80% of mutations are found in MYH7 and MYBPC3 About 10% of mutations are in Troponin-coding TNNT2 and TNNI3, Clinical sensitivity of the four-gene panel is ~50% Haploinsufficiency can be demonstrated in MYBPC3 by the lack of incorporation of truncated proteins into HCM cardiac tissue (evidence against dominant-negative effect), along with a lowered expression level of full-length protein, which suggests haploinsufficiency Interaction of multiple genes in a large system (presumably requiring cooperation & fixed stoichiometry between gene products) is characteristic of a haploinsufficiency syndrome, and probably explains some of the variability in presentation & phenotype.

Answer 80

PAX6 mutaion result in lack of irises. other symptoms include: nystagmus, cataracts, defects in vision. PAX6 is a control gene involved in eye development with very high conservation in all organisms with eyes Homozygous loss of PAX6 is known to cause wide-ranging defects including complete lack of eye formation and is fatal in mice. WAGR syndrome is caused by a contigous deletion on 11p13 and includes WT1 (wilm tumour gene) and PAX6 resulting in Wilms tumor, aniridia, genitourinary anomalies and mental retardation syndrome.

Answer 81

HNPP is charactersied by focal pressure neuropathies- carpal tunnel syndrome, peroneal palsy and foot drop Due to LOF of PMP22- 80% are due to a recurrent 1.5Mb deletion mediated by NAHR between CMT1A-REPS. 20% are due to LOF sequence mutations. PMP22 encodes an essential component of the peripheral myelin sheath reciprocal dup results in the more severe CMT1A shows that gene is HI and TS

Answer 82

DiGeorge syndrome, 22q11.2 deletion on one allele causing haploinsufficiency of the TBX1 T-box transcription factor gene (important in developmental regulation).

Answer 83

Cri-du-chat syndrome caused by deletions of 5p15, - a critical region between 5p15.2 is responsible for the observed dysmorphism and intellectual disability - the proximal region of 5p15.3 is associated with the cat-like cry and speech delay.

Answer 84

Mutated in over 50% of all tumours. - Germline mutations responsible for Li-Fraumeni syndrome (LFS) (early-onset breast and multiple other poor prognosis soft tissue & bone cancers).

Answer 85

TSG mutated in a wide array of tumours - Germline mutations cause Cowden syndrome & PHTS. - PTEN is a “gatekeeper” that negatively regulates cellular proliferation. - “obligate haploinsufficiency”; heterozygous loss is more tumourigenic than homozygous loss. Reason for this is a “failsafe” p53-dependent cellular senescence mechanism that works when PTEN is completely lost; this “masks” the cellular proliferation signal that would be the result of losing both copies of PTEN, so heterozygous PTEN loss is more tumourigenic. Loss of p53 (e.g. in tumours) prevents the “failsafe” senescence mechanism, so cases with complete loss of both PTEN AND p53 show faster rates of tumour development than heterozygous PTEN losses.

Answer 86

TSG associated with hereditary breast cancer: women carrying a heterozygous inactivating mutation have an 85% lifetime risk of developing breast cancer, and increased risk of other cancer types. - Conforms to the two-hit model of tumorigenesis ( - BRCA1 -/- mice show embryonic lethality:

Answer 87

result in increase in gene expression/product or gene developing a new aberrant function

Answer 88

- usually dominant as the presence of the normal allele does not prevent the mutant allele from functioning aberrantly - usually involve genes that control cell signalling- e.g. constitutively active - product can obtain a novel function e.g. fusion gene due to translocation - usually require a much more specific mutation than LOF e.g. mutation in the channel pore domain of an ion protein

Answer 89

PMP22- GOF CMT1A (dup) and LOF HNPP (del) AR- triplet repeat expansion >35 = SBMA (GOF), LOF SNV = AIS

Answer 90

Unstable triplet repeats- HD, DM!, SCA Overexpression - CMT1A novel function - BCR-ABL1 t(9;22)(q34;q11) Highly mutable codon- Achondroplasia

Answer 91

HD is caused by a CAG repeat expansion (>36 variable penetrance- 40rpts = disease) in the 1st exon of the HTT gene at 4p16.3 result in a polyglutamine tract which is though to develop novel deleterious function when expanded

Answer 92

- deletions and translocation affecting HTT do not result in HD - the phenotype of a homozygote is the same as a heterozygote - dominant phenotype - Levels of HD protein transcribed are the same in normal and mutant patients.

Answer 93

he presence of intranuclear inclusions is the characteristic sign of HD and are more abundant in the brains of patients with juvenile onset HD it is thought that the polyQ expansion results in the formation of intranuclear inclusions containing HTT, chaperone proteins and ubiquitin. HOWEVER, the inclusions do not appear to cause the disease themselves. In mouse models the location of inclusions does not correlate with cell toxicity.

Answer 94

the seq of pathogenesis in HD is unclear Mutant HTT forms abnormal protein structures - Bsheets and is truncated by caspase-6 into toxic N-terminal fragments. this is though to lead to altered processing of abnormal proteins in HD Mutant Htt interferes with gene transcriptions (PGLC1a) and may have a direct or indirect affect on the mitochondria = affecting metabolism and leading to oxidative stress there is also abnormal vesicle transport and release of BDNF and increased exocitotoxicity

Answer 95

DM1 is caused by a CUG repeat expansion in DMPK

Answer 96

Though to act via a toxic RNA GOF mechanism Repeat structures in RNA form stable hairpin structures that sequester RNA binding proteins CUG-BPI and MBNL in riobonuclear inclusion. This result in upregulation of CUG-BP1 and down regulation of MBNL. the altered expression of these affects alternative splicing and embryonic splicing patterns are seen instead of adult patterns in patients with DM1

Answer 97

Achondroplasia is the most common inherited disproportionat short stature incidence is 1 in 26-28,000 caused by mutations in the Tm domain of FGFR3

Answer 98

Due to a highly mutable codon - GOF FGFR3 is a TM tyr kinase receptor responsible for -vely regulating bone growth. Mutations that constitutively activate the receptor result in reduced bone growth 99% of disease is due to 2 mutations - achondroplasia is relatively common considering it requires very specific gene mutations- it has been suggested that the high de novo rate is because there is a proliferative advantage in spermatogonal cells. other mutations in FGFr3 result in different disorders e.g. thanapophoric dysplasia and hypochondroplasia

Answer 99

found in nearly all CML (major breakpoint) and some ALL (minor breakpoint) fusion gene formed by the t(9;22)(q34;q11) rearrangement resulting in the formation if a constitutively active tyr kinase - aberrant signalling promotes genome instability treated by TKI imatinib

Answer 100

CMT1A is caused by gene overexpression 70-80% is due to a recurrent 1.5Mb duplication at 17p12 whihc includes PMP22. remaining cases are due to GOF SNVs. PMP22 encodes peripheral myelin protein and is present in the myelin membrane of peripheral neurons where it plays a role in arresting schwann cell division recurrent dup is due to NAHR between CMT1A reps which flank the duplicated region. Reciprocal deletion result in HNPP

Answer 101

Mutations generally impair the function of a protein that are involved in protein complexes or reduce the activity of the WT allele only seen inhets more severe than null alleles of the same goen MND probably developed to protect against dominant negative truncated proteins proteins that are part of multimeric structures are particularly vulnerable to dominant negative effects as they are dependent on oligomerisation for activity- in a multimer a variant subunit with intact binding but altered catalytic activity can affect the function of the entire multimer

Answer 102

dominant negative- result in deafness GJB2 and 6 encode connexin 26 and 30- these are major gap junction proteins expressed in the cochlear. connexins are TM proteins and 6 oligomerise to form to form a hemi channal (connexon)- connexons of neighboring cells align symmetrically to from continuous gap junctions- they can be homopolymeric or heteropolymeric with different functional properties Cx26 and 30 are involved in K+ recycling in the ear- K+ is required for NT release from hair cells of cochlear. dominant missense mutation in Cx26 result in the formation of full length aberrant proteins- these form gap junctions with WT Cx26 and 30 forming connexons with impaired permeability = hearing loss in hets

Answer 103

dominant negative mutations in CLO1A1 and COL1A2 encode fibrillar collagens which are the major structural proteins of connective tissues pre-pro collagen contains N and C terminal globular pro-domains flanking a central repeat seq with a gly every 3rd residue 3 pre-procollagen chain associate to forma triple helix under the control of the globular domain- C and N terminal domain cleaved to form mature collage and this process is disrupted in OI

Answer 104

Missense mutations result in the expression of abnormal protein and severe OI. - dominant -ve (type II, II, IV) - 80% of muts replace gly in triple helix domain - tupe 1 procollagen comprises 2 chains encoded by COL1A1 and COL1A2- helix assembly starts at c-terminal domain therefore mutations close to the c-terminus are more deleterious than those near the N-terminus OI type 1 - due to LOF mutations - reduced production of type 1 procollagen as abnormal protein degraded by NMD - less severe

Answer 105

Most commonly mutated gene in cancer and mutations can be LOF, GOF and dominant negative Normally TP53 acts as a TSG- transcription factor whcih activates transcription of genes involved in cell cycle control, damage repair, and apoptosis. missense mutations in the DNA binding domain affect the ability of the protein to recognise DNA or inactivates TP53 by altering the conformation - dominant neagtive as TP53 binds DNA as a tetramer - WT and mutant p53 proteins form tetramers with impaired ability to bind DNA and trnscriptional activity - c-terminal domain is requird for dimerisation therefore truncating mutations in this domain are not dominant -ve as they cannot bind WT

Answer 106

Mutations result in the connective tissue disorder Marfans fibrillin has a structural role in the walls of large arteries dominant negative variants: - missense and exon skipping variants result in a stable but altered protein - impared interactions between variant and WT fibrillin and other proteins results in impaired ECM LOF mutations - nonsense and frameshift result in NMD - decreases the amount of fibrillin in vasculature and the aortic wall strength is weakened - increased risk of cardiovascular disease

Answer 107

AR - shows horizontal inheritance with affected siblings born to generally unaffected parents - increased risk in consanguineous families - unaffected siblings of affected have a 2/3 risk of being a carrier (1/3 unaffected non-carrier)

Answer 108

- most common AR disease in UK with carrier freq of 1/25 (high carrier freq suggests het advantage like in sickle, advantage is unknown- may be associated with cholera) - affects 1 in 2500 - carrier freq depends on population and so specific frequencies should be used for risk calculations where possible - there is a good genptype/phenotype correlation between the CF mutation and pancreatic sufficiency but not pulmonary disease. - phedel508 is most common UK caucasian deletion ~75%

Answer 109

CFTR gene encodes a cAMP activated chlorine channel located in the plasma membrane of secretory cells e.g. in the respiratory tract, reproductive tract, kidney, pancreas, vas deferens, sweat ducts CFTR channels are responsible for moving chlorine out of the cell, this creates a trans-membrane gradient. and Na+ and water flow out of the cell down the concentration gradient. Mutations that result in a loss of function or reduce ability to function result in reduced Cl- transport and hence water resulting in increased viscosity of mucus

Answer 110

Sweat chloride concentration >60mm/L (raised compared to normal) - chronic cough and wheezing - recurrent chest infections - can be pancreatic sufficient/insufficient - CAVD/CBAVD- 95% make are infertile - failure to thrive - moconium ileus in newborns - fetal echogenic bowel- 4% of fetus with FEB have CF - salty skin

Answer 111

pancreatic sufficient variable lung disease lower sweat chloride levels

Answer 112

due to mild CF mutations e.g, R117H/5T results in only mild dysfunction in one organ and may have slightly elevated sweat chlorides - disseminated bronchiecstasis - CBAVD - chronic ideopathic pancreatitis - allergic bronchopulmonary aspergillosis

Answer 113

``` IRT testing- used for newborn screening Sweat chloride Trans nasal epithelial test Semen analysis- for CBAVD genetic testing ```

Answer 114

IRT- immunoreactive trypsinogen in newborn it is raised compared to normal neonates and is tested as part of the NBS blood spot screening using a guthrie card. Trypsinogen is released by the pancreas and is increased in CF regardless of pancreatic sufficiency- If the level is raised of the 95th percentile a second IRT measurement is taken. If still raised generic testing for the 4 most common CF mutations is carried out- F508del, Gly542X, Gly551Asp, c.489+1G>T 2 mutations = confirms CF 1 mutation - test for other common mutations- if not second mutation do another IRT. If raised = Cf suspected, if not raised = carrier suspected no mutation = do another IRT test- if above threshold CF susupected and if not it is not suspected testing offered as no cure but early treatment benefits outcome. Set-up of NBS aims to maximize sensitivity for CF whilst reducing the detection of carriers.

Answer 115

gold standard test for diagnosing CF. 2 reading >60mm/L is diagnostic of CF in 98% of patients

Answer 116

In UK ARMs PCR using the commercial CFEU2v1 kit is generally used diagnostically. Detects the 50 most common mutation in UK caucasian population - will diagnose 90% of cases (differs for other ethnicities)

Answer 117

shift in the B tube may indicate the presence of a insertion or deletion so the affected exon can then be sequenced to identify the mutation SNP under the primer binding site can result in a false result and appearance of homozygosity of the other allele (may miss a mutation)- this is why a positive control should be used to confirm that the familial mutation can be detected.

Answer 118

expploits the observation that a DNA primer can only be extended from with a perfectly matched 3' end - primers for the mutant and WT alleles are contained in 2 mixes and the presence of an allele peak indicates the presence of that allele (alleles allele zygosity to be determined) - products differentiated by different sized stuffer fragments - weak mismatches may have a second mismatch in the adjacent base - requires a taq pol which lack 3-5' exonuclease acitvity -

Answer 119

- misses 10% of mutations - routine testing for all possibel mutations is not practical or cost affective but some cases may go on to have sequencing if there is a diagnosis of CF but no second mutation detected - Y659D is not tested for by kit but is common (9.6%0 in indian sub continent so may need to be tested for separately in this population - cant detect deletions as the other allele will be amplified and will appear homozygous - wont detect copy number changes- there is an MLPA kit if this is suspected

Answer 120

Linkage may be used in families with a confirmed clinical diagnosis where both mutants have not been identified. Is used for PND and carrier testing. Need DNA from the affected individual and parents to determine phase - small risk of a double recombination and does not test for de novo mutations so can only reduce the risk of being affected and not completely exclude it

Answer 121

Important to test parent for cascade testing of family members and PND but it also allows confirmation if phase to be sure the detected variants are in trans ``` May not be confirmed if: - non paternity - one parent is a deletion carrier - UPD7 later 2 only possible for a proband with a homzygous result ```

Answer 122

The length of the polyT tract at the splice acceptor site of intron 8 has an affect on the splicing on exon and the shorter the tract the more exon 9 is skipped and missing form the mature transcript. the penetrance of the 5T allele is affected by the number of TG repeats (11-13) in this case the longer the TG tract the more exon 9 is skipped. 9T/F508 is in strong linkage disequilibrium so when detected together can assume they are on the allele.

Answer 123

5Tis not a classical Cf mutation but can be associated with CFTR-RD when found with a classic mutation e.g. F508 5T is known to modify the expression of R117H and is commonin CBAVD. R1117H is not considered a CF mutation when in cis with 9T - 5T/R117H & typical severe mutation- CF with variable severity (acts as a compound CF causing mutation) - 7T/R117H & typical severe mutation - CFTR-RD e.g. CBAVD - 9T & atypical severe mutation = not considered disease causing (benign) 5T/5T are very rare and variable phenotype- may be asociated with CFTR-RD 5T in cis withg TG 12 or 13 and in trans with a classic mutation can result in CFTR-RD

Answer 124

The 5T allele is not routinely tested for (polyT and TG tract is included in the ARMs PCR kit but not rouitnely interpreted or reported). Reflexively tested for: - in all males referred for infertility - in patients with disseminated bronchiecstasis and only 1 pathogenic mutaion - when R117H is detected because of the importance of the phase of the polyT allele parents may be required to determine phase (except for when F508 is detected as always with 9T) NOT TESTED FOR PRENATALLY unless 5T in cis with R117H as will not result in severe CF

Answer 125

Normal spermatogenesis but absence of the vas deferens results in obstructive azoospermia - 1-2% of infertile males and 95% of CF males - karyotype and y del testing should be offered to males with infertility and a negative CF result - If CF mutation is detected, partner can be screened to determine risk of affected offspring - if infertile male only has a 5T allele cascade testing to family members is not offered as it is unlikely to result in classical CF and counselling the reproductive risk to them is unclear - cascade testing can be offered for R117H/5T - for other mild mutations, the choice on whether to offer cascade testing is on a case-by-case basis ans requires referral to clinical genetics for accurate risk counselling.

Answer 126

To confirm a suspected or clinically confirmed diagnosis - suspiscion of CFTR-RD or CBAVD - PND - Carrier testing including partner of carrier without family history

Answer 127

CFTR modulators - readtrhrough therpay to correct NMD of truncated CFTR- amnioglycosides e.g. genatmicin can be used for readthrough of PTCs fo that the full length protein is produced- issues with ototoxicity with long term use corrector therapy- Lumacaftor: facilitates proper maturation if the CFTR protein and transport to the membrane. Corrects mutations that result in misfolding and degredation e.g. F508 potnetiator therapy- Ivacafer corrects mutations that cause gating inefficiency e.g. G551D DNA editing e.g. CRISPR-CAS9 to remove mutated CFTR followed by HR with WT

Answer 128

1. no synthesis- severe pheno due to nonsense, framshift, splice site mutations 2. Block in processing 3. block in regulation 4. altered conductance 5. Regulation of other ion channels

Answer 129

No synthesis mutation reduces the amount of CF e.g. Gly542X treatment- gentamicin amnioglycosidase readthrough of PTC e.g. Gentecin

Answer 130

result in protein misfolding and defective maturation- retention in ER and degredation e.g. F508del treated by correctors e.g. Ivacaftor (phase 3 trials = improved lung function)

Answer 131

reduce capacity to secrete Cl= due to defects in channel activation e.g G551D (Phase 3 trials- Ivacaftor = improved lung function, reduced salt in sweat and weight gain)

Answer 132

reduce the capacity for chlorine conductance across the membrane e.g. R117H, Asp1152HIs Flavanoids can act directly on the channel to increase the chance of it being oen Ivacaftor also in trials for R117H

Answer 133

mutations that affect regulation of other ions channels e.g. ENAC Na+ channel treated by compound that enhance CFTR retention/acnhoring.

Answer 134

FMR1 is found at Xq27.3 - encodes the RNA binding protein FMRP - expressed in many tissues including the brain testes and ovaries FMRP plays a role in the development of synapses and controls the production of other proteins. FMRP is though to act as a shuttle within cells transporting mRNA from the nucleus to areas of the cell where it is translated

Answer 135

due to a trinucleotide repeat of a CCg expansion in the 5'UTR of FMR1 in fragile X a FM mutation results in hypermethylation of the FMR1 promoter and gene silencing. ~1% are due to a LOF point mutation. Disease is caused by HI for FMR1 In PM carriers patients are found to have anhigher than normal level of FMR1 mRNA and normal levels of FMRP protein. This indicates that the mutation mechanism is different to Fragile X. It is possible that the excess of FMR1 mRNA could be responsible for a toxic gain of function phenotype resulting in FXTAS and POI.

Answer 136

Normal= up to 45 repeats - normal phenotype and inherited stably in almost all transmissions (30 is the modal number for caucasians. Will not expand to a FM in a single generation intermediate = 46-58 repeats PM= 55-200 (not hypermethylated) FM= 200+ repeats

Answer 137

46 to 58 repeats (under 50 likely to be stable, 50-58 may show instability). Hardest range for counselling as is the overlap between normal and PM. - it is not clear is alleles in this range are involved in PM related phenotypes - mores likely to be unstable than normal alleles but will not expand to a FM in a single generation - Instability is associated with a) total length of repeat; b) fewer interspersions and c) length of the longest uninterrupted CGG tract 41-43. Alleles with pure CGG repeat tracts or with only one AGG interspersion are considerably more unstable than alleles with at least two AGG interspersions.

Answer 138

According to BPG in UK 'As a precaution and to reflect standard errors in sizing between laboratories, prenatal diagnosis should be offered to all women with an allele of 55 CGG repeats or greater.'

Answer 139

PMs are not associate with Fragile X They are unstable and expand in most generations- usually by a couple of repeats- the size of the expansion increases with increasing PM size PMs are the smallest size that a FM expansion has been reported in a single generation- most premutations tested are found to lack AGG interspersions, though this observation is biased by ascertainment usually via a Fragile X proband The probability of conversion to a full mutation on maternal transmission in a single generation is low for premutations of 59-70 repeats but rises to >90% for premutations of more than 90 repeats. some guidance suggests that 55 repeats should be used as the lower bound of the PM as there has been a report of a 56rpt expansion expanding to a FM in a single generaton but UK BPG consider this to be very rare and that 9 rpts is a more realistic lower bound PM diagnostic reporting however carriers of 55+ can be offered PND

Answer 140

The presence or absence of AGG rpts has a significant impact on the meiotic stability of a repeat expansion. The impact of AGGs is greater the smaller the repeat as large repeats have a greater propensity to expansion. Since unstable premutations are usually pure CGG repeats or contain only a proximal AGG interspersion, it is assumed that the loss of one or both AGG motifs or their conversion to CGG in an intermediate allele would predispose it to instability. Whether or not risk of expansion based on the published data on AGG interruptions is used for counselling and reporting is depending on local policy and the nature of the referral. The Asuragen kit provides the opportunity to obtain this information

Answer 141

Fragile X is associated with hypermethylated alleles >200 repeats. A FM almost always leads to hypermethylation so the Asuragen diagnoses FRAX based on expansion size other the presence or absence of hypermethylation there are a few reports of high functioning FM males without significant hypermethylation small proportion are due to point mutation or large dels or dups- do not exhibit a fragile site or hypermethylation

Answer 142

Most common single gene cause of LD- incidence is 1 in 4-6000 in males (1 in 5-8000 in females) - in males characterised by moderate to severe LD and social impairment, macro-orchordism, joint laxity and characteristic facies (long face, pointed chin, large ears, prominent forehead) females with a FM have a variable phenotype depending on the level of skewed X-inactivation. Ranges from apparently normal (50%) to mild to moderate LD and social impairment

Answer 143

Expansion from a PM to an Fm is only possible via female meiosis. Paternal transmissions can be unstable but will never result in a FM. FM males where tested only have PM alleles in their sperm.

Answer 144

FRAXE is a distinct condition caused by mutation to FMR2 located at Xq28 - also caused by a CCG repeat in the 5'UTR - phenotype is less severe than for fragile X with no syndromic features and no phenotype associated with PMs - also associated with a fragile site

Answer 145

Do not result from lack of FMRP- there are normal amounts of FMRP and increased FMR1 mRNA leading to the proposition that they are due to a toxic mRNA GOF mutation rather than LOF as in Fragile X

Answer 146

POI/POF is associated with cessation of menses before 40yrs. Affects ~20% of PM carriers compared to 1% of the general population. The risk of developing POI is depending on the length of the CCG rpt but is not linear. Greatest risk is for PMs of 80-100 repeats and is lower for larger expansions. Risk cannot be excluded for any PM allele size

Answer 147

More common in males Characterised by late onset pregressive cerebellar ataxia and intention tremor - Onset is typically between ages 60 and 65 years. Both age of onset and disease severity are related to repeat length, sex, and other features. - increasing penetrance with age - linear correlation between repeat length and penetrance has been diagnosed in an individuals mosaic for a FM and PM and in methylation mosaics with a methylated and unmethylated FM

Answer 148

Diagnostic- for LD, ADHD/ASD, behavior and social issues, SLD - characteristic appearance does not become evident until puberty in males and is not present in females so fragile X is often performed in young children as an exclusionary test due to its prevalence and has a low pick up rate - may be a carried out secondary to aray as this has a higher detection rate carrier testing- usually from clinic and not in patients under 16 prenatal testing for carrier female or mother of an affected

Answer 149

quick,cheap simple PCR test using primers whihc flank the CCG repeat - will detect alleles up to ~70-80 so sufficient to detect normal, intermediate and small PM alleles. Can exclude a diagnosis of fragile X in single allele males and het females - need controls near size boundaries for accurate sizing - cant distinguish homozygous female form a female with an undetected expansion so all single allele females also need to be tested by asuragen - FH cases should all have asuragen in case of mosaicism for a FM or PM allele - preferential amp of smaller allele may cause expansion to be smaller/ missed and PM have a characteristic hedgehog appearance - will miss 47,XXY with a normal and expansion allele

Answer 150

2 allele male may be 47,XXY- confirm by karyotype or sex PCR or mosaic 3 allele female may be 47,XXX or mosaic NB females with a FM have an increased risk of haveing a 45,X cell line with loos of the X chromosome carrying the expansion- FM allele may appear weak on a southern blot

Answer 151

Rarely carried out unless there is a query about the methylation status of an allele. In general diagnostic testing FM alleles >200 are assumed to be methylated uses an Eag1 (methylation sensitiev), EcoR1 double digest. Methylated (inactive) alleles are cut only by one enzyme to give a 5.1 kb fragment, while unmethylated (active) alleles are cut by both enzymes to yield a 2.8 kb fragment. Male premutation carriers will manifest as single enlarged fragments above 2.8 kb, while in females four fragments corresponding to the normal active, mutant active (2.8 kb and above), normal inactive and mutant inactive (5.1 kb and above) will be observed if X-inactivation is random. In both males and females full expansions are seen as a band significantly larger than 5.1 kb. Full mutations can be distinguished from large premutations by their methylated status, even on the active X chromosome.

Answer 152

supports two different PCRs - gene specifif PCR primers give a full range product peak for each allele and a triplet primed PCR which primes form each CCG repeat to give a ladder of prducts. because there is no priming for AGG interruptions it can also detect there presence or absence in samples. doesnt give accurate sizing but can identify expansions in the PM and FM range - can confirm or exclude the presence of an expansion allele new kit available that has the same PCR reaction but then splits the products in 2 and uses a methylation specific digestion to work out the methylation. 1 tube shows allele size and the other determines methylation

Answer 153

need to use asuragen - high risk of potential false-negative interpretations of PCR results due to MCC of the CVS/AF is particularly acute in Fragile X testing because of the wide discrepancy in size between normal and expanded alleles, with consequent preferential amplification of the former. methylation status not usually set for FMR1 in CVS samples so if using southern blot distinction of FM and PM is based on size if a large PM is detected in CVS there is a potential risk fro size mosaicism for a FM. This may be present in the fetus but not the CVS so testing of AF may be appropriate run a familial control with the prenatal- useful for accuracy of sizing and to confirm the reaction has worked

Answer 154

Rarely used and direct testing preferred. May be used to confirm a result or if other prenatal testing is inconclusive useful for confirmation of a result if same as mothers as it is less sensitive to MCC use more then 1 frond and digest/chop to reduce risk of CPM

Answer 155

do not need to report size of normal alleles if the range is included on the report.

Answer 156

uses TP-PCR with additional HPAII to detect methylation - no digest control should show normal (unmethylated) and expansion allele peaks - digest should result in loss of normal peak and only methylated expansion remaining. - females will have some methylation of the normal allele so there will be a reduction in peak height but not completely lost

Answer 157

Imprinting describes a parent of origin specific gene expression pattern.

Answer 158

Imprinting genes are found in domains/clusters that are controlled by a single imprinting control region (ICR) - ICRs have parent of origin specific methylation patterns (DMRs) imprinting is achieved via CpG island methylation. Once set the pattern is set in the embryo it is stably maintained throughout development and life. In gametes the imprinting pattern is resent so that it reflects the pattern for the sex of the individual.

Answer 159

Imprinting disorders occur as the genes should be expressed from a single allele- increase or decrease affects gene regulation and results in disease. manifest as neurological/developmental condtions when they arise in early life and as cancer in adulthood ``` mechanisms: UPD chromosomal rearrangement Mutation Epimutation ```

Answer 160

Result in whole chromosome or region being inherited from a single parent. If the affected region includes a imprinting centre there will be disregulation of the imprinted gene - recurrence risk is <1% - should be considered in carriers of balanced rearrangements involving a imprinted gene, in such cases the recurrence risk may be higher

Answer 161

deletion- loss of ICR or genes that should be expressed from that parental allele duplication- over expresssion of genes that should be imprinted rearrangement may disrupt gene resulting in LOF of gene that should be expressed

Answer 162

genomic mutation can affect expression of an imprinted gene epimutation can affect an ICR resulting in aberrant hypo or hyper methylation

Answer 163

6q24 - Pat UPD (6) Transient neonatal diabetes mellitus 1 - MatUPD(6) is very rare and clinical significance is unclear 7 - Mat UPD(7)- SRS - Pat UPD(7 11p15. 5 - MatUPD SRS - PatUPD BWS 14 - Mat UPD(14) Temple syndrome - PatUPD(14) TKagami-Ogata syndrome 15q11. 2 - MatUPD/ pat deletion- PWS - PatUPD/ mat deletion - AS ``` 20 MatUPD(20) pseudohypoparathyroidism patUPD(20) pseudopseudohypoparathyroidism ```

Answer 164

Mat UPD and maternally imprinted genes are associated with undergrowth paternally imprinted genes are associated with overgrowth

Answer 165

TNDM1 is most common cause of TNDM - hypoglycaemia and IUGR due to insulin insufficiency - spontaneously resolves ~18 months but risk of relapse to permanent form of diabetes in childhood or adulthood. caused by patUPD6 in majority of cases, also due to pat6q25 duplications and hypomethylation of mat DMR results in overexpression of PLAGL1 and HUMAYI- this results in abnormal development or absence of pancreas/islets and b cells so there is not enough insulin. Insulin is also involved in promoting growth in early development so this accounts for the IUGR

Answer 166

imprinted region is at 14q32.2 - paternal allele has paternally expressed protein coding genes (PEGs) - maternal allele has maternally expressed non-coding genes (MEGs) controlled by DMRs that are methylated on the paternal allele and unmethylated on the maternal allele

Answer 167

Temple syndrome - macrocephaly - obesity - short stature - feeding difficulties - hypotonia - early onset puberty matUPD majority of cases, also reported with epimutations and microdels of 14q32.2

Answer 168

Kagami-Ogata syndrome - more severe than matUPD - can be lethal in utero - USS = small bell shaped thorax, polyhydramnios, placentomegaly - PatUPD in majority of cases, epimutation and maternla microdels at 14q32.2 also reported

Answer 169

Associated with differences imprinting at the GNAS locus which gives rise to several imprinted transcripts by the use alternative promoters and splicing patUPD(20) - psuedohypoparathyroidism - resistance to parathyroid hormone in kidney and increased parathyroid hormone levels MatUPD(20) - pseudopseudohypoparathyroidism - rare so with few patients described - similar presentation to SRS

Answer 170

There is a correlation between ART (IVF, ICSI, etc) and the presence of normally rare imprinting disorders suggested that ART may interfere with the proper erassure and resetting of imprinting patterns that occurs in gameteogenesis. Timing of ART coincides with when this occurs and the gametes a manipulated and freeze thawed and all of this could contribute ART population is different to normally conceiving population as they are usually older with reduced fertility so these factors may also play a role

Answer 171

Only known pure maternal affect AR iherited disorder. Homozygous females are unaffected and can get pregnant but only the outer trophoblast develop and there is early embryo demise. Due to genome wide failure to set the correct imprinting pattern. Genes NLRP7 and KHDC3L are implicated

Answer 172

15q11.2 imprinted region on chromosome 15 AS is due to lack of the maternal contribution - patUPD - mat del - IC defect (non deletion) - IC deletion - UBE3A deletion PWS is due to a lack of the paternal contribution - MatUPD - pat deletion - IC defect (non deletion) - IC deletion

Answer 173

UPD, IC defect, de novo deletion all have low recurrence risk <1% IC deletion and UBE3A mutation has a recurrence risk of up to 50% - can be carried silently by a parent. e.g female can inherit a UBE3A mutation from her father but not get AS as they still get a functioning copy of UBE3A from the mother (passes silently as not expressed from paternl allele) - this will then result in AS in her offspring as she should be contributing the maternal specific UBE3A but it is mutated.

Answer 174

- neonatal hypotonia and failure to thrive (simillar to SMA and DM1 and often tested together as part of floppy baby trio) - poor feeding initially but develop hyperphagia and obesity - hypogonadism - small hands and feet - mild to moderate ID and LD - sleep disturbance and behavioral problems

Answer 175

- severe ID, LD - seizures - characteristic hand flapping - inappropriate laughter - gait ataxia - microcephaly - speech delay

Answer 176

Imprinted genes are present in clusters and there activity is controlled by and ICR acting in cis - UBE3A & ATP10A expressed in the brain only on the maternal allele. Paternal alleles are methylated and silenced - paternal allele the SnoRNAs, SNURF-SNRPN, NDN, MAGEL3 and MKRN3 are expressed. SNURFN-SNRPN genes have tissue specific promoters abs alt spliced transcripts. One of the longer transcripts in the brain includes the snoRNAs and the UBE3A-AS -UBE3A-AS is targeted to UBE3A and prevents is expression. therefore on the pat allele SNURF-SNRPN is umthethylated an expressed resulting in expression of UBE3A-AS and silencing of UBE3A on the pat allele. On the mat allele the pat genes are methylated and silenced so there is no expression of UBE3A-AS and UBE3A is expressed. loss of expression of UBE3A is the pathogenic mechanism in AS. Specific genes for PWS are not determined but the best condidates are SNURF-SNRPN and SNORD116

Answer 177

ICR controls the imprinting in the PWS AS region - deletion affecting only the PWS ICR will result in PWS when inherited paternally but not maternally - deletions involving only the AS ICR will causeAS when inherited maternally but not paternally

Answer 178

recurrent 4Mb deletion at 15q11q13 is the most common cause of PWS and AS - there are 5 common breakpoint BP1-BP5 - common del is between BP1 or 2 and BP3 - small proximal del between BP1 and BP2 included NIPA1 and is associated with susceptibility to NDD

Answer 179

Mosaicism is more common in AS than PWS. Mosaic AS can present with a PWS like phenotype - 1/2 AS patients with an ID defect are mosaic - MS-MLPA can detect mosaicism to~30%

Answer 180

MS-MLPA- can detect all dels and dups and the methylation status (standard MLPA split in 2 tubes and 1 treated with a methylation sensitive restriction enzyme (Hha1) which will not cut methylated DNA. 1 tube gives CN and the other gives methylation in AS there will be complete digestion (all pat and unmethylated) and in PWS there will no digestion (all mat and methylated) - MLPA is semi-quantitative and can determeine the presence of dels and dups in the PWAS region - methylation analysis allows genetic distinction between PWS and AS - probes can also detect IC microdeletions - cannot distinguish UPD from an IC defect without a del - cannot identitfy UBE3A mutations- this requires sequencing - SNPs under probe binding sites can give false results - alway be wary of single probe deletions- may need to confirm my another method - can detect AS mosaicism but will miss low level cases Array may be performed first if case is referred for general LD but will require further testing to determine mechanism UPD can be tested for by QF-PCR but requires parental samples It is important to determine if the mechanism is an imprinting centre deletion as the reucrrence risk is up to 50%

Answer 181

Methylation of the SNRPN exon 1 is reliably set early in embryonic development so methylation of this region can be used for prenatal diagnosis

Answer 182

PWS - neonatal SMA and DM1 - Mat UPD14 - beidl bardet syndrome and cohen syndrome (obesity) AS - Rett syndrome - Mowatt wilson - Pitt hopkins - lennox gestaut etc

Answer 183

No current cure and treatment aims to reduce/manage symptoms e.g. medication for seizures in AS In the future restore UBE3A expression in the brain could be a treatment for AS- can iinhibit expression of the UBE3A-AS to allow expression of paternal UBE3A

Answer 184

- request parents in LH for a 15q del in case is the result of a rearrenagment for FISH/kary0 - offer PND in case of germline mosaicism and for IC deletions - if UPD detected karyotype in case there is a parental rearrangement

Answer 185

11p15.5 | contains imprinting centres IC1 and IC2

Answer 186

IC1 AKA H19DMR regulated H19 and IGF2 - telomeric - contain H19 which is a lnRNA- maternally esporessed in the placenta and developing embryo and silenced in most issues after birth - H19 is only expressed on the mat allele - H19 may also have a role as a tumour supressor -IGF2 is a fetal growth factor that is paternally expressed in the fetsu and placenta and biallelically expressed i the liver after birth

Answer 187

IC2 AKA KuDMR - centromeri - includes KCNQ1 whihc is maternally expressed in early development and biallelically expressed in fetal development - KCNQ1 regulates cell cylce progression by inhibiting cylin dependent kinases and results in arrest in G1 (negatively regulates cell growth and proliferation) - also includes KCNQ1OT1 whihc is a paternally expressedlnRNA antisense to KCNQ1 IC2 is maternally methylated and controls (in cis) the maternally expressed genes of IC2

Answer 188

IC1/ H19DMR is regulated by CTCF which is found between IGF2 and H19 IN MICE ... - on the mat allele it binds the IC1 resulting in expression of H19 and silencing of IGF2 - on the pat allele methylation of the ICR preevent CTFC binding so there is IGF2 expression and H19 is silenced

Answer 189

Mat exoressed genes = H19, CDKN1, KCNQ1 pat expressed genes = IGF2, KCNQ1OT1 normally the paternal allele is methylated at IC1 and the waternal allele is methylated at IC2

Answer 190

Increase in paternally expressed IGF2 and a decrease in CDKN1 - due to IC2 hypomethylation resulting in depression in KCNQ1OT1 and downregulation of CDKN1C on the mat allele - hypermethylation of IC1 resulting in decreased expression of H19 and expression if IGF2 from the mat allele - Pat UPD for at least 11p15.5 i.e. hypomethylation of IC2 (downregulation of CDKN1) and hypermetylation of IC2 (increase IGF2) - CDKN1 mutation- found in familial cases of BWS - pat duplication at 11p15.5

Answer 191

increased risk of Wilms tumour and major cause of pediatric overgrowth major: - +ve BWS family history (15% familial AD and associated with CDKN1C point mutations) - large birth weight - abnormal ear lobes/ pits - large tongue - exomphalos - visceromeglay - assymetric overgrowth - renal abn minor - polyhydramnios - prematurity - hypogylcaemia - hemangioma - characteristic facies - cardiomeglay clinical diagnosis with 2 major & 1 minor clinical feature

Answer 192

MS-MLPA is a robust method for detecting the majority of epigenetic changes associated with BWS - can detect dels and dups at 11p15.5 and DNA methylation including UPD. Fir low level UPD it is best to perform microsatellite analysis especially for hemihypertrophy cases.

Answer 193

Simpson Golabi Behmel syndrome sotos syndrome weaver syndrome all overgrowth syndromes

Answer 194

- IUGR - post natal growth retardation - body assymetry - small triangular face freq 1 in 100,000 but likely to be underdiagnosed due to the broad range of features diagnosed in the presence of 3 major or 2 major and 1 minor feature major - IUGR - short stature - normal head circumference - limb/body assymetry minor - triangular face - 5th finger clinodactyly - frontal bossing - short arm span

Answer 195

Hypomethylation at IC1 resulting in H19 expressed from both alleles = growth restriction maternal duplication of 11p15.5 mat UPD11p15.5 deletion and UPD both result in biallelic expression of H19 and IGF2 silencing can also be caused by maternal UPD for chromosome 7

Answer 196

``` FA, BLM as both result in IUGR 3M syndrome Short syndrome temple syndrome 15q26 microdel syndrome ```

Answer 197

Significant number of patients with SRS and BWS have been reported to have aberrant methylation at multiple imprinted loci (muli locus imprinting defect) no significant difference in phenotype between patients with SRS and BWS with cingle or multip locus defects.

Answer 198

Pleitropy descibes when a single gene infulences more than 1 seemingly unrelated genetic traits- 1 gene many phenotypes

Answer 199

clinical heterogeneity is one gene causing multiple diseases

Answer 200

Ret is an RTK and a proto-oncogene recpetor dimerisation results in phosphorylation of tyrosine residue for downstream signalling Constitutive GOF mutations in RET are associated with MEN2 - 3 types of MEN2 all are associated with and increased risk of medullary thyroid cancer 1. MEN2A = early adulthood MTC + phaeochromocytoma and hyperparathyroidism 2. MEN2B is more severe with onset in childhood = MTC + ganglioneuromas and marfanoid features 3. familiary medullary thyroid carcinoma = MTC in midle adulthood Constitutive LOF mutations in RET are associated with hirschprungs disease - also an example of locus hetergoeneity as Hirschsprungs can also be caused by mutations in ERDNRB and EDN3 somatic mutations in RET occur in cacners and are found in NSCLC and thyroid cancers

Answer 201

COL2A1 encodes the alpha chain of type II collagen- involved in endochondral ossification and the replacement of cartilage with bone Mutations result in a spectrum of skeletal disorders Missense mutations result in the expression of abnormal protein and severe OI. Mutations replace a gly residue in the triple helix so that the collagen fibre does not form properly due to expressed abnormal protein (dominant negative) - dominant -ve (type II, II, IV) - 80% of muts replace gly in triple helix domain - type 1 procollagen comprises 2 chains encoded by COL1A1 and COL1A2- helix assembly starts at c-terminal domain therefore mutations close to the c-terminus are more deleterious than those near the N-terminus OI type 1 - due to LOF mutations - reduced production of type 1 procollagen as abnormal protein degraded by NMD - less severe

Answer 202

FGFR3 is a TM tyr kinase receptor responsible for -vely regulating bone growth. Mutations that constitutively activate the receptor result in reduced bone growth Achondroplasia is due to 2 relatively common AD mutations (suggesting it is a highly mutable codon) other mutations in FGFR3 result in different disorders e.g. thanapophoric dysplasia and hypochondroplasia Somatic activating mutations are associated with bladder cancer

Answer 203

PMP22 is found at 12p12. Expressed by schwann cells in the peripheral nervous system and is involved in the differentiation and regulation of schwann cells.

Answer 204

PMP22 is a doage sensitive gene increased dosage (dup or GOF mutation) is associated with CMT1A. The increased dosage of PMP22 protein means that it is not processed effectively in the ER and golgi reducing the amount of folded protein and this impairs the formation of the myelin sheath in HNPP HI ( deletion or LOF mutation) results in a decrease of PMP22 protein reducing the amount of myelin and making nerves more susceptible to mechanical forces e.g. presssure.

Answer 205

CMT is the most common inherited peripheral neuropathy - pes cavus - proximal to distal progressive muscle weakness - reduced sensory and motor nerve conduction velocities - Decreased sensation in hands and feet - Reduced or absent deep-tendon reflexes 1. Demyelinating (velocity <38 m/second), CMT1 2. Axonal (reduced amplitudes with >38 m/second), CMT2 CMT is a genetically heterogeneous condition, with over 90 genes and loci known to cause the condition when mutated.

Answer 206

- repeated focal pressure neuropathies such as carpal tunnel syndrome - peroneal palsy with foot drop. - Onset is usually in 20s-30s and a full recovery can be made. If recovery is not complete the disability is generally mild. In HNPP the deletion accounts for 84% of cases. Loss of function mutations in PMP22 also result in HNPP.

Answer 207

Duplications/deletions are associated withCMT1A-REPs. >99% of rearrangements are mediated by non-allelic homologous recombination (NAHR). CMT1A-REPs flank the region duplicated in CMT1A and act as substrates for NAHR. The proximal CMT1A-REP and distal CMT1AREP share 24,000bp of approximately 99% DNA sequence identity. Misalignment of the two repeat units allows unequal crossing over to take place resulting in duplications and deletions. The do novo rate of duplication is estimated to be 10-20%.

Answer 208

AR is an X-linked gene There is a CAG repeat in the 1st exon. Expansion over 38 is associated with SBMA which results in progressive muscel weakness, cramps, twitching in males. females are generally asymptomatic but may have milde features. - shows anitcipation LOF SNVs that partially or fully impair the AR gene are associated with androgen insensitivity. The androgen receptor is crucial for primary and secondary male sexula development in response to testosterone - CAIS = female genitalia, raised as females and not suspected until puberty. Associated with mutations throughout the whole gene - PAIS nealry normal female genitalia or ambiguous - mild AIS mlae genitalia but may be small- mainly muts in steroid and DNA binding domains

Answer 209

One disease many genes

Answer 210

CMT is the most common inherited neuropathy with a prevalence of 1 in 2500-3000 in European populations. CMT encompasses a range of diseases which are clinically similar but genetically heterogeneous. CMT is also known as Hereditary Motor and Sensory Neuropathy (HMSN). CMT is caused by reduced nerve conduction velocities which can be demyelinating (CMT1) or axonal (CMT2). All inheritance patterns described. AD most common, then XL and AR More than 90% of CMT cases in which a molecular diagnosis has been reached are associated with changes in four genes (PMP22, GJB1, MFN2 and MPZ). e.g. PMP22 GOF/dup associated with most common form CMT1A MPZ - major myelin protein in PNS - MPZ mutations can cause a demyelinating phenotype (CMT1B) or an axonal phenotype (CMT2I/2J) as well as intermediate forms GJB1 Loss of function mutations in GJB1 are the primary cause of CMTX1. - X- linked second most common form MFN2 - mitochondrial membrane protein - associated with CMT2 (AD)

Answer 211

left ventricular hypertrophy in the absence of other cardiac or systematic disease. Can range from asymptomatic and heart palpitations to heart failure and sudden cardiac death. Due to mutations in sarcomere proteins - can be dominant negative where incorporation of mutant gene interacts with WT and disrupts sarcomere function - GOF - some mutations in MYH7 and TNNT2 result in increased contracile forces adn Ca2+ release and impaired relaxation - HI e.g. lack of detectable MYBPC3 due to NMD

Answer 212

is a genetic condition characterized by kidney disease, hearing loss, and eye abnormalities. People with Alport syndrome experience progressive loss of kidney function and hematuria which indicates imparied kidney function 85% are XLD due to mutations in COL4A5 gene (encode type IV collagen) 15% are autosomal (mainly due to COL4A4 and COL4A3) and can show AD or AR inheritance.

Answer 213

The liklihood of a sinlge variant causing a specific phenotype can be expressed as a percentage. PRS aim to quantify the cumulative effect of a number of genes whihc individually only have a small affect GWAS has been used to study PRS for complex diseases e.g. diabetes and coronary artery disease.

Answer 214

- personalised preventative measures - could be used to identify high risk groups to target for screening of preventative treatment if available - useful in instances where family history is unknown e.g. adoption, ovum/sperm donor - can be combined with other risk factors e.g. lifestyle, sex, age to help define the clinial action threshold for intervention challenges - not diagnostic, a high risk scorfe does not mean an individual will develop a disease and vice versa- so risk needs to be carefully communicated to patients - most scores have been calculated in EU caucasian data sets so are likely to less accurate for other populations

Answer 215

Most common inherited ataxia- incidence of 1/50,000 with carrrier freq ranging from 1/50-100 - AR - Due to a LOF GAA repeat expansion in intron 1 of the FRXN gene

Answer 216

characterised by progressive ataxia and hypertrophic cardiomyopathy - average age of death is 37 from cardiac dysfunction - pateints become wheelchair bound within 10 yrs of onset of symptoms from muscle weakness

Answer 217

98% have an expansion mutation on both alleles, remainder have 1 expasnion allele and 1 point mutation. No reports of patients with 2 point mutations- assumed to be embryonic lethal as FA results from a deficiency of FXRN protain not a complete absence

Answer 218

Nuclear encoded mitochondrial protein bind Fe and is required for the formation of FE-S clusters and therefore for synthesis of respiratpry chain complexes I, II, III and aconitase shares symptoms with mitchondrial diseases MELAS and MERRF

Answer 219

RNA-DNA hybrids are formed called R-loops during transcription when the nascent RNA bind to the DNA template behind the RNA pol- these block the transcriptional machinery from proceeding along the DNA = reduced FRXN protein due to block of elongation transcriptional initiation is also affected the mechanism is unclear

Answer 220

Large overlap between repeat sizes and demarcation between normal and FM is not determined normal = 5-53 PM = 34-64 - not associated with FA but may expand on transmission Borderline = 44-64 - shortest allele reported with FA is 44 FM 66-~17,000

Answer 221

- interruptions are associated with increased stability - maternal transmission is associated with expansion and contractions - paternal transmisson is associated with contractions there is high mitotic instability resulting in somatic mosaicism

Answer 222

Complete penetrance but age of onset varies from 5-50 due tot the large range of expansion sizes. In general the size of the smaller expansion accounts for 50% in the variation in age of onset. - late onset > 25 yrs 1 allele < 500rpts - v. late onset > 40 yrs 1 allele <300rpts

Answer 223

- Sizing PCR across GAA repeat can exclude a diagnosis in the presence of 2 normal alleles - to detect and expansion allele TP-PCR or southern blot is performed - sequencing or MLPA may be required is only 1 expansion is detected but there is strong clinical suspiscion of a second mutation. Need to be wary of high carrier freq and the possibility of an alternative diagnosis. Protein based assay can also be used to determine the conc of FRXN protein in the blood as a deficiency of the protein is causative

Answer 224

Carriers are unaffected so aim is to increase protein levels to that of a carrier 1. increase transcriptions of FRXN1 using a histone deacetylase inhibitor to increase initiation. But non-specific 2. Use synthetic nucleaic acids to bind to the GAA repeat and inhibit R-loop formation 3. INFgamma upregulates FRXN1 levels in all cell types and clinical trials in children are promising 4. Fe transport molecules and antioxidants

Answer 225

1, aggregation of toxic products- but in HD the presence of NI does not correlate with the location of neuronal death (pathognomic but not causative 2. toxic fragments- cleavage of mutant Htt by caspases results in the formation of toxic n-terminal fragments 3. transcriptional dysregulation - polyQ expanded proteins accumulate in the nucleus and interfere with transcription factors and regulators 4. mutant proteins interfere with cytoskeletal and axonal transport resulting in accumulated cargo 5. mutant proteins affect non neuronal cells types e.g. microglia are the immune cells of the CNS and are activated in HD

Answer 226

IONIS-HTTRX (roche) is designed to inhibit expression of the expanded mRNA to reduce the concentration of mutant Htt

Answer 227

TNR are dynamic mutations show anticipation expansion or contraction thought to occur due to strand slippage during replication in actively dividing cells e.g. germ cells. In non actively dividing cells e.g. neurons expansion occurs by transcription mediated repair pathways

Answer 228

5'UTR - fragile X CCG - LOF - SCA 8, 10, 12 1st exon - HD CAG- GOF - SBMA CAG - SCA 1,2,3,6,7,17 CAG - DRPLA 1st Intron - Freidreich ataxia GAA- LOF 3'UTR - DM1 CUG- GOF

Answer 229

- adult onset (juvenille cases rare and if seen are paternally transmitted due to the high level of meiosis in spermatogenesis - progressive - show anticipation with a threshold level of repeat that must be met for the disease phenotype to present. - gene is ubiquitously expressed - mutant proteins accumulates in ubiquitinated neuronal intranuclear inclusions

Answer 230

SCA- Ataxia, abnormal limb movements, slurred speech and lack of coordination DRPLA- CVAG expansion in ATXN1 and result in ataxia, choreoathetosis and dementia. Myoclonus epilepsy also seen in cases under 20yrs and associated with increased expansion size SBMA- CAG expansion in AR gene. Affects males but females spared due to low levels of circulating androgens and lower level of AR recpetor stimulation. Males may also present with gynaecomastia, reduced fertility and testicular atrophy as a result of mild androgen insensitivity

Answer 231

HD is a AD disease caused by a CAG repeat expansion in the first exon of the Htt gene. Incidence of 5-10 per 100,000. Mean age of onset i3 30-60 with a peak at 40-45yrs account for 90% of chorea with a genetic cause characteristic finding is the present of ubiquitinated neuronal intranuclear inclusion in the brains of HD pateints (insoluble aggregates of mutant Htt and ubiqutiin)

Answer 232

Movement - chorea, dystonia, ataxia Psychiatric - depression, irritability, psychosis- may proceed movement changes neurologic - dementia

Answer 233

- rare and associated with paternal transmission - onset of symptoms <20 - first signs are usually behavioural disturbances at school and the development of twitchy movement, chorea is rarely seen in the 1st decade.

Answer 234

HTT is found at 4p16.3 HTT protein is ubiquitiously expressed and involved in normal development

Answer 235

The CAG repeat is transcribed and this results in a conformational change in the Htt protein- it becomes sticky and forms aggegates NII's Clinical features are associated with the degeneration of the CNS with loss of striatal neurons whilst large interneurons are spared. It is unclear why cell death is confined to particular neuronal cell types.

Answer 236

``` Normal - up to 26 repeats Intermediate - 27-35 reduced penetrance 36-39 Full penetrance - 40+ Juvenile - 60+ ```

Answer 237

Found in 6% of the general population- relatively common and so the possibility fo detecting one should be covered in pre-test counselling. May be found in a diagnostic case with 1 allele in the affected and 1 allele in the IA range, therefore identifying a risk of HD in the non-HD side of the family. Not associated with phenotype but risk of expansion to HD in single transmission so PND can be offererd risk of expansion depends on: sex- more likely in male transmission - family history, more likely if previous expansion of an IA in the family - genetic variation - Glu2645del poly more common in HD alleles than general population - If the 30 CAA has changed to CAG expansion is more likely

Answer 238

36-39 Low penetrance and may never develop HD in their lifetime. - 40% will be HD free at 65yrs and 30% at 70yrs - unstable and risk of HD in offspring so PND available - if detected in a diagnostic case reported as being consistent with a diagnosis of HD - if detected in a PST reported to have in increased risk of developing HD - can offer cascade testing to family members

Answer 239

1% of HD cases are not confirmed molecularily- phenocopies ``` differential diagnoses includes: HD-like 1 HD-like 2 DRPLA SCA17 Freidreich ataxia Wilson disease Neurocanthosis benign familial chorea ( ```

Answer 240

Homozygous HD has same onset (depending on repeat length plus other modifiers) and severity but the progression may be faster - reveals risk of HD on non-HD side of the family. both parents are either carriers of affected siblings have a 75% of risk of carrying one or both alleles

Answer 241

1. sizing PCR across the CAG repeat- can size alleles up to ~80rpts so usually sufficient for exclusion or confirmation of a diagnosis - uses 2 primers, 1 amplifies the CAG repeat to accurate sizing. a second amplifies the CAG repeat plus a polymorphic GC rich repeat. This is beneficial as patients unlikely to be homozygous for CAG and GC repeat so can confirm if a patient is homoxygous for a normal allele - rare poly can cause primer looping and 2 rpoduct peaks one repeat apart for a single allele TP-PCR is therefore used in cases when there is: - only 1 allele detected using both primer sets - 2 peaks 1 rpt apart as may be from the same allele - generally only required for juvenile cases as 55+ repeats expected to have onset by 35 and would be detected by sizing PCR need to use controls are the borders of the size ranges with known repeat sizes as CAG repeats run anonymously in electrophoresis which can make the size ladder unreliable

Answer 242

Diagnostic- patients with features of HD- accepted from neurologist or other relevant speciality. Referral from clinical genetics if patient is under 16 PST- must come from clinical genetics and requires at least 2 counselling sessions a couple of months apart. Preferably need a confirmed diagnosis in a family memeber, if not a negative result cannot rule out them being at risk of a different disorder PND- can be direct if affected parent has been tested or indirect for fetuses at 25% risk if the at risk parent does not want to be tested.

Answer 243

Use family member as a positive control. If mother is affected need to be wary of MCC- PCR test is more sensitive than the MCC test so may be affected by levels not detected by MCC exclusion. Should be wary of results with the same expansion size as the mother or very low peak and may wish to confirm by linkage which is less sensitive to MCC

Answer 244

need a sample from parents of parent at 50% risk to determine the high risk haplotype- preferably affetected parent - if fetus inherits high risk haplotype 50% risk of being affected and parents counselled that if they are undertaking the test they should terminate in this circumstance if not it is a PST on a minor without permission which is unethical - low risk haplotype reduced risk of HD- small risk that other parent carries an IA (65) or recued penetrance allele and is unaware - 2% risk of recombination so need to use marker across the gene to reduce the risk of a double recombination - ideally work up should be done before getting pregnant

Answer 245

yes embryos biopsied at the 8 cell stage and use linked markers in karyomapping to see if the high risk haplotype has been inherited

Answer 246

Dominant inheritance not found in patient with LOF mutations or dels CAG repeat is trascribed HD hets are clinically the same as HD homs

Answer 247

1. accumulation of toxic aggregates- NIIs are characteristic but are not causative as they do not cooincide with the timing or location of pathogenesis- part of the process but may not be toxic per se 2. toxic fragments- abnormal HTT is a substrate for proteolytic cleavage by caspases and calpains. amnio teminal fragment expessed in mice is sufficient to induce a HD like phenotype 3. transcription dysregulation- ployQ expanded fragments accumulate in the nucleaus and interfere with normal transcription 4. defect is cytoskeletal and axonal transport- disruption of transport results in aggregation of accumulated cargo and neuronal death ad dysfunction 5. effects on non-neuronla cell types - astocytes and microglia. Strong evidenc that microglia (neuronal immune cells) are activated in HD and level of activation correlates with level of neuronal pathology

Answer 248

Most common form of adult onset dystrophy 1 in 8,000 characterized by myotonia and progressive muscle weakness mean onset at 20-50yrs with death at 60 from cardiac failure AD and shows anticipation

Answer 249

Mild- late onset with and may only show mild myotonia, cataracts and normal life span Classic - myotonia, progressive muscle weakness, gait disturbances - cardiac conduction abnormalities - baldness and testicular artrophy - may also include catarcats, IDDM, digestive tract problems and hypersomina - onset in 2nd or 3rd decade Juvenile similar to classic DM but earlier onset and can include cognitive and behavioral difficulties Congenital - presents at birth with extreme hypotonia - prenatal polyhydramnios and reduced fetal movement - often have respiratory insufficiency resulting in early death - ID and motor developmental delay

Answer 250

19q13.3 98& of cases are due to CTG expansion in the 3'UTR, does not affect coding sequence and is transcribed as a CUG repeat in mRNA

Answer 251

- not due to HI as point mutations not detected in DM1 patients and KO mice do not show DM1 phenotype - CTG repeats may lead to changes in the chromatin structure and silence neighboring genes but this does not explain the full phenotype - RNA GOF expanded CUG repeats accumulate in nuclear foci and have been visualised in affected tissues - increased repeat length correlates with the accumulation of mutant transcripts expression of expanded 3'UTR is sufficient to inhibit myogenesis - DM2 produces a similar phenotype but due to an expansion in a different gene CUG repeat regions interacts with RNA binding proteins which are involved in splice regulation. MBNL1 and CUGBP1- these usually act antagonistically and interaction with CUG rpt results in functional down-regulation of MBNL1 and up-regulation of CUGBP1. This results in aberrant splicing of targets and embryonal splicing patterns are seen patients instead of adult splicing patterns.

Answer 252

expansions form as a result of the generation of secondary structures during processes which separate the DNA strands e.g. replication. once a CUG has at least 11 repeast it has the propensity to fold into a hairpin like secondary structure with pairing between C-G and U-U mismatches.

Answer 253

- correction of aberrant splicing of MBNL1 and CUGBp1 targets - forced nuclear export of expanded RNA - inhibition of protein binding to expanded repeats - elimination of expanded mRNA by CRISPR - reduce levels of mutant RNAs using ASOs

Answer 254

Normal - 5-35 Intermediate 36-50 No DM1 but may be unstabe; Full mutation 50-150 associated with mild, classi or asymptomatic DM Full mutation >150 associated with classic, juvenile and congenital DM

Answer 255

Instability is skewed toward expansion intermediate alleles show highest instability when paternally inherited. in the disease range all expansion are likely to be unstable regardless of parental gender Congential DM1 is almost exclusively inherited maternally in a mechanism which is not well understood somatic instability results in somatic mosaicism especially in cardiac and skeletal muscle 5% of DM1 patients have non CTG interruptions. - these are generally more stable on transmission and gross changes in expansion length occur in the uninterrupted part of the rpt proximal to the interruption.

Answer 256

Clinical features: - muscle pain and stiffness - progressive muscle weakness and myotonia - male hypogonadism and azoospermia - may also have ID, hypersomnia, tremor, hearing loss and male frontal balding

Answer 257

CCTG repeat in intron 1 of the CNBP gene normal alleles have 26 rpts disease alleles have 75->11,000 (mean 5,000) repeats does not show anticipation lower prevalence and more common in the Finnish and German populations

Answer 258

1. Sizing PCR using primers which flank the CUG rpt - uses 2 primer pairs to give a forward and reverse amplification - 2 primers reduce the chance of false -ves whihc can occur if there a non-CTG interruptions in the 3' of the expansion (5%) 2. TP-PCR - used if a sinlge normal allele is detected by sizing PCR whihc could indicate: - homoxygous for a normal allele - undetected large expansion allele - undetected second allele sue to SNP under primer binding site (long range PCR and southern blot can also be used but lonog range PCR may fail to amplify very large expansions and southern blot is time consuming and requires a lot of high quality DNA)

Answer 259

offered to carriers of IA and FM alleles - CTG PCR and TP-PCR - dilute CVS samples to prevent inhibition from heparin media - MCC- TP-PCR is more sensitive to MCC that the MCC assay, therefore may need to confirm a +ve result by linkage or southgern blot whihc are less sensitive to MCC Confirmation not required if: - father is affected/carrier - allele is a different size to the maternal expansion - fetus has not inherited the mothers normal allele - negative result and 2 normal alleles in fetus linkage - use linked markers. Aim to use multiple markers to reduce the chance of a double recombinations

Answer 260

PCR can be used to detect smaller alleles. Accurate sizing is not required due to the large size difference between the normal and affected ranges - quadruplet primed PCR to detect large expansions - expansions may appear as a diffuse smear by southern blot sue to somatic mosaicism- this limits the sensitivity of detection and requires good quality DNA

Answer 261

imperfect triplet repeats GCN (GCA, GCG,GCC, GCU) Present in >500 genes and expansions are implicated in 9 disorders, 8 of which affect transcription factors

Answer 262

found mainly in transcription factor, expecially homobox containing proteins Act as a spacer between functional regions and are key for allowing correct folding and conformation of proteins. Expansion of the repeat is though to dysregulate protein and in turn transcription of genes involved in developmental processes.

Answer 263

500 proteins with polyalanine repeats - shorter repeats than polyQ disorders - expansions of 7-14 rpts undertake variable levels of conformational transition from a-helix to B-sheet. - peptides with>19 rpta are completely converted to B-sheets and the proteins aggregate and form intranuclear inclusions

Answer 264

- once a threshold rpt lenght is met (>19) there is protein misfolding resulting in aggregation, degrdation, mislocalisation or aberrant interactions. - aberrant B-sheet proteins form intranucelar inclusion and sequester WT indicating that they can act in a dominant -ve manner

Answer 265

There is a correlation between increasing repeat length and severity of the disease for SPD1 and CCHS - largest recorded expansion is 33 in CCHS (PHOX2B gene)

Answer 266

- shorter expansions than other TNRs - stable in meiosis and mitosis - expansion is by uneven crossing over between mispaired normal alleles.

Answer 267

Chaperones are involved in protein folding - chaperones can become sequestered in the expanded protein aggregates along with ubiquiting and proteosome subunits. - formation of aggregates occurs whent he cells chaperone system cannot keep up and the build up unfolded proteins eventually results in apoptosis - also observed in polQ diseases indicating that misfolded proteins are recognised by their non-native conformation and are targeted to the ubiquitin-proteosome pathway

Answer 268

1. agregated proteins become dysfunctional 2. protein aggregates can recruit essential cellular componenets and compromise there function- dominant -ve 3. expansions may result in protein mislocalisation without aggregation resulting in aberrant DNA or protein interactions

Answer 269

chaperones- involved in protein folding and degradation and can protect cells from apoptosis - inducing HSP70 and 40 has been shown to reduce cellular toxicity in cells with expanded PHOX2B in patients with CCHS

Answer 270

CCHS- congential central hypoventialtion syndrome - PHOX2B exp - GOF and LOF mechanisms - autonomic nervous system abnormalities - also caused by SNVs syndromic and non-syndromic XLR mental retardation - ARX expansion - also caused by SNVs - GOF - MR, infantile seizures

Answer 271

Facioscapulohueral muscular dystrophy - assymetric and progressive proximal muscle weakness presenting in the face and progresssing to the scapula, arm, hip and legs. Often show scapular winging

Answer 272

- due to expression of the DUX4 transcript on chr 4q35 | - due to 2 different mechanisms in FSHD1 and 2

Answer 273

there is a tandem array of D4Z4 repeats at 4q35- each contains a copy of the gene DUX4 - DUX4 is normally epigenetically silenced in the majority of adult cells and tissues. - DUX4 repeat size is normally 11-100, in the disease range it is reduced to 1-10 a reduction in the DSUX4 repeat length is associated with a loss of chromatin compaction and CpG methylation resulting in DUX4 expression from the final D4Z4 unit broad inverse correlation between the repeat length and disease severity and patients with intermediate length repeats have a milder form without facial involvement Requires a permissive allele to develop disease. There is a 4qA or 4qB poly distal to the D4Z4 repeat. FSHD1 is only seen when there is repeat length contraction occurs on the permissive 4qA allele. AD inhertitcance

Answer 274

southern blot to detect repeat length

Answer 275

Digenic inheritance 1-5%of FSHD (majority is type 1) due to mutations in SMCHD1 + 1 permissive allele - SMCHD1 is an epigenetic modifier of D4Z4 and LOF mutations result in chromatin relaxtion and hypomethylation allowing expression of DUX4 digenic inheritance means risk to offspring is 25-50% depending ont he number of pathogenic haplotypes in the family and can make genetic counselling difficult FSHD1 risk to offspring is 50% SMCHD1 can also be a disease modifier in FSHD1- results in ealrier onset and more severe disease and there is DUX4 expression0 by 2 mechanisms.

Answer 276

Methylation specific pyrosequencing to detect the methylation status of D4Z4 and SMCHD1 screening to identify pathogenic mutations

Answer 277

deletions- if the gene(s) in the interval are HI and fully or partially deleted duplications- Ts genes or a duplication that disrupts a Hi gene- intragenic duplication( depends on whether reading frame is disrupted and functional domains)

Answer 278

Mediated by NAHR between LCRs - segmental dups (10-400kb) with high degree of homology (97%)- should get a reciprocal deletion and duplication but deletions are over represented, partially due to ascertainment bias as they are more likely to result in a severe phenotype. LCRs are misaligned in meiosis so there are regions with the same sequence but different locations.

Answer 279

Minimum efficient processing segment- kinimum stretch of homologous sequence required to enable homologous recombination - the further apart the LCRs the longer the MEPs need to be - Meiosis @300-500bp and shorter regions are required for mitosis

Answer 280

- phenotype often due to just 1 or 2 genes in the region e.g. RAI1 HI in smith magenis - often show variable expressivity, reduced penetrance and syndromic features to to disruption of >1 gene

Answer 281

mediated by NAHR between SMS-REPS - distal middle and proximal REPs - common 4Mb del is between the distal and proximal REPs

Answer 282

Smith Magenis= Deletion of 4Mb at 17p11.2 - distinctive facial features (brachycephaly, broad face, tented upper lip - DD and cognitive impairment - hypotonia in infancy - behavioral abnormalities - due to HI of criticla gene RAI1 Potocki-Lupski - 4Mb recurrent duplication at 17p12 - ID, DD, ASD, failure to thrive and hypotonia

Answer 283

del 7p11.2- mediated by NAHR between LCRs

Answer 284

- elfin like facial features - connective tissue abnormalities - ID (usually mild) - friendly - growth abnormalities - endocrine problems generally de novo but ~25% due to a normal parent with a parecentric inversion of chr 7

Answer 285

due to HI of the ELN (elsastin gene)- responsible for connective tissue and cardiac diseases.

Answer 286

characteristic facial features and severe impariment of expressive language

Answer 287

Due to recurrent deletion at 22q11.21 - common deletion is 3Mb bp A and D - smaller dels have vairable or milder features TBX1 is found in the region between bp A and B and is though to be responsible for the cardiac abnormalities.

Answer 288

Highly variable, reduced penetrance and may be inherited from a normal parent- makes genetic counselling difficult as cant be sure if offspring will be affected or how severely. - cardiac abnormalities - cleft palate - ID - thymic hypoplasia - speech and language delay - hypocalcaemia

Answer 289

17p13.3 deletion critical genes- LIS1 and YWHAE

Answer 290

Lissencephaly (LIS1) microcephaly, severe MR - majority de novo but 20% inherited from a parent with a balanced chromosome rearrangement

Answer 291

deletion at 8q24 critical gene are EXT1 and TRPS1

Answer 292

``` Mutliple exotoses (EXT1) bone and craniofacial abnormalities (TRPS1) ```

Answer 293

WAGR del 11p13 Wilms tumour (WT1) , aniridia (PAX6), genitourinary abnormaliies and mental retardation

Answer 294

Deletion of NF1 at 17q11.1 multiple cafe au lait spots, benign neurofibromata also cause by LOF mutations in NF1

Answer 295

4pter (4p16.3) | contiguous del

Answer 296

Greek warrior helmet facial features (wide spaced eyes, wide nasal bridge) - seizures - LD - growth delay and IUGR

Answer 297

Majority are de novo dels but ~40% have a WHS deletion and a partial trisomy for the terminal region of a different chromosome as it is inherited from an unbalanced rearrangement of the parental rearrangements.

Answer 298

dle 5pter variable breakpoints and the larger the deletion the more severe the phenotype. cat like cry associated with proximal 5p13.3 dysmorphic features and ID associated with 5p15.12 including CTNND2

Answer 299

``` cat like cry dysmorphic features- hypertelorism, low set ears and micrgnathia severe LD/DD low birthweight hypotonia ```

Answer 300

Gene disrupted by breakpoints of a balanced rearrangement or can result in the generation of a new fusion gene (more relevant to oncology e.g. BCR-ABL1) microdel/dup at breakpoint that is not genetically visible- likely to be detected by array positional affects cryptic imbalance disturbance of imprinting UPD balanced X chromosome rearrangments Mosaicism co-incidental finding- may have another genetic abnroality present that has not been detected by G-banding

Answer 301

Both chromosomes will look the ame by G-banding and arrayCGH. Need a SNP array to be detected. - can result in phenotype as disruption to imprinting pattern can result in loss or gain of expression of a gene that is normally expressed in a parent of origin specific manner e.g. chr 6,7,11,14,15,22

Answer 302

- move a gene away from its enhancer element - reducing expression - move a gene away from its inhibitor/silencer- inappropriate expression - move a gene into the control of an enhancer of a a different gene. E.g. in Burkitts lymphoma the t(8;14) rearangement puts the MYC oncogene under the control of the immunoglobulin gene enhancer resulting in increased expression and - rearrangement that juxtaposes heterochromatin with euchromatin can result in the heterochromatin region spreading to the euchromatin and silencing euchromatic genes

Answer 303

Abnormality may be present which is not seen in blood e.g. pallister killian iso 12p can be detected in prenatal samples and skin etc but is not seen in blood

Answer 304

- disruption of the critical reagion Xq13-22 or Xq22-26 can result in gondal dysfunction and infertility in females - in male carriers of X;A translocation are infertile due to disruption of the sex vesicle in meiosis and spermatogeneic arrest - Y;A - infertile due to spermatogenic arrest - if the X inactivation centre is tanslocated this can result in silencing of the centromeric autosome region (functional monosomy) and functional disomy for the centromeric X chromosome- this result in a high level of imbalance.

Answer 305

ABCR are associated with infertility (especially in males) as they can affect gametogenesis - thought to be that failure of pairing of the quadrivalent in meiosis 1 interferes with the X-Y bivalent and the sex vesicle resulting in spermatogenic arrest - may result in recurrent miscarriage which can manifest as infertility depending on gestation of loss

Answer 306

- genomic content- OMIM morbid genes etc need to consider whether the imbalance is a del of dup of disrupting the gene and whether the gene is HI or TS - genetic emahcnism of gene in region is key, deletion of a gene associated with missense GOF mutation is unlikely to be pathogenic - size- larger calls are more likely to be pathogenic as there could be greater imbalance but very blunt tool and large imbalances can be benign and small one pathogenic - inheritance from a normal parent is more like to be benign but many recurrent NDD regions show reduced penetrance so may not always be informative - some imbalances may suggest a large structural rearrangement as the cause and should be followed up by FISH or G-banding to determine the recurrence risk e.g. 15q11.2 NIPA1 del or 1q21.1 del, 16p11.2 - normal and disease databases- present in patients with same phenotype is evidence for pathogenic- need to be careful of study method and only compare imbalances with the same genes e.g. decipher and pubmed. on the other hand presence in normal individuals >1% is evidence for being benign

Answer 307

- pathogenic variants relevant to the referral reason - Neurosusceptibility loci associated with USS anomalies- reportable list included in BPG - high penetrance neurosusceptibility loci with high penetrance - deletion of certain cancer associated genes - SASI guidelines - carrier status if relevant to family members e.g. DMD del in a female fetus so mother can be tested do not report findings not linked to the abnormalities seen in the pregnancy VUS low penetrance neurosusceptibility genes het dels of AR genes not linked to the USS abnormalities. For complex result MDT with clinical genetics should be undertaken to discuss the results in terms of the pregnancy and presenting feature before reporting. On occasion parental samples may be requested to support results in interpretation.

Answer 308

collaboration between the NHS and wellcome sanger institute - array and trio exome of pateints with idiopathic LD - identified 12 new disorders - grew out of decipher database and aims to extend the reach of decipher to diagnoses a broader spectrum of disorders