Specialist OSFA (genetics) Flashcards

1
Q

What are the risks for a carrier of a balanced Robertsonian translocation?

A
  1. Infertility (male)
  2. Offspring with trisomy: (if chromosome 13 or 21 involved) - risk 10% if female carrier, 1% if male carrier - if isochromosome: risk is 100%
  3. Offspring with UPD: Trisomy or monosomy rescue could lead to UPD: 0.5-1% risk - if 14 or 15 involved this could lead to UPD 14mat (Temple syndrome) or UPD 15mat (Prader-Willi syndrome) - and UPD 14pat or UPD 15pat (Angelman syndrome)
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2
Q

What does standard analysis in constitutional cytogenetics work consist of?

A
  1. Minimum 2 cells analysed and cleared - if mosaic: minimum 1 cell from each cell line
  2. Minimum quality:
    CVS/AF: 3 (2 if confirming aneuploidy, 4-5 if looking for small structural rearrangements)
    Blood: 6
    Microdeletion syndromes: 7
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3
Q

What are the cytogenetic reporting targets?

A

Prenatal: Rapid QF-PCR/FISH 3 working days; karyotype: 14 calendar days
Postnatal: Rapid aneuploidy: 3 working days; Karyotype: Urgent: 10 days; Routine: 28 days; Tissue: 28 days
Haematology: Rapid PCR/FISH: 3 working days; karyotype: Urgent: 14 days, Routine: 21 calendar days

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4
Q

What should be done in postnatal constitutional analysis if mosaicism is suspected?
In which cases should mosaicism be investigated?

A

Extended scoring or analysis protocols for G banding:
• A minimum of 30 cells
• Duplicate cultures
• More than one tissue type
FISH may be more suitable if probes are available
Referring clinicians should be made aware that it is not possible to reliably exclude mosaicism from any analysis and specifically those not
targeted for extended counts

Extended analysis should be considered in cases presenting with the following
reasons for referral:
• Ambiguous genitalia /indeterminate sex
• Clinical details suggestive of known autosomal mosaic syndromes
e.g. trisomy 8; + i(12)(p10); +dic(15)(q12)
• Clinical features suggestive of a specific aneuploidy syndrome, but which have a normal karyotype on standard analysis
• Diagnosed or suspected cases of sex chromosome aneuploidy, known to be associated with mosaicism e.g. Turner syndrome
• Follow-up of a prenatal diagnosis of a possible mosaicism of
clinical significance in an affected child after birth
• Karyotypically normal parents of more than one child with the
same, or a related chromosome abnormality

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5
Q

What should always be included in reports?

A
  1. Recipient
  2. Lab identification
  3. Patient and sample identification
  4. Result summary - Use correct nomenclature (ISCN/HGVS)
  5. Restate clinical question
  6. Description of findings in words
  7. Name of associated disease/syndrome/prognosis
  8. Interpretation: In context of relevant information (e.g. clinical features, family history, ethnic background, other investigations)
  9. Assessment of recurrence risk (use Bayes if possible)
  10. Further testing required
  11. Basis of test and limitations
  12. Authorised by
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6
Q

What are the minimum FISH analysis recommendations for constitutional genetics?

A

Metaphase: Minimum 5 cells analysed (2 of which are checked)
Interphase: Aneuploidy: 30 examined, microduplication/deletion: 15 examined

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7
Q

Which sources of information are available for cytogenetic analysis?

A
  1. Departmental SOPs
  2. Association for Clinical Genomic Science (ACGS) best practice guidelines
  3. Gardner and Sutherland
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8
Q

For which referrals can microarray be used as a front line test?

A
Learning difficulties
Developmental delay
Dysmorphic features
Congenital abnormalities
(If baby/child with features of trisomy then do QF-PCR first)
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9
Q

What are the requirements for excluding mosaicism in CVS and AFs?

A

Depending on the abnormality, a basic, moderate or extensive work-up is required. All of them require more than one culture to be investigated.
Abnormalities in single cells normally only require basic work-up (except autosomal trisomies).
For chromosomes that are known to be involved in UPD (7, 11, 14, 15), further studies
should be considered.
For level III mosaicism in a CVS, follow up amniocentesis or fetal blood
sampling along with detailed ultrasound assessment of fetal morphology should be
advised.
The report must include a statement, that the level of mosaicism is not necessarily reflect the proportion in the fetus.
Use Hsu guidelines.

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10
Q

For which chromosomes should we be concerned about UPD?

A

If there is apparent CPM for chromosome 7, 11, 14, 15 or marker chromosomes originating from these.
Mosaic chromosome 16:If UPD is excluded, there is still a significant risk of an adverse outcome.

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11
Q

Which referral reasons are there for CF testing?

A

Diagnostic (newborn screening, meconium ileus, chest infections, CBAVD/infertility/obstructive azoospermia, bronchiectitis, pancreatitis, classical CF)
Confirmation of CF
Relatives of CF patients (risk of having children with CF)
Partners (especially if accurate pregnancy risk required)
Gamete donors
Fetal echogenic bowel (test parents first for carrier status)
First cousins
Not recommended to test children under 16 for carrier status

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12
Q

When should reflex testing for the intron 8 polyT tract in the CFTR gene be carried out?

A
  1. All males with obstructive azoospermia (could be 5T homozygote)
  2. Patients with bronchiectasis or pancreatitis where 1 mutation has been found
  3. R117H mutation detected (can modify severity)
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13
Q

What can be detected on 1st trimester scan and what is the significance?

A
  1. Raised nuchal translucency (indicator of genetic testing if >3.5 mm) - can indicate trisomy 13, 18 or 21 or 45,X.
  2. Cystic hygroma - can indicate 45,X or Noonan syndrome
  3. Echogenic bowel - can indicate trisomy 21 or CF - important to know local CF positive echogenic bowel cases for calculation of residual risk
  4. Choroid plexus cysts - can indicate +18 or +21
  5. Atrioventricular septal defect (AVSD) (+21)
  6. Ventricular septal defect (VSD) (+13,+18,+21)
  7. Diaphragmatic hernia (+18,+21, i12p)
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14
Q

What can be detected on 2nd trimester scan and what is the significance?

A
  1. Cardiac abnormalities (21, 18, 13 and 45,X)
  2. Features of Patau (+13): Holoprosencephaly (forebrain fails to develop into two hemispheres), Bilateral cleft lip, Polydactyly (extra digits), Talipes/club foot
  3. Features of Down syndrome (+21): Duodenal atresia (absence or closure of first section of small intestine) – is seen as two tubes appearing on ultrasound scan (“double bubble”)
  4. Features of Edwards (+18): Unilateral cleft lip, Micrognathia, Fisted hand/clenched fist, Talipes/club foot
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15
Q

What sizes of bands are expected on a EcoRI/EagI Southern blot of a:

1) Normal female patient
2) Normal male patient
3) FRX premutation carrier female
4) FRX premutation male
5) FRX full mutation carrier female
6) FRX full mutation male

A

1) 2.8 (EcoRI+EagI) and 5.2 kb (EcoRI only)
2) 2.8 kb
3) 2.8 and 5.2 kb + >2.8 and >5.2 kb
4) >2.8 kb
5) 2.8 and 5.2 kb +&raquo_space;5.2 kb or smear
6)&raquo_space;5.2 kb or smear

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16
Q

What are the expansion ranges in Fragile X syndrome?

A

<46: Normal
46-58: Intermediate allele - normal phenotype, very rare expansion to premutation in 1 generation, to full mutation in 2 generations
59-200 and unmethylated: Premutation - can expand to full mutation in 1 generation, may be affected with FXTAS, females: FXPOI, children with FXS
>200 or methylated (no expression): Full mutation, males affected, females: 50-60% affected

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17
Q

Reporting FRX results:

1) Normal/intermediate allele male
2) Normal/intermediate allele female
3) Premutation male
4) Premutation female
5) Full mutation male
6) Full mutation female

A

1) FRX unlikely (rare point mutation/deletion), possible mosaicism - refer to clinical genetics if >50
2) FRX unlikely (rare point mutation/deletion), possible mosaicism - FXPOI/FXTAS excluded - refer to clinical genetics if >50
3) FRX unlikely (rare point mutation/deletion), possible mosaicism, possible tissue mosaicism
4) Carrier of FXS - clinical symptoms of FXTAS or FXPOI may be attributable to expansion, but could be due to something else
5) FXS due to full mutation confirmed - Males with a full mutation rarely have children, all daughters are expected to carry premutation - male offspring are normal
6) Patient is a carrier of FXS - Symptomatic females generally less affected than males - Risk for female transmitting full mutation is 50%

Genetic counselling to mother of patients and her family should be recommended.

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18
Q

What is the location of the PWS/AS critical region?

A

15q11.2q13.1

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19
Q

What are the possible mechanisms of PWS and their frequency?

A

Deletion: ~70-75%
Uniparental disomy: ~25-29%
Imprinting centre defect: <1%
UBE3A gene mutation: n/a

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20
Q

What are the possible mechanisms of AS and their frequency?

A

Deletion: ~68%
Uniparental disomy: ~7%
Imprinting centre defect: ~3%
UBE3A gene mutation: ~11%

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21
Q

Testing strategy for PWS/AS referrals?

A

1) Microarray
2) If microarray normal - MS-PCR/MS-MLPA to see if maternal/paternal methylation present
3) If microarray deletion in 15q11-q13 region - MS-PCR/MS-MLPA to see if maternal or paternal allele missing - request parental samples to see if balanced rearrangement in a parent to assess recurrence risk (but most often sporadic)
4) If abnormal MS-PCR - repeat and request parental samples for UPD studies - if UPD then unlikely recurrence - IC defect: Normally sporadic, but deletions can be inherited (silent if mat allele with pat del)

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22
Q

Testing strategy for DMD referrals?

A

1) Diagnostic:
MLPA (2 kits) to detect deletions and duplications in dystrophin gene (70% of patients)
Sequencing available on request to detect point mutations
If a single exon deletion or duplication is found confirm by multiplex PCR or sequencing
Frameshift model is correct in 90% of cases (frameshift/nonsense mutations cause DMD, in-frame mutations cause BMD - use frame checker)
2) Carrier testing:
Look for familial mutation by appropriate method (MLPA/sequencing) or if no mutations has been identified do linkage
3) Prenatal testing:
Available to female carriers and females with affected sons (risk of mosaicism)
First do fetal sexing (invasive/non-invasive) - if male do invasive test (MLPA/sequencing) or NIPD

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23
Q

How can a female be affected by classical DMD?

A

1) Non-random X-inactivation due to X-autosome translocation unmasking a pathogenic dystrophin variant or unexplained non-random X-inactivation (in skeletal muscle tissue)
2) Uniparental disomy for X with pathogenic dystrophin variant
3) Turner syndrome with pathogenic dystrophin variant
4) Homozygosity or compound heterozygosity for pathogenic dystrophin variant

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24
Q

What are the clinical features of DMD and BMD?

A

DMD:
Progressive muscular weakness (mainly proximal) - wheelchair dependency before 13 years
Waddling gait, difficulty climbing
Developmental delay and learning difficulties (30-50%)
Dilated cardiomyopathy
Mean age of death at 25 years (main causes cardiomyopathy and respiratory insufficiency)
Gower’s sign
Serum creatine kinase (CK or SCK) levels raised

BMD:
Maybe late learning to walk
Muscle weakness around 11 years
Muscle cramps
Lose ability to walk at 40-50 years
No learning difficulties
Survive to middle age and beyond (mean age of death mid-40s, main cause: cardiomyopathy)
Serum creatine kinase levels >5x normal

Carrier females:
5-10% of carriers have cramps or mild muscle weakness
Usually not noticed until in 30s
Carriers of BMD less affected than DMD carriers
20% of carriers have evidence of dilated cardiomyopathy – should have 5 yearly echo/ECG
Serum creatine kinase (CK) levels 2-10x normal in 50% of cases

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25
Q

What to remember when reporting a DMD MLPA result?

A

1) Negative MLPA result:
Diagnostic: MLPA result does not exclude a diagnosis of DMD as deletions and duplications only occur in approximately 70% of patients
Sample can be sent away for point mutation analysis on request
Carrier testing:
Reduces the risk of being carrier - Bayes calculations can be included - (de novo risk is high in DMD)
Does not exclude germline mosaicism (9% in mothers with an affected son and no previous family history)
prenatal testing available in future due to relatively high risk of germline mosaicism
2) Positive MLPA result:
Deletion/duplication predicted to be in-frame/out-of-frame
Confirms diagnosis of BMD or DMD
Referral to clinical genetics recommended for counselling and carrier testing of female relatives
Prenatal testing available in future

26
Q

What are the clinical features of SMA?

A

•Degeneration of anterior horn cells of spinal cord
•Progressive symmetric muscle weakness and atrophy, proximal more severely than distal
•Poor weight gain, growth failure, may need gastronomy tube
•Restrictive lung disease
•Scoliosis, may require surgery
•Joint contractures
•Sleep difficulties
•Normal to elevated CK levels (indicating muscle damage)
4-5 classifications with different ages of onset (prenatal to adulthood) and lifespan (<6 months to normal)

27
Q

What is the difference between SMN1 and SMN2?

A

Inverted repeat on 5q13.2 has caused SMN1 and and SMN2 genes
They differ by 5bp at 3’ end
Exon 7:
o Stop codon near end
o Synonymous C>T conversion in SMN2 near beginning
o Disrupts exon splice enhancer (ESE), leading to exon 7 skipping
o SMN1: ~90% correct splicing
o SMN2: ~10% correct splicing

28
Q

What causes SMA?

A

Deletion or gene conversion of SMN1: 95-98%
Most people have 1 copy of SMN1 on a single chromosome [1+1], but 5-8% of population are carriers with [2+0] configuration – this gives false negative MLPA result (for carriers)
2-5% are compound heterozygotes for deletion/conversion and point mutation

29
Q

What is the testing strategy for SMA?

A

Diagnostic testing:
MLPA: Can distinguish between SMN1 and SMN2 exon 7 and 8
If 1 copy of SMN1 seen: recommend point mutation analysis - (if negative: Can do linkage if have family history)

Carrier/prenatal testing:
MLPA: If negative, include risk calculation: Could be [2+0], point mutation, de novo in index case, germline mosaic in parent
If suspect [2+0] do linkage analysis

30
Q

Which prior and conditional probabilities should be used for Bayes calculations in SMA?

A

Population carrier frequency: 1/50 (for Northern Europe)

Proportion of chromosomes with 2 copies of SMN1 on same allele: 4/100 (for Northern Europe)

De novo point mutations occur in 2/100 of individuals with SMA

31
Q

What are the clinical features of CMT?

A
  • Slow progressive weakness in distal limb muscles
  • Atrophy, “stork leg”
  • Mild to moderate sensory loss in distal limbs
  • Bilateral foot drop resulting in steppage gait, ankle sprains
  • Pes cavus due to intrinsic foot muscle weakness (high-arched feet)
  • Other findings: Hearing loss and hip dysplasia.
  • Parkinsonism, tremors, pyramidal tract signs (upper motor neurons from cerebral cortex to spinal cord), intellectual disability, optic atrophy also associated with axonal CMTX subtypes
  • Nerve conduction velocity (NCV):
  • Demyelinating CMT = CMT1: Reduced NCV (< 38 m/s)
  • Axonal CMT = CMT2: Normal or slightly reduced NCV (>38 m/s)
  • Onset: First or second decade
32
Q

What can cause CMT?

A
  • > 90 genes implicated
  • 33% of CMT mutations are de novo
  • In more than 90% of individuals with a CMT1 phenotype a pathogenic variant is found in one of three genes (PMP22, MPZ, GJB1)
  • in 70-80% of CMT1 cases the cause is a 1.5 Mb tandem duplication at 17p12 including PMP22
33
Q

What is the testing strategy for CMT1 and HNPP?

A

1) Do MLPA for PMP22 deletion (HNPP) or duplication (70-80% of CMT1)
2) If negative offer Sanger sequencing of PMP22, MPZ and GJB1 (detects >90% of CMT1)
3) If negative: CMT NGS panel available and GJB1 MLPA available if deletion suspected

34
Q

What is the testing strategy for CMT2?

A

Sanger sequencing of MFN2 (CMT2A - 11-22% of CMT2) - not part of core service

35
Q

What are the clinical features of HNPP?

A

Hereditary neuropathy with liability to pressure palsies
• Recurrent sensory and motor pressure neuropathies in single nerve
o E.g. carpal tunnel syndrome,
o E.g. peroneal palsy with foot drop
 Peroneal = branch of sciatic nerve, movement and sensation to lower leg, foot and toes
 Palsy = paralysis – especially accompanied by involuntary tremors
• Muscle weakness
• Atrophy
• Onset: Adolescence/young adulthood

36
Q

What are the clinical features of FAP?

A

Familial adenomatous polyposis, autosomal dominant
100-1000s of polyps in rectum by 2nd decade
Extracolonic features e.g. congenital hypertrophy of retinal pigmented epithelium (CHRPE)
Attenuated FAP: May have <100 polyps and therefore resemble MYH-associated polyposis (but this is autosomal recessive)

37
Q

What are the clinical features of HNPCC?

A

Hereditary non-polyposis colon cancer, autosomal dominant
Familial colon or endometrial cancer (rarely also other malignancies)
Mutations in MSH2 and MLH1 account for over 90% of cases
Approximately 80% lifetime risk of colon cancer (average 61 years) – women: 20-60% lifetime risk of endometrial cancer (average 46-62 years)
Mismatch repair deficiency syndrome (MMR-D): Caused by biallelic mutations in MMR genes (additional findings: early onset haematological malignancy, café-au-lait spots)

38
Q

What are the clinical features of VHL?

A

Von Hippel-Lindau syndrome, autosomal dominant
Variety of malignant and benign neoplasms: Retinal, cerebellar, and spinal haemangioblastoma, renal cell carcinoma, pheochromocytoma, pancreatic tumours

39
Q

What are the clinical features of MEN2?

A

Multiple Endocrine Neoplasia type 2, autosomal dominant
3 subtypes:
Familial medullary thyroid cancer, FMTC: Age of onset in middle age
MEN2A: Increased risk of phaeochromocytoma, parathyroid adenoma/hyperplasia, medullary thyroid cancer in early adulthood
MEN2B: Same features as MEN2A, but onset of thyroid cancer in early childhood. Also other features including: Mucosal neuromas of lips and tongue, distinctive facies with enlarged lips

40
Q

What are the clinical features of BRCA1/2 pathogenic mutations?

A

Breast/ovarian/prostate cancer, autosomal dominant
Early onset breast cancer (<50 years)
Personal or family history - BRCA1 and BRCA2 carrier probability calculation (e.g. BOADICEA or Manchester scoring system)
Overrepresentation of bilateral/multifocal breast cancer, simultaneous breast and ovarian cancer and male breast cancer compared to sporadic cases
Personal history of breast cancer and Ashkenazi Jewish or Polish ethnicity (due to founder mutations)
Triple-negative breast cancer (15%): negative for oestrogen receptors (ER-), progesterone receptors (PR-), and HER2 (HER2-) – does not respond to hormonal therapy, but may respond better to chemotherapy
CA125 blood levels (ovarian cancer)
Prostate specific antigen (PSA) levels (prostate cancer)

41
Q

What are the clinical features of Li-Fraumeni syndrome?

A

Predisposition to wide range of cancers: Sarcomas, breast cancer, brain tumours, adrenocortical carcinoma, acute leukaemia and others
Affects children and young adults
– therefore if see family with breast cancer, but also sarcoma and young age of onset: Both BRCA1/2 testing and TP53 testing may be considered

42
Q

What are the clinical features of Gorlin syndrome (GS)?

A

Autosomal dominant
Naevoid basal cell carcinoma syndrome: Multiple jaw keratocysts, (typically 2nd decade of life), and/or basal cell carcinomas (typically 3rd decade of life)
Characteristic facies including macrocephaly bossing of the forehead, coarse facial features and facial milia
Complete penetrance - approximately 20-30% of cases are sporadic

43
Q

Which referral reasons are there for cancer predisposition variants?

A

Diagnosis: Disorders associated with several genes can be assigned a panel - disorders where only one gene is investigated (e.g. VHL) can be assigned a full gene screen - if mosaicism is suspected then NGS is the better option - genes with deletions or duplications can be assigned MLPA as well

Presymptomatic: Test familial vairant only (sequencing/MLPA)

Indirect testing: At risk individuals, where no familial variant has been detected -test as would diagnostically

Confirmation: Affected individuals with confirmed diagnosis in family member

Family studies: To strengthen the interpretation of VUS

Tumour studies: To strengthen the interpretation of a germline VUS (LOH points to pathogenicity) - or to detect variant, where no germline variant has been found

Prenatal testing: Available where there is early/childhood onset (e.g. VHL)

44
Q

What is the testing strategy for HNPCC?

A

Immunohistochemistry (ICH) and microsatellite instability (MSI) are cheap and quick ways of pre-screening patients to select only cases with loss of MMR protein function for genetic testing

ICH: staining for MMR proteins: 2nd hit in tumour DNA resulting in loss of protein can be seen -loss of MLH1 may appear as loss of both MLH1 and PMS2; loss of MSH2 may appear as loss of both MSH2 and MSH6 - missense mutations leading to normal expression of protein, but loss of function
may result in false negative IHC

MSI: Detects loss of the function of the MMR proteins - contraction and/or expansion of repeat motifs occur in tumour DNA where a 2 hit has occurred - seen as hedgehog peaks appearing as 2 hedgehogs - Low instability (1/5 markers) has been linked with high risk of endometrial cancer
and MSH6 mutations – IHC analysis can be offered

Loss of MLH1 or MSH2 activity can be further investigated for presence of p.Val600Glu in BRAF and/or MLH1 hypermethylation studies, which indicate the tumour is likely sporadic

If not likely sporadic the patient is then tested for a germline mutation by sequencing of the MMR genes

45
Q

What is the testing strategy for Huntington disease?

A

Diagnostic: Do Flanking PCR (HD1/3 primers) - can size repeat (if not too big)
If 2 alleles in normal range (except 16/17, 17/18, 18/19): Report
If expansion allele seen or only 1 allele seen: Do TP-PCR or flanking PCR with HU3/4 primers (includes CG-rich adjacent repeat) - these techniques cannot size the repeat

Presymptomatic: Set up both flanking and TP-PCR at same time to meet TAT

Prenatal: Do direct testing (parental status revealed) or indirect linkage studies (parental status not revealed)

46
Q

What are the clinical features of myotonic dystrophy?

A
  • Muscle weakness (affects skeletal and smooth muscle), especially of distal leg, hand, neck and face
  • Myotonia (sustained muscle contraction, difficulty releasing grip)
  • Cataracts
  • Frontal balding
  • Hypogonadism
  • Diabetes
  • Cardiac involvement (including arrhythmia)
  • Serum CK concentration may be mildly elevated (indicating muscle damage)
  • Anticipation: Increasing disease severity or earlier age of onset observed in successive generations

Mild: Normal lifespan, maybe just cataracts or mild myotonia - Often not recognised until more severely affected individuals in subsequent generations are diagnosed

Classic/adult: All symptoms can be present, shortened lifespan and physical disability

Congenital: Hypotonia and severe general weakness at birth, respiratory insufficiency, Facial diplegia (paralysis of symmetrical parts of body, typical tent-shaped lip), Intellectual disability, Early death (25% within 18 months of age), Usually maternally inherited

47
Q

What is the testing strategy for myotonic dystrophy?

A

Diagnostic: Do flanking PCR - can size repeat (if not too big)
If 2 alleles in normal range: Report
If expansion allele or only 1 allele detected: Do TP-PCR Antisense and sense (interruptions in the repeat can flatten out peaks and give false negative result) - cannot size repeat
If sizing of larger allele required: Do Southern blot, but can only estimate (+/-100)

48
Q

Repeat size categories for Huntington disease?

What is the repeat, and where in the gene is it located?

A

Normal: 6-26 stable, no phenotype
Intermediate: 27-35, may be unstable, no phenotype
Incomplete penetrance: 36-39, unstable
Full mutation: 40+, unstable, affected

CAG in exon 1 of HTT gene - translated into polyGln tract

49
Q

Repeat size categories for myotonic dystrophy?

What is the repeat, and where in the gene is it located?

A

Normal: 5-34, stable, no phenotype
Premutation: 35-49, may be unstable, no phenotype
Mild/carrier: 50-100, unstable, no or mild phenotype
Adult: 100-700, unstable, classical adult onset
Congenital: 700-4000, unstable, Congenital or juvenile onset

CTG in 3’UTR of DMPK

50
Q

Repeat size categories for fragile X syndrome?

What is the repeat, and where in the gene is it located?

A

Normal: - 45, stable, no phenotype
Intermediate: 46-58, unstable, no phenotype
Premutation: 59-200, unmethylated, unstable, risk of FXTAS (mostly makes) and females: FXPOI, offspring with FRX
Full: 200, methylated, unstable, FRX in males and 50% of females, males only have premutation in sperm

CGG in 5’UTR of FMR1 gene

51
Q

What are the characteristics of of a t(8;21) in AML?

A

t(8;21) RUNX1-RUNX1T1 fusion (RQ-PCR), usually younger patients, >70% show additional abnormalities (-X, - Y, del9q), good prognosis, 20-25% show KIT mutations

52
Q

What are the characteristics of of a inv(16) in AML?

A

inv(16) incl. centromer, CBFB-MYH11 fusion (RQ-PCR), consider FISH (subtle), additional abnormalities include +22, usually only with inv(16), good prognosis, 30% have KIT mutations

53
Q

What are the characteristics of of a t(15;17) in AML?

A

t(15;17), PML-RARA fusion (RQ-PCR), APML, risk of blood clotting, very urgent, good prognosis due to ATRA, additional abnormalities in 40%, +8,

54
Q

What are the characteristics of of a t(9;11) in AML?

A

t(9;11), MLLT3-KMT2A, break-apart FISH probe, many fusion partners for KMT2A, intermediate prognosis in adult and paediatric (in adult depends on KMT2A partner)

55
Q

What are the characteristics of of a inv(3) in AML?

A

inv(3), RPN1-EVI1break-apart FISH probe, EVI1 breakage involved in many 3q abnormalities, poor prognosis for any EVI1 rearrangement

56
Q

What are the characteristics of of a t(12;21) in AML?

A

t(12;21) ETV6-RUNX1, RUNX1 FISH probe detects t(12;21), iAMP21 and hyperdiploidy,

57
Q

Favourable prognosis karyotypes in ALL?

A

High hyperdiploidy

t(12;21) ETV6-RUNX1

58
Q

Intermediate prognosis karyotypes in ALL?

A

Normal karyotype

t(1;19) TCF3-PBX1

59
Q

Poor prognosis karyotypes in ALL (examples)?

A
Low hypodiploidy
Near haploidy
t(9;22) BCR-ABL1 fusion
KMT2A rearrangements esp. t(4;11) fusion
iAMP21
t(17;19) TCF3 break-apart 
IGH rearrangements
60
Q

Presentation of ?ALL - what do you do?

A

Direct culture (ALL cells apoptose)
FISH:
BRC-ABL1 (poor prognosis)
KMT2A (chromosome 11 - esp. t(4;11) poor prognosis)
ETV6-RUNX1 (t(12;21), good prognosis - also detects iAMP (poor prognosis) and hyperdiploidy (good prognosis))

G-banding

61
Q

Presentation of ?AML - what do you do?

A

G-banding - consider FISH if unsure of inv(16) (+22 or immunology type (M2/M4) may indicate inv(16))

If ?APML then direct FISH for PML-RARA (t(15;17))

RNA for gene fusion monitoring (base-line), (RUNX1-RUNX1T1, CBFB-MYH11, PML-RARA)
RNA for FLT3 and NPM1 mutations

DNA for myeloid panel and AID13 studies depending on FLT3-itd ratio (>0.25)

DNA: If CBF (RUNX1-RUNX1T1 and CBFB-MYH11) then test for KIT mutations.