Case 16: genetics 2 Flashcards
1
Q
Application of NIPT
A
- Aneuploidy testing based on DNA molecule counting (abnormal number of chromosomes)
- Technique: single molecule DNA counting
- Analyse and sequence all foetal DNA. Analyse ratio of DNA to chromosomes to assess disease status
- Then confirm positive result with CVS/amniocentesis
- Can look at alleles and see ratio of those that contain a mutation to those that don’t to assess for recessive conditions (Homozygous or Heterozygous)
2
Q
NIPD/T limitations
A
- Maternal factors: Some women have very low foetal DNA fractions (due to women’s weight or foetal age). Lab techniques may not pick it up. Underlying chromosomal abnormality or tumour may affect results
- Pregnancy factors: Twin pregnancies (especially for NIPT), Resolving second gestational sac, Placental mosaicism (the foetal blood is mostly from the placenta)
3
Q
Testing for cord blood
A
only done if implications for management. Otherwise wait till they consent at 18
4
Q
Overview of indications for NIPD/T
A
- NIPD: determining foetal sex, testing for a specific mutation in a single gene disorder
- Aneuploidy testing
5
Q
Presentations of gene abnormality resul example:
- CFTR c.1521_1523delCTT p.F508del
Heterozygous
A
- CFTR gene- causative gene in Cystic Fibrosis
- Specific change in DNA coding sequence- CTT deleted between position 1521 & 1523
- Effect of DNA change on the protein produced (p.F508del) Phenylalanine missing at position 508 of the amino acid sequence
- Heterozygous: Present on one allele (one copy of the CFTR gene)
6
Q
Autosomal inheritance
A
- The mutation is present on both copies of the gene in order for the disease to develop
- Has to be on chromosomes 1-22 (the autosomes)
7
Q
Definitions: Heterozygous, Compound Heterozygous and Homozygous
A
- Heterozygous: Variant present on one allele, the other is normal. In autosomal recessive condition this means they are a carrier
- Compound Heterozygous: Both alleles contain a different variant, two different mutations present. No functioning copy of the gene so is affected by the recessive condition
- Homozygous: both alleles contain the same variant. Means the individual is affected by the recessive condition
8
Q
Cystic fibrosis pathophysiology
A
- CFTR gene codes for the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein, a cell membrane chloride transporter
- The gene is on chromosome 7
- Most common mutation: Delta F508
- Insufficient functioning CFTR protein for normal chloride transport, resulting in the production of thick sticky mucus production
- Multi-system disorder (lungs, intestines, pancreatic ducts, sweat glands, and reproductive organs).
9
Q
Cystic fibrosis inheritance
A
- Autosomal recessive inheritance
- Two functioning copies of the CFTR gene: Non carrier, not affected
- Mutation present on one copy of the CFTR gene: carrier not affected
- Mutation present on both copies of the CFTR: affected by CF
- Carrier frequency of CF: 1 in 25
10
Q
Risk of a child being affected by CF if one parent is a known carrier
A
- 1 in 100
- known carrier: probability of being a carrier is 1
- partner: probability of being a carrier is 1 in 25 (population risk)
- 1 in 4 chance of both passing on the mutation
- therefore overall risk of pregnancy being affected is 1 x 1/25 x 1/4 = 1/100
11
Q
Genetic testing: CF
A
- Partners of carriers are offered testing for the 50 most common CFTR mutation (account for 90% of mutations in Northern Europe)
- If no mutation is identifies it reduces risk of being a carrier from 1 in 25 to 1 in 250 (still some chance)
- Different mutations in different ethnic groups
12
Q
CF: Diagnosis
A
- Through newborn blood spot screening programme: measure trypsinogen (IRT) in blood samples. Refereed for further testing
- Sweat chloride test: gold standard, diagnosed if >60 (30-60 require further investigations)
- Genetic tests: not all mutations are detectable
- If clinical features are highly suggestable and investigations are negative then can still be diagnosed. If investigations positive but no symptoms then still diagnose
- After diagnoses refer to a cystic fibrosis centre
13
Q
CF: Monitoring
A
- Regular sputum cultures
- Pulmonary function tests (PFT): Spirometry and lung volume measurements
- CXR and CT: evaluate lung disease severity, identify complications like bronchiectasis
- Oral glucose tolerance test: screen for cystic fibrosis related complications
- DEXA
14
Q
CF presentation: age
A
- Infant: Meconium ileus
- Older child: chronic cough, recurrent wheezing, chronic respiratory infections, Malabsorption, failure to thrive
- Adult: cystic fibrosis related diabetes, infertility (absence of vas deferens (CBAVD), irregular menstrual cycle)
15
Q
CF: respiratory
A
- Persistent cough:Productive or non-productive, often exacerbated by mucus accumulation and infections.
- Wheezing and dyspnea:Resulting from airway obstruction and bronchospasm.
- Recurrent respiratory infections: pathogens such asStaphylococcus aureus,Haemophilus influenzae, andPseudomonas aeruginosa.
- Nasal polyps and chronic sinusitis
16
Q
CF: GI
A
- Meconium ileus:Neonates with CF may present with intestinal obstruction due to thickened meconium.
- Pancreatic insufficiency:Steatorrhea, weight loss, and malabsorption of fat-soluble vitamins due to pancreatic duct obstruction.
- Distal intestinal obstruction syndrome (DIOS):Partial or complete intestinal obstruction due to inspissated faecal material.
- Biliary cirrhosis:Impaired bile flow leading to liver damage, portal hypertension, and potential liver failure.
- Gastroesophageal reflux disease (GERD)
17
Q
CF: other clinical features
A
- Cystic fibrosis-related diabetes (CFRD):Insulin deficiency and impaired glucose tolerance caused by progressive pancreatic damage.
- Growth failure:Delayed growth and pubertal development due to malabsorption, chronic inflammation, and increased energy expenditure.
- Male infertility:Congenital bilateral absence of the vas deferens (CBAVD)
- Female fertility: irregular menstrual cycles, and decreased fertility
- Clubbing:Chronic hypoxia may lead to digital clubbing, a sign of advanced lung disease.
- Salt loss syndrome:Excessive sodium chloride loss in sweat can lead to hyponatraemic dehydration and metabolic alkalosis, particularly in infants.
- Bone disease:osteoporosis due to malabsorption of calcium and vitamin D
18
Q
CF management: conservative
A
- Chest physiotherapy:Techniques such as active cycle of breathing, autogenic drainage, and positive expiratory pressure devices help mobilize and clear mucus from the airways.
- High-frequency chest wall oscillation:Devices like the Vest® Airway Clearance System use rapid oscillations to loosen and clear mucus from the airways.
- Exercise
- Patients with CF should try tominimise contact with each otherto prevent cross infection withBurkholderia cepaciacomplex andPseudomonas aeruginosa
19
Q
CF: Medical management
A
- Mucolytics:dornase alfa and hypertonic saline reduce mucus viscosity
- Bronchodilators: Salbutamol and anticholinergics
- Anti-inflammatories:Beclomethasone Inh and Ibuprofen (NSAIDs) po help improve lung function.
- Antibiotics:Regular use of inhaled antibiotics (e.g., tobramycin, aztreonam) helps manage chronic infections, particularly Pseudomonas aeruginosa.
- CFTR modulators:ivacaftor, lumacaftor, and elexacaftor target specific CFTR mutations, improving protein function and clinical outcomes. Selection depends on the patient’s specific CFTR genotype.
20
Q
CF: surgery and CF modulators
A
- Lumacaftor/Ivacaftor (Orkambi): in CF who are homozygous for delta F508
- Lung transplant: in advanced lung disease. chronic infection withBurkholderia cepacia is a contraindication
21
Q
CF nutritional support
A
- Pancreatic enzyme replacement therapy (PERT):given with meals to assist digestion and absorption of nutrients.
- Fat-soluble vitamin supplementation:vitamins A, D, E, and K
- High-energy diet
22
Q
CF prognosis and complications
A
- Reduced life expectancy: early 40’s
- Dependence on presence of complications like cystic fibrosis related diabetes (CFRD) and liver disease
- Liver disease:Bile duct obstruction can progress to cirrhosis, portal hypertension, and hepatic encephalopathy, requiring liver transplantation in severe cases.
- Respiratory failure: may require supplemental oxygen or lung transplantation.
- Nephrolithiasis:Dehydration, alkaline urine, and hyperoxaluria increase the risk of kidney stones, which may require medical or surgical management.
23
Q
Tay Sachs disease
A
- HEXA gene encodes part of the beta-hexosaminidase A enzyme which plays a key role in the breakdown of toxic products in the brain and spinal cord.
- Autosomal recessive condition
- Severe neurodegenerative condition
24
Q
Consanguinity
A
- A consanguineous relationship is one between individuals who are second cousins or closer i.e. when two first cousins marry
- Important to ask- increased risk of recessive disorders. On a family tree is denoted with a double horizontal line between husband and wife (=)
- Doubles the risk of serious congenital and genetic disorders for children of first cousins
- More common in parts of the Middle East, South Asia, certain religious communities and amongst Irish travellers
25
Q
Carrier testing for CF and other autosomal recessive conditions: Familial risk
A
- Initially offered to first degree relatives
- Checks if they are a carrier
- Main indication is to find out the chance of having an affected child
- Specifically test for the mutation identified in the family
- For children testing should be deferred until old enough to consent
26
Q
Pharmacogenetics
A
explores the ways in which the persons genome contributes to a persons response to drugs
27
Q
What does Pharmacogenetics affect
A
- Pharmacokinetics: influences what the body does to the drug
- Pharmacodynamics: what the drug does to the body
28
Q
When is it indicated to use Pharmacogenetics in medicine
A
- Drugs with a narrow therapeutic index and a serious adverse drug reaction i.e. chemotherapy
- Genes can encode for liver enzymes which metabolise the drug, if there is a mutation this can cause the enzyme to be inactive
- The P450 (CYP) liver enzyme encodes for genes which metabolise warfarin, Clopidogrel, antidepressants and analgesics
- The plasma concentration of the drug varies signicantly depending on the activity of the enzymes
29
Q
The 5 drug gene pairs in which testing occurs relatively routinely
A
- azathioprine:TPMTandNUDT15;
- abacavir:HLA-B;
- fluoropyrimidines:DPYD;
- carbamazepine:HLA-AandHLA-B; and
- aminoglycoside antibiotics:MT-RNR1.
30
Q
Variants in which genes can affect warfarin sensitivity
A
- CYP2C9: codes for an enzyme primarily responsible for warfarin metabolism
- VKOR1: codes for the warfarin drug target
- Variants cause warfarin dosing issues/longer time to stabilise INR and increased risk of life threatening bleeding events
31
Q
DPYP gene
A
- Tested prior to prescribing fluorouracil based chemo
- Inherited variants in DPYD can result in deficiency of the enzyme encoded by this gene which can result in severe toxicity to drugs like 5-fluorouracil
32
Q
Direct to consumer genetic testing
A
- Tests are marketed via a range of web- and print-based media, including social media platforms; they can even be bought over-the-counter
- DNA sample are typically collected using saliva kits and sent directly to the testing laboratory by the consumer
- Results are uploaded to a secure website or provided in a written report format.
- Dont need to speak to doctor/clinician
- Can have access to raw data allowing other people to reanalyse the data to include other disorders/trait
33
Q
What can direct to consumer genetic testing offer
A
- Disease risk prediction
- Carrier status: for common autosomal conditions i.e. cystic fibrosis
- Mendelian disease i.e. BRCA.
- Lifestyle testing
- Ancestry
- Privacy: data stored safely
- Reanalysis
34
Q
What do direct to consumer genetic tests offer: disease risk prediction
A
- Risk of developing a number of common condition:
- Dementia / Alzheimer’s disease, IBD, T2D, Coeliac disease, Autoimmune disease, Parkinson’s disease
- Looks at genes which are present with individuals who have these which may not be relevant to that patient. Based in control of people who bought the test which causes a bias as it doesn’t represent the whole population
- Many of the diseases are multifactorial i.e. diet, smoking and family history which are not considered in direct to consumer genetic tests
35
Q
Direct to consumer genetic tests: carrier status
A
- Doesn’t report on all autosomal recessive conditions
- Doesn’t look for all pathogenic variations (only a small number of mutations)
36
Q
Direct to consumer genetic tests: Mendelian disease
A
- Normally only done after the patient has undergone genetic counselling
- Variations may be ethnic specific and when excluded have no clinical significance
- Only look at a few mutations
37
Q
Direct consumer genetic tests: Lifestyle testing
A
- Fitness and exercise capacity
- Nutrition, metabolism and weight
- Sleep preferences
- Skin care
- Taste i.e. wine
- The link between genomic variation and trait may be indirect or even unknown
38
Q
Direct to consumer genetic tests: Ancestry
A
- Compares your data to standards across the world so based on current population distribution rather than bone/teeth samples
- These traits are based on conjecture and observation- other people filling in questionnaires and comparing their genes
39
Q
Direct to consumer genetic tests: privacy
A
- What does the company do with the consumer’s DNA sample once the analysis is complete? Will it be stored, shared, sold, or destroyed?
- Who owns the consumer’s genetic data? Is it the company? Do have a right to decide how the data are used?
- Can the consumer delete their data?
- What are the company’s data security measures? How are the data stored? Can the data be accessed for unauthorised use?
40
Q
Direct to consumer genetic tests: Reanalysis
A
- When you download the raw data and ask a third party to look at it
- The original DNA analysis often includes false positive findings, which are carried through to re-analysis.
- 40% of reported findings were not confirmed in a clinical laboratory.
- Once the consumer has downloaded their raw data file, it is no longer protected by the original service’s privacy policy.
- Third-party re-interpretation services are usually unregulated.
41
Q
Pro’s and cons of direct to consumer genetic tests
A
- Pro’s: sample collection is easy, doesn’t require blood. Broad selection of tests, Quick results. Can use data in research and product development
- Cons: expensive, risk of false positives and negatives. Results can give false reassurance. Little evidence with some traits. Largely unregulated and privacy might not be guaranteed
