Genomics for Diagnosis and Disease Monitoring Flashcards
How are rare diseases caused by germline variants
- Variants are present in the gamete
- Variation presents in every cell of the body, including those of the germline
- Variants can be passed on to the offspring
How is cancer caused by somatic variants
- The variant would be absent in the gamete
- Variation can occur during foetal development or anytime after birth in any cell of the body, except those of the germline
- Variants are not passed onto the offspring
How does NGS DNA sequencing work
1) Genomic DNA is fragmented and baited with barcodes
2) It is then enriched with gDNA for regions containing target sequence
3) This is followed by parallel sequencing and bioinformatics
What are Gene Panels
- Simultaneous analysis of 50-1000 genes
- Can be applied to germline of somatic genomes
- Useful when selection of a single candidate gene is difficult
- Multiple genetic changes may be present
- Cost effective
What is whole genome sequencing
- Covers coding region of most genes as well as introns, untranslated regions, regulatory regions
- Applied somatic and germline samples
- Rapid and inexpensive
- Detects single nucletoide variants insertions/deletions, many copy number variants
What are the benefits of WGS in haematological malignancy
1) Comprehensive somatic genotping for diagnostic variants
- custom gene panels
- Reanalysis of stored data if new genes are discovered
2) Overview of total variant burden of disease
3) Added value
- Tissue typing/blood group
- Detection of inherited susceptibility
- Pharmacogenomic safety
- Detection of other diseases/risk factors
What is Haemophilia A
Protein defect - coagulation factor VIII deficiency
Gene: F8 - Xq28
What is Haemophilia B
Protein defect - Coagulation factor IX deficiency
Gene: F9 (Xq27.1)
What are haemophilia bleeding symptoms
- Thigh/calf bleeds
- Deltoid/forearm bleeding and bruising
- Buttock bleeding
- Neck swelling: EMERGENCY (potential airway compromise)
- Soft tissue bleeds and bruising
What are the haemophilia phenotype-genotype relationship
- Severe haemophilia
- Causal variant: Insertion/deletion
Stop gain/loss
Splice
Some missense - Moderate haemophilia
- Causal variant:
Missense - Mild Haemophilia
- Causal Variant
Missense
What are the other phenotypes of haemophilia
- Chronic synovitis
- Haemophilic Arthropathy
- Treatment acquired by HIV
- Treatment acquired HCV
How has genetic testing helped
- Confirmation of diagnosis
- Diagnostic test for other family members
- Option for ante-natal diagnosis (pre-implantation, first or third trimester)
- Improved accuracy of prognostic estimates
- Management of delivery
- Future bleeding phenotype
- Complications of therapy (inhibitor risk)
What is Chronic Myeloid Leukaemia
- Clonal proliferation of late myeloid cells
- Increased circulating white cell count
- Splenic Enlargement
What is an effective therapy for CML
Imatinib is a synthetic specific inhibitor of the Bcr-Abl fusion protein
How does acquired resistance to TK inhibitors arise
- Somatic single nucleotide variants in the Abl are frequent
- Those that are missense and confer imatinib resistance undergo positive selection
- New Abl inhibitors are less vulnerable to acquired resistance:
- Ponatinib
- Dasatinib
- Nilotinib
- Bosutinib
How has genetic testing helped with CML
1) there is a confirmation of diagnosis in CML
2) Informing choice of first line treatment
3) Monitoring of disease activity
4) Selection of personalised therapy for relapsed disease
