Companion Diagnostics Flashcards
What is companion diagnostics?
Devices that provide information that helps determine if a particular drug is likely to benefit a patient.
What are the benefits of CDx?
Can gain information to:
Identify patients who will benefit from the therapy and for early diagnosis.
Identify patients who will have increased adverse effects due to a therapy (Patient risk stratification).
Monitor responses to treatment to improve disease management.
What is fluorescence in situ hybridisation (FISH)?
A powerful technique used in the detection of chromosomal abnormalities.
Detects chromosome deletions / rearrangements
What is polymerase chain reaction (PCR)?
Allows identification of pathogenic organisms that are difficult to culture by detecting their DNA or RNA.
Detection of the presence of genes, or large mutations.
Gel electrophoresis separates DNA fragments based on their size.
How does Sanger sequencing work?
Sanger sequencing results in the formation of extension products of various lengths terminated with dideoxynucleotides at the 3′ end.
The extension products are then separated by Capillary Electrophoresis or CE.
The molecules are injected by an electrical current into a long glass capillary filled with a gel polymer.
What is NGS (next generation sequencing)?
Any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing.
What is immunohistochemistry (IHC)?
The most common application of immunostaining.
Detection of proteins e.g. receptors, HLA, enzymes.
What is enzyme-linked immunoabsorbant assay (ELISA)?
A biochemical technique used mainly in immunology to detect the presence of an antibody or an antigen in a sample.
Darker colour = higher amount of protein.
What is Maraviroc?
Treatment for HIV-1.
HIV envelope protein binds to receptor (CD4) and co-receptor.
R5-tropic HIV uses CCR5.
X4-tropic HIV uses CXCR4.
Maraviroc inhibits CCR5 binding.
Explain CDx for HIV-1 tropism:
PCR to select and amplify HIV envelope sequences from patient sample.
Generate a library of all the envelope sequences present in the patient.
Use this library in phenotypic or genotypic assay for HIV-1 tropism.
Phenotypic assay:
Preferred test in clinical practice.
Clear result of tropism.
Requires ~2 weeks to perform and is more expensive.
Genotypic assay:
Alternative test to predict HIV-1 tropism based on presence of certain mutations.
Explain phenotypic assay for HIV-1 tropism:
Patient envelope sequences used to generate HIV-1 particles that express luciferase reporter gene.
HIV-1 particles used to infect cells expressing either CCR5 or CXCR4.
Only cells that get infected with the virus express luciferase, measured as luminescence.
Explain genotypic assay for HIV-1 tropism:
PCR to select and amplify V3 loop of HIV envelope sequences from patient sample.
Sequencing to determine the V3 loop sequence, analysed by bioinformaticians to infer co-receptor usage.
What is the treatment of drug-resistant TB?
First line treatment for TB:
2 antibiotics (isoniazid and rifampicin) for 6 months. 2 additional antibiotics (pyrazinamide and ethambutol) for the first 2 months of the 6-month treatment period.
Resistance to isoniazid and rifampicin = multidrug-resistant TB (MDR-TB).
MDR-TB patients are treated with fluoroquinolones and injectable second-line drugs.
CDx tests to predict patient’s response to treatments is required.
How does drug susceptibility testing work?
Bacteria is grown in the presence of antibiotics.
High accuracy.
Bacteria is slow-growing so can take 4-6 weeks to get a conclusive result.
Agar culture plates show resistance to drugs tested.
What are line probe assays?
Newer methods detect presence of mutations that are known to confer resistance.
