Diagnostics Flashcards
Why do we do tests?
- Confirming the diagnosis
- Shot in the dark- allows the diagnosis to be narrowed down
- Assessing stages of severity
- Medico-legal reasons (paternity test)
What are the downsides of tests?
- Costs
- Inaccuracies
- Invasiveness of some tests and anxiety
Describe a diagnostic pathway
- Demographics
- Symptoms
- Physical examination
Simple bedside tests - Diagnostic test- surrogate biomarker which substitutes for clinical endpoint
- Real disease
- Many diagnoses are made through screening rather than patient presentation
Describe the ideal test
- Identifies every case of disease (100% sensitive)
- Does not predict anyone from the healthy group as sick (100% specific)
- Non-invasive
- Cheap
- Instant
- Easy to interpret data- presence of marker being actual marker
Describe how to develop a test- looking for a biomarker
- Comparing an equal number of healthy/diseased individuals
- If threshold too low, many people could be falsely classified
- Gold standard vs new test
- Validation with gold standard- e.g. confirmation through biopsy
- How often does the test match the biopsy
What is sensitivity?
Proportion of true positives that are correctly identified
What is specificity?
Proportion of true negatives that are correctly identified
What is a type 1 error?
- False positive
What is a type 2 error?
- False negative
What is the equation for sensitivity?
True positive/ (true pos + false neg)
What is the equation for specificity?
True negative/ (true neg + false pos)
What is the positive predictive value?
Proportion of patients with a positive test who are correctly diagnosed
What is the negative predictive value?
Proportion of patients with a negative who are correctly diagnosed
What is the equation for PPV?
True pos/ (true pos + false pos)
What is the equation for NPV?
True neg/ (true neg + false neg)
Which description should be used to determine the usefulness of the diagnostic test in a clinical setting and why?
- PPV
- Information gathered from population studies rather than case control studies
How is the choice of test determined?
- By the physical properties of the biomarker
What are the genetic categories of diagnostic tests?
- Cytogenetic
- Sequence dependent
What are the types of tests in cytogenetic diagnostics?
- Fluorescence In Situ Hybridisation (FISH)
- Chromosome Microarray Analysis
- Amniocentesis/ Chorionic villous sampling
- These help identify chromosome abnormalities
Describe fluorescence in situ hybridisation
- Sequenves specific to each chromosome pair labelled with specific dye colour
- Chromosomes and DNA heat treated and cooled together
- Complementary strands hybridised and become fluorescent
- Chromosomes imaged using fluorescent microscope
- Able to identify single genes on chromosomes
What are the types of tests in sequence dependent diagnostics?
- Polymerase Chain Reaction
- Clinical uses of PCR
- Whole genome sequencing
Describe the polymerase chain reaction
- Amplifies specific desired regions of genome in an exponential manner
- Requires DNA, primers, oligonucleotides and DNA polymerase
- Primers complementary base pair to specific area of gene sequence
- Sequential heating and annealing followed by DNA replication- polymerase
- Increases amount of material to be sequenced
What are clinical uses of PCR?
- Pathogen detection- viruses, bacteria and fungi- if viruses, some are RNA
- Oncology- mutations associated with transformation of cell can predict response to anti-tumour drugs (KRAS confers resistance to anti-EGS-R therapy)
- Mutation analysis, e.g. cystic fibrosis transmembrane conductance regulator CTFR (pre-implantation)
- HLA typing for organ/tissue donors
Describe whole genome sequencing
- Determines the entire DNA sequence in one go
- Being introduced clinically
- Personalised medicine- vital for guiding therapeutic intervention)
- Splicing variation
- Copy number variation
- Single nucleotide variation
