Molecular diagnostics in Medicine Flashcards
Types of genetic tests (hint: screening to diagnose and predict prognosis)
“screening to diagnose and predict prognosis”
Screening Test
Diagnostic test (e.g. CF)
Predictive test (e.g. BRCA/cancer)
Prognostic test (cancers)
Test characteristics (2 categories)
APSS (technical)
Accuracy
Precision
Sensitivity
Specificity
(clinical/patient related)
Clinical Validity
Clinical Utility
Personal Utility
Clinical validity
Accuracy of disease prediction/how well test predicts disease
Clinical utility
Usefulness of test results treatment/patient management
Personal utility
Effect of test results on patient (patient’s life basically)
Categories of etiologies
Point mutations
Copy number changes
Repeat expansions
Epigenetic changes
Point mutation types
Frameshift
Missense (conservative vs nonconservative)
Nonsense
Silent
Conservative vs Nonconservative missense mutations
Conservative - results in AA change; new AA resembles WT AA in function (so no functional difference)
Non-conservative - results in AA change; new AA functionally different from WT AA (gain or loss of function)
Types of Copy number changes
Aneuploidy; Translocation
Microdeletion/duplication (e.g. CF = loss of 1 bp)
Gene gain/loss
Exon gain/loss
Repeat expansion types and locations
Trinucleotide expansion (CGG) or Dinucleotide
Located within gene, promoter or intron
Epigenetic changes
Methylation of CpG islands
Molecular diagnostic techniques
“RFLP e sequence”
“Microsatellites methylate ASO’s”
RFLP
Sequencing
Microsatellite analysis
Methylation testing (via Southern)
Allele-specific oligonucleotide
RFLPing the sequence!!
Microsatellites methyl8 ASO’s!!
Point mutation genetic test used
RFLP (SNP type)
Sequencing
Test for repeat expansions
Microsatellite analysis
Test for methylation
Southern Blot
Test for copy number changes
Microarray
Multiplex ligation-dependent probe amplification
Multiplex ligation dependent amplification
Essentially, PCR with 2 primers >>
each w/ probe on one end>>
If mutated sequence = amplification but wrong size
If no mutation = amplification + right size
Next generation sequencing types
Targeted gene panels
Exome sequencing (highest coverage) [coding regions only]
(Whole) Genome sequencing
3 false negative scenarios
Sequence interpretation
Down Syndrome etiologies
Tests for DS
Test to order for DS
Fragile X Syndrome etiology
Tests for Fragile X Syndrome
Which test would you order for Fragile X?
Trinucleotide repeat analysis
Intepret the Southern Blot below of Fragile X patients. Give reasons for each intepretation.
Prader Willi Syndrome etiologies
PWS testing
Why would you choose methylation testing for PWS and not any of the other tests?
MLPA and FISH will only detect gain/loss of genetic info
Microarray won’t detect UPD
UPD analysis won’t detect deletion
How do you interpret results of PWS detection using UPD analysis?
Look at peak size
Look at genes present (from both parents) in proband
How do you interpret the results of PWS detection by Microarray?
As with any other microarray (discussed in this lecture), compare the patient’s genetic profile to that of the control
Summary of disease examples
