Genetic Tests And Technologies Flashcards
Types of genetic tests: Clinical genetics
•Diagnostic
•Carrier
•Predictive
•Prenatal tests incl. NIPT
Types of genetic tests: Clarify familial relationships
Paternity testing
Types of genetic tests: Determine identity
Genetic finger printing
What are the roles of genetic testing?
•To confirm a clinical diagnosis
•To give information about prognosis
•To inform management
•Allow pre-symptomatic/predictive testing in close relatives
•Carrier testing
•To give accurate recurrence risks
•Prenatal diagnosis
Genetic testing in the clinic
•What is the condition?
•Can a diagnosis be made clinically?
•Is the genetic cause(s) known?
•Is a genetic test available?
•service versus research tests
•not all genes are known!
•What type of test
•diagnostic, carrier or predictive
•Is consent full & informed
•who else does the result affect?
•testing children & adults with learning difficulties
•Any other implications? - employment, insurance etc.
What is Sanger sequencing?
•Developed by Frederick Sanger
in 1977
•Uses PCR to amplify regions of interest followed by sequencing of products
•Useful for single gene testing
What is next generation sequencing?
•High throughput or massively parallel sequencing
•Can sequence whole human genome in one day
•Multi-gene panels, whole exome/genomes
What are features of Sanger sequencing?
•Single start point (primer)
•Single DNA fragment sequenced
•High cost per gene
•Time consuming
•Simple analysis (read the sequence)
•Very accurate
•The gold standard
What are features of next generation sequencing?
•Library of DNA fragments
•Massively parallel sequencing
•Low cost per gene
•Fast
•Huge amounts of raw data to interpret
•Moderately accurate
What is NGS Data analysis?
•NGS generates millions of short DNA fragments (reads) the need to be filtered for quality and aligned to a reference sequence.
•Reference genome
•Identify variants
•Interpret variants
•Insilico tools (bioinformatics)
How to interpret variants?
•Has the variant been previously reported?
•- in the literature
•- present on variant or reference databases
•Type of mutation – nonsense, frame shift, splice site, missense etc
What to do when interpreting unclassified variants?
•Type of mutation
•Population Frequency
•Literature search
•Evolutionary conservation – domain context
•Severity of amino acid substitution
•Splice site prediction
•Functional studies – protein and/or mRNA analysis
•Genotype-phenotype correlation – importance of clinical assessment
•Family studies - analysis of affected and unaffected individuals
•De-novo variant
Databases of disease mutations
•Drawn from literature collected over decades with variable standards
•Up until relatively recently there were no large reference databases. This meant many variants misinterpreted as pathogenic/causative.
•New databases more careful about evidence
What are incidental/secondary findings?
Additional findings concerning a patient or research participant that may, or may not, have potential health implications and clinical significance, that are discovered during the course of a clinical or research investigation, but are beyond the aims of the original test or investigation
What are examples of incidental/secondary findings?
•Non-paternity on examination of a family trio
•Variant known to confer high risk of adult-onset disease
•Variants of uncertain clinical significance, possibly requiring further investigation
•Need to consider whether and when to disclose
•Importance of full and informed consent prior to test
•Use of clinical judgement
