Lecture 5 Flashcards
what is the best diagnostic approach in regards to testing an affected persons close relatives?
test the affected family members first - if we detect a genetic variation, possibly associated with a clinical phenotype, then we can perform the familiar segregation in other familiar cases
if the aunt of the proband turns out to be positive for a variant, who would we test next?
the probands father
if the aunt and father have the mutation, is it wise to test all the other related aunts and uncles?
yes - they have a chance to have the same mutation of the affected family member
why is Sanger sequencing considered to be the gold standard?
it is characterized by a very high accuracy
what are some downsides to Sanger sequencing?
it is very high cost and can take a long time
what is the main causative gene in Brugada Syndrome?
SCN5A
what does the SCN5A gene code for?
encodes for the sodium gated channels expressed in the cardiac muscle - responsible for the action potential during the electrical activity of the heart
If genetic testing does not confirm the clinical diagnosis, what occurs?
the clinical diagnosis still remains the same
what is LQT?
a disease characterized by an abnormally long QT interval in an electrocardiogram
LQT is caused by thousands of genes, but what are the three main causatives?
thee genes that code for the potassium-gated channel and sodium-gated channel (SCN5A)
when we have known causative genes, how do we go about analyzing them?
we analyze the first causative gene, then it is negative we can test the second one; if it is negative too then we analyze the third and so on
when sanger sequencing was the only diagnostic tool being used, what was the waiting time for results called?
the diagnostic odyssey - it took several months to have a final and conclusive genetic analysis
what is the advantage of whole genome or whole exon sequencing?
allows for the analysis of all the genes at the same time, and if we would like to reanalyze a sample we already have all of the data
what is a disadvantage to whole genome or whole exon sequencing?
there is a big risk of detecting a lot of variations not associated with the clinical phenotype
what is the best situation to use whole genome sequencing?
during the research approach - when we don’t know what is the molecular basis of that phenotype and would like to investigate it
what is the accuracy of NGS related to?
the number of reads that cover the gene (coverage)
what are we at risk of detecting when running whole genome sequencing?
incidental findings → variations that are not related with the clinical phenotype, but that are causative for other human disorders, that out patients don’t present in that specific moment
now that NGS is in place, how fast is genetic testing now?
2-8 weeks
what is an advantage of NGS vs Sanger in regards to amount data obtained?
we can analyze an entire panel of genes in a single run with multiple causative agents tested at a time
what is the list of causative genes called?
a core disease gene list
what is a core gene list according to the American Society of Human Genetics (ASHG)?
the list of genes that are already associated with the clinical phenotype - only genes with a known relationship between the aberrant genotype and the pathology should be included in analysis
what does clinical utility refer to?
the genetic results that are important to confirm the diagnostic hypothesis, as well as are important for the management of other family members affected or at risk of developing the disorder
what is the best approach for diagnostic testing?
performing a targeted sequencing → focusing on the core disease list in the NGS data analysis, in order to have the final clinical utility
what is the type of disease referred to if the parents and siblings of the proband are unaffected for the causative mutation?
de novo mutation
who decides what the “disease list” is for comparison in NGS analysis?
there are no indications or clear guidelines that indicate the respective gene list, so there is a heterogeneity among laboratories → there are several publications with lists of genes associated with specific pathologies (OMIM, PubMed, etc), so it is just important to state on the clinical report which genes have been analyzed so that it is possible to re-evaluate a case at a later time if some genes are not previously analyzed
what is an incidental finding defined as when performing during genomic research?
a finding concerning an individual research participant that has potential health or reproductive importance and is discovered in the course of conducting research but is beyond the aims of the study
is it possible to notify the clinician about an IF, but not the patient?
yes, so they can watch out for symptoms in the future
what is the debate on IF centered around?
the pros and cons of telling a patient about the incidental findings if they are not currently experiencing symptoms of the disease
what is the practice in the US regarding incidental findings?
the American college of genetics indicates a list of 50 genes, that if discovered, must be reported to both the clinician and the patient
a genetic variant can be organized into what five classes?
- benign
- likely benign
- variation of unknown significance
- likely clinically relevant (pathogenic)
- clinically relevant (pathogenic)
what is the organization of the given classes dependent on?
performed based on the different filtering criteria the have been applied during the NGS analysis
what different criteria must be considered for the different filtering classifications?
- population data
- computational and predictive data (in silicon prediction, tools that we use to possibly predict the effect of the variants)
- functional data (publications)
- segregation data
if a variant is common in the population, what is it most likely considered as?
benign
what class do most variants obtained from NGS fall into?
class III
why is the fact that the majority of variants found by NGS fall into class III an issue?
it is a limitation → since we do not know the role of these variants, and they must be reevaluated in the future to find out their true relevance
