Lecture 5

Question 1

what is the best diagnostic approach in regards to testing an affected persons close relatives?

Answer 1

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

Question 2

if the aunt of the proband turns out to be positive for a variant, who would we test next?

Answer 2

the probands father

Question 3

if the aunt and father have the mutation, is it wise to test all the other related aunts and uncles?

Answer 3

yes - they have a chance to have the same mutation of the affected family member

Question 4

why is Sanger sequencing considered to be the gold standard?

Answer 4

it is characterized by a very high accuracy

Question 5

what are some downsides to Sanger sequencing?

Answer 5

it is very high cost and can take a long time

Question 6

what is the main causative gene in Brugada Syndrome?

Answer 6

SCN5A

Question 7

what does the SCN5A gene code for?

Answer 7

encodes for the sodium gated channels expressed in the cardiac muscle - responsible for the action potential during the electrical activity of the heart

Question 8

If genetic testing does not confirm the clinical diagnosis, what occurs?

Answer 8

the clinical diagnosis still remains the same

Question 9

what is LQT?

Answer 9

a disease characterized by an abnormally long QT interval in an electrocardiogram

Question 10

LQT is caused by thousands of genes, but what are the three main causatives?

Answer 10

thee genes that code for the potassium-gated channel and sodium-gated channel (SCN5A)

Question 11

when we have known causative genes, how do we go about analyzing them?

Answer 11

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

Question 12

when sanger sequencing was the only diagnostic tool being used, what was the waiting time for results called?

Answer 12

the diagnostic odyssey - it took several months to have a final and conclusive genetic analysis

Question 13

what is the advantage of whole genome or whole exon sequencing?

Answer 13

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

Question 14

what is a disadvantage to whole genome or whole exon sequencing?

Answer 14

there is a big risk of detecting a lot of variations not associated with the clinical phenotype

Question 15

what is the best situation to use whole genome sequencing?

Answer 15

during the research approach - when we don’t know what is the molecular basis of that phenotype and would like to investigate it

Question 16

what is the accuracy of NGS related to?

Answer 16

the number of reads that cover the gene (coverage)

Question 17

what are we at risk of detecting when running whole genome sequencing?

Answer 17

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

Question 18

now that NGS is in place, how fast is genetic testing now?

Answer 18

2-8 weeks

Question 19

what is an advantage of NGS vs Sanger in regards to amount data obtained?

Answer 19

we can analyze an entire panel of genes in a single run with multiple causative agents tested at a time

Question 20

what is the list of causative genes called?

Answer 20

a core disease gene list

Question 21

what is a core gene list according to the American Society of Human Genetics (ASHG)?

Answer 21

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

Question 22

what does clinical utility refer to?

Answer 22

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

Question 23

what is the best approach for diagnostic testing?

Answer 23

performing a targeted sequencing → focusing on the core disease list in the NGS data analysis, in order to have the final clinical utility

Question 24

what is the type of disease referred to if the parents and siblings of the proband are unaffected for the causative mutation?

Answer 24

de novo mutation

Question 25

who decides what the “disease list” is for comparison in NGS analysis?

Answer 25

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

Question 26

what is an incidental finding defined as when performing during genomic research?

Answer 26

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

Question 27

is it possible to notify the clinician about an IF, but not the patient?

Answer 27

yes, so they can watch out for symptoms in the future

Question 28

what is the debate on IF centered around?

Answer 28

the pros and cons of telling a patient about the incidental findings if they are not currently experiencing symptoms of the disease

Question 29

what is the practice in the US regarding incidental findings?

Answer 29

the American college of genetics indicates a list of 50 genes, that if discovered, must be reported to both the clinician and the patient

Question 30

a genetic variant can be organized into what five classes?

Answer 30

1. benign
2. likely benign
3. variation of unknown significance
4. likely clinically relevant (pathogenic)
5. clinically relevant (pathogenic)

Question 31

what is the organization of the given classes dependent on?

Answer 31

performed based on the different filtering criteria the have been applied during the NGS analysis

Question 32

what different criteria must be considered for the different filtering classifications?

Answer 32

• 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

Question 33

if a variant is common in the population, what is it most likely considered as?

Answer 33

benign

Question 34

what class do most variants obtained from NGS fall into?

Answer 34

class III

Question 35

why is the fact that the majority of variants found by NGS fall into class III an issue?

Answer 35

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