Lecture 1 Flashcards
What are the possible uses of genetic testing? In other words, why and when can genetic testing be useful for clinical management?
- patient has a disease and we want to confirm the molecular cause of the disease
- evaluate the predisposition to develop pathological phenotype
- screening (like prenatal screening)
- identify cause of disorder
- pharmacogenetic reasons to choose the best / most appropriate treatment
- prognosis based on molecular basis
- follow the progression of a disorder in the patient by measuring circular DNA
- verify the presence of bacteria or viruses (molecular approach)
- identify the presence of a disease during the pre-symptomatic era
- useful for patients’ relatives
What is the most sensible data we have?
DNA
What information does a predicative gene test provide?
The test identifies the presence of the disease before the disese presents its phenotype.
Why is a predicative gene test helpful?
If the molecular basis is identified before the occurrence of the disorder, the lifestyle of the patient can be modified to avoid the occurrence of the disorder.
What is an example of a disease that a predicative teat is useful for?
thrombophilia
Is a gene test for Parkinson’s necessary?
No, because there are no known preventative measures at the time
What is familiar thrombophilia?
case of atypical thrombus that occurs in early age
What are the benefits of gene testing?
benefits are in the diagnosis, prognosis, screening and risk stratification of the patient
When should genetic testing be done?
only if there is clinical suspicion
List the risks associated with genetic testing:
over treatment
physiological impact of results without clinical diagnosis
higher risk for the patients’ assurance
procedure risks with amniocentesis and villocentesis
identification of genes that are not related to clinical implications
What is the problem with online genetic testing services?
it is hard to manage the amount of information provided by genetic testing services
they also use 2nd and 3rd generation sequencing, so the results are not very accurate since they only identify some variants
Why is it important to use 1st generation sequencing?
it is used by certified, high quality labs to avoid the occurrence of false positives
Are there ethical issues with genetic testing?
Since DNA gives paternal and private information about a patient, it is importnat to to have consent from the patient
Why is pre-testing genetic counseling important?
It is important because the genetic counselor meets with the patient and insures the patient feels comfortable with the process and understands the benefits
What is a problem with genetic testing in terms of storage? Why not store the information in a cloud?
After sequencing the DNA of a patient, the sequence requires terabytes of storage. It would not be appropriate to use a cloud simply for privacy reasons.
What is molecular diagnostics?
genetic diagnosis based on molecular analysis through the identification of pathogenetic mutations in DNA or RNA samples to facilitate identification, diagnosis, classification, prognosis, and monitoring
What are the goals of genetic testing?
genetic diagnosis of the clinical phenotype
identification of molecular basis that underline the clinical phenotype
classification: genetic testing can help identify the subtype of the diagnosis
prognosis: to have an idea of the prognosis related to the specific alteration
monitoring: helps analyze somatic molecular alterations
What mutations are analyzed when studying inherited disorders?
germ line mutations are analyzed because the muations of the germ line can help diagnose and classify
What should be performed first: clinical diagnosis or genetic testing?
Clinical diagnosis must be done before genetic testing because genetic testing should be used to confirm the clinical diagnosis. If the genetic test does not confirm the clinical diagnosis, the patient can still be affected, especially since not all molecular bases are well characterized.
An example is cardiomyopathy, which often has false negatives.
What was an important milestone in being able to perform genetic testing for students?
discovery of the DNA double helix
Who discovered how to amplify DNA?
Kary Mullis
What is another name for first generation sequencing?
Sanger Sequencing
What are some benefits to second generation sequencing?
reduction of costs and time
ability to analyze many patients and genes at the same time
What is the gold standard to DNA sequencing?
Sanger sequencing
What kind of genetic testing cvan be performed in diagnostic laboratories? What are its limitations?
second generation sequencing
if a causitive mutation is detected, first generation sequencing must be used to ensure the variant exists before reporting it to the patient
What are some examples of Mendelian disorders?
Haemophilia
Cystic Fibrosis
Define Mendelian disorder:
disorder in which one gene is causative and the presence of that variant is related to a pathological phenotype.
What is a classical example of a Mendelian disorder that is autosomal recessive?
Cystic Fibrosis
What is affected in a patient with a homozygous variant on the CFTR gene?
Cystic Fibrosis (autosomal recessive)
What are susceptibility genes?
variants on genes that may increase the risk of developing a disease
Is having a genetic variance enough to show clinical phenotype? Name an example
No, an example is the inheritance of a mutation on the BRCA1 gene. Individuals with the mutation are at a higher risk for breast cancer, but it does not mean they will develop it.
What are chromosomal alterations?
conditions in which we don’t use the sequencing approach but instead use, for example, cytogenetic analysis
analysis is not focused on the DNA, but instead on the karyotype
What is carrier testing?
genetic testing done on an individual that is not affected, but we would like to know if they the individual carries a mutation or variation.
What is an example as to why carrier testing would be done?
if a couple carries cystic fibrosis genes, carrier testing can be done to know whether or not the variants can be trasmitted to the baby
What kind of genetic testing deals with testing affected patients?
mendelian disorder testing
susceptibility testing
chromosomal alteration
Why and when do you analyze carriers that are going to develop the disease?
test is performed if it is suspected or other family members of the disorder are carriers
it can be performed prenatally or postnatally
What kind of testing can be performed prenatally?
pre-implantation genetic diagnosis (PGD)
cell-free fetal DNA testing
Chorionic Villus Sampling (CVS)
Amniocentesis
What are some examples of post natal testing?
carrier testing
testing for the identification of mutations in the newborns or adults when a genetic disorder occurs
What is the most appropriate genetic test that we can perform?
disease-specific testing
whole genome sequencing
What kind of genetic testing is useful for Disease-Specific Testing?
next generation sequencing (NGS)
Advantages of Whole Genome Sequencing
analysis can be focused on only the gene that is associated
if in the future new genes are associated with that disorder, the new genes can be re-analyzed
the quality of the data produced is high
Disadvantages of Whole Genome Sequencing
detection of accidental findings
it would be difficult to choose the correct ethical approach
What are some goals of the diagnostic laboratory?
reduce processing time and costs
minimize number of replicated tests
accurate and precise analytical data
What helps reduce processing time and cost in diagnostic laboratories?
Next Generation Sequencing
Sanger sequencing is a lot more expensive
Who is the alpha and the omega during genetic testing?
the patient
What is genetic testing?
evaluation of clinical data
pedigree and family history
identification of the appropriate genetic test
useful for informed choices
evaluation of the recurrence of the disease in the family
information about the inheritance of the disease
