Lecture 1

Question 1

what does a predictive test provide?

Answer 1

provides evidence of the presence of a specific disease before the disease phenotype becomes evident in the patient

Question 2

what can we gain from a predictive test?

Answer 2

if we have the genetic variant based on the genetic results we may suggest changes in treatment or in the lifestyle to avoid the occurrence of that specific phenotype

Question 3

how can predictive testing be used? (ex of disease)

Answer 3

if we detect mutations on the factor V coagulation cascade (Leiden factor) knowing that an individual carrying the alteration is at a higher risk for thrombus compared to the general population we can treat accordingly → if a patient has this mutation and is pregnant, the gynecologist will be able to choose the best drug for that patient and will be much more careful when monitoring the patient throughout the pregnancy

Question 4

what are the 5 potential goals of genetic testing?

Answer 4

1. genetic diagnosis
2. identification of the molecular basis underlying a phenotype
3. classification of a disease
4. prognosis
5. monitoring

Question 5

when genetic testing is performed, what is the driving force?

Answer 5

the clinical diagnosis → genetic testing is used as the confirmation of the clinical diagnosis

Question 6

what do most research studies use to better investigate and understand the molecular basis for a disease?

Answer 6

the reference genome

Question 7

if a diagnostic laboratory performs genetic testing using NGS and discovered a causative mutation, what occurs?

Answer 7

before reporting this mutation to the patient we must validate that mutation using first generation sequencing on the portion of the genome containing the mutation to make sure that the variant actually exists in the patient

Question 8

what are the four inheritance models?

Answer 8

autosomal dominant, autosomal recessive, X-linked, and Y-linked

Question 9

what is important to keep in mind in regards to inheritance models and genetic testing?

Answer 9

which type of inheritance pattern we have as well as that some disorders may have more than one

Question 10

what is a Mendelian disorder?

Answer 10

when we have one gene that is causative / in which the presence of that variant is related with a pathological phenotype → presence of that variant is sufficient to have an altered phenotype

Question 11

what is the classic example of a mendelian disorder?

Answer 11

cystic fibrosis: autosomal recessive - if I have a homozygous variant on the CFTR gene, the patient is affected

Question 12

what are susceptibility genes?

Answer 12

means that we have variants of genes that may increase the risk of developing a disease, but having that variant is not sufficient to have the clinical phenotype

Question 13

what are chromosomal alterations?

Answer 13

condition in which we don’t use the sequencing approach but we use for example cryogenic analysis (the analysis of the karyotype) in order to detect if there are numerical alterations, in case of syndromes that are diagnosed such as trisomy 21 → focused not on just the DNA sequence but the entire karyotype

Question 14

what is carrier testing?

Answer 14

genetic testing on an individual that is not affected but we would like to know if that individual carries a mutation or variation

Question 15

what are the four types of pre-natal testing?

Answer 15

1. pre-implantation genetic diagnosis (PGD)
2. cell-free fetal DNA testing
3. chorionic villus sampling (CVS)
4. amniocentesis

Question 16

describe pre-implantation genetic diagnosis:

Answer 16

before implantation of the embryos, we can perform the genetic testing on the embryos to investigate if there are chromosomal aberrations or to look for a specific mutation that is transmitted in the family

Question 17

what is chorionic villus sampling?

Answer 17

performed on the villocentesis and amniocentesis → quite invasive because they extract the fetus’ DNA for the analysis of the karyotype or for the analysis of specific familial mutations

Question 18

describe the cell-free fetal DNA testing?

Answer 18

there is free-circulating fetal DNA found in maternal blood, so a peripheral blood sample can be taken from the mother for the analysis of fetal DNA

Question 19

what is the downside to cell-free fetal DNA testing?

Answer 19

the accuracy of this approach is lower than the other two types of investigation - also, if variants are detected its necessary to confirm this alterations with the fold standard approach which is villocentesis or amniocentesis

Question 20

what are the two types of post-natal testing?

Answer 20

carrier testing and whole genome sequencing

Question 21

what is the advantage of NGS?

Answer 21

we can analyze the entire panel of associated genes at the same time, in the same analysis, or we can choose to focus on only the causative genes that are already associated with the clinical phenotype

Question 22

what is an advantage to only selecting a few causative genes to sequence?

Answer 22

the quality of the sequencing is higher than whole exon sequencing because the sequence only has to focus on ten genes instead of 22,000 → the quality of the sequencing is fundamental for the quality of the diagnostic testing

Question 23

what are the 6 components of a clinical molecular laboratory?

Answer 23

1. skilled and trained staff
2. dedicated instruments
3. organization of spaces to avoid the possible contamination
4. automation
5. centralization
6. high-throughput technologies

Question 24

describe the organization of a clinical molecular laboratory in order to avoid contamination:

Answer 24

separate areas for the blood to be stored, the extraction of DNA, preparation for amplification, sequencing

Question 25

what is centralization in regards to clinical molecular laboratories?

Answer 25

due to the high cost of instruments and precisely trained staff, usually there is one lab for multiple clinics / hospitals

Question 26

describe the flow that a genetic sample goes through in terms of people involved in its analysis:

Answer 26

clinician (diagnostic request), medical geneticist (informed consent), laboratory technicians biologist, geneticists and bioinformaticians ( lab work), medical geneticist (interpretation and analysis), and clinician (final report)

Question 27

what is the most important part of genetic testing?

Answer 27

informed consent → the patient MUST agree with the type of analysis

Question 28

what is the job of the bioinformatician?

Answer 28

newest figure in gene analysis → terabytes of data are generated, and therefore someone is needed to generate a bioinformatic pipeline in order to evaluate, classify, and generate a report to be given to the medical geneticist and then the clinician

Question 29

what is the most difficult phase of analysis?

Answer 29

the analysis of data and the creation of the report and findings