Basic science - Genetic testing (finish)

Question 1

How many pair of chromosomes - human

Answer 1

23 pairs of chromosomes, 22 autosomes and 1 pair of sex chromosomes

Question 2

5 types of DNA variants

Answer 2

• single-nucleotide variants (SNVs)
• Small insertions/deletions (indels)
• Structural variants
• inversions
• multi-copy-number variants

Question 3

difference between germline variants and somatic variants

Answer 3

germline: present in gametes and can be passed onto offspring
somatic: acquired during lifespan

Question 4

Simple vs complex genetic traits

Answer 4

Simples: medelian (monogenic) conditions, like cystic fibrosis
complex: traits influenced by genetic (polygenic) and environmental factors, like type 2 D

Question 5

For which type of conditions genetic testing is currently mostly offered

Answer 5

Medelian conditions

Question 6

by what is cased a mendelian disorder

Answer 6

by alteration(s) in a single gene

Question 7

prevalence in population vs individual of medelian disorder

Answer 7

individually rare, collectively frequent

Question 8

Difference between Allelic heterogeneity and locus heterogeneity

Answer 8

Allelic: different DNA variants in the same gene cause the same disease
Locus heterogeneity: a similar disease results from variants in different genes (hearing loss e.g.)

Question 9

Penetrance vs expressivity

Answer 9

Penetrant: refers to the probability of a gene or trait being express (BRCA1 and predisposition to breast cancer, e.g.)

Expressivity: Refers to variation in phenotypic expression when an allele is penetrant (FBN1 in Marfan syndrome)

Question 10

how do we assess the clinical relevance of a DNA variants?

Answer 10

Question 11

3 ways of detecting SNVs and small indels

Answer 11

• genotyping methods (for known variants)
• sanger sequencing
• Next-generation sequencing

Question 12

4 ways of detecting structural variants

Answer 12

• karyotyping
• chromosomal microarray
• multiplex ligation-dependent Probe amplification (MLPA)
• Next generation sequencing

Question 13

applications of sanger sequencing

Answer 13

• for individual genes and known variants
• widely used for small-scale test
• confirmation of variants detected by NGS

Question 14

advantages of sanger sequencing

Answer 14

• fast, cheap and accurate (for small scale projects)
• more than 40 years of technology improvement

Question 15

limitations of sanger sequencing

Answer 15

low throughput (800 bp-1kb) (?)

Question 16

principle of MLPA

Answer 16

amplification of multiple targets and dosage analysis

Question 17

application of MLPA

Answer 17

detection of copy number variants such as deletions/duplication at a given locus

Question 18

advantages of MLPA

Answer 18

Detection of small CNV

Question 19

limitations of MLPA

Answer 19

targeted analysis

Question 20

applications of chromosomal microarray

Answer 20

detection of unbalanced chromosomal abnormalities (net gain of loss of genetic material) genome-wide

Question 21

advantages of chromosomal microarray

Answer 21

• genome-wide approach
• higher resolution than karyotyping and no cell culture required

Question 22

limitations of chromosomal microarray

Answer 22

• Can’t detect small CNVs (e.g. single-exon deletions)
• Can’t detect balanced chromosomal abnormalities (e.g. reciprocal translocations, inversions, ring chromosomes)

Question 23

other name for next-generation sequencing

Answer 23

parallel sequencing

Question 24

principle of NGS

Answer 24

sequencing millions of shor DNA fragments in parallel

Question 25

advantages of genome sequencing

Answer 25

one-test-fits-all, it examines all types of variants genome wide
- possible to revisit data
- technically easier

cost 1000$ per sample

Question 26

advantages of exome sequencing

Answer 26

1-2% of the genome for 80-90% of disease-causing variants - very cost effective!
- good comprehensiveness
- best suited for disorders that are genetically hetereogenous and/or difficult to recognize clinically
- data reanalysis possible

Question 27

Challenges in genetic investigation

Answer 27

Infrastructure & expertise
- High-throughput sequencers & high-performance computing and storage required
- Multidisciplinary expertise required

Technological & knowledge limitations
- All laboratory tests have limitations
- The challenge of variant interpretation

Ethical, legal and social implications
- Secondary/incidental findings
- Test reimbursement (public vs. private systems)
- Risk of inequality and genetic discrimination
- Social acceptance