Basic science - Genetic testing (finish) Flashcards
Students should be able to: Describe the range of DNA variation in the human genome Outline the main laboratory methods used in molecular genetics Identify the main applications of DNA sequencing for Mendelian disorders
How many pair of chromosomes - human
23 pairs of chromosomes, 22 autosomes and 1 pair of sex chromosomes
5 types of DNA variants
- single-nucleotide variants (SNVs)
- Small insertions/deletions (indels)
- Structural variants
- inversions
- multi-copy-number variants
difference between germline variants and somatic variants
germline: present in gametes and can be passed onto offspring
somatic: acquired during lifespan
Simple vs complex genetic traits
Simples: medelian (monogenic) conditions, like cystic fibrosis
complex: traits influenced by genetic (polygenic) and environmental factors, like type 2 D
For which type of conditions genetic testing is currently mostly offered
Medelian conditions
by what is cased a mendelian disorder
by alteration(s) in a single gene
prevalence in population vs individual of medelian disorder
individually rare, collectively frequent
Difference between Allelic heterogeneity and locus heterogeneity
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.)
Penetrance vs expressivity
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)
how do we assess the clinical relevance of a DNA variants?
3 ways of detecting SNVs and small indels
- genotyping methods (for known variants)
- sanger sequencing
- Next-generation sequencing
4 ways of detecting structural variants
- karyotyping
- chromosomal microarray
- multiplex ligation-dependent Probe amplification (MLPA)
- Next generation sequencing
applications of sanger sequencing
- for individual genes and known variants
- widely used for small-scale test
- confirmation of variants detected by NGS
advantages of sanger sequencing
- fast, cheap and accurate (for small scale projects)
- more than 40 years of technology improvement
limitations of sanger sequencing
low throughput (800 bp-1kb) (?)
principle of MLPA
amplification of multiple targets and dosage analysis
application of MLPA
detection of copy number variants such as deletions/duplication at a given locus
advantages of MLPA
Detection of small CNV
limitations of MLPA
targeted analysis
applications of chromosomal microarray
detection of unbalanced chromosomal abnormalities (net gain of loss of genetic material) genome-wide
advantages of chromosomal microarray
- genome-wide approach
- higher resolution than karyotyping and no cell culture required
limitations of chromosomal microarray
- Can’t detect small CNVs (e.g. single-exon deletions)
- Can’t detect balanced chromosomal abnormalities (e.g. reciprocal translocations, inversions, ring chromosomes)
other name for next-generation sequencing
parallel sequencing
principle of NGS
sequencing millions of shor DNA fragments in parallel
advantages of genome sequencing
one-test-fits-all, it examines all types of variants genome wide
- possible to revisit data
- technically easier
cost 1000$ per sample
advantages of exome sequencing
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
Challenges in genetic investigation
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
