Lecture 5: Diagnostic Technologies Flashcards
What are the three basic types of FISH?
Repeat sequences
Single copy DNA - subtelomere FISH
Chromosome painting - multi-color
Where are repeated sequence FISH probes isolated from?
temlomere or centromere
Where are single copy FISH probes isolated from?
unique sequence
cloned DNA of a disease-causing gene, or fragment of DNA of known location associated with a particular disease-causing gene
Where are subtelomere FISH probes isolated from?
distal ends of chromosomes, proximal to actual telomere regions
Why is subtelomere FISH very useful?
subtelomere regions are gene-rich
can see cryptic (very small) deletions and rearrangements which cannot be seen by standard karyotype analysis
Which FISH technique is useful for seeing cryptic (very small) deletions and rearrangements which cannot be seen by standard karyotype analysis?
Subtelomere FISH
Which FISH technique is used to detect the source extra material of unknown origin in a chromosome, complex rearrangements, or marker chromosomes?
Chromosome painting
Why can’t some deletions be seen by karyotype analysis? what technique should be used instead?
too small
subtelomere FISH
What size are typical FISH probes?
10Kb
What size FISH probe is necessary to detect velocardiofacial syndrome (VCFS)? What is the problem with this size?
3Mb - too big; probe is only 10Kb
What are regions in the genome with clusters of closely associate genes (all related to a clinical outcome) whose functions are usually unrelated?
Continuous Gene Syndromes
What is FISH used to detect within Continuous Gene Syndromes?
microdeletions or microduplications
What is the lower limit of abnormalities detected by karyotype analysis?
3Mb
How large are microdeletions and microduplications?
0.5-6Mb
How large is the common delta F508 mutation in cystic fibrosis?
3bp
What are 6 Continuous Gene Syndromes?
WAGR - 11p Miller-Dieker/Lissencephaly - 17p Williams syndrome - 7q Velocardialfacial syndrome - 22q 1p-syndrome Prader Willi/Andelman Syndrome
What causes coarse skin and hair, lack of flexibility in the aorta, and supravalvular aortic stenosis associated with Williams syndrome?
Deletion on elastin gene (ELN) on xs 7
What causes autistic-like behavioral problems associated with Williams syndrome?
deletion on a gene adjacent to elastin gene
How is Williams syndrome classified?
Continuous gene syndrome - deletion of several adjacent genes
connective tissue disease (deletion of elastin gene)
What are the 1st and 2nd most common syndromes known in humans?
Down syndrome Velocardiofacial syndrome (VCFS)
Where is the deletion in velocardiofacial syndrome? How is it detected?
xs 22
FISH
Difficulty feeding, cardiac defects, facial dysmorphologies are all seen infants, and learning disabilities, short stature, and conductive hearing loss as an individual ages are seen in what condition? How is this syndrome characterized?
Velocardiofacial syndrome
Continuous gene syndrome
How does the deletion associated with velocardiofacial syndrome arise?
misalignment during meiotic crossing over
Why do 10-15% of patients with velocardiofacial syndrome have a more severe condition than their parents with the same deletion?
Parent’s normal chromosome 22 can compensate
Affected child’s second chromosome 22 doesn’t have the alleles which can compensate
In a genetic microarray, what does a green signal mean?
excess of reference DNA
–> deletion in test DNA
In a genetic microarray, what does a red signal mean?
excess test DNA
–> duplication in test DNA
polymorphisms, mutations, and copy number variations (CNVs) can all be detected by _______
gene arrays
Will gene arrays detect balanced rearrangements?
no - total amount of DNA is conserved, no change in relative amounts detected
What does a red signal in an expression array mean?
increased expression
What does a green signal in an expression array mean?
decreased expression
What does a peak mean in a chromosome microarray?
gain of segments - duplication
What does a valley mean in a chromosome microarray?
loss of segments - deletion
What do chromosome microarrays view?
copy number variants
What is the SOX5 gene involved in?
development - mutation can cause dysmorphic features
What kind of next gen sequencing is used for genetic disorders, oncology, infectious disease, reproductive health, population genetics, forensics, and agriculture?
target sequencing
Next gen sequencing has been used to develop panels. What information do these provide?
particular genes or regions of genome known to be associated with particular classes of disease
Which type of genetic technology is used for relatively large (>3Mb) numerical and structural abnormalities, and is genome wide?
karyotype analysis
Which type of genetic technology is used for well-defined, specific, very small (1-300bp) mutations, with targeted testing?
molecular diagnostics
Which type of genetic technology is used for well-defined, specific, medium sized (10Kb-10Mb) mutations, with targeted testing?
FISH
Which type of genetic technology is used for generalized genome-wide screening for small (1Kb) to large mutations, and will not detect balanced rearrangements?
microarray
Which type of genetic technology is used for high resolution for targeted regions to detect mutations to a single base level?
DNA sequencing
