Cytogeneomic Mechanism of Disease 1 Flashcards
Karyotyping: (definition)
- resolution
- coverage
Karyotyping: a subjective whole genoma test of limited resolution
- coverage: complete
- resolution: > 5-10 Mb (lowest)
Karyotyping is ideal for
larger chromosome abnormalities
Karyotyping identifies chromosomes by
chromosomes identified by size and banding pattern
karyotyping has low yield for detecting
low yield for detecting small rearrangments associated with intelectual disabilities, congenital anomalies, autism/ASD
benefits of karotyping
=view entire genome
-can visualize individual cells and individual chormosomes
limits of karyotyping
- low resolution
- need actively growing source of cells
what can you detect with karyotyping? (4)
1) aneuploidy (too many or too few chromosomes = trisomy or monosomy)
2) deletions (missing part of chromosome = partial monosomy)
3) duplications (extra part of chromosome = partial trisomy)
4) inversions and translocations (balanced and unbalanced) if large enough
Fish is more sensitive than ___ but ___
FISH is more sensitive than keryotyping but only interrogates a specific genomic regoin of interest
FISH is useful for
Useful for suspected microdeletion/microduplications, prenatal aneuploidy detection, detection of common rearrangements in neoplasia, and FISH panels for hematolymphoid disorders
FISH coverage and resolution (2)
coverage:
-probe specific
resolution:
- FISH (interphase) >20kb
- FISH (metaphase) >100kb
How FISH works
MOLECULAR CYTOGENETICS
- make probe = fluorescendtly labelled segment of DNA complementary to chromosome region of interest
- hybridization: denatured chromosomes fixed on a microscopic slide exposed ot prob, hybridization (attachment) occurs between probe and complementary chromosomal DNA
- DNA sample and color detected (usually with chromosmes in metaphse because condensed and coiled)
4 types of FISH probes (generally)
- gene specific probe
- centromeric probe ( repetitive sequence probe)
- telomeric probe (repetitive sequence probe)
- chromosome painting probe
Dual color fusion probe
- detects both derevative chromosomes (normal and abnormal) after rearrangment
- decreases false negatives
- fusion color = rearrangement
- single color = normal
dual color break apart probe
- detects translocations which “breaks apart” overlapping fusion signals into single probe colors
- fusion = normal
- rearranged gene split apart into 2 single colors (transloation = 2 seperate colors)
DiGeorge Syndrome is an example of what assay
example of FISH assay
- green dot = ARSA gene on tip of chromosome 22
- red hybridizing to digeorge syndrome critical region of 22 q
- when red signal gone (where just green) = delection of chromosome 22 so patient is positive for digeorge syndrome
3 examples of FISH assay
1) Digeorge syndrome
2) prenatal aneuploidy (trisomy 18)
3) SRY gene - CEP X (did not go over)
can use FISH for
deletions, insertions, translocations
chromosome microarray/single nucleotide polymorphism (SNP) array analysis
- resolution
- coverage
resolution: 50kb/SNP 1 bp
coverage: Complete
Chromosome microarray analysis (CMA) is more sensitive than ___ but does not detect ___
Chromosome microarray analysis (CMA) with oligonucleotides or SNPs is a whole-genome test with much greater sensitivity than karyotyping
Higher diagnostic yield in many patient groups
Does not detect balanced rearrangements
single nucleotide polymorphism (SNP)
A SNP is a change in 1 nucleotide or base-pair within a codon in the DNA.
SNP chromsome microarray involves:
amplify pt. DNA and apply to SNP array with probe, undergo hybridization
AA = homozygous A
BB = homozygous B
AB = heterozygous
A - = dletion of one
B - = deletion of one
-/- = homozygous deletion (no signal)
AABB, AAAA, AAAB, ABBB, BBBB = gains
a virtual karyotype produced by an SNP array analysis can do 2 things:
1) use SNPs for genotyping (acn look for heterozygosity)
2) use CNV for copy number variations (identify regions of chromosomes gained or lost = duplicted or deleted)
