Cytogenetics Flashcards
numerical abnormalities
- change number of chromosomes
structural abnormalities
- change structure of chromosomes
robertsonian translocation
- fuse two small chromosomes into a very large chromosome
historically
- chromosome rearrangements have involved large regions of genome because they have been detected by karyotyping
limits of karyotyping
- requires viable cells
- low resolution limited to 3-5 MB or greater
karyotyping used for
- permits evaluation of entire genome
- used to detect gains and losses of entire chromosomes and fairly large chromosomal regions
why do chromosome abnormalities result in disease
- cause an increase and/or decrease in gene products
- alter the gene product itself by producing a fusion protein with altered function
what phenotypes are typically associated with chromosome abnormalities
- cancer
- abnormal growth and development in children or pregnancies
- early death
- clinically normal individuals with a personal or a family history of clinical abnormal offspring, miscarriages, or infertility
FISH
- high resolution - usually 100 KB
- requires clinically directed search
- very specific search
- interphase FISH can be performed on nonviable cells
FISH technique
- chromosome prep and denaturation
- labelled probe and denaturation
- in situ hybridization
- detection
micro deletion and micro duplicating syndromes characterized by
- by small, recurring interstitial deletions or duplications
- each associated with a well described phenotype
DiGeorge syndrome
- facial features - prominent nose w/ squared nasal root, small yes, small ears with abnormal folding
- abnormal palate
- heart abnormalities
- learning disabilities
- hypocalcemia
- immune deficiency
- psychiatric disorders
DiGeorge syndrome FISH
- green control maps just fine
- red probe which normally maps to DiGeorge critical region does not hybridize
- that region is deleted on chromosome 22
microarray tech allows us to
- survey entire genome for gains and losses
- very high resolution
- can use nonviable cells
- allow us to identify consanguinity and probably uniparental disomy
how affymextrix cytoscan array works
- patient DNA is labelled with fluorochrome probe and allowed to hybridize to a chip containing arrayed DNA of interest
- intensity of hybridization signal at each locus is compared to the in silico data obtained from 270 normal controls to assess copy number
- data for each locus plotted as a log 2 ratio of 0
when above the 0 log
- duplication or amplification
when below 0 log
- deletion
importance of follow up by FISH due to changes identified in microarray
- provides info about mechanisms responsible for the gain/loss identified by microarray
- less expensive test to do follow up parental testing
best test to determine if a parent carries a balanced translocation?
- metaphase FISH
uniparental disomy
- the inheritance of both copies of an allele from a single parent
- detected by SNP microarray
consanguinity
- mating between related individuals
- detected by SNP microarray
importance of consanguinity
- related individuals more likely than unrelated individuals to carry same mutant recessive genes
- offspring more likely to manifest a recessive disorder
hallmarks of consanguinity
- long stretches of homozygosity scattered throughout genome in offspring
greater level of consanguinity
- the greater number and length of homozygous stretches
what tier test is the chromosomal microarray
- first tier
microarray exceptions that it can’t recognize
- balanced rearrangements
- low level mosaicism
