Molecular diagnostics Flashcards
what is karyotyping used for?
large structural or numerical abnormalities, whole genome, miscarriage history
why is karyotyping not ideal?
need actively dividing cells, time for growth, cells can get contaminated, can’t get small changes less than 5mB, cant detect single gene rearrangements
what types of tissues can you karyotype?
prenatal: amniotic, chorionic villi, umbillical blood, perinatal/postnatal=fibroblasts and blood,tumors
what phase are cultures harvested in?
metaphase
light and dark in chrom?
light is euk. dark and hetero
3 types of chromosomes?
acrocentric (small top), submetacentric (medium top), and metacentric (big top)
What is FISH
flouresecnt in Situ hybridization
Why is FISH not ideal?
have to know what you’re FISHING for, limited # of colors to use, relies on eyes so poor resolution
types of fish probes?
"Aneuploidy detection/enumeration Locus or gene-specific Whole chromosome paint (metaphase) Subtelomeric Rearrangement detection (break apart and fusion)
what are centromeric probes good for?
to see loss or gain
what are subtelomeric good for?
see deletion
what do break apart probes show?
for 1 gene 2 regions close to eachotherÉif you see that they’re seprated means something bad happened since they should be together
what do fusion probes show?
for 2 genes..if you see they’re together itÕs a problem bc they should be separated
what is fish good for??
targeted cytogenetics - structural abnormalities (aneusomies)
what phases for FISH?
interphase and metaphase
What is array CGH
(array competitive genomic hybridization)
When is array CGH good?
like a molecular karyotype whole genome
good for small unbalanced changes (gain or loss), copy # changes
high resolution/sensitivity,
good 1st test retardation
when array bad?
cant detect balanced translocations (need gain or loss)
cant find super small microdeletions
chimerism: 2+ genotypes from zygotes
mosaicism: 2 cells w dif genotypes mixing
what is the difference bw unbalanced and balanced DNA rearrangements?
unbalanced there is loss of genetic material..balanced you can’t tell with an array anything has changed
What is a robertsonian translocation?
whole arm exchange of acrocentric chromosomes. usually lose the short ones that join together
what is DNA sequencing best for?
mutations and small insertions/deletions
specific diagnosis and genotyping
Tumors: diagnosis and targeted therapy - Constitutional defects: hearing loss, cardiomyopathy, syndromes Genotyping: HLA testing, paternity, forensics Pharmacogenetics: drug metabolism
list cytogenetic analysis methods from big to small
o Karyotype mFISH chromosome
o array CGH gene
o Dna sequencing exon, and genome
