Molecular diagnostics

Question 1

what is karyotyping used for?

Answer 1

large structural or numerical abnormalities, whole genome, miscarriage history

Question 2

why is karyotyping not ideal?

Answer 2

need actively dividing cells, time for growth, cells can get contaminated, can’t get small changes less than 5mB, cant detect single gene rearrangements

Question 3

what types of tissues can you karyotype?

Answer 3

prenatal: amniotic, chorionic villi, umbillical blood, perinatal/postnatal=fibroblasts and blood,tumors

Question 4

what phase are cultures harvested in?

Answer 4

metaphase

Question 5

light and dark in chrom?

Answer 5

light is euk. dark and hetero

Question 6

3 types of chromosomes?

Answer 6

acrocentric (small top), submetacentric (medium top), and metacentric (big top)

Question 7

What is FISH

Answer 7

flouresecnt in Situ hybridization

Question 8

Why is FISH not ideal?

Answer 8

have to know what you’re FISHING for, limited # of colors to use, relies on eyes so poor resolution

Question 9

types of fish probes?

Answer 9

"Aneuploidy detection/enumeration
Locus or gene-specific 
Whole chromosome paint (metaphase)
Subtelomeric
Rearrangement detection (break apart and fusion)

Question 10

what are centromeric probes good for?

Answer 10

to see loss or gain

Question 11

what are subtelomeric good for?

Answer 11

see deletion

Question 12

what do break apart probes show?

Answer 12

for 1 gene 2 regions close to eachotherÉif you see that they’re seprated means something bad happened since they should be together

Question 13

what do fusion probes show?

Answer 13

for 2 genes..if you see they’re together itÕs a problem bc they should be separated

Question 14

what is fish good for??

Answer 14

targeted cytogenetics - structural abnormalities (aneusomies)

Question 15

what phases for FISH?

Answer 15

interphase and metaphase

Question 16

What is array CGH

Answer 16

(array competitive genomic hybridization)

Question 17

When is array CGH good?

Answer 17

like a molecular karyotype whole genome
good for small unbalanced changes (gain or loss), copy # changes
high resolution/sensitivity,
good 1st test retardation

Question 18

when array bad?

Answer 18

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

Question 19

what is the difference bw unbalanced and balanced DNA rearrangements?

Answer 19

unbalanced there is loss of genetic material..balanced you can’t tell with an array anything has changed

Question 20

What is a robertsonian translocation?

Answer 20

whole arm exchange of acrocentric chromosomes. usually lose the short ones that join together

Question 21

what is DNA sequencing best for?

Answer 21

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

Question 22

list cytogenetic analysis methods from big to small

Answer 22

o Karyotype mFISH chromosome
o array CGH gene
o Dna sequencing exon, and genome