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Genetics > Molecular Diagnostics - 3 lectures > Flashcards

Molecular Diagnostics - 3 lectures Flashcards

1
Q

difference between direct and indirect methods

A

indirect - looking at markers that tend to be close to disease allele (think recombination)

direct - everything else

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2
Q

purpose of linkage analysis

A

to find a genetic loci that is associated with a disease

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3
Q

what phase does crossover happen in the DNA

A

prophase of meiosis I

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4
Q

which loci experience crossover more - ones that are farther apart or closer together

A

farther apart

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5
Q

marker that is usually inherited with the disease causing mutation

A

polymorphic marker

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6
Q

genes or marker that are not close together or on different chromosome experience what percentage of recombination requency

A

50% recombination frequency (independent assortment) and are considered not linked

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7
Q

genes that are close together experience what percentage of recombination frequency

A

less than 50% and are considered linked

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8
Q

particular arrangement of a chromosome that is inherited together

A

haplotypes

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9
Q

low or high frequency of recombination - two loci that are close together

A

LOW

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10
Q

how are disease causing gene actually identified

A

sequencing nearby regions of the genome or using human genome data

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11
Q

restriction enzymes cutting at palindromic sequences is used in what method

A

PCR RFLP analysis

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12
Q

a disease individual without the marker being used or a non affected person with the diseased marker is a result of?

A

recombination

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13
Q

challenges to linkage analysis

A

recombination and loci heterogenity(same phenotype but different loci)

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14
Q

methods that query the whole gene

A

karyotyping (G banding), array CGH, SNP chip, expression arrays, special karyotyping, and next gen sequence

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15
Q

significance of a single bp difference every 1000bp

A

digestions of DNA from different individuals will result in different patterns of DNA fragment

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16
Q

what happens at restriction sites that have single bp change

A

they are destroyed

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17
Q

RFLP data was originally obtained from what other method

A

southern blotting

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18
Q

disadvantage of southern blotting

A

lengthy procedure, not automated, radioactivity, expensive

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19
Q

as of now RFLP data is obtained using what?

A

PCR which uses restriction enzymes

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20
Q

Direct RFLP used to diagnose what illness

A

sickle cell anemia

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21
Q

data for direct RFLP depends on what?

A

locus and restriction enzyme

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22
Q

ASO used for diagnoses of what diseases

A

cystic fibrosis and hemochromatosis

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23
Q

when do ASO become less useful

A

as the disorder exhibits more allelic or genetic heterogenity

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24
Q

ASO bind to what

A

single allele of a gene - only possible if exact mutation has been identified

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25
what are the triple repeat disorders and what method is used to detect them
fragile X, huntingtons, myotonic dystrophy PCR
26
how can PCR tell you it is triple repeat disorder
the size of the PCR product - the genotype will have a lot more than normal repeats
27
how will the PCR product of a person with triple repeat disorder show on the agarose gel
the DNA wouldn't travel as far as the normal one because it is too big
28
PCR can be used to detect
Duchenne because it is a deletion
29
limitations to PCR
difficult to optimize so can't detect carriers
30
can be used to detect aneuploidy, insertions, deletion, large translocations
karyotyping (G banding)
31
disadvantages to karyotyping
only detects large alterations (deletion >5kb or even more) and has low resolution
32
in G banding, the dark and light bands represent what
dark: A-T rich region light: C-G rich region
33
keypoint of FISH
resolution is improved over G banding
34
how long are the probes in FISH
10-100kB
35
difference between the two types of FISH (SKY FISH and chromosome specific)
SKY FISH - paints the whole chromosome a specific color chromosome specific - hybridizes to a specific locus on the chromosome (only one locus)
36
DiGeorge's Syndrome or 22q11.2 is detected using what method
FISH can also use G banding but might not get great results
37
what is abnormal in digeorges
pharyngeal arch development
38
symptoms of digeorge's
CATCH22 | cardiac anomaly most important
39
advantage of FISH
better resolution of G banding
40
disadvantage of FISH
have to know exactly what you are looking for
41
FISH can be used to detect what disorder
trisomy
42
SKY FISH most importantly used to detect
translocations since it colors each chromosome a specific color
43
disadvantage of SKY FISH
can't detect small deletions since whole chromosome is painted one color
44
if you suspect a patient of having digeorge's and you do FISH method and you have a red signal in both chromosome 22s, what doest that mean
patient does not have digeorge's since red signal is present in both chromosomes - would have been digeorge's if red signal only present in one chromosome
45
advantage of array CGH
can detect copy number changes in DNA throughout the genome, genome amplification, deletions (CNV - copy number variant)
46
disadvantage of array CGH
does not detect balanced rearrangements
47
array CGH detect deletions and insertion at very high or very low resolution?
high resolution
48
what method can detect gain or loss of DNA copies
array CGH
49
why cant array CGH detect Philadelphia chromosome (translocation between 9 and 22)
it can only detect additions and deletions of chromosomes and not balanced translocations
50
why can SKY FISH detect Philadelphia chromosome (translocation between 9 and 22)
because each chromosome is painted a different color so it will show chromosomes having two different colors in this case
51
FISH can detect deletions at about how bp levels
~100,000 bp
52
involves labeling genomic DNA fragments and allowing them to hybridize to DNA spots adhered onto a microarray slide where each spot represents various alleles of a gene.
SNP microarray chips
53
advantage of SNP
identify hundreds of thousands of polymorphic sites in a single experiment
54
CYP450 is used for?
phase I metabolism of about 20% of prescribed drugs
55
can a person's allele affects how drug is metabolized
yes
56
DNA is isolated from a patient who was born with congenital malformation of several different organs. The patient’s DNA was broken into small pieces, labeled, and then compared to an equal amount of a reference standard by hybridization to an array of DNA probes that represent sequential regions of the genome separated by 50 kb. what technique is this?
array CGH - we are comparing to a reference
57
A patient is identified to have Prader Willi syndrome as a result of uniparental disomy. In this case, he has lost the paternal contribution of chromosome 15 and instead he has two copies of his maternal chromosome 15 which are sister chromatids (the non-disjunction occurred in meiosis 2). Which technology would best diagnose this condition?
SNP chip
58
microarray that contains features representing a set of known expressed (transcribed) sequences
cDNA microarray
59
what can cDNA be used for
May be used to identify a set of genes or all genes that are expressed in a cell or tissue May be used to compare gene expression between cell or tissue samples
60
are prices of sequencing genome going up or down
down
61
a method to obtain the base pair sequence of a piece of DNA
Sanger (dideoxy) sequencing
62
what does the dideoxynucleotide do to the DNA strand in sanger sequencing
it terminates the synthesis of the DNA strand by making sure the free 3' OH is absent
63
current method of sequencing uses what
fluorescence label and capillary electrophoresis
64
how can one tell the position of the base relative to the primer and the type of base in sequencing
position of the base - length of DN sequence | type of base - color of the DNA
65
A patient is suspected to have a genetic cause associated with his symptoms. A test is given which detects a deletion of 500,000 basepairs of DNA from his chromosome 7. What test was used to detect this?
array CGH could also use FISH - since you know exactly what you are asking for
66
what happens if you sequence a gene and you find a base pair that is altered on the second run, what do you infer?
could be a mistake or not so you run the sequence many more times
67
what happens if you sequence a gene and for a particular bp, half of the time, the bp shows T and the other half it shows as G. what do you infer?
polymorphism or mutation
68
analysis that can be used to detect and quantify the amount of a particular protein
western blotting
69
detection using a labeled antibody system (typically an enzyme label and a chemiluminescent substrate)
western blotting
70
methods that only focus on one gene
southern, northern, western, sequencing of PCR product, ASO detection on DNA, allele specific primers for PCR
71
Techniques that can detect only what is asked for
ASO blot, PCR, FISH, southern
72
point mutation that does not change the AA code
silent mutation
73
point mutation that changes the protein
missense mutation
74
point mutation that creates a stop code
nonsense mutation
75
mutation that changes base from one purine to another purine, or one pyrimidine to another pyrimidine
transition mutation
76
mutation when a purine is replaced by a pyrimidine or vise versa
transversion mutation (less common)

Genetics (19 decks)

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