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Genetics > Molecular Diagnostics - 3 lectures > Flashcards

Molecular Diagnostics - 3 lectures Flashcards

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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
Q

what are the triple repeat disorders and what method is used to detect them

A

fragile X, huntingtons, myotonic dystrophy

PCR

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26
Q

how can PCR tell you it is triple repeat disorder

A

the size of the PCR product - the genotype will have a lot more than normal repeats

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27
Q

how will the PCR product of a person with triple repeat disorder show on the agarose gel

A

the DNA wouldn’t travel as far as the normal one because it is too big

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28
Q

PCR can be used to detect

A

Duchenne because it is a deletion

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29
Q

limitations to PCR

A

difficult to optimize so can’t detect carriers

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30
Q

can be used to detect aneuploidy, insertions, deletion, large translocations

A

karyotyping (G banding)

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31
Q

disadvantages to karyotyping

A

only detects large alterations (deletion >5kb or even more) and has low resolution

32
Q

in G banding, the dark and light bands represent what

A

dark: A-T rich region
light: C-G rich region

33
Q

keypoint of FISH

A

resolution is improved over G banding

34
Q

how long are the probes in FISH

A

10-100kB

35
Q

difference between the two types of FISH (SKY FISH and chromosome specific)

A

SKY FISH - paints the whole chromosome a specific color

chromosome specific - hybridizes to a specific locus on the chromosome (only one locus)

36
Q

DiGeorge’s Syndrome or 22q11.2 is detected using what method

A

FISH

can also use G banding but might not get great results

37
Q

what is abnormal in digeorges

A

pharyngeal arch development

38
Q

symptoms of digeorge’s

A

CATCH22

cardiac anomaly most important

39
Q

advantage of FISH

A

better resolution of G banding

40
Q

disadvantage of FISH

A

have to know exactly what you are looking for

41
Q

FISH can be used to detect what disorder

A

trisomy

42
Q

SKY FISH most importantly used to detect

A

translocations since it colors each chromosome a specific color

43
Q

disadvantage of SKY FISH

A

can’t detect small deletions since whole chromosome is painted one color

44
Q

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

A

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
Q

advantage of array CGH

A

can detect copy number changes in DNA throughout the genome, genome amplification, deletions (CNV - copy number variant)

46
Q

disadvantage of array CGH

A

does not detect balanced rearrangements

47
Q

array CGH detect deletions and insertion at very high or very low resolution?

A

high resolution

48
Q

what method can detect gain or loss of DNA copies

A

array CGH

49
Q

why cant array CGH detect Philadelphia chromosome (translocation between 9 and 22)

A

it can only detect additions and deletions of chromosomes and not balanced translocations

50
Q

why can SKY FISH detect Philadelphia chromosome (translocation between 9 and 22)

A

because each chromosome is painted a different color so it will show chromosomes having two different colors in this case

51
Q

FISH can detect deletions at about how bp levels

A

~100,000 bp

52
Q

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.

A

SNP microarray chips

53
Q

advantage of SNP

A

identify hundreds of thousands of polymorphic sites in a single experiment

54
Q

CYP450 is used for?

A

phase I metabolism of about 20% of prescribed drugs

55
Q

can a person’s allele affects how drug is metabolized

A

yes

56
Q

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?

A

array CGH - we are comparing to a reference

57
Q

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?

A

SNP chip

58
Q

microarray that contains features representing a set of known expressed (transcribed) sequences

A

cDNA microarray

59
Q

what can cDNA be used for

A

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
Q

are prices of sequencing genome going up or down

A

down

61
Q

a method to obtain the base pair sequence of a piece of DNA

A

Sanger (dideoxy) sequencing

62
Q

what does the dideoxynucleotide do to the DNA strand in sanger sequencing

A

it terminates the synthesis of the DNA strand by making sure the free 3’ OH is absent

63
Q

current method of sequencing uses what

A

fluorescence label and capillary electrophoresis

64
Q

how can one tell the position of the base relative to the primer and the type of base in sequencing

A

position of the base - length of DN sequence

type of base - color of the DNA

65
Q

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?

A

array CGH

could also use FISH - since you know exactly what you are asking for

66
Q

what happens if you sequence a gene and you find a base pair that is altered on the second run, what do you infer?

A

could be a mistake or not so you run the sequence many more times

67
Q

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?

A

polymorphism or mutation

68
Q

analysis that can be used to detect and quantify the amount of a particular protein

A

western blotting

69
Q

detection using a labeled antibody system (typically an enzyme label and a chemiluminescent substrate)

A

western blotting

70
Q

methods that only focus on one gene

A

southern, northern, western, sequencing of PCR product, ASO detection on DNA, allele specific primers for PCR

71
Q

Techniques that can detect only what is asked for

A

ASO blot, PCR, FISH, southern

72
Q

point mutation that does not change the AA code

A

silent mutation

73
Q

point mutation that changes the protein

A

missense mutation

74
Q

point mutation that creates a stop code

A

nonsense mutation

75
Q

mutation that changes base from one purine to another purine, or one pyrimidine to another pyrimidine

A

transition mutation

76
Q

mutation when a purine is replaced by a pyrimidine or vise versa

A

transversion mutation (less common)

Genetics (19 decks)

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