Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

fall 2022 > exam 2 > Flashcards

exam 2 Flashcards

1
Q

normalized melting curves use

A

melting temp or dyes that fluoresce in the presence of dsDNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

unlabeled probe genotyping

A

used when greater detail or exact genotyping is needed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

snapback primer

A

unlabeled probes on the 5’ end of a primer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

snapback or unlabed primers are used for

A

common disease variants
subtyping viruses
epidemiology

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

factor V leiden genotyping

A

small amplicons, unlabeled probes, or snapback primers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

gilbert syndrome

A

increased drug toxicity
TA repeats in promoter or UGT1A1
small amplicon genotyping is used

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

methylation analysis is used to

A

dx imprinting disorders
give degree of methylation
(unmethylated CG are converted to TA in pretreatment bc methylation is lost in PCR)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

competitive PCR

A

used to detect exomic delections, trisomies, sex chromosome abnormalities

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

epigenetics

A

the study of mitotically heritable changes of a phenotype that do not result from changes in the genetic code

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

epigenetics are mediated by

A

postranscriptional histone modifications
histone variants
atp-dependent chromatin
small and noncoding RNAs
DNA methylation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

DNA methyhlation is

A

methyl group on 5’ position of cytosines in the context of a GpG that interferes with binding of transcriptional activators

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

CpG

A

75% methylated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

CpG islands

A

mostly actively transcribed
1-4kb
methylated islands are on inactivated chromosomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

theory of methylation

A

is essential for mammalian embryogenesis
origin of disease hypothesis
environmental influences
imprinting

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

there is altered methylation patterns in

A

cancer
neurodegenerative disorders
metabolic disorders
autoimmune disorders like lupus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

increase of methylation in promoter regions of tumor suppressors and signal transduction genes

A

APC

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

methylation of DNA repair

A

MGMT
MLH1
BRCA1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

methylation of detox genes

A

GSTP1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

methylated cell cycle regulators

A

p15
p16
RB

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

angiogenesis

A

THBS1
VHL

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

apoptosis

A

caspases
p14
DAPK

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

clinical application of methylation

A

determine ratio of meth:unmeth CpGs
- independent of starting material and expression levels
- can be done on almost any specimen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

changes in methylation

A

precede genetic changes
hypermethylation is seen prior to dysplastic changes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

DNA methylation as a prognostic indicator

A

ID tumor growth and recurrence
predict survival time
stratify tumor to aid in therapy decision
predict response to chemo

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
methylation content has cons like
no info on location of DNA meth on genome
26
genome wide analysis of methylation
-measures mRNA expression after treating cells w/ a methylation inhibitor -requires cell culture -leads to expression of epigenetically silenced genes -target and non target genes activated
27
other methods for genome wide methylation analysis
NGS anti-methyl cytosine antibodies purification of methylated DNA w/ MBD proteins
28
analysis of individual CpGs requires
PCR of MS digested DNA MS multiplex ligation dependent probe amplification (MS-MLPA)
29
Methylation‐specific PCR (A) consists of two primers binding to sites with one or more CpGs. When the correct methylation pattern is present, in this case complete methylation, an amplicon is formed that can be detected on a gel.
true
30
Maxam Gilbert Sequencing
a chain breakage at specific NTs are then separated by gel electrophoresis and detected by autoradiography read 5' to 3'
31
dimethyl sulfate
breaks at a G
32
Formic Acid
breaks at a G+A
33
Hydrazine
T and C
34
Hydrazine and salt
C
35
sanger sequencing is
modified DNA replication growing chains are terminated by ddNTPs
36
why can't ddNTPs bind
the 3'OH group is missing
37
sequencing ladder
fragments electrophoresed in 4 sample tubes and 4 lanes
38
Cycle sequencing utilizes
chain termination in a thermal cycler, uses one tube/capillary a dye primer heat stable DNA pol
39
cycle sequencing labels
fluorescein and rhodamine each letter has its own color which corresponds to peaks and are read on an electrophoretogram
40
dye primer is on
5'
41
dye terminator is on
3' end or ddNTPs
42
pyrosequencing is based on
light generated through release of a ppi on NT addition
43
pyrosequencing equation
PPi + APS -> ATP ATP + luciferase -> oxyluciferin + light
44
Next Gen Sequencing requires
a library custom linkers a solid surface/interface
45
NGS steps
1. shear high MW DNA 2. polish ends 4. ligate DNA adapters 4. produce fractions and quantitate 5. amplify on flow cell surface 6. denature to ssDNA 7. hybridize seq primers to the ssDNA 8. sequence or hybrid capture
46
issues w/ PCR
preferential amplification/jackpotting false + due to substitution errors bias in high and low C/G fragments
47
hybrid capture
fragments from WGS library are selected w probes that match target can purify w/ magnets
48
multiplex PCR
1. design overlapping primers from gene of interest 2. group primers according to G/C content/Tm 3. amplify 4. create library by ligation 5. sequence
49
single nucleotide RT sequencing/SMRT
phi 29 DNA pol very processive phospholinked florescent dNTPs
50
false negatives are often due to
lack of coverage
51
false positives are due to
variants in one strand variant at end of strand poor coverage or matching gene has paralogue increased sensitivity variant algorithims
52
application of NGS technology
WGS req database for spec mutations exome sequencing still need to consider regulatory region mutations*
53
targeted sequencing
isolate a subset of genes allows ID of rare variants
54
plasma DNA seq
ID fetal and tumor genetic material circulating in blood
55
transcripteomics
total mRNA req gives view of transcriptional profile
56
epigenetics
methylation sequencing CHIP seq bisulfite seq
57
whole genome seq
finds SNVs, deltetions, amplifications, translocations, inversions, indels, etc.
58
exome sequencing
validates WGS
59
ref-seq
over expression metrics SNVs gene fusions
60
ribosomal profiling
IDs rate of protein synthesis for predicting protein abundance translation control shows protected mRNA fragments
61
what does WGS analysis yield?
single nucleotide variants amplifications deletions translocations inversions indels
62
current limitations of WGS
order of variants on parental xsome is not retained difficulty mapping repetitive sequences incr error rates thousands of cells needed which excludes many cell types
63
WGSs clinical application
1st line of dx in sick children dx of developmental delay ID de novo mt/recessive alleles
64
goals of the non-invasive prenatal test
reduce exposure of fetus to risk reduce false pos enable incr detection easy testing available to all preg ppl
65
NIFTY -- non invasive fetal trisomy test
based on free fetal DNA in mom circulation good for detecting aneuploidy but not enough resolution to detect smaller variants causing disease
66
cancer profiling
focus on a select group of known cancer causing genes problems: tumor material % NL DNA vs tumor DNA formalin or parafin fixed
67
WGS in susceptibility testing
culture dependent no reliance on primers ascertain resistance by phenotype
68
whole meta-genome sequencing in susceptibility testing
culture independent determines relative abundance of resistance in a pop can't ID specific gene to a sub species or strain can ID AMR genes that are divergent
69
culture based analysis of S. aureus
spp ID in 4 hr MALDI-TOF confirmation at 12 hr further susceptibility testing w disks another 12-18 hrs
70
sequence vs culture based AMR analysis
sequencing is faster

fall 2022 (6 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions