Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

AMT II > AMT II FINAL > Flashcards

AMT II FINAL Flashcards

1
Q

do all cells that express Class II
HLA proteins also express Class I?

A

yes

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

what do EGFR mutations in NSCLC cause?

A

constitutively active tyrosine kinase activity

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

is TMA/NASBA performed at one constant temperature?

A

yes

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

after virologic suppression, an isolated detectable HIV-RNA level that is followed by a return to virologic suppression

A

Virologic blip

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

the range of results expected in the “normal population”

A

reference range

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

what is TMA/NASBA primarily used to detect?

A

RNA viruses
CTNG testing
CMV & HIV viral load quantification
M. Tuberculosis detection in positive respiratory smears

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

the UGT1A1 *28 allele is associated with…..

A

irinotecan toxicity

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

-annotation of variants for sense making
-visualization for further QA/QC
- interpretation and disease association

A

tertiary analysis

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

S. aureas confers resistance to what bc of what gene?

A

oxacillin; mecA

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

comparing the consensus to a reference sequence
ex: comparing a patients BRCA gene with the normal published BRCA gene

A

alignment

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

what is LAMP best for?

A

rapid detection of a single target in a field or mobile lab setting

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

what does the c.-1639G>A mutation in VKORC1 cause?

A

the A allele reduces gene expression, warfarin has higher impact on the enzyme to lower active vit K and reduce clotting

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

what does a 1 mean in the context of ddPCR?

A

a signal was detected

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

what does molecular diagnostics of cancer tell us?

A

details on cancer typing, prognosis, and prediction of response to therapy

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

disease is present, molecular diagnosis established its characteristics to provide actionable information for treatment

A

diagnosis

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

how much of a viral load change is enough to be clinically or statistically significant?

A

0.5log change

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

if TMPT is deficient what does this mean for thiopurine drugs?

A

they will not be inactivated, causing toxicity

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

what is the read length for illumina and ion torrent sequencing?

A

100-600bp

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q
  • instrument specific steps to call base pairs and compute quality scores
  • demultiplexing, adapter trimming, quality control
A

primary analysis

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

what is the goal of prenatal diagnosis?

A

inform couples of the risk for birth defects and provide informed choices. testing fetus “at known risk”

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

number of reads that cover a specific locus

A

coverage

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

How can donor cells be differentiated from recipient cells when a bone marrow transplant has been done?

A

STR analysis by fragment analysis

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

CYP2D6 activates ____ and deactivates _______

A

codeine; tricyclic antidepressants

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

if your VKORC1 genotype is G/A, what does that mean?

A

intermediate drug response; medium dose needed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Hepatitis C virus
5' untranslated UTR
26
if you have cervical cancer do you likely have HPV?
yes
27
what does CYP2C19 loss of function cause?
prevent the conversion to the active drug, reduced inhibition of clotting | redueced inhibition: body's natural mechanisms for preventing excessive
28
what is the goal of HIV therapy?
to get the viral load below the limit of detection of the assay (<20cp/mL)
29
what is the mutation for the KRAS codon 12?
G12V: 35G>T
30
two consecutive plasma HIV-RNA levels >200 copies/mL after 24 weeks on an ARV regimen in a patient who has not yet had documented virologic suppression on that regimen
incomplete virologic response
31
Does ddPCR allow for relative or absolute quantification?
absolute
32
- quality control of raw reads (FASTQ) - alignment or de novo assembly of reads (BAM) - quality filtering and variant calling (VCF)
secondary analysis
33
mycoplasma pnuemoniae
16S rRNA
34
is RNA the final result of amplification in TMA/NASBA?
yes
35
neisseria gonorrhoeae
opa
36
what kind of file is used for coverage and variant calling?
VCF
37
what are the most common high risk strains of HPV?
16 and 18
38
after virologic suppression, confirmed HIV-RNA level >200 copies/mL
virologic rebound
39
m. tuberculosis confers resistance to what antibiotic because of rpoB?
rifampin
40
what is the formula for positive predictive value?
TP/TP+FP
41
what are the most common mutations in EGFR in NSCLC
LREA exon 19/20 deletion and exon 21 point mutation L858R
42
what are limitations of NIPS?
mosaicism, disease incidence, not definitive
43
if you are an ultra rapid metabolizer for codeine what does that mean?
increased morphine formation; avoid (toxic)
44
bordatella pertussis
IS 481
45
"final sequence" determined by the assembled reads
consensus sequence
46
what are the limitations of TMA/NASBA?
- increased risk of cross contamination - RNA degradation - cannot distinguish between transient infections or on-going infections
47
mutations that cause either duplications or deletions of large sections of a gene, an entire gene, or genomic segment containing several genes
copy number variants
48
what fold change is a 0.5log change?
3-fold
49
if your VKORC1 genotype is A/A, what does that mean?
high drug response; low dose
50
this is done to assess cancer risk,, likelihood of being diagnosed in the future
screening
51
the full range of reported values
reportable range
52
- reversible termination - fragments captured on a lawn of adapter complementary oligos -bridge amplification -paired-end reads
Illumina sequencing
53
chlamydophila pneumoniae
MOMP
54
the comparison of certain assay performance characteristics to parameters that are already established
verification
55
what HLA class II molecule must you identify for a bone marrow transplant?
HLA-DR
56
if you are a poor metabolizer for codeine what does that mean?
no pain relief; avoid bc ineffective
57
what are limitations of pharmogenomics?
- star allele nomenclature does not capture nuances between variants - assays have limited test targets - physicians largely uneducated - need more studies
58
what does UGT1A1 do?
conjugates glucuronic acid, allowing for liver or kidney excretion of the drugs
59
what is the most common target for HIV viral load assays?
gag gene
60
defined as lowest viral quantity that can be quantified
lower limit of quantification
61
a sequenced molecule
read
62
salmonella confers resistance to what antibiotic because of gyrA, gyrB, parC, parE?
quinolones
63
HLA Class II proteins are present where and on which types of cells?
on the surface of professional antigen presenting cells B-lymphs, monocytes, macrophages, and dendritics cells
64
how can you detected the UGT1A1 *28 allele?
fragment analysis on the capillary electrophoresis instrument
65
chlamydia trachomatis
MOMP
66
what does CRISPR stand for?
Clustered Regularly Interspaced Short Palindromic Repeats
67
EGFR is ___ in colorectal cancer
overexpressed/amplified
68
defined as the lowest viral quantity that can be detected
limit of detection
69
if you have HPV do you have cervical cancer?
no
70
which monoclonal antibody can be used to treat an EGFR mutation in colorectal cancer?
cetuximab
71
what is the mutation for the KRAS codon 13?
G13D: 38G>A
72
what can microarrays be used to detect?
SNPs, measure gene expression, or chromosomal abnormalities
73
what is the formula for clinical specificity?
TN/TN+FP
74
RSV
Fusion glycoprotein F gene Nucleoprotein N gene
75
what molecular technique is described below: DNA will hybridize with the probes, extend, and the fluorescence will be recorded. Any DNA that does not bind with the immobilized probes is washed away.
microarray
76
the range of results expected in the normal population
reference range
77
what does a 0 mean in the context of ddPCR?
a signal was not detected
78
this kind of screening used HPV as the first line test for cervical cancer risk analysis (pap smear is only done as a follow up)
primary screening
79
if you have a KRAS mutation do you have a BRAF mutation?
no they are mutually exclusive
80
- ZMW has a polymerase molecule immbolized at the bottom - phospholinked fluorescent nucleotides are pushed through the ZMW - as nucleotides are incorporated, fluorescence is cleaved, signal is produced
SMRT sequencing (pac-bio)
81
- relies on the release of a hydrogen ion during base incorporation - detected with a semi conductor - worlds smallest pH meter - if two of the same nucleotides are incorporated in a row, the signal is twice as high - bead cluster amplification by emulsion PCR
ion torrent chemistry
82
streptococcus pnemoniae
lytA
83
the inability to achieve or maintain suppression of viral replication to HIV-RNA level <200 copies/mL
virologic failure
84
gram- negatives confer resistance to _______ because of _______(gene)?
beta lactams; tem,shv,oxa,ctx-m
85
what are the benefits of TMA/NASBA??
high sensitivity, isothermal, fast can be done in 15-30 minutes
86
confirmed detectable HIV-RNA level <200 copies/uL
low-level viermia
87
what is the common gene of interest for HIV drug resistance testing?
pol gene
88
if you are a poor metabolizer for tricyclic antidepressants, what does that mean?
reduced inactivation of active drug; drug concentration is high in the plasma; avoid bc toxic or reduce dose by 50%
89
a confirmed HIV-RNA level below the LLOD of available assays
virologic suppression
90
what does SMRTs stand for
single molecule real time sequencing
91
the usefulness of a test for clinical practice - test leads to different treatment - test leads to fewer additional test - test leads to decision not to treat (benign vs malignant)
clinical utility
92
What is the point of CRISPR?
CRISPR/Cas is a gene editing tool used on cells, tissues, and whole organisms. scientists can modify the sequence before DNA is repaired naturally
93
HLA class I proteins are present where and on which types of cells?
surface of all nucleated cells and platelets
94
the full range of reported values
reportable range
95
what is the purpose of TMPT?
inactivate drugs used for ALL and inflammatory diseases
96
number of bases in the read
read length
97
what kind of file is used for alignment where the reads are compared to a reference sequence?
SAM/BAM
98
sorting the reads together using overlapping areas taking a few reads together and building contigs and then scaffolds
assembly
99
required for laboratory developed tests or if an FDA approved test is modified
Validation
100
what kind of file is used for primary analysis (sequencing) and base calling?
FASTQ
101
-immobilized pores pull molecules of DNA through pore - each nucleotide interrupts ion-flow and that change is recorded - no PCR -no DNA synthesis
Nanopore
102
what is the formula for clinical sensitivity?
TP/TP+FN
103
m. tuberculosis confers resistance to isoniazid because of what genes?
katG,inhA
104
If your VKORC1 genotype is G/G what does that mean?
low drug response; high dose needed
105
Streptococcus pneumoniae confers resistance to _____ because of ____(gene)?
penicillin; pbp1a and pbp1b
106
in which codons are the mutations in KRAS present?
12 and 13
107
what are the 3 parts of the pol gene?
protease, reverse transcriptase, and integrase
108
what is the goal of prenatal screening?
identify pregnancies for which prenatal diagnosis should be offered. tests for birth defects/ disorders "without a known risk"
109
mycobacterium tuberculosis
16S rRNA
110
if you are an ultrarapid metabolizer for tricyclic antidepressants, what does that mean?
build up of inactive metabolites; inaffective
111
which HPV genes are targeted when looking for cancer?
E6 & E7
112

AMT II (5 decks)

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