AMT II FINAL Flashcards
do all cells that express Class II
HLA proteins also express Class I?
yes
what do EGFR mutations in NSCLC cause?
constitutively active tyrosine kinase activity
is TMA/NASBA performed at one constant temperature?
yes
after virologic suppression, an isolated detectable HIV-RNA level that is followed by a return to virologic suppression
Virologic blip
the range of results expected in the “normal population”
reference range
what is TMA/NASBA primarily used to detect?
RNA viruses
CTNG testing
CMV & HIV viral load quantification
M. Tuberculosis detection in positive respiratory smears
the UGT1A1 *28 allele is associated with…..
irinotecan toxicity
-annotation of variants for sense making
-visualization for further QA/QC
- interpretation and disease association
tertiary analysis
S. aureas confers resistance to what bc of what gene?
oxacillin; mecA
comparing the consensus to a reference sequence
ex: comparing a patients BRCA gene with the normal published BRCA gene
alignment
what is LAMP best for?
rapid detection of a single target in a field or mobile lab setting
what does the c.-1639G>A mutation in VKORC1 cause?
the A allele reduces gene expression, warfarin has higher impact on the enzyme to lower active vit K and reduce clotting
what does a 1 mean in the context of ddPCR?
a signal was detected
what does molecular diagnostics of cancer tell us?
details on cancer typing, prognosis, and prediction of response to therapy
disease is present, molecular diagnosis established its characteristics to provide actionable information for treatment
diagnosis
how much of a viral load change is enough to be clinically or statistically significant?
0.5log change
if TMPT is deficient what does this mean for thiopurine drugs?
they will not be inactivated, causing toxicity
what is the read length for illumina and ion torrent sequencing?
100-600bp
- instrument specific steps to call base pairs and compute quality scores
- demultiplexing, adapter trimming, quality control
primary analysis
what is the goal of prenatal diagnosis?
inform couples of the risk for birth defects and provide informed choices. testing fetus “at known risk”
number of reads that cover a specific locus
coverage
How can donor cells be differentiated from recipient cells when a bone marrow transplant has been done?
STR analysis by fragment analysis
CYP2D6 activates ____ and deactivates _______
codeine; tricyclic antidepressants
if your VKORC1 genotype is G/A, what does that mean?
intermediate drug response; medium dose needed
Hepatitis C virus
5’ untranslated UTR
if you have cervical cancer do you likely have HPV?
yes
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
what is the goal of HIV therapy?
to get the viral load below the limit of detection of the assay (<20cp/mL)
what is the mutation for the KRAS codon 12?
G12V: 35G>T
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
Does ddPCR allow for relative or absolute quantification?
absolute
- quality control of raw reads (FASTQ)
- alignment or de novo assembly of reads (BAM)
- quality filtering and variant calling (VCF)
secondary analysis
mycoplasma pnuemoniae
16S rRNA
is RNA the final result of amplification in TMA/NASBA?
yes
neisseria gonorrhoeae
opa
what kind of file is used for coverage and variant calling?
VCF
what are the most common high risk strains of HPV?
16 and 18
after virologic suppression, confirmed HIV-RNA level >200 copies/mL
virologic rebound
m. tuberculosis confers resistance to what antibiotic because of rpoB?
rifampin
what is the formula for positive predictive value?
TP/TP+FP
what are the most common mutations in EGFR in NSCLC
LREA exon 19/20 deletion and exon 21 point mutation L858R
what are limitations of NIPS?
mosaicism, disease incidence, not definitive
if you are an ultra rapid metabolizer for codeine what does that mean?
increased morphine formation; avoid (toxic)
bordatella pertussis
IS 481
“final sequence” determined by the assembled reads
consensus sequence
what are the limitations of TMA/NASBA?
- increased risk of cross contamination
- RNA degradation
- cannot distinguish between transient infections or on-going infections
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
what fold change is a 0.5log change?
3-fold
if your VKORC1 genotype is A/A, what does that mean?
high drug response; low dose
this is done to assess cancer risk,, likelihood of being diagnosed in the future
screening
the full range of reported values
reportable range
- reversible termination
- fragments captured on a lawn of adapter complementary oligos
-bridge amplification
-paired-end reads
Illumina sequencing
chlamydophila pneumoniae
MOMP
the comparison of certain assay performance characteristics to parameters that are already established
verification
what HLA class II molecule must you identify for a bone marrow transplant?
HLA-DR
if you are a poor metabolizer for codeine what does that mean?
no pain relief; avoid bc ineffective
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
what does UGT1A1 do?
conjugates glucuronic acid, allowing for liver or kidney excretion of the drugs
what is the most common target for HIV viral load assays?
gag gene
defined as lowest viral quantity that can be quantified
lower limit of quantification
a sequenced molecule
read
salmonella confers resistance to what antibiotic because of gyrA, gyrB, parC, parE?
quinolones
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
how can you detected the UGT1A1 *28 allele?
fragment analysis on the capillary electrophoresis instrument
chlamydia trachomatis
MOMP
what does CRISPR stand for?
Clustered Regularly Interspaced Short Palindromic Repeats
EGFR is ___ in colorectal cancer
overexpressed/amplified
defined as the lowest viral quantity that can be detected
limit of detection
if you have HPV do you have cervical cancer?
no
which monoclonal antibody can be used to treat an EGFR mutation in colorectal cancer?
cetuximab
what is the mutation for the KRAS codon 13?
G13D: 38G>A
what can microarrays be used to detect?
SNPs, measure gene expression, or chromosomal abnormalities
what is the formula for clinical specificity?
TN/TN+FP
RSV
Fusion glycoprotein F gene
Nucleoprotein N gene
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
the range of results expected in the normal population
reference range
what does a 0 mean in the context of ddPCR?
a signal was not detected
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
if you have a KRAS mutation do you have a BRAF mutation?
no they are mutually exclusive
- 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)
- 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
streptococcus pnemoniae
lytA
the inability to achieve or maintain suppression of viral replication to HIV-RNA level <200 copies/mL
virologic failure
gram- negatives confer resistance to _______ because of _______(gene)?
beta lactams; tem,shv,oxa,ctx-m
what are the benefits of TMA/NASBA??
high sensitivity, isothermal, fast can be done in 15-30 minutes
confirmed detectable HIV-RNA level <200 copies/uL
low-level viermia
what is the common gene of interest for HIV drug resistance testing?
pol gene
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%
a confirmed HIV-RNA level below the LLOD of available assays
virologic suppression
what does SMRTs stand for
single molecule real time sequencing
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
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
HLA class I proteins are present where and on which types of cells?
surface of all nucleated cells and platelets
the full range of reported values
reportable range
what is the purpose of TMPT?
inactivate drugs used for ALL and inflammatory diseases
number of bases in the read
read length
what kind of file is used for alignment where the reads are compared to a reference sequence?
SAM/BAM
sorting the reads together using overlapping areas
taking a few reads together and building contigs and then scaffolds
assembly
required for laboratory developed tests or if an FDA approved test is modified
Validation
what kind of file is used for primary analysis (sequencing) and base calling?
FASTQ
-immobilized pores pull molecules of DNA through pore
- each nucleotide interrupts ion-flow and that change is recorded
- no PCR
-no DNA synthesis
Nanopore
what is the formula for clinical sensitivity?
TP/TP+FN
m. tuberculosis confers resistance to isoniazid because of what genes?
katG,inhA
If your VKORC1 genotype is G/G what does that mean?
low drug response; high dose needed
Streptococcus pneumoniae confers resistance to _____ because of ____(gene)?
penicillin; pbp1a and pbp1b
in which codons are the mutations in KRAS present?
12 and 13
what are the 3 parts of the pol gene?
protease, reverse transcriptase, and integrase
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”
mycobacterium tuberculosis
16S rRNA
if you are an ultrarapid metabolizer for tricyclic antidepressants, what does that mean?
build up of inactive metabolites; inaffective
which HPV genes are targeted when looking for cancer?
E6 & E7
