Angela's Laboratory Tests and Stats Flashcards
What does Western blot evaluate?
Protein
- Measure whether a specific protein is expressed in a sample by running it on a gel, transferring the resolved proteins onto a special piece of membrane, which will be exposed to an antibody to the specific protein of interest. The antibody is labeled with a molecule that can be visualized, indicating whether the protein of interest is expressed in this sample and how abundant it is, as well as understanding what size the protein is.
What is the screening test for HIV?
Elisa
Up to date: Preferred testing algorithm uses a combination antigen/antibody HIV-1/2 immunoassay (detects IgM and IgG to HIV1 and 2 and p24 antigen) which is more sensitive, followed by a confirmatory HIV-1/HIV-2 antibody differentiation immunoassay if the antigen/antibody screening test is positive. HIV1/2 immunoassay detect HIV-1 and HIV-2 antibody as early as 3 weeks after exposure.
ELISAs antibody only tests (IgM and IgG to HIV1 only) can also be used as initial screening test, although have Iesser sensitivity for detecting acute infection compared with the immunoassy test above.
What is the confirmatory test for HIV?
For example: the screening test is +, which test do you order to confirm this?
up to date answer: HIV-1/HIV-2 differentiation immunoassay (targets antibodies to HIV1/HIV2 antigents) is the preferred confirmatory test.
Angela’s answer: Western Blot also acceptable.
In the past, it was the Western blot but takes days to weeks to return.
*Some patients may have a positive antigen/antibody test followed by a negative confirmatory test. This is considered an indeterminate test result and should typically be evaluated with an HIV RNA assay. HIV RNA testing should also be performed if there is concern for acute HIV infection.
Herpes Simplex Virus testing?
DNA detection via PCR or culture of the virus
*PCR is the most SENSITIVE
HPV testing?
Angela’s: PCR
Up to date: situ hybridization or PCR which both detect HPV DNA (Head and Neck Testing). Pap smear HPV testing doesn’t specifically say PCR.
What is the best test to amplify small quantities of DNA?
PCR
What does FISH test for?
Chromosomal analysis identifying gene copy number and location at a specific locus.
The number of chromosomes or their structural makeup:
Duplication/amplification
Deletion
Translocation
Aneuploidy and the presence of derivative (structurally rearranged) chromosomes.
Which test should be used to confirm number of DNA gene copies of ERBB2 prior to initiating treatment?
FISH
*Overexpression of the HER2 protein product – Western blotting, enzyme-linked immunosorbent assay (ELISA), or immunohistochemistry (IHC).
*HER2 gene amplification by in situ hybridization (ISH) – Fluorescence in situ hybridization (FISH), chromogenic in situ hybridization (CISH), silver-enhanced in situ hybridization (SISH), or differential polymerase chain reaction (PCR).
Which test would be used to confirm loss of heterozygosity in tumor suppressor genes?
FISH
What is the best way to identify a tumor suppressor gene in the lab?
Test for loss of heterozygosity
What does comparative genomic hybridization do?
Assesses the whole genome for gene copy number, a microarray platform
analysing copy number variations (CNVs) relative to ploidy level in the DNA of a test sample compared to a reference sample
*Analyse copy number variations relative to ploidy level in the DNA of a test sample compared to a reference sample. It aims at quickly and efficiently compareing two genomic DNA samples arising from two sources, which are most often closely related, because it is suspected that they contain differences in terms of either gains or losses of either whole chromosomes or subchromosomal regions. CGH is only able to detect umbalanced chromosomal abnormalities.
CGH
Comprehensive (whole genome)
Genome
H kind of looks like # for number
What does Southern Blot evaluate?
DNA - by breaking into DNA fragments and labelling
Southern blot analysis can be used to investigate whether a gene is amplified, deleted, or structurally rearranged in cancer cells as compared to normal cells.
Looking at a compass: South is on the bottom because DNA is the foundation / building block of life
What does Northern blot evaluate?
A northern blot is a laboratory method used to detect specific RNA molecules among a mixture of RNA. Northern blotting can be used to analyze a sample of RNA from a particular tissue or cell type in order to measure the RNA expression of particular genes.
Which is larger, standard deviation or standard error of the means?
Standard deviation
Standard deviation measures the variability from specific data points to the mean. (One experiment)
Standard error of the mean measures the precision of the sample mean (our one experiment) to the population mean that it is meant to estimate (repeat the experiment with different groups ten times and take the mean) aka the mean of the mean
What is the best test to compare values from the same patient before and after a drug is used?
Paired t test
What is a students t-test?
A test used to provide a confidence interval for an estimated mean or difference of means
used to determine if the means of two (normally distributed) groups are statistically different when the Standard Dev is unknown
students T test=unpaired T test
What is type 1 error?
Incorrect rejection of the null
(Null is correct, you aren’t)
Difference found by chance
What is alpha error?
A test’s probability of making a type 1 error
Difference found by chance
What does an alpha of .05 mean?
There is a 5% chance of making a type 1 error
What is the confidence level?
Confidence level = 1-alpha
The confidence level equals 100*(1 - alpha)%, or in other words, an alpha of 0.05 indicates a 95 percent confidence level.
What is type 2 error?
Incorrect failure to reject the null (Beta)
(Null is wrong but you think it’s correct)
There was a difference that you did not detect
What is beta error?
A test’s probability of making a type 2 error
There was a difference that you did not detect
What does a beta of 10% mean?
there is a 10% chance of making a type 2 error
What is the power?
Power=1-beta
Reflects the ability of a study to detect an actual effect
🙌 you have the power 🙌
What is a receiver-operator curve (ROC)?
A plot of sensitivity by 1-specificity
1- Specificity = Probability that a true negative will test positive. = FP / N Also referred to as False Positive Rate (FPR)
True positive (y-axis) vs. False positive (x-axis)
What does a receiver-operator curve (ROC) tell you?
The performance of a diagnostic test
AUC 1.0 is perfect test
AUC 0.5 is chance
What “cutpoint” are you looking for when you look at a receiver-operator curve (ROC)?
The point that optimizes sensitivity and specificity
Ideally AUC closest to 1
In what study do you use an odds ratio?
Case-control
What is an odds ratio?
Odds of exposure in the disease group divided by odds of exposure in the non-diseased group
Estimate of relative risk
The odds ratio (OR) is a measure of how strongly an event is associated with exposure. The odds ratio is a ratio of two sets of odds: the odds of the event occurring in an exposed group versus the odds of the event occurring in a non-exposed group. Odds ratios commonly are used to report case-control studies
What is the most appropriate initial type of study to determine risk factors for a rare disease?
Case control
In what study do you use relative risk?
Prospective studies like Cohort studies and clinical trials
What does relative risk measure?
Risk of disease or death in a population exposed to some factor of interest divided by the risk in those not exposed
Absence of association RR=1
Exposure may indicate increased risk RR>1
Exposure may indicate decreased risk RR<1
[a/(a+b)] / [c/(c+d)]
What is the best initial test to perform to determine the relationship between prenatal vitamin use and ovarian cancer?
Case control
What is variance?
The sum of the squared deviations of measurements from their mean
variance measures how far each number in the set is from the mean (average), and thus from every other number in the set
Square of standard deviation
What is standard deviation?
The square root of the variance
Fixed value reflecting variability within a single population
Given Gausian distribution, how many scores should fall within one standard deviation of the mean? two? three?
One: 68%
Two: 95%
Three: 99.7%
Given Gausian distribution, what percentage of people lie greater than two standard deviations above the mean? below?
Above 2.5%
Below 2.5%
How does the standard deviation change as the population increases?
Trick question!
It doesn’t
What is standard error?
The measure of the variability of the sample mean. It reflects how much the average value you get from a sample (of any size) might deviate from the true population mean. As the sample size increases, the standard error tends to decrease because a larger sample provides a more precise estimate of the population mean.
How does the standard error change as the population increases?
It becomes smaller
The SE is standard deviation divided by the square root of the sample size
Standard deviation measures the variability from specific data points to the mean. (One experiment)
Standard error of the mean measures the precision of the sample mean (our one experiment) to the population mean that it is meant to estimate (repeat the experiment with different groups ten times and take the mean) aka the mean of the mean
Is the standard error of the mean larger or smaller than the standard deviation?
Smaller
Which of the following is dependent on prevalence of disease?
a. positive predictive value (PPV)
b. sensitivity
c. specificity
PPV
A PPV cannot be calculated from a case-control study
How do you compare survival rates among groups?
Kaplan Meier (curve)
Estimate, graphical representation
Use log-rank to mathematically test for a difference between the two groups
What does ROC stand for?
Receiver operator curve
What affects positive predictive value?
Prevalence of disease
You have a nominal variable with normal distribution. What test do you use?
Chi square
chi-square test is used to help determine if observed results are in line with expected results and to rule out that observations are due to chance
A chi-square test is appropriate for this when the data being analyzed are from a random sample, and when the variable in question is a categorical (or nominal) variable AND normally distributed
A nominal variable is one that describes a name, label or category without natural order. Sex and type of dwelling are examples of nominal variables
If paired (nominal) data, use McNemar’s test
What is attributable risk?
Attributable risk (AR) or risk difference
(Risk of disease or death in an exposed population) - (risk in unexposed population)
A number >0 may indicate exposure increased risk of disease
A number <0 may indicated exposure decreases risk
What is a case-control study?
Diseased and non-diseased populations are selected, existing or past characteristics (exposures) are assessed to determine the possible relationship between exposure and disease
*Start with diseased cases, then select sample of non-diseased controls who are representative of the underlying population that gave rise to the cases
What is a cohort study?
Groups to be studied are defined by characteristics (or exposures) that occur before the disease of interest, and the study groups are followed to observe the risk f disease in the cohorts
*Start with exposed and non-exposed individuals who are monitored over time to identify the number of diseased cases that develop
What is a chi-square test?
Tests the null hypothesis that proportions are equal or that nominal/categorical variables are independent (per B&H)
a.k.a. compare the observed values in your data to the expected values that you would see if the null hypothesis is true
data must be from a random sample and variable must be nominal / categorical
Non-parametric
What is an unpaired t-test?
Compares two means from independent samples
testing mean = parametric/normal distribution data (AW)
use for continuous data (AW)
What is a paired t-test?
Compares the difference or change in a numerical variable for matched or paired groups or samples
compares means of two paired or same groups-at diff time points (reminder, mean=parametric data) (AW)
used on continuous numerical data (AW)
What are the two types of validity?
Internal=freedom from bias; bias refers to a systematic error in design, conduct or analysis of a study that results in a mistaken conclusion; types of bias= observation, selection, confounding
External=ability to generalize the results observed from one study population to another
What does it mean to stratify groups?
To examine the association of interest within groups that are similar with respect to a potential confounder
used to control confounding bias in the analytic portion of a study (AW)
What is multivariate analysis?
Technique that controls for several confounders simultaneously
What criteria are important in judging an epidemiologic study?
Biologic credibility
Effect of removing the causal agent
Strength of the association
Temporality-exposure precedes disease
Consistency
Dose-response
BEST CD
What does a meta-analysis study?
Results from independent studies examining the same exposure (or treatment) and outcome are combined so that a more powerful test of the null hypothesis may be conducted
What is the log-rank test?
Used in survival analysis to compare the distribution of time to event/survival distributions in two independent samples
Used in simple situations with a single factor with only two values (ex: difference in survival time when two different drugs are given)
Cox regression used in more complicated situations
AKA Mantel-Cox test. Best in right skewed (nonparametric) data (AW)
What is used to compare the relative risk associated with multiple variables in a stepwise fashion?
Multiple regression analysis
aka multiple linear regression = continous dependent variables
multiple logistic regression = noncontinous/categorical dependent variables
What is multiple regression analysis?
analyzes the relationship between a single dependent variable and several independent variables. The objective of multiple regression analysis is to use the independent variables, whose values are known, to predict the value of the single dependent value.
The goal of multiple linear regression is to model the linear relationship between the explanatory (independent) variables and response (dependent) variables
aka multiple linear regression
When do you use a student’s t test v ANOVA?
Student’s t is used to compare means between two groups
ANOVA is used to compare the means among three or more groups
“Tea for TWO”
superNOVA = big = 3+…kinda a stretch
(AW)
both require parametric data (AW)
What is the Wilcoxon test?
Wilcoxon signed rank test
Tests whether the mean values of two dependent groups (paired data) differ significantly from each other
Non-parametric test = subject to fewer assumptions than its parametric counterpart the t-test for dependent samples
Wilcoxon test is used when the 6 required boundary conditions for the t-test for dependent samples are no longer fulfilled: Independent observations, Normality, Equal variances, Random sampling, Interval or ratio data, Homogeneity of variance.
What is the Mann-Whitney U test?
Tests whether there is a difference between two indepdendent/unpaired samples (groups) and the data need not be normally distributed.
It is the non-parametric counterpart to the t-test for independent samples–it is used when the requirement of normal distribution for the t-test is not met
What is cox regression?
used in survival time analysis: determine the influence of several different variables on survival time–variables can be continuous, binary, or categorical
Allows you to determine the effects of multiple independent variables on a time-to-event outcome either to test hypotheses about the independent variables or to build a predictive model (ex: effect of drug and age on survival time
aka Cox proportional hazards survival regression
Which condition will require a larger sample size to detect statistical significance?
An outcome with smaller effect size
What test do you use to determine effects of multiple factors on survival?
Cox regression
Cox proportional hazards regression
What tests can be used for independent variables?
ANOVA (for 3+ dependent or independent, parametric)
Mann-Whitney U (2 groups, nonparametric)
Kruskal-Wallis (3 groups, nonparametric)
Wilcoxon, paired t-test for dependent only
Unpaired T test/Students T test should also be for two independent variables, parametric data (AW)
What are examples of randomization strategies?
Simple: based on a single sequence of random assignments. “coin flip”
**Block: ** randomize participants into groups that result in equal sample sizes–ensure a balance in sample size across groups over time. groups may be generated that are not comparable in terms of certain covariates.
Stratified: addresses the need to control and balance the influence of covariates–achieve balance among groups in terms of participants baseline characteristics
Covariate adaptive: new participant is sequentially assigned to a particular treatment group by taking into account the specific covariates and previous assignments of participants–uses method of minimization by assessing the imbalance of sample size among several covariates
How do you calculate sensitivity, specificity, positive predictive value, negative predictive value?
Sensitivity= [a/(a+c)] x100
Specificity= [d/(b+d)] x100
Positive predictive value= [a/(a+b)] x100
Negative predictive vale=[d/(c+d)] x100
ab
cd
a=true positive (has the condition and tests positive)
b=false positive (doesn’t have the condition but tests positive)
c=false negative (has the condition but tests negative)
d=true negative (doesn’t have the condition and tests negative)
