Angela's Laboratory Tests and Stats

Question 1

What does Western blot evaluate?

Answer 1

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.

Question 2

What is the screening test for HIV?

Answer 2

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.

Question 3

What is the confirmatory test for HIV?

For example: the screening test is +, which test do you order to confirm this?

Answer 3

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.

Question 4

Herpes Simplex Virus testing?

Answer 4

DNA detection via PCR or culture of the virus

*PCR is the most SENSITIVE

Question 5

HPV testing?

Answer 5

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.

Question 6

What is the best test to amplify small quantities of DNA?

Answer 6

PCR

Question 7

What does FISH test for?

Answer 7

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.

Question 8

Which test should be used to confirm number of DNA gene copies of ERBB2 prior to initiating treatment?

Answer 8

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).

Question 9

Which test would be used to confirm loss of heterozygosity in tumor suppressor genes?

Answer 9

FISH

Question 10

What is the best way to identify a tumor suppressor gene in the lab?

Answer 10

Test for loss of heterozygosity

Question 11

What does comparative genomic hybridization do?

Answer 11

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

Question 12

What does Southern Blot evaluate?

Answer 12

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

Question 13

What does Northern blot evaluate?

Answer 13

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.

Question 14

Which is larger, standard deviation or standard error of the means?

Answer 14

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

Question 15

What is the best test to compare values from the same patient before and after a drug is used?

Answer 15

Paired t test

Question 16

What is a students t-test?

Answer 16

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

Question 17

What is type 1 error?

Answer 17

Incorrect rejection of the null

(Null is correct, you aren’t)

Difference found by chance

Question 18

What is alpha error?

Answer 18

A test’s probability of making a type 1 error

Difference found by chance

Question 19

What does an alpha of .05 mean?

Answer 19

There is a 5% chance of making a type 1 error

Question 20

What is the confidence level?

Answer 20

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.

Question 21

What is type 2 error?

Answer 21

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

Question 22

What is beta error?

Answer 22

A test’s probability of making a type 2 error

There was a difference that you did not detect

Question 23

What does a beta of 10% mean?

Answer 23

there is a 10% chance of making a type 2 error

Question 24

What is the power?

Answer 24

Power=1-beta

Reflects the ability of a study to detect an actual effect

🙌 you have the power 🙌

Question 25

What is a receiver-operator curve (ROC)?

Answer 25

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)

Question 26

What does a receiver-operator curve (ROC) tell you?

Answer 26

The performance of a diagnostic test
AUC 1.0 is perfect test
AUC 0.5 is chance

Question 27

What “cutpoint” are you looking for when you look at a receiver-operator curve (ROC)?

Answer 27

The point that optimizes sensitivity and specificity
Ideally AUC closest to 1

Question 28

In what study do you use an odds ratio?

Answer 28

Case-control

Question 29

What is an odds ratio?

Answer 29

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

Question 30

What is the most appropriate initial type of study to determine risk factors for a rare disease?

Answer 30

Case control

Question 31

In what study do you use relative risk?

Answer 31

Prospective studies like Cohort studies and clinical trials

Question 32

What does relative risk measure?

Answer 32

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)]

Question 33

What is the best initial test to perform to determine the relationship between prenatal vitamin use and ovarian cancer?

Answer 33

Case control

Question 34

What is variance?

Answer 34

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

Question 35

What is standard deviation?

Answer 35

The square root of the variance

Fixed value reflecting variability within a single population

Question 36

Given Gausian distribution, how many scores should fall within one standard deviation of the mean? two? three?

Answer 36

One: 68%
Two: 95%
Three: 99.7%

Question 37

Given Gausian distribution, what percentage of people lie greater than two standard deviations above the mean? below?

Answer 37

Above 2.5%
Below 2.5%

Question 38

How does the standard deviation change as the population increases?

Answer 38

Trick question!
It doesn’t

Question 39

What is standard error?

Answer 39

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.

Question 40

How does the standard error change as the population increases?

Answer 40

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

Question 41

Is the standard error of the mean larger or smaller than the standard deviation?

Answer 41

Smaller

Question 42

Which of the following is dependent on prevalence of disease?
a. positive predictive value (PPV)
b. sensitivity
c. specificity

Answer 42

PPV

A PPV cannot be calculated from a case-control study

Question 43

How do you compare survival rates among groups?

Answer 43

Kaplan Meier (curve)

Estimate, graphical representation

Use log-rank to mathematically test for a difference between the two groups

Question 44

What does ROC stand for?

Answer 44

Receiver operator curve

Question 45

What affects positive predictive value?

Answer 45

Prevalence of disease

Question 46

You have a nominal variable with normal distribution. What test do you use?

Answer 46

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

Question 47

What is attributable risk?

Answer 47

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

Question 48

What is a case-control study?

Answer 48

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

Question 49

What is a cohort study?

Answer 49

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

Question 50

What is a chi-square test?

Answer 50

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

Question 51

What is an unpaired t-test?

Answer 51

Compares two means from independent samples

testing mean = parametric/normal distribution data (AW)
use for continuous data (AW)

Question 52

What is a paired t-test?

Answer 52

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)

Question 53

What are the two types of validity?

Answer 53

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

Question 54

What does it mean to stratify groups?

Answer 54

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)

Question 55

What is multivariate analysis?

Answer 55

Technique that controls for several confounders simultaneously

Question 56

What criteria are important in judging an epidemiologic study?

Answer 56

Biologic credibility
Effect of removing the causal agent
Strength of the association
Temporality-exposure precedes disease

Consistency
Dose-response

BEST CD

Question 57

What does a meta-analysis study?

Answer 57

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

Question 58

What is the log-rank test?

Answer 58

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)

Question 59

What is used to compare the relative risk associated with multiple variables in a stepwise fashion?

Answer 59

Multiple regression analysis

aka multiple linear regression = continous dependent variables

multiple logistic regression = noncontinous/categorical dependent variables

Question 60

What is multiple regression analysis?

Answer 60

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

Question 61

When do you use a student’s t test v ANOVA?

Answer 61

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)

Question 62

What is the Wilcoxon test?

Wilcoxon signed rank test

Answer 62

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.

Question 63

What is the Mann-Whitney U test?

Answer 63

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

Question 64

What is cox regression?

Answer 64

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

Question 65

Which condition will require a larger sample size to detect statistical significance?

Answer 65

An outcome with smaller effect size

Question 66

What test do you use to determine effects of multiple factors on survival?

Answer 66

Cox regression

Cox proportional hazards regression

Question 67

What tests can be used for independent variables?

Answer 67

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)

Question 68

What are examples of randomization strategies?

Answer 68

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

Question 69

How do you calculate sensitivity, specificity, positive predictive value, negative predictive value?

Answer 69

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)