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GOBBLERS 2023 > Angela's Laboratory Tests and Stats > Flashcards

Angela's Laboratory Tests and Stats Flashcards

1
Q

What does Western blot evaluate?

A

Protein

*duplicate question: How do you evaluate protein? Western blot

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2
Q

What is the screening test for HIV?

A

Elisa

up to date: ELISAs that detect antibody to HIV are used as an initial test to screen for HIV.

These tests (HIV1/2 immunoassay in the algorithm) detect HIV-1 and HIV-2 antibody as early as 3 weeks after exposure

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3
Q

What is the confirmatory test for HIV?

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

A

up to date answer: HIV-1/HIV-2 differentiation immunoassay is the preferred confirmatory test.

Angele’s answer: Western Blot

In the past, it was the Western blot but takes days to weeks to return.

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4
Q

Herpes Simplex Virus testing?

A

DNA detection via PCR or culture of the virus

*PCR is the most SENSITIVE

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5
Q

HPV testing?

A

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.

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6
Q

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

A

PCR

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7
Q

What does FISH test for?

A

Chromosomal analysis identifying gene copy number and location at a specific locus

The number of chromosomes or their structural makeup:
Duplication/amplification
Deletion
Translocation

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8
Q

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

A

FISH

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9
Q

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

A

FISH

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10
Q

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

A

Test for loss of heterozygosity

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11
Q

What does comparative genomic hybridization do?

A

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

CGH
Comprehensive (whole genome)
Genome
H kind of looks like # for number

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12
Q

What does Southern Blot evaluate?

A

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

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13
Q

What does Northern blot evaluate?

A

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.

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14
Q

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

A

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

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15
Q

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

A

Paired t test

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16
Q

What is a students t-test?

A

A test used to provide a confidence interval for an estimated mean or difference of means

the t test determines a probability that two populations are the same with respect to the variable tested when samples are collected independently of one another

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17
Q

What is type 1 error?

A

Incorrect rejection of the null

(Null is correct, you aren’t)

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18
Q

What is alpha error?

A

A test’s probability of making a type 1 error

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19
Q

What does an alpha of .05 mean?

A

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

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20
Q

What is the confidence level?

A

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.

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21
Q

What is type 2 error?

A

Incorrect failure to reject the null (Beta)

(Null is wrong but you think it’s correct)

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22
Q

What is beta error?

A

A test’s probability of making a type 2 error

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23
Q

What does a beta of 10% mean?

A

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

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24
Q

What is the power?

A

Power=1-beta

Reflects the ability of a study to detect an actual effect

🙌 you have the power 🙌

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25
Q

What is a receiver-operator curve (ROC)?

A

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)

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26
Q

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

A

The accuracy of a test

AUC 1.0 is perfect test
AUC 0.5 is chance

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27
Q

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

A

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

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28
Q

In what study do you use an odds ratio?

A

Case-control

29
Q

What is an odds ratio?

A

Odds of exposure in the disease group divided by odds of exposure in the non-diseased group

Estimate of relative risk

(a/c) / (b/d) or ad/bc

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

30
Q

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

A

Case control

31
Q

In what study do you use relative risk?

A

Prospective studies like Cohort studies and clinical trials

32
Q

What does relative risk measure?

A

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)]

33
Q

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

A

Case control

34
Q

What is variance?

A

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

35
Q

What is standard deviation?

A

The square root of the variance

36
Q

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

A

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

37
Q

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

A

Above 2.5%
Below 2.5%

38
Q

How does the standard deviation change as the population increases?

A

Trick question!
It doesn’t

39
Q

What is standard error?

A

The same as the standard deviation but calculated for repeated samplings of a study statistic; important in confidence intervals around the mean

40
Q

How does the standard error change as the population increases?

A

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

41
Q

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

A

Smaller

42
Q

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

A

PPV

A PPV cannot be calculated from a case-control study

43
Q

How do you compare survival rates among groups?

A

Kaplan Meier

44
Q

What does ROC stand for?

A

Receiver operator curve

45
Q

What affects positive predictive value?

A

Prevalence of disease

46
Q

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

A

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

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

47
Q

What is attributable risk?

A

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

48
Q

What is a case-control study?

A

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

49
Q

What is a cohort study?

A

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

50
Q

What is a chi-square test?

A

Tests the null hypothesis that proportions are equal or that nominal/categorical variables are independent

data must be from a random sample and variable must be nominal / categorical

51
Q

What is an unpaired t-test?

A

Compares two means from independent samples

52
Q

What is a paired t-test?

A

Compares the difference or change in a numerical variable for matched or paired groups or samples

53
Q

What are the two types of validity?

A

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: observation, selection, confounding

External=ability to generalize the results observed from one study population to another

54
Q

What does it mean to stratify groups?

A

To examine the association of interest within groups that are similar with respect to a potential confounder

55
Q

What is multivariate analysis?

A

Technique that controls for several confounders simultaneously

56
Q

What criteria are important in judging an epidemiologic study?

A

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

Consistency
Dose-response

BEST CD

57
Q

What does a meta-analysis study?

A

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

58
Q

What is the log-rank test?

A

Used in survival analysis to compare the distribution of time to event in two or more 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

59
Q

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

A

Multiple regression analysis

60
Q

What is multiple regression analysis?

A

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.

61
Q

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

A

Student’s t is used to compare means between two groups

ANOVA is used to compare the means among three or more groups

62
Q

What is the Wilcoxon test?

A

Tests whether the mean values of two dependent groups differ significantly from each other

It is a non-parametric test and is subject to fewer assumptions than its parametric counterpart the t-test for dependent samples –a Wilcoxon test is used when the boundary conditions for the t-test for dependent samples are no longer fulfilled

63
Q

What is the Mann-Whitney U test?

A

Tests whether there is a difference between two 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

64
Q

What is cox regression?

A

Cox proportional hazards survival regression: used in survival time analysis to determine the influence of 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

65
Q

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

A

An outcome with smaller effect size

66
Q

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

A

Cox regression

67
Q

What tests can be used for independent variables?

A

ANOVA (for dependent or independent)
Mann-Whitney U

Wilcoxon, paired t-test for dependent only

68
Q

What are examples of randomization strategies?

A

Simple: based on a single sequence of random assignments

Block: randomize participants into groups that result in equal sample sizes–ensure a balance in sample size across groups over time

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

69
Q

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

A

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)

GOBBLERS 2023 (28 decks)

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