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Genomics/Pop Health Spring 2018 > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

Interpreting P Values:

if P > 0.1

A

no significant association

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2
Q

Interpreting P Values:

if 0.05 < P < 0.1

A

marginal association

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3
Q

Interpreting P Values:

if P < 0.05

A

significant association

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4
Q

Interpreting P Values:

if P < 0.01

A

very significant association

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5
Q

Interpreting Odds Ratio

if OR = 1

A

no association

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6
Q

Interpreting Odds Ratio

if OR > 1

A

potential increasing risk

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7
Q

Interpreting Odds Ratio

if OR < 1

A

potential decreasing risk

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8
Q

Interpreting 95% CI:

if CI is greater than 1

A

significant risk effect

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9
Q

Interpreting 95% CI:

if CI contains 1

A

no statistical significance

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10
Q

Interpreting 95% CI:

if CI is less than 1

A

significant protective effect

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11
Q

what can be used to correct for false positives with SNPs?

A

Bonferroni Correction

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12
Q

what is the bonferroni correction?

A

corrected p value = 0.05 / n

n = total number of SNPs

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13
Q

what is IEM

A

inherited Erythromelalgia – “man on fire” disease

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14
Q

IEM happens because?

A

Gain of function mutations of Nav1.7

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15
Q

what drug was found to have usefulness for pts with IEM/Nav1.7-V400M mutation

A

CBZ (carbamazepine)

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16
Q

_________ normalizes activation of Nav1.7-S241T & reverses hyper-excitability

A

carbamazepine

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17
Q

what is CYP2D6s clinical relevance

A

many relevant drugs (codeine, carvedilol, tramadol, fluoxetine, metoprolol, tamoxifen, hydrocodone, nortriptyline)

extreme variability in enzyme activity

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18
Q

If a pt is an ultra rapid metabolizer — what is the effect on prodrugs that relate to that gene

A

actually have increased toxicity risk (because it is being converted so fast to active drug)

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19
Q

clinical relevane of CYP2C9

A

s-warfarin; phenytoin; glipizide

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20
Q

CYP2C19 clinical relevance **

A

clopidogrel!!!
PPIs
Antidepressants

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21
Q

clinical relevance of CYP3A5

A

tancrolimus

need higher doses of it if CYP3A5 is expressed

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22
Q

what is glucuronidation

A

conjugation of glucose at a functional group

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23
Q

why is UGT1A1 important

A

bilirubin, sex-steroid hormones,and bile acid

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24
Q

why is it important to replicate GWAS?

A

one set of a population is not always indicative of the whole population…. need bigger samples…

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25
Q

GWAS can find _______ not _______

A

find correlation

not cause/effect

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26
Q

what is the null hypothesis

A

NO ASSOCIATION b/w two things

rejecting null happens when something is statistically significant

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27
Q

For IEM pts, CBZ can cause a ______ shift to the curve

A

right shift

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28
Q

what is CBZ normally used for?

A

normally for seizures, it is a non-selective sodium channel blocker

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29
Q

what are MEA’s used for?

A

MEA = Multi Electrode Array

they are used for extracellular recording of neuronal firing

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30
Q

CBZ tx in pts with the ______ mutation led a switch form chronic pain to acute pain

A

S241T

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31
Q

how where they able to measure “pain in a dish” for IEM

A

they took iPSCs (pluripotent stem cells) from IEM pts, treated with CBZ and saw sensory like neurons did not fire like normal (aka without CBZ)

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32
Q

which CYP affects warfarin

A

CYP2C9

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33
Q

which CYP affects Codeine

A

CYP2D6

34
Q

which CYP affects Clopidogrel

A

CYP2C19

35
Q

which CYP affects Simvastatin

A

CYP3A5

36
Q

which CYP affects Tacrolimus

A

CYP3A5

37
Q

which mutation affects Azathioprine/6-mercaptopurine

A

TPMT mutation

those drugs are substrates to TPMT

38
Q

which mutation affects Isoniazid (an abx)

A

NAT (N-acetyltransferase)

39
Q

which mutation affects Sulfonamides

A

NAT (N-acetyltransferase)

if pt is a slow acetylator..

40
Q

which mutation can affect simvastatin

NOT CYP tho

A

SLCO1B1

41
Q

which mutation can affect Methotrexate

A

SLCO1B1

42
Q

what genes are related to P-GP

A

MDR1
and
ABCB1

43
Q

what mutation can affect metformin

A

OCT1

44
Q

if an ACE-induced cough occurs what gene/gene product may be altered

A

Bradykinin B2 receptor

45
Q

if there is a gene alteration in Estrogen Receptor - alpha what may the effect be

A

increase in BMD (bone mineral density)

increase in HDL

46
Q

if there is a gene alteration in Arachidonate 5-lipoxygenase what may the effect be

A

improvement in FEV1 (the lipoxygenase is related to leukotriene inhibitors - aka monteleukast drug)

47
Q

what are the most common Adrenergic Beta 1 GPCR variants

A

Ser49Gly
and
Arg389Gly

48
Q

what are the most common Adrenergic Beta 2 GPCR variants

A

Gly16Arg
and
Gln27Glu

49
Q

the ADRB2 GPCR is located on chromosome _____ and is closely associated with ______

A

5;

asthma

50
Q

the ____ allele is associated with a more severe asthma phenotype

A

Gly16

51
Q

2 Main VKORC1 variants that matter

A

1639G>A
and
1173C>T

52
Q

how many h bonds b/w A and T in DNA

A

2 bonds

53
Q

how many h bonds b/w C and G in DNA

A

3 bonds

54
Q

how many DNA base pairs are there (in the human genome)

A

3 billion

55
Q

about how many genes are there in the human genome

A

20,000

56
Q

exons vs introns

which is coding and which is noncoding

A

coding: exons

non-coding: introns

57
Q

definition of locus

A

unique position of a nucleotide in the reference genome

58
Q

Chromatin vs Chromosome:

unwound DNA - accessible for transcription

A

chromatin

59
Q

Humans have _____ chromosomes

or _____ pairs of autosome

A

46 chromsomes

22 pairs

60
Q

what is the start codon in mRNA

A

AUG

61
Q

how many codons are there

A

64

62
Q

how many amino acids are there

A

20

63
Q

definition of haplotypes

A

inheritance of a cluster of single nucleotide polymorphisms (SNPs)

64
Q

definition of Non-Synonymous SNP

A

changing the AMINO ACID in the protein

65
Q

definition of Synonymous SNP

A

does not change amino acid in protein (prob not changing function of the gene)

66
Q

what are the types of Non-Synonymous SNPs

A

missense and nonsense

67
Q

what is Missense SNP

A

replacing an amino acid

68
Q

what is Nonsense SNP

A

amino acid changes to stop codon

69
Q

CYP2C19: pt is an ultra rapid metabolizer if their genotype is…?

A

1/17
or
17/17

70
Q

CYP2C19: pt is an normal metabolizer if their genotype is…?

A

1/1

71
Q

CYP2C19: pt is a poor metabolizer if their genotype is…?

A 
*2/*2
or 
*2/*3
or
*3/*3
72
Q

what is LD

A

linkage disequilibrium

NON-random assoc. at different loci on the SAME chromosome

73
Q

how to measure LD

A

R^2 – measuring correlation b/w two variables

74
Q

Measuring LD:

if R^2 = 0 ?

A

NO LD

75
Q

Measuring LD:

if R^2 = 1

A

complete LD/Perfect LD

76
Q

Measuring LD:

what R^2 values show strong LD?

A

R^2 > 0.8

77
Q

Goal of HapMap

A

to identify sequence variations in various populations

78
Q

Rank VKORC1: 1639 Genotypes

which one can have a normal/higher dose vs which ones need a lower one

A

GG - normal/higher
GA - need normal/medium dose
AA - need lower dose

79
Q

what CYP2C9 frequencies need lower warfarin doses

and which ones can do the normal starting dose

A

normal: 1/1 or 1/2

more *2 and *3 = need lower doses

80
Q

which population (race) is more likely to have the VKORC1: 1639G>A variant

A

Asians

white second

81
Q

which population (race) is more likely to have the CYP2C9 variations (*2 or *3)

A

white ppl

Genomics/Pop Health Spring 2018 (3 decks)

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