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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
GWAS can find _______ not _______
find correlation | not cause/effect
26
what is the null hypothesis
NO ASSOCIATION b/w two things | rejecting null happens when something is statistically significant
27
For IEM pts, CBZ can cause a ______ shift to the curve
right shift
28
what is CBZ normally used for?
normally for seizures, it is a non-selective sodium channel blocker
29
what are MEA's used for?
MEA = Multi Electrode Array they are used for extracellular recording of neuronal firing
30
CBZ tx in pts with the ______ mutation led a switch form chronic pain to acute pain
S241T
31
how where they able to measure "pain in a dish" for IEM
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)
32
which CYP affects warfarin
CYP2C9
33
which CYP affects Codeine
CYP2D6
34
which CYP affects Clopidogrel
CYP2C19
35
which CYP affects Simvastatin
CYP3A5
36
which CYP affects Tacrolimus
CYP3A5
37
which mutation affects Azathioprine/6-mercaptopurine
TPMT mutation | those drugs are substrates to TPMT
38
which mutation affects Isoniazid (an abx)
NAT (N-acetyltransferase)
39
which mutation affects Sulfonamides
NAT (N-acetyltransferase) | if pt is a slow acetylator..
40
which mutation can affect simvastatin | NOT CYP tho
SLCO1B1
41
which mutation can affect Methotrexate
SLCO1B1
42
what genes are related to P-GP
MDR1 and ABCB1
43
what mutation can affect metformin
OCT1
44
if an ACE-induced cough occurs what gene/gene product may be altered
Bradykinin B2 receptor
45
if there is a gene alteration in Estrogen Receptor - alpha what may the effect be
increase in BMD (bone mineral density) | increase in HDL
46
if there is a gene alteration in Arachidonate 5-lipoxygenase what may the effect be
improvement in FEV1 (the lipoxygenase is related to leukotriene inhibitors - aka monteleukast drug)
47
what are the most common Adrenergic Beta 1 GPCR variants
Ser49Gly and Arg389Gly
48
what are the most common Adrenergic Beta 2 GPCR variants
Gly16Arg and Gln27Glu
49
the ADRB2 GPCR is located on chromosome _____ and is closely associated with ______
5; | asthma
50
the ____ allele is associated with a more severe asthma phenotype
Gly16
51
2 Main VKORC1 variants that matter
1639G>A and 1173C>T
52
how many h bonds b/w A and T in DNA
2 bonds
53
how many h bonds b/w C and G in DNA
3 bonds
54
how many DNA base pairs are there (in the human genome)
3 billion
55
about how many genes are there in the human genome
20,000
56
exons vs introns which is coding and which is noncoding
coding: exons non-coding: introns
57
definition of locus
unique position of a nucleotide in the reference genome
58
Chromatin vs Chromosome: | unwound DNA - accessible for transcription
chromatin
59
Humans have _____ chromosomes | or _____ pairs of autosome
46 chromsomes 22 pairs
60
what is the start codon in mRNA
AUG
61
how many codons are there
64
62
how many amino acids are there
20
63
definition of haplotypes
inheritance of a cluster of single nucleotide polymorphisms (SNPs)
64
definition of Non-Synonymous SNP
changing the AMINO ACID in the protein
65
definition of Synonymous SNP
does not change amino acid in protein (prob not changing function of the gene)
66
what are the types of Non-Synonymous SNPs
missense and nonsense
67
what is Missense SNP
replacing an amino acid
68
what is Nonsense SNP
amino acid changes to stop codon
69
CYP2C19: pt is an ultra rapid metabolizer if their genotype is...?
*1/*17 or *17/*17
70
CYP2C19: pt is an normal metabolizer if their genotype is...?
*1/*1
71
CYP2C19: pt is a poor metabolizer if their genotype is...?
``` *2/*2 or *2/*3 or *3/*3 ```
72
what is LD
linkage disequilibrium NON-random assoc. at different loci on the SAME chromosome
73
how to measure LD
R^2 -- measuring correlation b/w two variables
74
Measuring LD: | if R^2 = 0 ?
NO LD
75
Measuring LD: | if R^2 = 1
complete LD/Perfect LD
76
Measuring LD: | what R^2 values show strong LD?
R^2 > 0.8
77
Goal of HapMap
to identify sequence variations in various populations
78
Rank VKORC1: 1639 Genotypes | which one can have a normal/higher dose vs which ones need a lower one
GG - normal/higher GA - need normal/medium dose AA - need lower dose
79
what CYP2C9 frequencies need lower warfarin doses and which ones can do the normal starting dose
normal: *1/*1 or *1/*2 | more *2 and *3 = need lower doses
80
which population (race) is more likely to have the VKORC1: 1639G>A variant
Asians | white second
81
which population (race) is more likely to have the CYP2C9 variations (*2 or *3)
white ppl

Genomics/Pop Health Spring 2018 (3 decks)

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