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Biol 439 > Final > Flashcards

Final Flashcards

1
Q

what method of genotyping is used by 23andMe

A

microarrays

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2
Q

what is the purpose of imputation in genetic analysis

A

predicting and filling in missing genetic information based in known patterns from a reference dataset

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3
Q

what drives overdominance and positive selection of beta thalassemia alleles (3)

A
  • cultural and geographic isolation
  • mate choice
  • malaria presence
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4
Q

what is 1 reason behind the prevalence of osteopetrosis in the jewish community

A

founder effect

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5
Q

a) what is the program that screens for genetic diseases?
b) what is 1 disease it screens for
c) what population would this program be useful to

A

a) Dor Yeshorim
b) tay-sachs
c) jewish

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6
Q

why are the thalassemia prevention programs very successful and approachable

A

does not need genetic testing just a blood test

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7
Q

what is the founder effect

A

small group of individuals forms a new population in a different geographical location –> loss of genetic variation

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8
Q

what is an ethnoreligious disease

A

prevalence is impacted by genetics and religious factors (e.g partner selection)

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9
Q

what is the most common type of sequencing used for
- sickle cell anemia
- tay sachs
- gaucher
- T2 diabetes
- hermansky- pudlak

A

DNA sequencing and blood sample analysis

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10
Q

what is 1 approach stop codon readthrough drugs could take to address nonsense mutations

A

inhibiting release factors

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11
Q

what is the most prevalent consequence of nonsense mutations

A

diseases

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12
Q

what does ataluren do to promote read-through of nonsense mutations

A

inhibits release factor binding

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13
Q

what is the standard number of individuals that need to be affected by a disease for it to classify as rare

A

there is no standard number

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14
Q

what barriers do rare disease patients face when getting treatment

A

treatment costs more than common disease treatment

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15
Q

what is an example of a promising treatment for rare diseases

A

Lenmeldy

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16
Q

what is a segmented aging disorder

A

disorder that causes premature localized aging

e.g Hutchinson- Gilford Progeria syndrome

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17
Q

how could apolipoprotein E2 be linked to longevity

A

lowers cholesterol levels

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18
Q

what results proved that ICMT gene inhibition is a viable treatment method for individuals with HGPS

A

ICMT inhibition showed improvements in phenotypic expression of HGPS and higher survival rates in mice

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19
Q

what is the common disease hypothesis

A

genetic component of common diseases is due to large amount of disease-causing alleles that occur often in populations

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20
Q

what type of study is used to identify alleles and loci associated with common symptoms

A

genome-wide association studies (GWAS)

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21
Q

what is an example of a gene associated with polycystic ovary syndrome (PCOS)

A

CYP11 alpha

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22
Q

how many proteins were found to be significantly enriched in patients with aggressive MS

A

7

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23
Q

what is 1 autosomal dominant gene related to Parkinson’s

A

SNCA

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24
Q

what is oncoproteomics

A

the use of proteomics to study cancer and tumorigenesis

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25
Q

a) what is an example of a gene variant that confers resistance to leprosy (Hansen’s disease)

b)which population is this variant commonly found in

A

a) HLA class II locus in HLA-DRB1 gene

b) European

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26
Q

a) what is a balanced polymorphism

b) what is an example of a balanced polymorphism

A

a) maintaining 2 versions of a gene in a population because one of them has an advantageous effect

b) malaria and sickle cell anemia

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27
Q

why is it likely that the deleterious B haplotype associated with the ERAP2 protein maintained at high freq in the population

A

balancing selection

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28
Q

What was a common hormone that influenced sex-specific disease risk?

A

estrogen

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29
Q

What is the triad of risk factors in Alzheimer’s Disease

A
  • age
  • APEO
  • sex
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30
Q

What do you need to check for when looking at odds ratio data and making associations?

A

confidence intervals

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31
Q

what are 5 risk factors for cancer

A
  1. age
  2. sex
  3. behavior
  4. geography (province)
  5. income
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32
Q

what is an added risk for breast cancer

A

family member with breast cancer

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33
Q

what does BRCA1 protein complex do

A

repairs chromosomal damage

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34
Q

what was the gene found in 1994 that linked early onset of familial breast cancer

A

BRCA1

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35
Q

do both copies of BRCA1 need to be mutated for cancer to develop

A

yes

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36
Q

what are 4 similarities with CFTR and BRCA1 research

A
  1. prenatal genetic diagnoses
  2. both have lots of mutations
  3. mutation prevalence varies among diff populations
  4. gene therapy
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37
Q

what is an implication of mutation prevalence being different all over the world

A

no standardized global screening

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38
Q

what lead researchers to target specific genes in CF and cancer studies

A

genetic markers with high LOD scores

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39
Q

what is a major difference in mutations in CFTR and mutations in BRCA1

A

CFTR mutation= CF is caused by mutations

BRCA1 mutation = might not get breast cancer/ disease is influenced by mutations

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40
Q

can you get breast cancer and not have any mutations in BRCA1 or BRCA2

A

yes

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41
Q

what was the aim in the retrospective cohort study in the prevalence and penetrance of BRCA1 and BRCA2

A

to quantify risk for ppl who have mutations in the genes but don’t come from a multi-case family

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42
Q

what is a retrospective cohort study

A

find out who has a mutation and then see who has developed a certain disease

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43
Q

what was the “exposed” and “non exposed” groups in the retrospective BRCA1 and BRCA2 cohort study

A

exposed = born with mutation in either gene

non exposed = non mutated genes

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44
Q

do case control studies have an order of events

A

no

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45
Q

extra factors that could enhance chance of exposure

A

confounding factors

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46
Q

what is an example of a confounding factor

A

allele that promotes smoking which causes cancer

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47
Q

study where you dont assign exposure and you monitor for it

A

prospective (observational) cohort

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48
Q

no one has exposure or disease –> assign exposure and non exposure to individuals –> subject the individuals to the exposure and wait for the disease to form

A

experimental cohort

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49
Q

order of events are known, exposure and disease are known

A

retrospective (observational) cohort

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50
Q

what is calculated in cohort studies

A

relative risk

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51
Q

what 2 types of mutations combine in certain tissues and causes cancer

A
  1. germline mutations
  2. sporadic mutations
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52
Q

how does a rare mutation end up being homozygous

A

consanguinity

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53
Q

what is calculated in case control studies

A

OR

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54
Q

problems with experimental cohort studies

A
  1. no one could end up getting the disease
  2. ethical issues if you suspect exposure causes disease and then subject patients to it
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55
Q

why have multicase families with linkage studies

A

better chance at finding risk alleles

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56
Q

what is it called when you run multiple PCRs on the same gel

A

multiplex heteroduplex

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57
Q

what are the 3 basic steps of heteroduplex

A
  1. amplify by PCR
  2. warm up
  3. cool down
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58
Q

what does a heteroduplex analysis look like on a gel

A

2 bands (1 wildtype 1 mutant) since ppl are heterozygotes

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59
Q

what was the main finding of the study of estimating the prevalence of BRCA mutations

A

mutations are not prevalent, most women with breast cancer dont have mutations

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60
Q

the proportion of individuals with a specific disease associated genotype who express corresponding disease with in a specific time period

A

penetrance

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61
Q

what is a key difference between BRCA1 and 2 and deltaF508

A

deltaF508 = very common
BRCA1 and 2 = not common

BRCA1 penetrance is high

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62
Q

what is an example of a high penetrance cancer gene

A

BRCA1 or BRCA2

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63
Q

what is an example of a moderate penetrance cancer gene

A

ATM

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64
Q

what is an example of a low penetrance cancer gene

A

COX11

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65
Q

how does a low penetrance mutation arise

A

sporadic

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66
Q

how does a moderate penetrance mutation arise

A

familial agrregation

67
Q

how does a high penetrance mutation arise

A

mendelian fashion (traced through families)

68
Q

what makes cancer risk/odds ration vary (4)

A
  • gene affected
  • gene variant
  • modifier genes
  • environment
69
Q

why should we do genetic cancer testing (2)

A
  • treatment decisions
  • know cancer risk for patient/ family
70
Q

what mechanism does PARP inhibitors utilize

A

synthetic lethality

71
Q

what is an example of a constitutively essential expressed gene that is essential for BRCA1 to function

A

PARP

72
Q

what needs to be inhibited to stop cancer cell production in synthetic lethality

A

both PARP and BRCA1

(just inhibiting 1 is not lethal)

73
Q

what does BRCA1 and BRCA2 proteins do

A

homologous recombination repair (HRR)

74
Q

what is required for HRR

A

functional BRCA1 and BRCA2

75
Q

what pathways repairs mutations if PARP enzymes are inhibited in cells lacking functional HRR proteins

A

non homologous end joining pathway

76
Q

what hypothesis is this called:

  1. individual carries a mutation in 1 copy of gene –> developes a mutation in the second cop –> cancer
A

2 hit hypothesis

77
Q

what may have a greater effect on cancer risk than BRCA mutations

A

multiple commonly occurring low-modest penetrant genes

78
Q

most important takeways from the study at Mount Sinai hospital in Toronto

A
  • SNPs did not have a significant OR on its own
  • combined SNPs had an association with breast cancer
79
Q

why would a cancer be less amenable to the benifits of periodic screening

A

fast growing

80
Q

what is a problem with overdiagnosis of a slow growing cancer

A

person might be older and making the cancer non effective since its slow growing but now they either have to get treatment or live with the fact that they have cancer

81
Q

what is the main problem with over diagnosis

A

unnecessary treatment

82
Q

what type of plot:

outcome is the same for everyone regardless of exposure but time to outcome varies

A

kaplan meier plot

83
Q

what does this suggest

A

65 isoleucine mutation delays progression of AIDS

84
Q

where does the single HR value come from in most studies

A

Cox proportional hazard model

85
Q

why is chemo not given to stage 1 lung cancer patients

A

it doesnt help (HR = 1)

86
Q

why is chemo useful in stage ii and iii lung cancer

A

HR is lower

87
Q

of the stage i lung cancer patients what 2 groups were they further divided into

A

HR = 0.33 = high risk
HR = 3.67 = low risk

88
Q

what did the 0.33 high risk group tell us

A

what chemo increases lifespan in high risk stage i cancer

89
Q

what did the 3.67 low risk group tell us

A

that chemo leads to a faster death in low risk stage i lung cancer

90
Q

what is the low risk stage 1 lung cancer and chemo treatment a result of

A

overdiagnosis

91
Q

what is an example of personalized medicine with CF patients with G551D mutation

A

Kalydeco (potentiator drug)

92
Q

what is an example of personalized medicine with BRCA1

A

double mastectomy or PARP inhibitors

92
Q

what is an example of personalized medicine with stage i lung cancer if the tumor has a high risk gene expression

A

chemo

92
Q

what are 3 things to consider in epidemiology with respect to cancer

A
  1. inherited variation (e.g BRCA1 alleles)
  2. gene expression profiling (e.g qPCR)
  3. cancer genome mutation profiling
93
Q

what does homozygous for the deletion in CCR5 do

A

resists HIV

94
Q

what does heterozygous for the deletion in CCR5 do

A

progression of AIDS is slowed

95
Q

in the smith 1997 AIDS study what type of study did they do

A

retrospective cohort

96
Q

in the smith 1997 AIDS study what what was the purpose

A

survey CCR2 to see if mutations were responsible for slow progression of AIDS

97
Q

what was the common allele at codon 64 in CCR2 gene

A

valine (GTC)

98
Q

what was the minor allele at codon 64 in CCR2 gene

A

isoleucine (ATC)

99
Q

what amino acid does the restriction enzyme cut in CCR2

A

ATC (isolucene)

100
Q

what restriction enzyme did the smith 1997 CCR5 study use

A

BsaB1

101
Q

when will you have a BsaB1 restriction site

A

if CCR2 encodes an isoleucine at position 64

102
Q

what does exposed mean int he CCR2 study

A

exposed to the 64 isoleucine mutation

103
Q

what is an example of a mutation that increases risk/ resistance

A

CCR2 (resistance)
BRCA1 (risk)

104
Q

what do you also have if you have a CCR2 V64I deletion

A

promotor mutation that stops CCR5 from being expressed

105
Q

why is the CCR2 V64I mutation and the promotor mutation inherited together

A

in complete linkage disequilibrium

106
Q

why is the CCR2 V64I mutation and promotor mutation good in linkage and GWAS studies

A

in complete linkage disequilibrium

107
Q

what is it called when alleles are close together on difference loci and are inherited together

A

linkage disequilibrium

108
Q

what was the purpose for the mis matched primers and restriction enzyme in the CCR2 study

A

proxy for the causative allele

109
Q

what is critical threshold

A

how many times you need to amplify pcr for it to show up on gel

110
Q

what 2 things does critical threshold depend on

A
  1. how many cycles of amplification
  2. how much protein the person produces
111
Q

what is the main takeaway from this graph

A

african origin have more copies of CCL3L1

112
Q

what does having a high copy # of CCL3L1 lead to

A

decrease risk in getting HIV

113
Q

how does CCL3L1 decrease risk for HIV

A

competes for receptor binding with HIV

114
Q

in who were fewer copies of CCR5 t cells expressed

A

in patients with extra CCL3L1 copies

115
Q

when did whole genome sequence data become available

A

2001

116
Q

what are the oligonucleotides complementary to in probes

A

all 4 alleles (A, T, C,G)

117
Q

if you have a C at a position in the sample what will show on the probe

A

G

118
Q

what is a specific combo of linked alleles

A

haplotype

119
Q

what does the HapMap project identify (2)

A
  • SNPs
  • haplotypes
120
Q

alleles are far away so there is no way to predict inheritence

A

linkage equilibrium

121
Q

pretty good indicator that 2 allelels will be inherited together

A

linkage disequilibrium

122
Q

2 alleles are so close that they are always inherited together

A

complete linkage disequilibrium

123
Q

why are there less discrete blocks of linkage disequilibrium in african population

A

lots of recombination and less LD

124
Q

perfect LD
alleles always inherited together

r2 value?

A

r2 = 1

125
Q

an allele is predicted correctly by the presence of another 80% of the time
r2 value?

A

r2 = 0.8

126
Q

why do african populations need more tagging SNPs

A

cus it is older and has more chance of recombination

127
Q

where are recombination hotspots

A

base of triangles

128
Q

–% of all recombination takes place in –% of sequence

A

80% of recombination takes place in 15% of sequence

129
Q

in HapMap what are the genetic markers proxies for

A

LD blocks in the genome

130
Q

why do you need your cases and control to be from the same ethnic region in GWAS

A

so that the only allele differences are associated with disease

131
Q

what were 2 results of the GWAS study in the UK

A
  1. within diff regions of Britain there is allelic variation
  2. identifies regions of the genome for 7 diff diseases
132
Q

how do you come up with a p vlaue threshold

A

simulations

133
Q

what is a cost-effective way to sequence both cases and controls (like in rare mutations)

A

just sequence exons (coding regions)

134
Q

what were some disease the were found to be associated with candidate genes in the agnostic GWAS study that they could pursue further

A
  • bipolar disorder
  • type 1 and 2 diabetes
135
Q

in the GWAS study why didnt it matter if some controls had type 1 diabetes

A

cus there were so many cases and controls it didn’t effect the study

large sample size

136
Q

what lead the researchers in the GWAS study to believe that a single locus does not fully explain the observation that many of these diseases run in the family

A

low ORs but significant

137
Q

what is a cultural problem with 23andMe and biobank

A

heavily skewed towards ppl of European ancestry

138
Q

what % of mutations are found in the coding regions (about 1% of the genome is coding)

A

85%

139
Q

what are most genetic diseases caused by

A

coding sequence change

140
Q

what type of variants are responsible for most human disease

A

rare varients

141
Q

what type of disorder is bartter syndrome

A

autosomal recessive

142
Q

by screening the individual for Bartter’s syndrome at homozygous intervals what did this reveal

A

a misdiagnosis
he actually had Gitelman syndrome

143
Q

in a given individual how many cSNVs (coding single nucleotide variant) are conserved

A

40

144
Q

why isn’t there more disease prevalence since we all have quite a bit of cSNVs in conserved locations

A

these are recessive mutations

145
Q

example of a supressed disease causing allele (HIV)

A

CCR5 suppression due to mutation in CCR2 + promotor mutation = resistant to HIV

146
Q

example of a supressed disease causing allele (CF)

A

deltaF508 + R553Q mutation = lesser symptoms of CF

147
Q

an issue with the resilience project

A

unable to recontact patients

148
Q

what differentiates a high risk type i lung cancer with low risk type ii lung cancer

A

gene expression profiles

149
Q

personalized medicine example (HR+ breast cancer)

A

Tamoxifen –> competes with estrogen for receptor binding

150
Q

personalized medicine example ERBB2(HER2)+ tumors,

A

Trastuzumab
antibody thearpy

151
Q

what appears to be associated with consistently better response to
trastuzumab

A

high HER2 copy numbers = high mRNA copies = high protein copies

152
Q

what 2 things should be considered in cacncer therapy with HER2+ cancers

A
  • HER2+ expression
  • HER2+ copy #
153
Q

how do you know if you have more HER2+ copies than average using FISH

A

fluorescent markers bind to HER2+ and CEP17
- if there are more HER2+ signals than CEP17 you have more copies

154
Q

what is CEP17 a marker for

A

HER2+

155
Q

what is an Additional breast cancer gene expression profile test

A

Oncotype DX test

156
Q

why do targeted drugs kill the entire cancer, why is there still some cells left over?

A

gene expression changes in different regions of the tumor

157
Q

example of personalized medicine for G551D CF patients

A

Ivacaftor potentiator

158
Q

example of personalized medicine for BRCA1 or BRCA2 mutations

A

PARP inhibitors

159
Q

how did they go about running a pcr when the CCR2 gene sequence BsaB1 (restriction enzyme) recognition site

A

used a mismatched primer to add nucleotides

160
Q

What are two DNA repair pathways exploited during CRISPR-Cas9-
mediated gene targeting?

A

1.Non-homologous end joining
2. Homology-directed repair

161
Q

What is the name of the fetal haemoglobin repressor knocked-out by
CRISPR therapy?

A

BCL11A

162
Q

What genetic condition can be caused by germline editing past the
single-cell stage? (Hint: This term describes the distribution of CCR5
alleles in the first CRISPR babies).

A

mosaicism

Biol 439 (1 decks)

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