Final Flashcards
what method of genotyping is used by 23andMe
microarrays
what is the purpose of imputation in genetic analysis
predicting and filling in missing genetic information based in known patterns from a reference dataset
what drives overdominance and positive selection of beta thalassemia alleles (3)
- cultural and geographic isolation
- mate choice
- malaria presence
what is 1 reason behind the prevalence of osteopetrosis in the jewish community
founder effect
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) Dor Yeshorim
b) tay-sachs
c) jewish
why are the thalassemia prevention programs very successful and approachable
does not need genetic testing just a blood test
what is the founder effect
small group of individuals forms a new population in a different geographical location –> loss of genetic variation
what is an ethnoreligious disease
prevalence is impacted by genetics and religious factors (e.g partner selection)
what is the most common type of sequencing used for
- sickle cell anemia
- tay sachs
- gaucher
- T2 diabetes
- hermansky- pudlak
DNA sequencing and blood sample analysis
what is 1 approach stop codon readthrough drugs could take to address nonsense mutations
inhibiting release factors
what is the most prevalent consequence of nonsense mutations
diseases
what does ataluren do to promote read-through of nonsense mutations
inhibits release factor binding
what is the standard number of individuals that need to be affected by a disease for it to classify as rare
there is no standard number
what barriers do rare disease patients face when getting treatment
treatment costs more than common disease treatment
what is an example of a promising treatment for rare diseases
Lenmeldy
what is a segmented aging disorder
disorder that causes premature localized aging
e.g Hutchinson- Gilford Progeria syndrome
how could apolipoprotein E2 be linked to longevity
lowers cholesterol levels
what results proved that ICMT gene inhibition is a viable treatment method for individuals with HGPS
ICMT inhibition showed improvements in phenotypic expression of HGPS and higher survival rates in mice
what is the common disease hypothesis
genetic component of common diseases is due to large amount of disease-causing alleles that occur often in populations
what type of study is used to identify alleles and loci associated with common symptoms
genome-wide association studies (GWAS)
what is an example of a gene associated with polycystic ovary syndrome (PCOS)
CYP11 alpha
how many proteins were found to be significantly enriched in patients with aggressive MS
7
what is 1 autosomal dominant gene related to Parkinson’s
SNCA
what is oncoproteomics
the use of proteomics to study cancer and tumorigenesis
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) HLA class II locus in HLA-DRB1 gene
b) European
a) what is a balanced polymorphism
b) what is an example of a balanced polymorphism
a) maintaining 2 versions of a gene in a population because one of them has an advantageous effect
b) malaria and sickle cell anemia
why is it likely that the deleterious B haplotype associated with the ERAP2 protein maintained at high freq in the population
balancing selection
What was a common hormone that influenced sex-specific disease risk?
estrogen
What is the triad of risk factors in Alzheimer’s Disease
- age
- APEO
- sex
What do you need to check for when looking at odds ratio data and making associations?
confidence intervals
what are 5 risk factors for cancer
- age
- sex
- behavior
- geography (province)
- income
what is an added risk for breast cancer
family member with breast cancer
what does BRCA1 protein complex do
repairs chromosomal damage
what was the gene found in 1994 that linked early onset of familial breast cancer
BRCA1
do both copies of BRCA1 need to be mutated for cancer to develop
yes
what are 4 similarities with CFTR and BRCA1 research
- prenatal genetic diagnoses
- both have lots of mutations
- mutation prevalence varies among diff populations
- gene therapy
what is an implication of mutation prevalence being different all over the world
no standardized global screening
what lead researchers to target specific genes in CF and cancer studies
genetic markers with high LOD scores
what is a major difference in mutations in CFTR and mutations in BRCA1
CFTR mutation= CF is caused by mutations
BRCA1 mutation = might not get breast cancer/ disease is influenced by mutations
can you get breast cancer and not have any mutations in BRCA1 or BRCA2
yes
what was the aim in the retrospective cohort study in the prevalence and penetrance of BRCA1 and BRCA2
to quantify risk for ppl who have mutations in the genes but don’t come from a multi-case family
what is a retrospective cohort study
find out who has a mutation and then see who has developed a certain disease
what was the “exposed” and “non exposed” groups in the retrospective BRCA1 and BRCA2 cohort study
exposed = born with mutation in either gene
non exposed = non mutated genes
do case control studies have an order of events
no
extra factors that could enhance chance of exposure
confounding factors
what is an example of a confounding factor
allele that promotes smoking which causes cancer
study where you dont assign exposure and you monitor for it
prospective (observational) cohort
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
experimental cohort
order of events are known, exposure and disease are known
retrospective (observational) cohort
what is calculated in cohort studies
relative risk
what 2 types of mutations combine in certain tissues and causes cancer
- germline mutations
- sporadic mutations
how does a rare mutation end up being homozygous
consanguinity
what is calculated in case control studies
OR
problems with experimental cohort studies
- no one could end up getting the disease
- ethical issues if you suspect exposure causes disease and then subject patients to it
why have multicase families with linkage studies
better chance at finding risk alleles
what is it called when you run multiple PCRs on the same gel
multiplex heteroduplex
what are the 3 basic steps of heteroduplex
- amplify by PCR
- warm up
- cool down
what does a heteroduplex analysis look like on a gel
2 bands (1 wildtype 1 mutant) since ppl are heterozygotes
what was the main finding of the study of estimating the prevalence of BRCA mutations
mutations are not prevalent, most women with breast cancer dont have mutations
the proportion of individuals with a specific disease associated genotype who express corresponding disease with in a specific time period
penetrance
what is a key difference between BRCA1 and 2 and deltaF508
deltaF508 = very common
BRCA1 and 2 = not common
BRCA1 penetrance is high
what is an example of a high penetrance cancer gene
BRCA1 or BRCA2
what is an example of a moderate penetrance cancer gene
ATM
what is an example of a low penetrance cancer gene
COX11
how does a low penetrance mutation arise
sporadic
how does a moderate penetrance mutation arise
familial agrregation
how does a high penetrance mutation arise
mendelian fashion (traced through families)
what makes cancer risk/odds ration vary (4)
- gene affected
- gene variant
- modifier genes
- environment
why should we do genetic cancer testing (2)
- treatment decisions
- know cancer risk for patient/ family
what mechanism does PARP inhibitors utilize
synthetic lethality
what is an example of a constitutively essential expressed gene that is essential for BRCA1 to function
PARP
what needs to be inhibited to stop cancer cell production in synthetic lethality
both PARP and BRCA1
(just inhibiting 1 is not lethal)
what does BRCA1 and BRCA2 proteins do
homologous recombination repair (HRR)
what is required for HRR
functional BRCA1 and BRCA2
what pathways repairs mutations if PARP enzymes are inhibited in cells lacking functional HRR proteins
non homologous end joining pathway
what hypothesis is this called:
- individual carries a mutation in 1 copy of gene –> developes a mutation in the second cop –> cancer
2 hit hypothesis
what may have a greater effect on cancer risk than BRCA mutations
multiple commonly occurring low-modest penetrant genes
most important takeways from the study at Mount Sinai hospital in Toronto
- SNPs did not have a significant OR on its own
- combined SNPs had an association with breast cancer
why would a cancer be less amenable to the benifits of periodic screening
fast growing
what is a problem with overdiagnosis of a slow growing cancer
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
what is the main problem with over diagnosis
unnecessary treatment
what type of plot:
outcome is the same for everyone regardless of exposure but time to outcome varies
kaplan meier plot
what does this suggest
65 isoleucine mutation delays progression of AIDS
where does the single HR value come from in most studies
Cox proportional hazard model
why is chemo not given to stage 1 lung cancer patients
it doesnt help (HR = 1)
why is chemo useful in stage ii and iii lung cancer
HR is lower
of the stage i lung cancer patients what 2 groups were they further divided into
HR = 0.33 = high risk
HR = 3.67 = low risk
what did the 0.33 high risk group tell us
what chemo increases lifespan in high risk stage i cancer
what did the 3.67 low risk group tell us
that chemo leads to a faster death in low risk stage i lung cancer
what is the low risk stage 1 lung cancer and chemo treatment a result of
overdiagnosis
what is an example of personalized medicine with CF patients with G551D mutation
Kalydeco (potentiator drug)
what is an example of personalized medicine with BRCA1
double mastectomy or PARP inhibitors
what is an example of personalized medicine with stage i lung cancer if the tumor has a high risk gene expression
chemo
what are 3 things to consider in epidemiology with respect to cancer
- inherited variation (e.g BRCA1 alleles)
- gene expression profiling (e.g qPCR)
- cancer genome mutation profiling
what does homozygous for the deletion in CCR5 do
resists HIV
what does heterozygous for the deletion in CCR5 do
progression of AIDS is slowed
in the smith 1997 AIDS study what type of study did they do
retrospective cohort
in the smith 1997 AIDS study what what was the purpose
survey CCR2 to see if mutations were responsible for slow progression of AIDS
what was the common allele at codon 64 in CCR2 gene
valine (GTC)
what was the minor allele at codon 64 in CCR2 gene
isoleucine (ATC)
what amino acid does the restriction enzyme cut in CCR2
ATC (isolucene)
what restriction enzyme did the smith 1997 CCR5 study use
BsaB1
when will you have a BsaB1 restriction site
if CCR2 encodes an isoleucine at position 64
what does exposed mean int he CCR2 study
exposed to the 64 isoleucine mutation
what is an example of a mutation that increases risk/ resistance
CCR2 (resistance)
BRCA1 (risk)
what do you also have if you have a CCR2 V64I deletion
promotor mutation that stops CCR5 from being expressed
why is the CCR2 V64I mutation and the promotor mutation inherited together
in complete linkage disequilibrium
why is the CCR2 V64I mutation and promotor mutation good in linkage and GWAS studies
in complete linkage disequilibrium
what is it called when alleles are close together on difference loci and are inherited together
linkage disequilibrium
what was the purpose for the mis matched primers and restriction enzyme in the CCR2 study
proxy for the causative allele
what is critical threshold
how many times you need to amplify pcr for it to show up on gel
what 2 things does critical threshold depend on
- how many cycles of amplification
- how much protein the person produces
what is the main takeaway from this graph
african origin have more copies of CCL3L1
what does having a high copy # of CCL3L1 lead to
decrease risk in getting HIV
how does CCL3L1 decrease risk for HIV
competes for receptor binding with HIV
in who were fewer copies of CCR5 t cells expressed
in patients with extra CCL3L1 copies
when did whole genome sequence data become available
2001
what are the oligonucleotides complementary to in probes
all 4 alleles (A, T, C,G)
if you have a C at a position in the sample what will show on the probe
G
what is a specific combo of linked alleles
haplotype
what does the HapMap project identify (2)
- SNPs
- haplotypes
alleles are far away so there is no way to predict inheritence
linkage equilibrium
pretty good indicator that 2 allelels will be inherited together
linkage disequilibrium
2 alleles are so close that they are always inherited together
complete linkage disequilibrium
why are there less discrete blocks of linkage disequilibrium in african population
lots of recombination and less LD
perfect LD
alleles always inherited together
r2 value?
r2 = 1
an allele is predicted correctly by the presence of another 80% of the time
r2 value?
r2 = 0.8
why do african populations need more tagging SNPs
cus it is older and has more chance of recombination
where are recombination hotspots
base of triangles
–% of all recombination takes place in –% of sequence
80% of recombination takes place in 15% of sequence
in HapMap what are the genetic markers proxies for
LD blocks in the genome
why do you need your cases and control to be from the same ethnic region in GWAS
so that the only allele differences are associated with disease
what were 2 results of the GWAS study in the UK
- within diff regions of Britain there is allelic variation
- identifies regions of the genome for 7 diff diseases
how do you come up with a p vlaue threshold
simulations
what is a cost-effective way to sequence both cases and controls (like in rare mutations)
just sequence exons (coding regions)
what were some disease the were found to be associated with candidate genes in the agnostic GWAS study that they could pursue further
- bipolar disorder
- type 1 and 2 diabetes
in the GWAS study why didnt it matter if some controls had type 1 diabetes
cus there were so many cases and controls it didn’t effect the study
large sample size
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
low ORs but significant
what is a cultural problem with 23andMe and biobank
heavily skewed towards ppl of European ancestry
what % of mutations are found in the coding regions (about 1% of the genome is coding)
85%
what are most genetic diseases caused by
coding sequence change
what type of variants are responsible for most human disease
rare varients
what type of disorder is bartter syndrome
autosomal recessive
by screening the individual for Bartter’s syndrome at homozygous intervals what did this reveal
a misdiagnosis
he actually had Gitelman syndrome
in a given individual how many cSNVs (coding single nucleotide variant) are conserved
40
why isn’t there more disease prevalence since we all have quite a bit of cSNVs in conserved locations
these are recessive mutations
example of a supressed disease causing allele (HIV)
CCR5 suppression due to mutation in CCR2 + promotor mutation = resistant to HIV
example of a supressed disease causing allele (CF)
deltaF508 + R553Q mutation = lesser symptoms of CF
an issue with the resilience project
unable to recontact patients
what differentiates a high risk type i lung cancer with low risk type ii lung cancer
gene expression profiles
personalized medicine example (HR+ breast cancer)
Tamoxifen –> competes with estrogen for receptor binding
personalized medicine example ERBB2(HER2)+ tumors,
Trastuzumab
antibody thearpy
what appears to be associated with consistently better response to
trastuzumab
high HER2 copy numbers = high mRNA copies = high protein copies
what 2 things should be considered in cacncer therapy with HER2+ cancers
- HER2+ expression
- HER2+ copy #
how do you know if you have more HER2+ copies than average using FISH
fluorescent markers bind to HER2+ and CEP17
- if there are more HER2+ signals than CEP17 you have more copies
what is CEP17 a marker for
HER2+
what is an Additional breast cancer gene expression profile test
Oncotype DX test
why do targeted drugs kill the entire cancer, why is there still some cells left over?
gene expression changes in different regions of the tumor
example of personalized medicine for G551D CF patients
Ivacaftor potentiator
example of personalized medicine for BRCA1 or BRCA2 mutations
PARP inhibitors
how did they go about running a pcr when the CCR2 gene sequence BsaB1 (restriction enzyme) recognition site
used a mismatched primer to add nucleotides
What are two DNA repair pathways exploited during CRISPR-Cas9-
mediated gene targeting?
1.Non-homologous end joining
2. Homology-directed repair
What is the name of the fetal haemoglobin repressor knocked-out by
CRISPR therapy?
BCL11A
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).
mosaicism
