Genetics SSN Flashcards
CHEK2, BRCA1/2
breast cancer mutations
AD predisposition to arrhythmia
Long Qt syndrome
KCNQ1, KCNH2
treat with beta blockers
KCNH2
avoid hypokalemia
SCN5A
mexilitine and pacing to stop bradycardia
aggravated by exercise, adrenaline
Long QT 1
aggravated by sudden unexpected sound
Long QT 2 and 3
AD, repsonse to certain meds (anesthesia)
malignant hyperthermia
extra or missing chromosomes, most common reason for spontaneous abortion
aneuploidy
Trisomy 16 is ____ common than trisomy 21/22
more
most aneuploidy happenis in
oogenesis
Meiosis 1 errors are ____ common than meiosis 2 errors
much more common
chromosomes condense, centromeres separate, interphase Mts break down, spindle Mts assemble
prophase
nuclear envelope breaks down, Cr attach to spindle Mts and start to move
prometaphase
Cr align at spindle equator, metaphase plate, bipolar spindle assembly complete
metaphase
sister chromatids separate, spindle poles move apart
anaphase
daughters arrive at poles and decondense, nuclear envelope reassembles, contractile ring assembles
telophase
two new cells separate
cytokinesis
when no meitosis is happening
interphase
only in gonads, cells go from diploid to haploid
meiosis
males perform meiosis
life long
females perform meiosis
14 weeks into gestation
Meiosis 2 occurs in females
after gestation
cells commit to meiosis
leptotene
homologous pairs line up
zygotene
crossing over occurs, at least once per Cr, via chiasmata for proper segregation
pachytene
homologous chromosomes repel each other
diplotene
greatest contraction of chromosomes
diakinesis
homologs separate in
meiosis one
sister chromatids separate in
meiosis two
abnormal disjunction occurs in which phases
Anaphase, metaphase
in meiosis 1, both chromosomes pulled into one daughter cell together, giving one trisomic embryo and one monosomic embryo
true nondisjunction
in meiosis 1, both chromosomes pulled into same daughter cell separately (failure to pair)
achiasmate nondisjunction
no synapsis, no recombination, independent segregation of homologs
in achiasmic nondisjuction
one full and one half chromosome pulled into daughter cell
premature separation of sister chromatids
primary error source in meiosis
premature separation of sister chromatids
crossing over not at hotspots ____ chances of aneuploidy
increases
sister chromatid cohesion is facilitated by
cohesin
release of cohesion complexes from chromatin at meta/anaphase is facilitated by
separase
inhibits separase until ubiquinated by anaphase
securin
advanced maternal age associated aneuploidy is caused by
defective cohesion complexes
when some cells have different # of chromosomes in same tissue
mosiacism
mosiacism is caused by
Post-zygotic (mitotic) chromosome malformation
CdK, activated by cyclin and dephosphorylation to phosphorylate other proteins
cell cycle control system
Cdk-inhibitor OR ceased production of control system parts
override control system, as in cancer
prevent Cdc20 from interacting with APC/C cyclosome
checkpoint proteins
APC/C cyclosome sends securing and cyclin B to proteasome to
free separase (separate sister chromatids)
different mutations within same gene result in similar phenotype with varied severity
allelic heterogeneity (as in CF)
delta F508
most common CF mutation
causes defective prossessing so CTFR protein gets stuck in cell
delta F508
mutations within gene at different loci cause same phenotype
locus heterogeneity
hyperphenylalaninemia
example of locus heterogeneity, phenotypic heterogeneity
classic from in mutated PAH, other varients in BH4 metabolizing enzymes
hyperphenylalaninemia
one gene involved, different mutations in same gene result in very different phenotypes
phenotypic heterogeneity
different mutations in PAH gene may cause
very different severity of phenotype
most mutations, point and truncations
loss of function
50% of normal levels results in abnormal phenotype
haploinsufficiency
haploinsufficeincy example, causes hyperglycemia after a meal
mature onset diabetes of youth
gene becomes superactive or aquires new function
gain of function mutation (huntingtons)
more polyglutamine repeats causing earlier onset of disease (worse as inherited)
anticipation (huntingtons)
rare in humans, e.g. tempature sensitive mutations in androgen receptor
conditional mutations
50% of normal levels is poison (actively does something detrimental)
dominant negative mutation, e.g. osteogenesis imperfecta
AD mutatio nin procollagen gene, form defective collagen fibrils causing poor mineralization of bone
osteogenesis imperfecta
enzyme deficiency inheritance is almost always
AR, since 50% is usually sufficient
treat phenylalaninemia with restricted diet, other BH4-requiring end-products such as
serotonin, L-dopa
humans have this many pairs of chromosomes
23
how many base pairs per set of chromosomes
three billion
how many genes
twenty thousand, many more gene products
how many bases
five
purines, have three H bonds
G, C
pyramidines, have 2 H bonds
C, U, T
RNA has ____ on 2’ C, DNA has ____
hydroxy, H
5’ end, near transcription start site
promoter
contain coding sequence
exons
silent mutations are possible because
DNA code is redundant
always ATG (methionine)
start codon
UAA, UAG, UGG in humans
stop codon
polyA signal (AATAAA)
generates polyA tail in mature RNA
5’ cap added onto mature RNA
CAP site
GT
5’ splice site
A
branch site
AG
3’ splice site
Short non-mRNAs, loads RNA silencing complex (RISC), translational repression of mRNA or mRNA destruction
microRNA
pase pairs per histone
200
changes activity at different histones
methylation, acetylation
tightly packed, low transcriptional activity
heterochromatin
satellite DNA (tandem repeats clustered together) often found
heterochromatin
loose chromatin, high transcriptional activity
euchromatin
regulate genes nearby
Cis regulatory elements
can be far away, brought near by 3D folding
trans regulatory elements
may occur due to misalignement in mitosis, may lead to divergence of function e.g. globins
gene duplication
can move gene fragments around, e.g. hemophilia
transposable elements
transcript destroyed if stop codon inserted too early
Nonsense-mediated decay
disease prevalence
q squared
caculate carriers (heterozygotes)
2pq
point mutation example: from FGF receptor GOF mutation (g to A or C)
achondroplasia (also, cancer, due to defects in DNA proofreading or repair
repeat expansion examples
fragile X, huntington’s
reduced penetrance causes
induced by age (Huntington’s, colon cancer), sex-limited (male pattern baldness)
expressivity (severity) example
neurofibromatosis: cafe au lait spots
one genetic change, wide array of effects in multiple organ systems (e.g. Marfan’s, eye bone and heart)
pleitropy
unfavorabley lyonization, homozygous, 45X or 46XY females
female shows phenotype in X-linked recessive conditions
maternal inheritance, many children, many organs (esp. brain, heart, muscle), phenotype depends on heteroplasmy
mitochondrial inheritance
mRNA detection, mRNA expression to deterine under or over expression of genes
Northern Blot, RNA by in situ hybridization
protein detection, e.g. dystrophin in Duchenne’s muscular distrophy
Western Blot
detect protein via fluorescent Ab in tissue
immunocytochemistry
uses restriction enzymes to cut DNA and run on fluorescent gels to bind and visualize DNA fragments
southern blot
southern blot probe must be
1000 bps long, or allele-specific oligonucleotides
use for tandem repeats (huntingtons) large deletions, missense mutations
southern blot
don’t use for missense mutation, deletion or transloacation may not be detected at restriction site or by probe
southern blot
???
use PCR
don’t use for allele dropout of enzyme, large deletions on only one chromosome
PCR
can detect heterozygote deletion
quantitative PCR (multiple ligation primary annealing PCR)
use: single bp or other small deletion, missense mutation, etc
genome sequencing
don’t use for tandem repeats, copy number variations
genome sequencing
don’t use for detecting missense and most other mutations
multiple ligation primary annealing PCR
use for constitutional deletiona nd duplication for large scale mutations (chromosome imbalance) e.g. in cancers
comparative genomic hybridization
don’t use for small mutations (current chip density is 3Mb)
comparative genomic hybridization
detect gene expression and visualize via Manhattan plots
Genome-wide association studies
can see heterozygote and homozygote missense mutations. Not used for mutations involving many base pairs
Genome-wide association studies
Safer (.5% chance of miscarriage), done at week 16-20
amniocentesis
Riskier (1%), but done at week 10-12
CVS
classic example of at-birth genetic screening
phenylketonuria (PKU)
true positives/(true positives + false negatives)
sensitivity
higher sensitivity means fewer
false negatives
true negatives/(true negatives + false positives)
specificity
higher specificity means fewer
false positives
changing gene expression patterns via DNA methylation and histone modification
epigenetics
disease phenotype in Turner’s syndrome (XO) proves
some genes escape X activation
dominant mechanism of X inactivation, transcribed but not translated
Xist
areas of DNA that have high concentration of adjacent Cs and Gs
CpG islands
methylation silences genes ____, by recruiting proteins that modify chromatin to block Tfs
indirectly
propagates methylation pattern from parent cell to daughter cell
DNA methyltransferase
when bad Xs die faster than they are replaced, so good X dominates
phenotypic rescue
rescue example, where B cells only have good X activated
X-linked Agammaglobulinemia
accidental activation of more of good X than bad in target tissue explains
why rarely a woman may have XlD Duchene’s muscular distrophy
XlD that effects only females, because males die in utero, causes rapid neuropsychiatric decline in childhood
Rett’s syndrome
silencing the expression of just one allele on a gene, depends on sex of parent who gave it
imprinting
how does imprinting lead to disease?
it doesn’t. Disruptions in imprinting lead to disease
materal imprint restricts growth, paternal imprinting speeds growth
Haig hypothesis
Are most fetal genes controlling growth imprinted?
Nonsense-mediated decay
disruption of imprinting due to loss or gain of methylation
epimutation
empty egg with double-dose of dad’s imprinting genes
hydatidiform mole (tumor)
promotes fetal growth, paternally activated (methylated) DMR region does not allow silencing CTCF to bind
IGF2
caused by gain of function mutation that allows materal allele DMR region to be methylated
Beckwith-Weidmann Syndrome (giant baby with tumors)
dad’s DMR region is not methylated; all IGF2 is restricted
Silver Russell Syndrome: severe interuterine growth restriction
phenotypes of imprinting lesoins involve abnormal growth or behavior, not
anatomical malformations
proportion of individuals carrying a gene variant who express a particular phenotype.
penetrance
proportion of variance in phenotype expression in a populatoin that can be accounted for by genetics
heritability
difference in concordance between monozugotic and dizygotic twins is attributed to
50% difference in genes
genetic loci coordination with disease varies greatly why?
overestimation of heritability, rare variants with large impact not picked up, genome duplication/deletion not measured well
polygenic disease example
obesity/type II diabetes, FTO and MC4R
in mice, leptin mutations and feeding in first five weeks of life
influenced resulting phenotype
inhibits appetite
leptin
in urea cycle disorders, excrete hippurate using
sodium benzoate (diversion)
in familial hypercholesterolemia, reduce bile saltes with ____ and inhibit HMG CoA reductase with ____
cholestyramine, statins (diversion)
in hemochromatosis, use ____ to deplete excess iron
phlebotomy (depletion)
In LDL recepter deficiency, use
plasmapheresis (depletion)
in PKU, cofactor to increase enzyme activity
cofactor BH4
in Gaucher, help mutant protein to fold correctly using
chaperone AT2101
in MPS 1,2,4; Gaucher, Fabry and Pompe, use
protein replacement therapy
treat hereditary agiodema (caused by mutation in esterase inhibitor)
danazol to increase expression
treat sickle cell/thalassemia with ____ to decrease methylation of fetal Hgb
butryate
treat dominant negatives with ____ to initiate degradation of mutant allele
RNAi
due to loss of cells in anterior horn of spinal cord, caused by mutations in Survival Motor Neuron genes SMN1/2
Spinal Muscular Distrophy (no effect on cognition)
When SMN1 lacks ____, it is unstable and rapidly degrades, leading to SMA
Exon 7
this is used to enhance normal splicing of SMN1/2
SR
use this to increase the expression of SMN2, lessening the phenotype severity
Sodium Phenylbutyrate
treat nonsense mutations in CF and Duchenne MD with ____ that read through stop codons
aminoglycosides
corrects delta508 mutations, allow mutant protein to not get stuck in RER, get to the cell surface
curcumin
convert duchenne MD to becker MD, a less severe form
modify splicing to restore normal reading frame.
transplantation treats
genetic diseases with single organ involvment
treat hemoglobinopathies, immunodeficiencies, storage disorders
bone marrow transplant
treat small amounts of cells in babies and kids
cord blood
many inborn errors of metabolism
liver transplant
treat fetus with cortisol to prevent virilizatoin of females and reduce shock due to low Na and high K
congenital adrenal hyperplasia, prenatal treatment
gene addition is performed with
vectors: naked DNA, adenoviruses, oncoretroviruses, lentiviruses
can correct single gene defects, can add new functions to cells, can increase immune response to cancer
gene addition
abnormal beta globin
sickle cell disease, can be treated with gene therapy
decreased or absent beta globin due to point mutations
beta thalassemia, can be treated with gene therapy
normal immune function in 9/10 children, 3/10 developed leukemia due to insertion near oncogene
SCID severe combined immunodeficiency
cerebral demyelination in children with enzyme deficiency, treated with lentivirus, no evidence of mutagenesis
adrenoleukodystrophy
early onset blindness, focused on RPE65, inserted directly into eye to avoid mutation
leber congential amaurosis: restored light and some gross vision
viral replication leads to infection, insertional mutagenesis, benign and malignant tumors, clonality
safety issues of gene therapy
federal law stating that insurers and employers cannot discriminate based on genetic information
GINA
Does GINA protect against discrimination in life insurance, disability insurance or long-term care?
No
Robbery with a deadly weapon not excsued by 47 XYY aneuploidy
Millard v. State of Maryland
successfully sued Arizona SU after blood samples donated for diabetes research were being used to research inbreeding and schizophrenia
Havasupai Tribe
In NY, can patients be genetically tested without giving consent?
No
doctors must
inform patients of risk, explain implications for family, offer services
genetic information must be shared with family?
no, it is confidential to the individual
hospital, doctor or testing company can be sued for ___ if a test is misread, leading to the birth of a baby that the parents would have wanted to abort
wrongful birth
encourages private companies to invest in genetic research
argument for gene patenting
lack of incentive to improve testing, high price, slow turn-around times, no means of independent conformation
argument against gene patenting
is preimplantation genetic diagnosis regulated?
no, is now used for controversial traits such as gender selection
Trisomy 21, 18, 13
Non-fatal autosomal aneuplodies
maternal meiosis 1 non-disjunction, hypotonia, low ears, simian crease, tow space, declined cognitive development, risk of leukemia and heart defects
Trisomy 21, Down syndrome
clenched fists, rocker bottom feet, small gestational aga, 90% heart defect, 10% 1 year survival
Trisomy 18, Edward Syndrome
95% abort, 75% due to meiotic nondisjuntion, 20% translocations, holoprosencephaly, cleft lip and palate, eye problems
Trisomy 13, Patau Syndrome
short, infertile, broad chest, webbed neck, 1:5000 female birth, 80% due to loss of pateral X
Monsomy X, Turner syndrome
sterile, small testes, low testosterone, gynecomastia, tall, 1o point lowered IQ, 1:1000 males
XXY, Klinefelter’s syndrome
Klinefelter with triple X
possible sterility
Klinefelter with XYY
possible rediction in IQ, tall
maternal age correlates with all aneuploidies except
45X and XYY
chmsm 5p, chmsm 4p
deletion examples
mewing cry, microcephaly, mental retardation
chmsm 5p, Cri-du Chat
distinct face, 87% due to pateral de novo deletion
chmsm 4p, Wolf-Hirschhoron
mitogens (PHA)
stimulates mitosis
Colchicine
spindle poison, stops mitosis in metaphase
route for banding, trypsin and giemsa
G banding
R banding
G banding reversed
centromeres and heterochromatin
C banding
first method, quinacrine
Q banding
short arm is called
p
long arm is called
q
size: acro is ___ than sub-meta is ___ than metacentric
smaller than
Chmsm 1, 9,16, Y
large heterochromatic regions
Chmsm 13, 14, 15, 21, 22 (also Y)
acrocentric
how many proteins in the proteosome?
80-100000
What’s worse, monosomy or trisomy?
monosomy
have no gain or loss of genetic material
balanced translocations
results in partial monosomy and partial trisomy
unbalanced translocations
translocation of acrocentric chmsm, fusion at centromeres, and loss of short arm fusion
robertsonian translocation, carriers have 45 chmsm
two breaks in one chmssm
inversion
pericentric v. paracentric inversion
peri inludes the centrosome
crossover leads to duplication/deletion of distal DNA
pericentric inversion
crossover leads to acentric fragment and dicentric chmsm (both lethal to offspring)
paracentric inversion
small centromere containing fragments from trisomy rescue
marker chmsm
misegregations lead to duplications of shirt or long arm (and absence of counterpart) in daughter cell
isochromosomes
Hybridzing DNA probes to pateints chromosomes: good for microdeletoins (~1Mb loss)
FISH: fluorescent in situ hybridization
paternal deletion of 15q11.2, floppy at birth, hungry, underweight, small genitalia
Prader-Willi
Maternal deletion of 15q11.2 innappropriately happy, speech delay, excitable
Angelman
microdeletion of 22q11.2
DeGeorge
FISH has subtelomere probes b/c
telomeres have highest concentration of genes, thus biggest impact of deletions
FISH for CVS or amniocentesis
interphase fish, results in 1-2 days, v. 7-10 for conventional cytogenetics
advanced maternal age, abnormal maternal serum (risk for trisomy 18 or 21), risk of neural tube defects, prenatal ultrasound abnormalities
use Interphase FISH
limits of interphase FISH
reduced sensitivity, or recognizes most frequent abnormalities
preimplantation genetic diagnosis is done with
polar bodies from oocytes, blastomeres from embryos
what guides choice of FISH probes?
clinical phenotype
scrape marker off of chromosome, use it to make probe
reverse FISH, very expensive
spectral karyotyping
multicolored FISH
stain normal chromosome with DAPI, label control and experiment
comparative genomic hybridization (CGH)
only detectsimbalances greater than 3-10 Mb, depends on banding resolution which varies between preparations
CGH limitations
like CGH but w/representative DNA sequences (not whole chromosomes) affixed to plate
microarrays
small gains or deletions not seen with large probes, probes may skip site of gain/deletion,
microarray limitations
detects greater than 100-200kb changes
BAC platform (microarray)
detects greater than 1-100kb changes
oligonucleotide platform (microarray)
single neucleotide polymorphism olionucleotide microarray analysis
SOMA
benign variation, aneuploidy, partial aneuploidy, microdeletions and duplications far below traditional thresholds, long stretchs of homozygosity,
SOMA
