Week 1 Flashcards
Penetrance
on/off switch
- If person has mutation they either effected or not effected
- NOT influenced by level of phenotype expression
Expressivity
dimmer function
- Light is on, but trying to determine SEVERITY / range of expressivity
- Patient has mutation, but there is a range of severity levels
Pleitropy
gene that has multiple effects within the body
- How broad/how many different areas are effected
- Polysystemic or Monosystemic
Mendel’s 2 laws are…
- Mendel’s Law of Segregation: Alleles segregate (at meiosis) into the gametes
- Mendel’s Second Law of Independent Assortment: the segregation of each pair of alleles is independent
3 threats to mendelian inheritance
penetrance
pleitropy
expressivity
The human genome is _________ and organized in a ______________
dynamic
non-random manner
There is an average of _______ SNPs every _________ bp between any two randomly chosen human genomes.
We are 99.9% identical but this still means we have _________ differences
1
1000 bp
3 million
The 4 types of variations that can occur between genomes are…
1) Insertion/Deletion Polymorphisms
2) Single Nucleotide Polymorphisms
3) Copy Number Variations
4) Other structural variations (inversion, duplications, translocations, large scale insertions/deletions)
Minisatellites are ____________ polymorphisms and consist of ___________. They are also known as _____________
insertion-deletion polymorphisms
consist of tandemly repeated 10-100 bp blocks of DNA
(aka Variable Number Tandem Repeats VNTR)
Microsatellites are _____________ polymorphisms and consist of __________. They are also known as ___________ and a common example is ____________
insertion-deletion polymorphism
di-, tri-, tetra- nucleotide repeats
AKA Short Tandem Repeat Polymorphisms (STRP)
EX) CAG repeats - abnormal CAG repeats in Huntington’s disease dictate if individual gets disease or not
SNPs can be detected by _________, and are used in _________ because they are so widely distributed
PCR
can be used in genetic fingerprinting
Copy Number Variations can vary in size from _______-______ and are the primary type of ________ variation.
200bp - 2 Mb
structural
CNV can be identified using ________
array comparative genomic hybridization
microarray, but with DNA
1q21 is a region on the genome that is _______ and is associated with _______ different diseases
unstable
12 different diseases
1q21
- contains duff 12-20, highly variable protein coding region
- humans have most copies
- farther you get from humans the less copies
- thought to be involved in human brain evolution
- more instability in 1q21 = increase duff 1220 copy number –> increase in brain size
1q21 deletion –>
1q21 duplication –>
deletion –> schizophrenia, microcephaly
duplication –> autism, macrocephaly
G-C rich regions make up ____% of the genome, and A-T rich regions make up ____%
GT = 38% AT = 54%
GC and AT rich regions are used in finding _________
chromosomal banding patterns
Genome sequencing is focused on _____ regions with > ______ sequence gaps still remaining, and there is no completely sequenced and assembled human genome.
euchromatic, >200
Genome Composition:
1) _____ = translated (protein coding)
2) 20-25% = __________
3) ______% = “single copy” sequences
4) 40-50% = _________
1) 1.5% is translated (protein coding)
2) 20-25% is represented by genes (exons, introns, flanking sequences involved in regulating gene expression)
3) 50% “single copy” sequences
4) 40-50% classes of “repetitive DNA”
NextGen sequencing relies on ______ sequences, therefore _________ regions are typically unexamined such as _______
short read
complex, highly duplicated regions
such as 1q21
Missing Heritability
defined as the fact that single genetic variations cannot account for much of the heritability of diseases, behaviors, and other phenotypes.
Explain the relationship between gene duplication and evolution and problems with this
- CNV involved in rapid, recent evolutionary change
- link between evolutionarily adaptive copy number increases and increase in human disease
- one gene copy carries out critical function, the other is free to vary
CNV regions are often enriched for _________, __________, and __________
human specific gene duplication
genome sequence gaps
recurrent human diseases
Gene families
- composed of genes with high sequence similarity that may carry out similar but distinct functions
- Arise through gene duplication
- play major role in evolutionary change
____% of the genome is comprised of segmental duplications
5
Tandem Repeats (aka satellite DNAs) are used for _________ and some are found as part of ___________ on long arms of Chromosome 1, 9, 16, and Y
cytogenetic banding
human-specific heterchromatin
a-satellite repeats are _______ bp repeat units found _______. They are important for ________ and ________.
171
found near centromeric regions of all human chromosomes
important for chromosome segregation in mitosis and meiosis
Dispersed Repetitive Elements include _____ and _______ families. These can be responsible for _________
Alu
L1
responsible for aberrant recombination events between different copies of dispersed repeats (–> disease)
Alu Family, aka _________. Comprised of _____ bp, with ________ copies in the genome
SINE (short interspearsed repeat elements)
300 bp, 500,000 copies
L1 Family, aka _________. Comprised of _____ kb, with ________ copies in the genome
LINE (long interspersed repeat elements)
6kb, 100,000 copies
Retrotransposition may cause _________ of genes, and is due to what process?
insertional activation
mRNA –> cDNA (introns all gone) –> cDNA reinserted into genome
-can be innocuous or detrimental
There are ____ (#) of cross-over events of homologous chromosomes, and each cross-over contains a physical link between homologs called a ________
2-3
chiasma
Genetic variability among offspring is due to ________ and _________
Recombination/Crossing-over and Independent assortment
Independent assortment
Chromosomes can align in many different ways before being pulled apart (2^23 possible combinations)
In Prophase I of meiosis, ______ and _______ occur, such that homologous chromosomes are brought into alignment along the entire length of the chromosome and swap parts. These ______ are held together in _________.
synapsis and recombination
bivalents, held together in syntaptonemal complex
In metaphase I chromosomes undergo _________ when they line up at the metaphase plate
independent assortment
Homologous chromosomes separate in _________, and this process can result in ________
anaphase I
disjunction
At the end of meiosis I you go from _______ to __________
1 4n cell –> 2 2n cells
Sister chromatids separate in ________
anaphase II
At the end of meiosis II you create ________
4 haploid cells that are all genetically different
Nondisjunction in meiosis I =
100% abnormal gametes
2 cells = N+1
2 cells = N-1
Nondisjunction in meiosis II =
50% abnormal gametes
2 cells = N
1 cell = N+1
1 cell = N-1
Two possible mechanisms of nondisjunction
chiasmata positioning
freqeuncy of cross-over events
Chiasmata positioning results in nondisjunction because
cross over event occurs too near or too far from the centromere
Metacentric
centromere is located in the middle of the chromosome, such that the two chromosome arms are approximately equal in length.
Submetacentric
centromere is slightly removed from the center.
Acrocentric
- centromere is near one end of the chromosome.
- everything on short arm is repetitive satellite and ribosomal DNA
_____ and ______ are dyes used in banding pattern staining to allow unequivocal identification of each chromosome
Giemsa and DAPI
Polyploidy
“many-ploidy” having a chromosome number that is more than double the basic or haploid number – 69, etc.
- Triploid (3 sets) – 69
- Tetraploid (4 sets) – 92
Aneuploidy
abnormal number of chromosomes
EX) Monosomy, trisomy
Mosaicism
presence of at least two genetically different cells in a tissue that is derived from a single zygote
Maternal age effect: Two-Hit Theory
1) More risk of non-disjunction because of diminished recombination due to lack of chiasma or mislocalization
2) Diminished ability of oocytes to successfully complete chromosome segregation in the presence of unfavorable recombination events
Maternal Age effect: Cohesion Complex Theory
- Degradation of cohesion complexes established during fetal development between sister chromatids and homologs with age because of extended meiosis I
- -> Terminalization (premature separation of homologs/sister chromatids –> aneuplodiy)
Balanced Structural Rearrangments
- all genomic material is present, even though it is arranged differently
- No loss or gain of genetic material
- No phenotypic effect for heterozygote carrier
- EXCEPTION: breakpoint in a gene, disrupting function
- Can increase risk of producing abnormal gametes, risk to subsequent generations
3 examples of balanced structural rearrangments
1) Robertsonian Translocations
2) Inversions
3) Reciprocal translocations
Reciprocal translocations results in ________ formation when chromosomes of a carrier pair in meiosis, leading to either _______ or _______ segregation
quadrivalent formation
adjacent
alternate
Reciprocal translocation
- reciprocal exchange of broken segments between non-homologous chromosomes
- balanced structural rearrangement
When adjacent segregation of quadrivalents occurs this leads to the formation of __________
100% unbalanced gametes
When alternate segregation of quadrivalents occurs this leads to the formation of __________
1/2 normal gametes, 1/2 balanced reciprocal translocation gametes
Robertsonian translocation
- Most common structural chromosomal rearrangement
- Fusion of two acrocentric chromosomes → loss of both short arms (NOT deleterious, only satellite DNA)
→ reduction of chromosome number, but still considered balanced
-Normal phenotype in carrier, but can lead to unbalanced karyotypes in offspring (monosomies and trisomies)
Two types of inversions
pericentric
paracentric
Inversions
- chromosome undergoes two double strand breaks of the DNA backbone, and the intervening sequence is inverted prior to the rejoining of the broken ends
- formation of loop when homologous chromosomes are paired in recombination
- can increase risk of abnormal gametes
Pericentric Inversions
- Include the centromere
- Can result in gametes with duplication and deficiency of chromosome segments
-½ balanced, ½ unbalanced
Peracentric Inversions
- excludes centromere
- can result in acentric or dicentric chromosomes after crossing over (unstable)
-1/2 balanced, 1/2 inviable
Unbalanced Structural Rearrangements
abnormal chromosomal content, deletion or duplication in multiple genes
Duplication results in gametes with _________ and deletion results in gametes with _________ (after fertilization with a normal gamete)
duplication –> partial trisomy
deletion –> partial monosomy
Del (22)(q11.2) results in ________ and _______ syndromes due to a deletion of 3 Mb within 22q11.2 in one cope of chromosome 22. Symptoms include _______, ________, _________, _________
- DiGeorge Syndrome, Vel-Cardio-Facial Syndrome
- Results in: heart defects, craniofacial anomalies, intellectual disability, and immunodeficiency
DiGeorge Syndrome and Vel-Cardio-Facial Syndrome are a result of ___________
Del(22)(q11.2)
-deletion of approximately 3 Mb within 22q11.2 in one copy of chromosome 22
Epigenetics
mitotically and meiotically heritable variations in gene expression not caused by changes in DNA sequence
EX) reversible, post-translational modifications of histones and DNA methylation
DNA methylation of CpG islands results in ______, but some DNA methylation can result in __________
recruitment of silencing complexes, and silencing of gene expression
gene expression activation
Genetic imprinting is _________ and is present in ___% of genes in the human genome
sex dependent epigenetic modulation of regulatory regions such as promoter sequences
10%
DNA methylation of genetically imprinted genes have 3 main qualities…
1) established in the gamete
2) stably maintained in somatic cells after fertilization
3) reversible
Imprinted DNA methylation is maintained in somatic cells by ________ when DNA is replicated
maintenance methyltransferases
Imprinted DNA methylation is reversible because _________
it can be reset during gametogenesis to transfer the appropriate sex-specific imprint to progeny (based on their sex)
Uniparental Disomy is _____________ and often results due to __________
the presence of two chromosomes only inherited from one parent
trisomy rescue
Types of FISH probes include ________, _________ and __________
Centromere, Locus Specific, and Dual Fusion
FISH probes use _________ which hybridize to cells and can identify _______ by looking for ________
fluorescently labeled specific DNA probes (no more than 200kb)
-can identify translocations by looking for fusion signals
Centromere FISH probe is used for ________
EX) ______
enumeration
EX) ALL panel
Locus Specific FISH probe is used for _________
EX) ______
identifying deletions/duplications
EX) p53
Dual Fusion FISH probe is used for __________
EX) ______ and _______
identifying translocations
EX) BCR-ABL and PML-RARa
Chromosomal microarray (CMA) can detect _______ but not ________, and has limited ability to detect _________
genomic deletions and duplications
NOT translocations
mosaicism
Lab test diagnosis protocal includes these 3 steps:
1) Chromosomal Microarray (CMA)
- If duplication/deletion detected → consult Database of Genomic Variants (DGV) to see if it is a known disease region
2) Parental FISH studies – determine if finding is normal, rare, or familial
- Deletion/Duplication found on parent → further FISH testing of other family members
3) No deletion/duplication found, and no DGV hits, then do further data-base mining
Pharmacogenetics
- Variable response to individual genes
- The study of differences in drug response due to allelic variation in genes affecting drug metabolism, efficacy, and toxicity
Pharmacogenomics
- variable response due to MULTIPLE LOCI across the genome
- Concerned with assessment of common genetic variants in the aggregate for their impact on the outcome of drug therapy
Pharmacokinetics
- absorption, distribution, metabolism, and excretion of drugs
- whether, or how much drug reaches its target
Drug Metabolism Steps (2)
Phase 1: polar group added to compound –> makes more soluble (usually hydroxylation)
Phase 2: add sugar/acetyl group to detoxify drug –> easier to excrete
Pharmacodymanics
- relationship between drug concentration at site of action and the observed biological effects
- what happens when drug successfully reaches target
CYP450 gene family (50+ types): most function to _________, and 90% are active in ___________.
inactivate drugs
phase I metabolism of common drugs
______% of Codeine is inactivated by ______ and _____% of codeine is activated by _________
80% inactivated by CYP3A4
10% activated by CYP2D6
grapefruit juice acts to _______ CYP3A activity. Therefore, when grapefruit juice is combined with Felodipine (treats HTN) the result is _______________
inhibit
significant hypotension - low metabolism of drug because CYP3A is inactivated, thus over-activation of drug effects
_______ is used to treat fungal infections and acts to temporarily inhibit _______ metabolism of cyclosporine
Ketoconazole
CYP3A
When Ketocanazole is combined with ________, you must _________ or risk neprotoxicity because ________ is inhibited
cyclosporine
must decrease cyclosporine dose
CYP3A metabolism of cyclosprine
________ is a TB prophylaxis drug that acts to _______ thus ___________. Therefore, you must ________
Rifampin
CYP3A inducer thus increasing metabolism of cyclosporine.
Must increase dose of cyclosporin
CYP2D6
needed to activate codeine into morphine
VKORC1 = ? and is metabolized by _______
Warfarin (narrow therapeutic window)
CYP2C9
NAT = is a __________ enzyme whose rate is determined by ________. _______ (drug) is a TB prophylactic drug metabolized by NAT.
If drug is metabolized to fast –> ?
If drug is not metabolized enough –> ?
N-Acetyltransferase enzyme (important in phase II metabolism), reate determined by genetic polymorphisms
Isoniazid
If drug is metabolized to fast –> not effective in preventing TB
If drug is not metabolized enough –> liver damage/failure
TPMT (Thiopurine-S-methyltransferase) is used to treat ______
If drug is metabolized to fast –> ?
If drug is not metabolized enough –> ?
treats childhood leukemia
If drug is metabolized to fast –> not effective in treating leukemia
If drug is not metabolized enough –> immunosuppressant can cause death from bone marrow failure
G6PD deficiency
- X-linked Recessive
- most common human enzyme deficiency
- Increases malarial resistance (common among blacks)
- subject to hemolytic anemia after certain drug exposures
Population genetics
the study of allele frequencies and changes in allele frequencies in populations
Polymorphism
genetic variant (mutation) which is common (>1%) in the populations
Mutation rate (u)
Frequency of new mutations at a given genetic locus
Calculating mutation rate:
Direct method
Indirect Method
Direct method:
u = number of cases without family history/ (total population x 2 allels)
Indirect Method: used when f=0
I=2u
Fitness (f)
If F=1 ?
If F=0 ?
o Probability of transmitting one’s genes to the next generation
F=1 (same as normal population)
F=0 (gene(s) not passed on)
Coefficient of Selection (S)
S = 1 - f
Hardy-Weinberg Assumptions
1) Population is large and matings are random
2) Allele frequencies remain constant over time because:
- No appreciable rate of mutation
- All genotypes are equally fit (equal chance to pass alleles to next generation)
- No significant immigration/emigration of individuals with different allele frequencies
Carrier frequency =
2pq
when q is more rare than 1/10,000 can use 2q as an estimate for carrier frequency
p=?
q= ?
p = frequency of common allele q = rare allele
3 Types of Down Syndrome
- Trisomy 21 (95% of the time) (maternal nondisjunction in meiosis I usually)
- Unbalanced Translocation (3-4%) between chr21 and another acrocentric chromosome
- Mosaic Trisomy 21 (1-2%) – more mild phenotype
Down Syndrome Physical Features
- Flat faces
- prominent epicanthal folds
- Upslanting palpebral fissures
- Single palmar crease
- small ears
- gap between 1st 2 toes
- Large-appearing tongue
- Low muscle tone
- Increased joint mobility
Down Syndrome Medical Problems
Duodenal atresia Hirschsprung disease (constipation) Congenital heart disease (atrial septal defect) Early onset Alzheimer's Increased ALL risk
Other:
- Eye: myopia (near-sightedness), lazy eye, blocked tear ducts, nystagmus, cataracts
- ENT: ear infections, deafness, enlarged tonsils/adenoids
- Endocrine: diabetes, thyroid, reduced fertility
- Ortho: hips, joint subluxation, atlantoaxial subluxation
Down Syndrome Developmental and Behavior Phenotypes (6)
- Hypotonia – gross motor development effects
- Spectrum of intellectual disability (Mild-moderate usually)
- Speech problems
- Seizures
- Alzheimer’s
- Autism
Trisomy 18 (Edwards Syndrome)
Clinical Features (4)
- Small for gestational age
- Small jaw
- low-set ears
- Clenched fingers
- Rocker-bottom feet
-Very high lethality within 1 year
Trisomy 13 (Patau Syndrome)
Clinical Features
- Characteristic faces
- Severe intellectual disabilities
- facial clefts
- polydactyly
- renal anomolies
45XO is ___________
Turner Syndrome
47XXY is ___________
Kleinefelter Syndrome
Turner Syndrome clinical features
- short stature
- webbed neck
- broad chest
- low set ears
- cubitus valgus
- inner canthal folds
- blue sclera
- NORMAL INTELLIGENCE
- hormone dysfunction
- gonadal dysgenesis
- coarctation of the aorta
- Prolonged QTc
- scoliosis
Turner Syndrome prevalence
1/2500 newborn girls
99% do not survive to term
mosaic karyotypes thought to contribute to survival
Klinefelter Syndrome prevelance
47XXY
1/500-1/1000 newborn boys
can occur due to maternal or paternal meiosis I
Klinefelter Syndrome Clinical Features
- Tall stature
- Hypogonadism (small testes)
- gynecomastia
- usually sterile
- learning disabilities
- delayed speech/language
Prader-Willi Syndrome (PWS) can be caused 3 ways
1) 15q11-q13 deletion on paternal chromosome (70%)
2) Maternal uniparental disomy (20-30%)
3) Abonormalities in imprinting center (2.5%)
PWS 15q11-q13 deletion can be caused by _______ and can be detected with ______ and ________
Caused by misalignment during homologous recombination of repeats flanking 15q11-q13
Detect with FISH and Microarray
Maternal uniparental disomy is 2 copies of the ______ allele and can be detected with __________
maternal
detect with methylation testing
PWS abnormalities in imprinting center results when fertilization occurs by _________ causing the cell to think there is maternal UPD
sperm with abnormally persistent female imprinting
Detect abnormalities in imprinting center with ___________
methylation testing
PWS physical features (4)
-Changes in facial features (almond shaped eyes)
-Undescended testicles (males)
-Severe feeding problems (require G-tube) until 2-4 years when they completely reverse (insatiable appetite)
→ Obesity (can treat with Growth Hormone)
PWS medical problems
- Ortho: Scoliosis common
- Eyes: Nystagmus, strabismus
- Resp: obstructive sleep apnea
PWS developmental and behavioral problems
- mild-moderate cognitive disabilities
- behavioral issues are common
Angelman Syndrome can be caused 4 ways
1) 15q11-q13 deltion on maternal chromosome (70%)
2) Paternal uniparental disomy (7%)
3) Abnormalities in imprinting center (abnormally persistent male imprint) (3%)
4) Genetic mutation in UBE3A (10%)
UBE3A is usually only expressed from the ______ allele, so mutation can cause _______ 10% of the time
maternal
Angelman Syndrome
AS phenotype (6)
- mildly dysmorphic facial features
- hypotonia
- spasticity in older patients
- Intellectual Disability
- seizures
- autism
IDIC 15 (15q11-q13) is a _________ derived abnormality that causes ________. These patients are NOT ______ but often suffer from _______ and ________
maternally
causes autism
NOT dysmorphic
suffer seizures, and are hypotonic
Maternal 15q Interstitial Duplication only results in phenotypic effects if it is __________
maternally inherited
Maternal 15q Interstitial Duplication results in ______, with _____ and ______ common,. These patients are NOT _________
autism
seizures, hypotonia common
NOT dysmorphic
Chronic Myeloid Leukemia (CML) results from a ________ translocation involving chromosomes _____ and _____
BCR-ABL, chr 9 and 22
CML can be treated by ________
Gleevec
Gleevec is a _______ and acts to _________
- tyrosine kinase inhibitor
- targets novel protein (tyrosine kinase signaling molecule) generated by translocation
- -> Gleevec binds ATP binding site, inhibiting action
Acute Pro-Myeloid Leukemia (APML) results from a _______ balanced translocation involving chromosome _____ and _____
RERalpha and PML translocation
chr 15 and 17
RERa and PML translocation results in a _________ that acts to _________
- novel transcription factor
- bind to promoter elements in DNA, inhibiting transcription downstream
Acute Pro-Myeloid Leukemia is treated with ________ which acts to _________
Vitamin A
-bind novel protein TF–> changes protein conformation –> allows transcription to continue when coactivators bind
Childhood B-cell Leukemia:
Hypodiploid = ? Hyperdiploid = ?
Hypodiploid = 38 chromosomes in cancer cells (poor prognosis, needs aggressive treatment)
Hyperdiploid = 55 chromosomes in cancer cells (more favorable diagnosis)
47XYY = ?
Jacobs Syndrome
Jacobs syndrome clinical features and prevalence
-Learning disabilities
-Speech delays
-developmental delays
-emotional/behavioral difficulties
autism
-tall stature
1/1000 newborn boys
47XXX = ?
Triple X syndrome
Triple X syndrome clinical features/risks and prevalence
- Tall stature
- risk of learning disabilities, delayed speech/motor, seizures, kidney abnormalities
1/1000 newborn girls
Androgen Insensitivity Syndrome
46XY
- x-linked gene
- Androgen Receptor mutation
- Androgens (testosterone) is present, but body does not recognize/respond to it
5-alpha reductase deficiency
46XY
-Body can’t convert testosterone to dihydrotestosterone
-Phenotype: undervirilized male with increased virilization at the time of puberty
SRY disorders:
SRY deletion = ?
Presence of SRY in 46XX = ?
Mutations in SRY = ?
Deletion/Absence of SRY → phenotypically normal female
Presence of SRY in 46XX → phenotypically normal male
Mutations in SRY → decreased/absent AMH, under-virilization of a male
Denys-Drash and Frasier Syndrome (genotype = ?) results from a mutation in ________ which is a _________. Can result in ________, _________, and ______
46XY
WT1 gene, an SRY transcription factor
Can result in: kidney disease, increased tumor risk, and sex reversal
Congenital Adrenal Hyperplasia (genotype = ?) and results in ________, ________, and _________
46XY
ambiguous genitalia
21-hydroxylase deficiency
risk of salt wasting
Who am I?
- short stature
- webbed neck
- broad chest
- low set ears
- cubitus valgus
- inner canthal folds
- blue sclera
- NORMAL INTELLIGENCE
- hormone dysfunction
- gonadal dysgenesis
- coarctation of the aorta
- Prolonged QTc
- scoliosis
Turner Syndrom XO
