Genetics Flashcards
1
Q
Chiasmata
A
Physical linkages between homologs (maternal & paternal sister chromatids) during meiosis I
2
Q
Bivalents
A
During Prophase I of meiosis, maternal and paternal homologs become synapsed along their entire length
3
Q
Synaptonemal complex
A
Proteinaceous complex binding together maternal & paternal homologs, allowing for crossover.
Degrades at the end of Prophase I.
4
Q
What is the most error-prone part of the process of meiosis?
A
Meiosis I - when homologs are segregated to opposite poles
5
Q
Aneuploidy
A
The condition in which cells contain an abnormal number of chromosomes
6
Q
Polyploidy
A
Extra copies of all chromosomes; e.g., triploidy (3n) or tetraploidy (4n)
7
Q
Terminalization
A
Postulated model for abnormalities in aging maternal oocytes. As oocytes age, the cohesion complex between sister chromatids & homologs degrades –> chiasmata move towards the ends of the homologue pairs –> precocious separation of homologous chromosomes, leading to aneuploidy
8
Q
Mosaicism
A
The presence of two or more populations of cells with different genotypes in tissues derived from a single zygote.
Mosaic phenotypes are highly variable & results are difficult to predict.
9
Q
Down Syndrome
A
Trisomy 21
Characteristic facies, short stature, hypotonia, moderate intellectual disabilities
Congenital malformations – gastrointestinal anomalies, Hirschprung disease, early-onset Alzheimer’s
10
Q
Edwards Syndrome
A
Trisomy 18
Intrauterine growth retardation, characteristic facies, severe intellectual disabilities
Clenched hands, narrow hips
Congenital heart disease, CNS abnormalities
11
Q
Patau Syndrome
A
Trisomy 13
Normal or deficient growth, CNS abnormalities
Facial clefts, polydactyly
Renal dysplasia, congenital heart disease, omphalocele (midline defect –> abdominal organs develop externally in a sac)
12
Q
Klinefelter Syndrome
A
47, XXY
Tall stature, hypogonadism, gynecomastia, sterility, language impairment
13
Q
Turner Syndrome
A
45, X
Short stature, webbed neck, edema of hands and feet, broad shield-like chest, widely-spaced nipples, narrow hips, renal and cardiovascular anomalies, hormonal dysfunction, gonadal dysgenesis (failure of ovarian maintenance) = infertility
14
Q
Charcot-Marie-Tooth Disease
A
Cause = duplication of the gene for peripheral myelin protein 22 (PMP 22) 17p11.2
Characterized by weakness of foot & lower leg muscles, hammertoes, & weakness & muscle atrophy of the hands in late stages.
Affects the function of peripheral nerves
15
Q
Hereditary neuropathy with predisposition to pressure palsy (HNPP)
A
Cause by deletion of gene 17p11.2, containing gene for peripheral myelin protein 22 (PMP 22)
16
Q
What is a contiguous gene syndrome?
A
Disorder caused by overexpression or deletion of several genes adjacent to one another.
Examples: velocardiofacial syndrome, DiGeorge Syndrome
17
Q
Velocardiofacial syndrome
A
del 22q11
Cleft palate, septal defects
18
Q
DiGeorge Syndrome
A
del 22q11
Absent or hypoplastic thymus and parathyroids
Outflow tract defects in the heart
19
Q
What is the genetic basis for Prader-Willi Syndrome?
A
In 70% of patients, PATERNAL DELETION of homologue of Chr 15 (15q11-q13)
Maternal chr is methylated
20
Q
Angelman Syndrome
A
Characterized by unusual facial appearance, short stature, severe intellectual disabilities, autism, spasticity, and seizures
Have a MATERNAL DELETION on homologue of Chr 15. Paternal copy is methylated & inactive
21
Q
What is a horizontal inheritance pattern?
A
Disease shows up in siblings but not parents or offspring = autosomal recessive
22
Q
Allele, carrier, & disease frequencies?
A
Allele frequency = q
Disease frequency = q^2
Carrier frequency = 2pq = 2q
q is for recessive diseases
23
Q
What is allelic heterogeneity?
A
The presence of multiple common mutant alleles of the same gene in a population
24
Q
What is a compound heterozygote?
A
An individual who carries 2 different mutant alleles of the same gene
25
PKU
Phenylketonuria = Have problems metabolizing phenylalanine in the blood
>98% of time, defects in phenylalanine hydroxylase (PAH)
1-2% of time, defects in PAH cofactor BH4
High allelic heterogeneity. Compound heterozygosity leads to varied phenotype severity – depending on the allelic mutations, can be anywhere from 20-50% activity
26
What is PAH?
Phenylalanine hydroxylase; converts phenylalanine into tyrosine
27
What is BH4?
A cofactor for PAH. Also cofactor in creation of dopamine and serotonin – pts with deficiency have trouble making these neurotransmitters
28
Explain maternal PKU
Women went off PKU (low-protein) diets during pregnancy; led to increased miscarriage & babies with developmental delays.
They had too much Phe in blood --> gets to baby, is toxic for developing brain of baby
Solution: low-Phe diet lifelong, esp during pregnancy
29
How & when do you screen newborns for PKU?
Screen by measuring ratio of Phe:Tyr (babies with PKU have high Phe, low Tyr)
Need to screen multiple times to make sure you don't miss critical window; once 1-2 days after birth & once 10-14 days after birth
30
Clinical features of alpha-1 antitrypsin?
Increased risk for emphysema, liver cirrhosis, liver cancer
31
Which enzyme is the primary target for alpha-1 antitrypsin, and what does it do?
Elastase - helps break down elastin in lungs & maintain proper lung turnover
32
Mutant alleles involved in AAT?
Z allele is the most common
- Individuals with ZZ genotype have ~15% of normal SERPINA1 level (gene for AAT)
- Z allele makes a protein that isn’t folded properly & tends to accumulate in the ER of liver cells --> liver damage
S allele makes unstable protein (lower enzyme activity)
- Individuals with SS genotype have 50-60% of normal level
33
Tay-Sachs Disease
Lysosomal storage disorder caused by abnormal accumulation of GM2 ganglioside in lysosomes. Caused by a defect in HEXA gene, leading to faulty α subunit in Hexosaminidase A enzyme
34
What is GM2?
Lipid found in neuronal cell membranes
35
What is the molecular pathway of Tay-Sachs Disease?
GM2 gets removed from cell membranes by GM2AP in lysosomes. GM2AP transports it to Hex A (enzyme composed of α and β subunits). Subunits are encoded for by HEXA & HEXB genes, respectively
36
Sandhoff Disease
Caused by mutation in HEXB gene --> faulty β subunits --> defects in enzymatic activity --> accumulation of GM2 & other substrates acted upon by enzymes with β subunits
37
AB variant of Tay-Sachs Disease
Mutation in gene encoding for GM2AP protein = proper enzymatic function but no carrier protein --> accumulation of GM2 in lysosomes
38
What is the layout of the α- and β-globin gene clusters?
Two copies of α on Chromosome 16
One copy of β on Chromosome 11
α-cluster: zeta-alpha2-alpha1 (ζ-α2-α1)
β-cluster: epsilon-gammaG-gammaA-delta-beta (ε-γG-γA-δ-β)
39
What are the different forms of hemoglobin expressed during development?
Embryonic:
- Hb Gower 1: ζ2ε2
- Hb Gower 2: α2ε2
- Hb Portland: ζ2γ2
Fetal:
Hb F: α2γ2
Adult:
>95% Hb A: α2β2
3.5% Hb A2: α2δ2
1% Hb F
ζ to α (zeta during embryo --> at 6 weeks post-conceptual age (fetus) all α)
ε to γ (epsilon during embryo --> same as above)
Levels of γ start to decrease simultaneously with levels of β starting to increase (at birth)
Levels of δ (delta) start to increase during adulthood
40
What is the Locus Control Region?
Upstream promoter ~10kb away from coding sequence
Deletions of the entire LCR of the beta cluster cause beta-thalassemias
41
Mutation that causes sickle cell anemia?
```
Mutation in one codon (6)
Changes Glu (charged) --> Val (hydrophobic) on β6
```
HbSS = someone who has 2 alpha & 2 beta with sickle cell mutation
Hb S, when it becomes deoxygenated, loses solubility --> forms polymers --> sickle shape
42
Mutation that causes Hemoglobin C disease?
Mutation in same codon as sickle cell anemia (6)
Changes Glu --> Lys (neg charge --> pos charge)
HbCC = β subunit tends to form crystals & causes lysis of RBCs
43
How do you diagnose sickle cell anemia?
Mst II restriction enzyme recognizes a site on normal β subunits, cuts into pieces. Because of point mutation, it no longer recognizes site on βs subunit = longer fragments are obtained
44
What are the genotypes of α-thalassemias?
1. αα/αα = 100% ; normal
2. αα/α- = 75% ; silent carrier
3. αα/-- (α-thal 1) = 50% ; mild anemia
a. Southeast Asia
4. α-/α- (α-thal 2) = 50% ; mild anemia
a. Africa, Mediterranean, Asia
5. α-/-- = 25% ; severe anemia
a. = Hb H (β4)
6. --/-- = 0% ; fetal death (hydrops fetalis)
45
What are the geographic locations of the different types of α-thals?
α-thal 1 = αα/-- = Southeast Asia
α-thal 2 = α-/α- = African, Mediterranean, Asia
46
What is the genotype of Hb H?
α-/-- = 25% ; severe anemia (β4)
47
What is β-thalassemia minor (intermediate)?
You have one functional β allele and one either missing or mutant. Have 50% β globin amount and >50% β allele, respectively.
48
What is β-thalassemia major (Cooley's anemia)?
You either have 2 missing β alleles (β0-thal) or 1 missing and 1 mutant (β+-thal). End up with 0% β globin or <50% β globin, respectively.
49
What is a simple β-thalassemia?
Mutations affects only a single gene = β-globin chain gene
50
What is a complex β-thalassemia?
Affects expression of multiple genes in a cluster – caused by large deletions that remove β-globin gene plus genes in the β-cluster, or the LCR
51
Hereditary persistence of fetal hemoglobin (HPFH)
There is no δ or β synthesis because of deletions of both genes (which are typically expressed in adults). 100% of hemoglobin is HbF (α2γ2), which is ~17-35% of normal level of Hb production.
52
What mutations cause increased γ-globin expression?
1. extended deletion of additional downstream sequences, which likely brings a cis-acting enhancer element closer to the γ-globin gene
2. mutations in the promoter region of one of the two γ-globin genes that destroy the binding site of a repressor, thereby indirectly upregulating expression of γ
53
What is the geographic distribution of hemoglobinopathies?
SE Asia & West Pacific: α, β thalassemias & E
Africa: S, C, α, β thalassemias
East Mediterranean: β thalassemias and S
High prevalences:
- Africans = S
- SE Asians = E
- SE Asians & Mediterraneans = β-thal
54
What are reticulocytes?
Young RBCs
| sign of increased RBC production
55
What are the clinical features of Cooley's anemia?
- dense skull/marrow expansion
- osteopenia
- enlarged spleen
- iron overload
- growth & endocrine failure
- death usually results from iron deposition
56
Achondroplasia - basics
Most common form of dwarfism
- AD -
Skeletal dysplasia: 1 in 15,000-40,000 newborns
De novo mutations occur exclusively in paternal germline, and occur more with increasing age (>35 years)
57
What are the clinical characteristics of achondroplasia?
- small stature
- rhizomelic limb shortening (proximal limbs shorter than distal)
- short fingers
- trident hands
- large head/frontal bossing
- midfacial retrusion
- small foramen magnum
58
What is the mutation involved in achondroplasia?
FGFR3 = encodes fibroblast growth factor receptor 3
Inhibits bone growth --> this is a GAIN-OF-FUNCTION mutation
(Nucleotide on this gene has the highest new mutation rate known in man)
59
Neurofibromatosis Type I
Disease causing benign tumors on nerve tissues.
- AD -
1 in 3000 births
50% new mutation rate
60
What are the diagnostic criteria of neurofibromatosis Type I?
Two or more of following:
- 6 or more café-au-lait spots
- 2 or more neurofibromas = benign tumor of nerve sheath
- 1 plexiform neurofibroma = involving more than one nerve
- freckling in the axillary or inguinal area
- optic glioma
- 2 or more Lisch Nodules (brown spots in eyes)
- distinctive osseous lesions
- affected first degree relative
61
What is the mutation involved in neurofibromatosis Type I?
```
Protein = NF1
Gene = Neurofibromin-tumor suppressor gene on Chr 17
```
Loss of function mutation
>1000 mutations have been described. Although dominant, must have a mutation in both genes to demonstrate the phenotype
62
Polycystic Kidney Disease - basics
Causes large cysts on kidneys & occasionally other organs
- 1 in 1000 births
- 5% new mutation rate
63
What are the clinical manifestations of PKD?
- bilateral renal cysts
- cysts in other organs
- vascular abnormalities
- end stage renal disease in 50% by 60 years old
64
What are the mutations in PKD?
- 2 different ones, on 2 different genes! = locus heterogeneity
- PKD1 (Chr 16)
- PKD2 (Chr 4, 15%)
- Polycystin 1 & 2
- Produces a truncated protein
65
What are the clinical manifestations of familial hypercholesterolemia?
- high cholesterol (>310) and LDL levels (>190)
- xanthomas
- premature CAD & death
66
What are the mutations in familial hypercholesterolemia?
Locus heterogeneity --> mutations in 3 genes known to cause this:
- LDLK
- APOB
- PCSK9
67
What is anticipation in AD diseases?
Appearance of the disease at an earlier age as it is transmitted through a family, or severity of disease increases
68
What are the clinical manifestations of Huntington's Disease?
- progressive neuronal degeneration causing motor, cognitive, and psychiatric disturbances
- age of onset 35-44
- death approximately 15 years after onset
69
Huntington's Disease - basics
Trinucleotide repeat disorder (CAG)
Occurs 1 in 10,000
Anticipation & paternal transmission
70
What are the mutations involved in Huntington's Disease?
```
Gene = HTT (Chr 4)
Protein = Huntingtin
```
Expansion of glutamine may cause altered structure of biochemical property of the protein
Repeat count:
o 39 = full penetrance
o >60 = juvenile onset
71
What is a hemizygous chromosome?
The special case where a male has an abnormal allele for a gene located on the X chromosome and there is no other copy of the gene
72
Fragile X Syndrome - basics
X-linked dominant
Trinucleotide repeat disorder – CGG repeats in 5' UTR of FMR1 gene
(>200 repeats = full mutation)
More common in males
Most common cause of inherited developmental delay
anticipation
maternal transmission bias
73
Fragile X Syndrome - clinical manifestations
```
intellectual disabilities
dysmorphic features: large ears, long face, macroorchidism
autistic behavior
social anxiety
hand flapping/biting
aggression
```
74
What are the mutations involved in Fragile X Syndrome?
FMR1 & FMRP (protein); on X chromosome (obvs)
Protein is essential for normal cognitive development and female reproductive function
Increase in the trinucleotide repeats --> methylation of gene --> protein is not made
75
Duchenne's Muscular Dystrophy
- progressive muscular weakness, going from proximal --> distal
- calf hypertrophy
- dilated cardiomyopathy
- Creatine kinase levels 10x normal (indication of inflammation of muscles = myositis)
Onset before the age of 5
Wheelchair bound before 13
Death in their 30’s
Absence of Dystrophin protein
76
Hemophilia A
X-linked recessive
1 in 4,000 male births; about 10% of female carriers are affected
Clinical: spontaneous bleeds, excessive bruising, prolonged bleeding, delayed wound healing
Mutation in gene F8, encoding Factor VIII (a coagulation factor)
77
What is ataxia?
Lack of voluntary coordination of muscle movements
Leads to a jerky, unsteady, to-and-fro motion of the middle of the body (trunk) and an unsteady gait (walking style). It can also affect the limbs.
78
Difference between X-linked dominant and X-linked recessive?
X-linked dom:
- displays in male hemizygous and female heterozygotes
- much more likely to actually see the phenotype in females
X-linked recessive:
- phenotype is expressed in all males & homozygous females
- heterozygous females are carriers
79
Mitochondrial inheritance
Mother passes on to all her children. Men pass on to none of their children
Replicative segregation - multiple copies of mtDNA will segregate randomly during replication to mitochondria
Heteroplasmy - mitochondria will have more or less copies of mutated mtDNA
Threshold effect - once enough mutated mtDNA is present, disease phenotype presents
80
What are the clinical manifestations of mitochondrial diseases?
Heavily affect organs that require a lot of oxidative phosphorylation: brain, eyes, skeletal muscle, heart
81
What is a haplotype?
A given set of alleles at a locus or cluster of loci on a chromosome
82
What is linkage disequilibrium?
Certain alleles within chunks tend to stay together, because recombination within those chunks is uncommon
LD blocks (=chunks) 2x smaller in African populations than Caucasian or Asian b/c African pop. is more ancient
83
Candidate gene association studies
You guess what gene is relevant to a disease, and you test SNPs/sequencing in that gene
Depends on a priori biological/positional hypothesis
Best for common risk alleles with small-moderate effects
FATAL FLAWS:
- Publication bias
- True multiple-testing correction must include all tests, even those that never made it to publication
- Background genetic variation may vary among populations – your controls will never be identical to one another
84
Genome-wide association studies (GWAS)
Tests hundreds of thousands/millions of markers (SNPs) across entire genome
You know the number of tests performed genome-wide; can perform appropriate multiple-testing correction
Still need to match cases & controls ethnically; but because entire genome is represented, can detect & correct for population stratification
Create a Manhattan Plot to find statistically sig signals
Difficult to distinguish potentially causal variants from non-pathological
85
Genetic linkage study
Search genome for segments disproportionately inherited along with disease in family members that have a disease vs. family members that don’t have the disease
Best for Mendelian traits (uncommon alleles with strong effects); less powerful for “complex traits”
Functionality depends on recombination = loci close to each other undergo less separation by recombination, whereas the ones further apart undergo more recombination
86
Genetic recombination
Unit of genetic recombination = centiMorgan (cM)
1 cM = 1% recombination between two loci per meiosis
Statistical measure is LOD (log of odds) score
Significance level: LOD >= 3.0 is considered proof of linkage/gene localization
87
Allelic heterogeneity
Multiple mutations in a particular gene can cause disease
88
Genetic heterogeneity
Mutations in multiple genes involved in a particular phenotype
89
Chromosomal analysis
= Karyotyping. Used for suspected abnormalities of chromosome number or structure. Can diagnose aneuploidies, deletions, insertions, rearrangements, and duplications.
90
Fluorescence in-situ hybridization (FISH)
Can diagnose deletions, translocations, and abnormalities of copy number. Often used to detect cytogenetic changes that are not visible by chromosomal analysis.
You need to know the chromosomal deletion/etc. that you're testing for in order to correctly pick the probe!
91
Chromosomal microarray analysis
Look for chromosomal DNA losses & gains, small deletions & insertions. Great resolution.
92
DNA sequencing analysis
Used to identify sequence changes in specific genes - novel, polymorphic, etc. Only assays one region of a gene, though. Doesn't sequence promoters, introns --> not 100% sensitive.
93
What are the advantages/disadvantages of retroviral gene therapy?
Advantages: integrate into cell genome, minimal host immune reactions
Disadvantages: small max size of transgene, infect only dividing cells (not quiescent), risk of insertional mutagenesis/germline integration
94
What are the advantages/disadvantages of adenoviral gene therapy?
Advantages: wide variety of cell types can be infected; large insert size; stable & easy to get to high titers
Disadvantages: does not integrate into genome, expression can be transient, some risk of malignant transformation, immune reactions can be severe
95
What are the advantages/disadvantages of non-viral gene therapy?
Advantages: insert size can be very large (even mini-chromosomes), minimal immune response
Disadvantages: low efficiency, transient expression
96
Fabry Disease
X-linked disorder caused by deficiency of alpha-galactosidase A activity, which removes galactose from glycosphingolipids
97
Multiple Endocrine Neoplasia
AD
RET mutation --> high risk of thyroid cancer, but you can prophylactically remove thyroid & risk goes away
98
Aphasia
Damage to the part of the brain that regulates speech. Present with inability to speak, read, or write.
99
Hereditary hemorrhagic telangiectasia
A disorder that results from abnormalities in the blood vessels. Arteries go directly to veins, without intervening capillaries (arteriovenous malformations, or telangiectases). These can occur near the skin, leaving pink marks.
Hemorrhages can occur in the brain, liver, lungs, or other organs.
100
What is the amino acid substitution that occurs in achondroplasia?
Gly380Arg substitution
101
Syndromic deafness - types and causes
Retinitis pigmentosa --> Usher
Thyroid goiter --> Pendred
Arrhythmia or sudden death --> Jervell and Lange-Nielson syndrom
White forelock --> Waardenburg
8th nerve schwannomas --> Neurofibromatosis type II
102
What is the most common cause of congenital deafness?
Genetic, autosomal recessive, nonsyndromic deafness due to GJB2 mutation
103
What happens with the different amounts of repeats in Fragile-X Syndrome?
CGG repeats!
5-50 repeats --> normal
50-200 repeats --> increased expression of mRNA (bizarrely)
>200 repeats --> no mRNA --> no FMRP
104
What is Fragile X-associate tremor/ataxia syndrome (FXTAS)?
X-linked, lesser number of repeats than full Fragile-X Syndrome (50-199)
Adult onset --> ataxia, tremor, parkinson's symptoms, peripheral neuropathy.
More in men than women
105
When does premature ovarian failure occur?
When there's a pre-mutation number of CGG repeats (50-199; pre-Fragile-X Syndrome)
Women's ovaries fail early, before 40
106
What are some examples of loss-of-function mutations that lead to disease?
Duchenne's Muscular Dystrophy (and Becker's), HNPP, Osteogenesis Imperfecta Type I
107
Genetics of Duchenne's Muscular Dystrophy?
Mutation/deletion of DMD on Xp21.2 (X-linked inheritance)
Large deletions of multiple exons or nonsense mutations --> LOSS-OF-FUNCTION
108
What are the genetics of Becker muscular dystrophy?
In-frame deletions in the DMD XP21.2 gene - so instead of losing whole exons or nonsense, just lose a few aa. Milder form of disease than Duchenne's.
109
Hereditary neuropathy with liability to pressure palsies (HNPP)
Deletion of PMP22 gene --> LOSS-OF-FUNCTION
Autosomal dominant!!!
This protein is an integral glycoprotein in nerves --> repeated focal pressure palsies.
110
Genetics of CMT1A phenotype?
3 copies of the PMP22 gene --> GAIN-OF-FUNCTION --> Charcot-Marie-Tooth
Autosomal dominant!!!!
Clinically: demyelinating sensory & motor neuropathy. Presents with weakness in lower extremity, sensory loss, & muscle atrophy.
111
Osteogenesis Imperfecta Type I
AD!!
Collagen is made up of 3 chains, 2 proα1 and one proα2
Here, premature stop codon in COL1A1 --> mRNA unstable --> degraded --> only 1/2 as much COL1A1 & proper collagen produced
112
Osteogenesis Imperfecta Types II, III, and IV
Normal amounts of collagen are produced, but 1/2 are normal, 1/2 are not. Phenotype is much more severe than Type I
113
What are some disease examples of gain-of-function of the protein?
Hemoglobin Kempsey, Charcot-Marie-Tooth Syndrome Type 1A
114
Hemoglobin Kempsey
Mutation in beta globin (Asp99Asn) --> higher oxygen affinity. Hemoglobin remains locked in the "relaxed" state. Does not release oxygen appropriately in tissues --> body creates more RBCs --> polycythemia
115
What are some disease examples of novel property mutations?
Osteogenesis Imperfecta Types II, III, & IV; sickle cell anemia
116
What are the three different classes of trinucleotide repeat disorders?
1. Expansion of non-coding repeats and loss of function (Fragile X)
2. Expansion of non-coding repeats and gain of function (FXTAS, myotonic dystrophy types I & II)
3. Expansion of codons in exons (Huntington's)
117
Huntington's Disease
CAG repeats
Normal number is =40
36-39 = incomplete penetrance
Paternally inherited in children
118
Myotonic dystrophy
DMPK (gene that encodes a kinase)
Normal is 5-34 CTG repeats. Repeats expanded generationally. Maternal expansions more likely.
Clinically: myotonia, cataracts, cardiac arrhythmias, weakness, balding, respiratory defects, intellectual disability
119
What classes can genomic DNA be assigned to and what is the frequency of each class?
1.5% translated (protein-coding)
20-25% genes (introns, exons, flanking sequences for gene expression, etc.)
50% "single copy" sequences
50% "repetitive DNA" (millions of repeated sequences)
120
Describe the types of repetitive DNA that exist in the genome
Satellite DNAs (tandem repeats)
- Microsatellites: 2, 3, or 4-nucleotide repeats
- Minisatellites: 10-100 bp tandemly repeated blocks of DNA
- “α-satellite” repeats (171 bp) found near centromeres; may be important to chromosome segregation
Dispersed repetitive elements
- Short Interspersed Repetitive Elements (Alu family)
- Long Interspersed Repetitive Elements (L1 family)
- Medical significance: may facilitate non-allelic homologous recombination events, lead to aberrant genes
121
How many human genes are there?
25,000-30,000
122
What are the different types of genes?
Protein-coding genes
RNA-coding genes (rRNA, tRNA, etc.)
Psueodogenes: intron-containing, retroposed pseudogenes (cDNA from RNA)
123
What is the advantage of gene duplication?
When a gene duplicates, it frees up the other gene to vary while it still carries out an essential function
124
What are the some of the symptoms/diseases associated with aberrant CNVs on 1q21.1?
Deletions in this region lead to microcephaly & schizophrenia
Duplications in this region lead to macrocephaly and autism
125
What is the "missing heritability" problem in genome sequencing?
Individual genes cannot account for much of the heritability of diseases.
Large studies implicating local SNPs account for only a fraction of the expected genetic contribution
126
What does this mean?
46,XX,ins(2)(p13q21q31)
An insertion of segment 2q21-q31 into the breakpoint at 2p13
127
What does this mean?
46,XY,t(2;6)(q35;p21.3)
A reciprocral translocation with breakpoints in chromosomes 2q35 and 6p21.3
128
What does this mean?
45,XY,der(14;21)(q10;q10)
A Robertsonian translocation: fusion with breaks near the centromeres in acrocentric chromosomes 14q10 and 21q10
der = derivative chromosome
129
What are paracentric and pericentric inversions?
Paracentric: inversion does NOT include centromere (can lead to acentric or dicentric chromosomes during meiosis)
Pericentric: inversion includes centromere (can lead to duplications or deletions)
130
What are the ways that reciprocal translocation can go wrong during segregation in meiosis?
Adjacent-1: two chromatids with partial monosomy – unbalanced, total loss of crucial genetic material
Adjacent-2: two chromatids with partial trisomy - duplication of genetic material. Can lead to CML
131
What is a Robertsonian translocation?
Fusion of two acrocentric chromosomes within their centromeric regions, resulting in the loss of both short arms (these short arms contain rDNA repeats, so the loss of these is not deleterious)
"pseudo di-centric"
132
What is an interstitial deletion?
A deletion that contains the centromere (goes from one arm to the other)
Can form into a ring chromosome
133
What is an isochrome?
A chromosome in which one arm is missing and the other is duplicated in a mirror-like fashion
134
What happens to the offspring of a carrier of isochrome 21?
100% are abnormal - either they have trisomy or monosomy (which is not compatible with life)
135
What does DNMT1 do?
It's a maintenance methyltransferase - it recognizes hemi-methylated DNA after duplication & re-methylates appropriately
136
What on earth is Waddington's epigenetic landscape?
Basics: a ball at the top of the hill; can roll down and enter many different valleys.
Biological: a stem cell has the potential to differentiate into many different types of cells, follow many different pathways. Potential for differentiated cells to de-differentiate into something else is decreased (hills on either side of valleys). Each cell state is a stable “low energy” state.
137
What turns histones on? ;)
Acetylation of lysines
Phosphorylation of serines
138
Tumor Suppressor Gene (TSG)
Methylation (silencing) of this can lead to cancer.
Potential therapies are un-methylating it.
139
What is cytogenetics?
Study of the structure & number of chromosomes
140
What are the two most common leukemia translocations?
t(9;22) is diagnostic for chronic myelogenous leukemia (CML). Treated with tyrosine kinase inhibitors (Gleevec)
t(15;17) is diagnostic for a specific acute promyeloid leukemia (APML).
141
Acute promyeloid leukemia (APML)
Result of translocation of 15;17.
Auer rods visible on slides
Treated with retinoic acid --> acts on RARα (retinoic acid receptor) to enable DNA coactivators --> differentiation therapy --> cure
142
How do the cytogenetic findings in childhood B-cell leukemia affect prognosis?
```
Low hyperdiploidy (47-50 chr) = poor prognosis
High hyperdiploidy (>50 chr) = good prognosis
```
143
What are the different types of FISH probes?
Centromere – used for enumeration (ALL panel, prenatal dx)
Locus specific – deletion/duplication (p53, cancer)
Dual fusion, fusion – translocation (BCR:ABL, PML:RARα --> cancer)
Break apart – translocation rearrangement (MLL --> cancer)
Whole chromosome paint (identifying markers, translocations)
144
Chromosomal microarray analysis
DNA from patient and from control is oligomerized and hybridized onto plate. One is labeled red, one labeled green. If everything's yellow, they exist in equal amounts. Can detect duplications, deletions -- but not translocations, as DNA is chopped up.
145
What is uniparental disomy?
In PWS, for example, 2 methylated copies from mom are inherited, nothing from dad.
146
What are the clinical features of Prader-Willi Syndrome?
Newborn: hypotonia (floppy babies), almond-shaped eyes, undescended testicles, lighter skin pigmentation than sibs
Child: early course of difficulty feeding & failure to thrive - until preschool, when child develops hyperphagia and gains weight dramatically
Mild-moderate developmental delays; ophthalmologic problems: strabismus (lazy eye), nystagmus (jiggly eyes); scoliosis; OSA
147
What is ptosis?
Falling or drooping of the eyelid
148
What is spasticity?
Stiff or rigid muscles. May also be called unusual tightness or increased muscle tone.
Reflexes (for example, a knee-jerk reflex) are stronger or exaggerated
149
What are the mechanisms that lead to Down Syndrome?
1. meiosis I nondisjunction (maternal) - 95% of cases
2. Robertsonian translocation (4%)
3. Isochromosome (21q21q translocation)
4. mosaic DS - phenotype typically milder, wider variability
5. partial trisomy 21 (very rare)
150
What is the phenotype of a patient with Down Syndrome?
Normal growth parameters
Midfacial hypoplasia (middle 1/3 of face develops slower than eyes, jaw, etc.)
Upslanting palpebral fissures
Epicanthal folds
Small ears, large-appearing tongue
Low muscle tone, increased joint mobility
Transverse palpebral fissures
Clinically: heart defects, diabetes, thyroid problems, GI structural abnormalities, OSA, increased risk of leukemia, early Alzheimer's
151
Fitness calculations
Autosomal dominant: μ = ½ F (1-f)
Autosomal recessive: μ = F (1-f)
X-linked recessive: μ = 1/3 F (1-f)
* μ = mutation rate/gene/generation
* F = frequency of disease
* f = reproductive fitness
152
What is the difference between pharmacogenetics and pharmacogenomics?
Pharmacogenetics: assessing pharmaceutical efficacy based on allelic variation in genes affecting drug metabolism. Looking at individual genes
Pharmacogenomics: assessing common genetic variants in the aggregate for their impact on drug responsiveness
153
Phase I & II drug metabolism steps?
Phase I: attach a polar group onto the compound to make it more soluble; usually a hydroxylation step
Phase II: attach a sugar/acetyl group to detoxify the drug and make it easier to excrete
154
What is the difference between pharmacokinetics and pharmacodynamics?
P-kinetics: the rate at which the body metabolizes, etc. the drug = whether or how much of the drug reaches its target
P-dynamics: the after-effects of the drug binding to its target (downstream effects) = what happens when the drug successfully reaches its target
155
CYP450 enzyme system
CYP450 genes encode enzymes that are active in liver, small intestine. Metabolize 90% of commonly used meds
156
CYP3A
Acts on cyclosporine.
Inhibited by ketoconazole, grapefruit juice.
Elevated (activity) by rifampin
157
CYP2D6
Acts on tricyclic antidepressants, opioids (codeine)
Inhibited by quinidine, fluoxetine, paroxetine
158
VKORC1 and CYP2C9
Act on Warfarin
159
NAT
N-actyltransferase enzyme
Acts on Isoniazid (drug for TB)
160
TMPT
1 in every 300-400 children do not have this enzyme – if you give these children with ALL (leukemia) the standard chemotherapeutic dose, you will kill the child due to immunosuppression
161
G6PD
Most common disease-producing enzyme defect in the world – 400 million ppl worldwide & 10% of African-American males are G6PD deficient
X-linked
Deficient individuals are susceptible to hemolytic anemia after drug exposures
Acts on sulfonamide, dapsone
162
What is a Barr body?
A clump/cluster of inactivated X chromosome
163
XIST
= a gene located on the X chromosome
Expressed only from the inactive X; inactivation can't occur in its absence
Majority of genes on inactivated X chr have promoters that have been methylated
164
Klinefelter's Syndrome
47, XXY
Learning disability, delayed speech & language, tall stature, small testes, reduced facial & body hair, gynecomastia
165
Jacobs Syndrome
47, XYY
Learning disability, speech/developmental delays, autism spectrum, tall stature
166
Triple X Syndrome
47, XXX
May have tall stature. Increased risk of learning disabilities, delayed speech, seizures, kidney abnormalities
167
What do Sertoli cells & Leydig cells turn into?
Sertoli = sperm
Leydig = interstitial cells; produce testosterone
168
Genital development in women
Paramesonephric (Mullerian) ducts result in female structures
169
Hormones involved in female genital development?
WNT4 = responsible for differentiation of ovaries; inhibited by SOX9
DHH = upregulated by WNT4; inhibits SOX9
RSPO1 = coactivator of WNT pathways
170
Genital development in men
Mesonephric (Wolffian) ducts results in male structures.
Ducts elongate to form vas deferens, epididymus, and seminal vesicles
171
Hormones involved in male genital development?
SRY & SOX9 = responsible for AMH hormone, regression of paramesonephric ducts
FGF9 = differentiation of testes
SF1/NR5A1 = stimulate differentiation of Sertoli & Leydig cells
