Genetics Final Exam Review

(Thanks to Musa Saeed)

Note: Blocked fields indicate information that is not required for final-
Spring2011 (Dr Agnihotri)
1 – Cell Biology:
- Mis-folded proteins end up in the ER (endoplasmic reticulum) before their destruction
- Mucopolysaccaridoses -> located in the lysosomes
- Clathrin coated pits are used for the uptake of LDL cholesterol via the LDL receptor
- Membrane structure: Phospholipids + Glycolipids + Cholesterol
- Microtubules: associated with mitosis and meiosis, move the chromosomes apart, attach to
kinetochores
- DON’T WASTE TIME ON THIS LECTURE!!!

2 – Cell Division:
- Chromosomes can be visualized only in M phase (not in G1, S or G2)
Cell Cycle:
Cyclin Dependent Kinases (CDK): phosphorylate enzymes to regulate cell cycle.
G1Phase -> Protein synthesis, organelles duplicated
G1Check point: Check for cell size, nutrients, growth factors and DNA damage can utilize p53 pathway
and Rb protein.
TP53 gene that codes for p53 protein, works by increasing expression of p21 which inhibits CDKs
and arrests the cell cycle. Also has potential to cause apoptosis.

Li Fraumeni Syndrome
Mode of Inheritance: Autosomal Dominant
Mutation: TP53 gene
Phenotype: Causing variety of cancers and multiple primary cancers. Mutation is usually germ
line, therefore inherited. (Two Hit Hypothesis)

Rb protein works by binding to E2F (transcription factor) and inhibits it, until a CDK phosphorylates it
and removes it from the E2F. Only then can required proteins for DNA replication can be synthesized
and cell cycle can continue to S phase. Mutations in the Rb protein will lead to loss of function of Rb
leading to the lack of inhibition of the E2F, and increased synthesis of replication proteins and increased
replication -> Retinoblastoma

S Phase -> DNA replication

G2 Phase -> Checkpoint/catch-up phase (has double the DNA from G1)
G2 Check point: Check for cell size and DNA damage
M Phase -> Cell duplication/division
- Condensation of chromosomes -> Prophase: start to see chromosomes
Metaphase: most condensed + shortest
Kinetochore -> protein complex located at the centromere that attached microtubules
Meiosis (germ line division):
- Most error prone step: Anaphase I
- Males: Happens all the time
- Females: Arrested in stages -> At birth: Primary oogonia arrested in Prophase I
At Puberty: Secondary oocyte arrested in Metaphase II
At fertilization: Complete Meiosis
Crossing over (exchange of DNA material between chromatids: Recombination) occurs in Pachytene of
Prophase I
Nondisjunction -> unequal distribution of chromosomes -> Aneuploidy (not a multiple of 23)

3 – The Human Genome:

Nuclear: 1 copy per cell (Size: 3 Billion bp)
Nucleosome (beads on a string = 10 nm fiber) -> DNA coiled around the histone core.
Histone Core: Octamer 2x (H2a, H2b, H3 and H4)
Linker Histone: H1
To make DNA Accessible:
Histone modification -> Acetylation of the Tails
DNA modification -> methylation (Heterochromatin/inactive) or demethylation (Euchromatin/active) of
Cystosine residues (CpG Islands)
Solenoid: 30 nm fiber -> can be classified as chromosome
Functional unit of replication -> chromosome loop

Mitochondrial: 1000 copies per cell (Size: 16,500 bp)

Circular DNA
Complete Maternal DNA
Has 13 OXPHOS genes -> Lots of RNA (making proteins for electron transport chain)
No introns only exons (tightly packed -> no extra garbage)
No checkpoints/repair mechanisms
Examples of mitochondrial diseases: LHON and MELA (Mitochondrial Myopathy Encephalopathy, Lactic
Acidosis) – Common symptoms: Neuromuscular problems -> since brain and muscles require lots of ATP

LHON (Leber’s hereditary Optic Neuropathy)

Mode of Inheritance: Mitochondrial
Mutation: Mitochondral DNA mutation in OXPHOS gene (Def: NADH dehydrogenase)
Phenotype: bilateral vision loss

No mutation in the mitochondrial DNA ≠ No mutation in any component of the electron transport chain
There are 60 other OXPHOS genes in the nuclear genome which can cause mutation

1% of DNA -> Single copy DNA

99% of DNA -> Spacer DNA + Repetitive DNA
If all in one place: Satellite DNA (Alphoid: Near Centromere)
Minisatellite >10bp
Microsatellile <10bp
Location: Y chr. And short arms of acrocentric chrs. (13, 14, 15, 21, 22)
Transposons: (able to move around the DNA -> like retroviruses)
Dispersed: LINE + SINE (Long and Short Interspersed Nuclear Elements
LINE: Duchene Muscular Dystrophy
SINE: Alu Family: Points of recombination -> BRCA genes
More SINE and LINE repeats = more mutation
4 – Mutations:
Genome mutations (most common)
Chromosomal mutations
Gene mutations
Mutation in regulatory element -> protein unaffected only production affected
ex: LCR (locus control region) for alpha and beta like globin genes, if mutation in LCR then no production
of any globin.
Most mutations = loss of function (ex: non-functional protein)
Gain of function -> ex: Burkitts Lymphoma (discussed in cancer)

Mutation in coding region -> Will change protein structure (Missense, Nonsense, Silent, Frameshift)
Ex: normal coding region: A B C D E F G
Mutation 1: A B C x Nonsense Mutation
Mutation 2: A B C F G 2 codon Deletion or splice site mutation

60 bp 60 bp -> normal protein

56 bp 56 bp -> 4 bp deletion + frameshift (more severe)
54 bp 54 b6 -> 6 bp deletion in frame

Triple repeat disorders: (DNA polymerase slips)

Huntington Disease
Mode of Inheritance: Autosomal Dominant
Mutation: CAG repeats (polyglutamine) in the coding region of huntingtin gene (malformed
protein product, too much glutamine)
Phenotype: neurodegeneration, cognitive impairment
 Fragile X Syndrome
Mode of Inheritance: X-linked Dominant (long arm of X chr)
Mutation: CGG repeats in the untranslated promoter region of the FMR-1 gene (decreased
expression since CGG look like CpG Islands -> hypermethylation of the DNA)
Phenotype: Big balls and jaw, Mental Retardation

Myotonic Dystrophy
Mode of Inheritance: Autosomal Dominant
Mutation: CTG repeats in the DMPK gene
Phenotype: myotonia and muscle weakness

Friedreich’s Ataxia
Mode of Inheritance: Autosomal Recessive
Mutation: GAA repeats in the Frataxin gene
Phenotype: muscle weakness, vision and hearing impaired, slurred speech

These diseases exhibit Genetic Anticipation: repeat gets longer every generation, increasing in severity
and decreasing the age of onset.

5 – DNA Damage & Repair:

Xeroderma Pigmentosum
Mode of Inheritance: Autosomal Recessive
Mutation: XPA and XPC proteins mutated required for excision repair pathway
Phenotype: sun sensitivity, neurological problems

HNPCC (Hereditary Non Polyposis Colon Cancer)

Mode of Inhertance: Autosomal Dominant
Mutation: MSH and MLH proteins mutated required for mismatch repair
Phenotype: Colon cancer with no polyps

Holliday Model: explains the homologous recombination

Ataxia Telangectasia
Mutation: ATM protein mutated involved in p53 pathway
Phenotype: lack of muscle control, spider veins in eyes

6 – Intro to Cytogenetics:
When to do chromosomal analysis:
Unexplained mental retardation/physical retardation
Abnormal growth/Cancer
Multiple still-births
Family History

1st Get Sample:

For Adult: Blood sample (make a karyotype)
For Fetus: Amniotic fluid
2nd Arrest the cell:
Use Colchicine (microtubule inhibitor) to arrest the cell in metaphase or pro-metaphase, pro-
metaphase is preferred since the chromosome are not yet fully condensed, more bands
available
Acrocentric chromosomes (13, 14, 15, 21, 22) have satellite DNA in their p arms and associated
with Robertsonian Translocations

3rd Visualize:
G Banding: (Giemsa stain) Light Bands = Euchromatin (gene rich)
Dark Bands = Heterochromatin (gene poor)
Q Banding: (Quinacrine stain) Non-Fluorescent Bands = Euchromatin (gene rich)
Fluorescent Bands = Heterochromatin (gene poor)
C Banding: (Giemsa stain only for centromere)

Other Techniques:
SKY (Spectral Karyotyping): Can pick out unknown translocations
Chromosome paint: To pick out known translocations (can’t say balance or unbalanced)
CGH (Comparative Genome Hybridization): Can pick out duplications
FISH (Fluorescent in situ Hybridization): Interpret microdeletions
Prophase: Metaphase:

Nomenclature:

Chromosomal Anomalies:
Euploidy: multiple of 23 (n)
Aneuploidy: not a multiple of 23
Triploidy: 3n = 69 chr (incompatible with life)
Tetraploidy: 4n = 92 chr (incompatible with life)
 If survives then must be a mosaic or wrong specimen
Balanced: All chromosomal present, not necessarily in the right spot
Inversions: Paracentric: Does not involve the centromere (one arm)
Pericentric: involves the centromere
Translocations: Reciprocal: exchange of chromosomal material (no loss
Robertsonian: between two acrocentric chromosomes, karyotype shows one less chromosome
(45)
Unbalanced: addition or deletion of some of the chromosomal material
Insertions
Deletions (partial monosomy)
Duplications (partial trisomy)

7 – Autosomal Cytogenetics:
Mosaic: Genetically different cells originating from one zygote
Chimera: Genetically different cells originating from more than one zygote
Most common cause of spontaneous abortions -> chromosomal defects (Turner syndrome)

Aneuploidies:
Down Syndrome
Aneuploidy: Trisomy 21 (Karyotype 47 Chrs)
Genes Involved: DSCR1 (Down Syndrome Critical Region) and DYRK1A on Chr 21
Mechanism: DSCR1 encodes for an inhibitor of CN (Calcineurin). Normally CN dephosphorylates
the NFATc (transcription factor) which then can enter the nucleus and activate genes for normal
neural development. If more DSCR1 present (trisomy 21) more inhibition of CN, which then can’t
dephosphorylate NFATc. Phosphorylated NFATc can’t enter nucleus, no neural development.
Common cause: Maternal Nondisjunction
Other causes: Translocations: (Karyotype 46 Chrs)
Robertsonian: [46,XX or XY, rob(14;21)(q10;q10),+21] (risk 1/3 for child)
21q21q: 100% risk for child to have Downs
Phenotype: Mental retardation, hypotonia, dysmorphic facial features, heart defects
Other associated disorders:
Alzheimer’s Disease, Premature aging and Leukemia
-> APP gene also located on Chr 21
Screening: Alpha-fetoprotein (AFP) -> if low indicates Downs syndrome

Patau Syndrome
Aneuploidy: Trisomy 13
Phenotype: Cleft lip and palate

Edwards Syndrome
Aneuploidy: Trisomy 18
Phenotype: Rocker bottom feet and fist clenching

Risk Factor for all -> Advanced Maternal Age -> Non-disjunction
Autosomal Deletion Syndromes:
Cri du Chat
Mutation: Large deletion of Chr 5p15
Phenotype: Cat like cry, mental retardation, fertile
El gato frances podia tener bebes aunque era anormal y lo compraron por $5.15

Wolf-Hirschhorn Syndrome
Mutation: Large deletion of Chr 4p16
Phenotype: Greek warrior helmet
El lobo tuvo un gran borron en el casco de guerrero que le costo $4.16 c

Autosomal Microdeletion Syndromes:

Williams Syndrome
Mutation: ELN (elastin) + LIMK1 gene
Phenotype: elfin like, hyperacusis, heart defects
William el de la cara de delfin, por escuchar mucho se le rompio el Corazon por culpa de ELN y
LIMK1 Geneo

DiGeorge/Velocardiofacial Syndrome
Mutation: TBX1 + CRKL gene
Phenotype: CATCH 22 (no thymus, immunodeficiency)

Miller-Dieker Syndrome
Mutation: LIS1 gene
Phenotype: lissencephaly (smooth brain)
Miller tuvo porblemas con LIS1 y se le puso sueve el cerebro

Examples of Genomic Imprinting:

Prader-Willi Syndrome
Mutation: Chr 15 (paternal missing)
Phenotype: Obesity
Prader y Willi a los 15 el papa se desaparecio y se pusieron gordos

Angelman Syndrome
Mutation: Chr 15 (maternal missing)
Phenotype: Mental retardation, spasticity
Angie a los 15 la mama se desaparecio y se volvio anormal

Genomic Imprinting: Both copies (maternal and paternal) are not required by all genes, one copy can be
methylated (turned off), regulated via Epigenetics. However, some genes do require both copies.

8 – Sex Chromosomal Cytogenetics:

Y Chromosome: SRY gene coding for TDF (testis determining factor)
AZF and DAZ genes (mutation in these can cause infertility)
X Chromosome: XIC/XIST gene -> active in Barr bodies
-> inactive in normal X Chromosome (transcriptionally active)
LYON’s Hypothesis: X-inactivation, occurs early in embryonic life
Random vs Selective inactivation (if some mutation)
Barr bodies:
Male with 2 barr bodies = XXXY -> Type of Klinefelters (Phenotype: Gynecomastia and infertility)
Female with 2 barr bodies = XXX

Sex Reversal: 46 XX male: SRY translocated on one of the X chr

46 XY female: SRY lost during crossing over

Aneuploidies:
Klinefelters (47 XXY) -> Variants can include more Xs (XXXXY) -> more severe
Common cause: non-disjunction in Paternal Meiosis I
Phenotype: Tall male, infertile, some learning difficulty

XYY Syndrome (47 XYY)

Cause: non-disjunction in Paternal Meiosis II
Phenotype: Tall male, fertile, some behavioural problems, acne

XXX Trisomy (47 XXX) -> Variants can include more Xs (XXXXX) -> more severe
Cause: non-disjunction in Maternal Meiosis
Phenotype: Tall female, fertile, some learning difficulty

Turners/Monosomy X (45 XO)

Cause: faulty sperm (no sex chr) result in high amount of spontaneous abortions
Phenotype: Short female, infertile, webbed neck
Not associated with advanced maternal or advanced paternal age

DAZ and SOX9 genes associated with gonadal differentiation and development

Female Pseudohermaphroditism/Congenital Adrenal Hyperplasia (CAH)

Karyotype: 46 XX
Mode of Inheritance: Autosomal Recessive
Cause: 21-alpha Hydroxylase deficiency
Phenotype: Ambiguous genitalia, male like genitalia in females (no change in males)

Male Pseudohermaphroditism
Karyotype: 46 XY
Androgen Insensitivity Syndrome (Testicular Feminization Syndrome)
Mode of Inheritance: X-Linked recessive
Cause: Androgen receptors absent, elevated LH and testosterone levels

5-alpha-reductase Deficiency
Mode of Inheritance: Autosomal Recessive
Cause: enzyme deficiency, no
active form of testosterone (DHT)
Phenotype: Female genitalia in males

9 – Autosomal Inheritance:
Pedigree symbols:
Incomplete Dominance: A heterozygote has an intermediate severity of disease compared to
homozygote
Co-Dominance: Full expression of both alleles, both detectable. Ex: Sickle Cell
Allelic Heterogeneity: Different mutations occurring at the same gene locus, causing spectrum of
severity in a disease. Ex: Hurler-Scheie
Locus Heterogeneity: Mutations on different chromosomes and loci causing same phenotype. Ex:
Osteogenesis Imperfecta
Penetrance: Probability that individuals with particular genotype will actually express the phenotype.
Reduced/Incomplete Penetrance: Individuals don’t show phenotype for the mutated genotype. Ex:
Familial Breast Cancer
Variable Expressivity: Same genotype but varying severity of the phenotype. Ex: Neurofibromatosis
Pleiotropy: Single abnormal gene having an effect on different organ systems. Ex: Marfan Syndrome
Late age of onset: Individuals with mutated gene, present with symptoms after they have passed on the
genes. Ex: Huntington’s Disease
Fitness: Probability that the mutation/gene would be passed on to the next generation
Coefficient of selection: measure of new mutations
Calculation of new mutation: S = 1 – f

Autosomal Dominant Pedigree:

Lots of people affected
At least one affected parent
Male to male Inheritance
Male and Females equally affected

Autosomal Recessive Pedigree:

People rarely affected
Female affected so likely not X-linked

X-Linked Recessive Pedigree:

People rarely affected
 Only males affected
No male to male inheritance

Mitochondrial Pedigree:
All progeny/kids affected
No male to male inheritance

Autosomal Dominant Diseases:

Neurofibromatosis
Mutation: NF1 gene
Phenotype: benign fleshy tumours or mild cafe-au-lait spots

Achondroplasia
Mutation: FGFR3 gene (increased risk with advanced paternal age)
Phenotype: Little people, lumbar lordosis

Familial Hypercholesteremia
Mutation: LDL receptor
Phenotype: xanthomas, Familial coronary heart disease, myocardial infarction

Autosomal Recessive Diseases: (likely seen in consanguineous matings -> higher risk)
Cystic Fibrosis
Mutation: CFTR gene (loss of Phenylalanine at position 508)
Phenotype: pulmonary dysfunction, pancreatic enzyme deficiency
Carlos Fue Tan Retrogrado que perdio a Pheny en el asiento 508 y le dio problemas de
pancreas y pulmonares como a Cyst

Tay-Sachs Disease
Mutation: Hex A gene (TATC insertion)
Phenotype: Accumulation of ganglioside GM2 in neurons, neurodegenerative disorder

10 – X-Linked Inheritance
X-Linked Recessive Diseases
Hemophilia A
Mutation: Factor VIII deficiency -> no fibrin formation
Phenotype: Prolonged bleeding time
 Duchene Muscular Dystrophy (Becker’s: mild form)
Mutation: Dystrophin gene
Phenotype: progressive muscle weakness

X-Linked Dominant Diseases:

Hypophosphatemic Rickets (Vit D resistant)
Phenotype: low phosphate reabsorption, rickets

Incontinentia Pigmenti Type 2 (IP2)

Phenotype: Microcephaly, mental retardation, skin rash

Uniparental Disomy: Both copies of the chr/gene inherited from only parent (euploidy)
11&12 – Hardy Weinberg
Gene/Allele frequency Calculations:

Autosomal Dominant (ex: FH)

Affected = p2 + 2pq
Non-affected = q2 = 1 – (p2 + 2pq)

Autosomal Recessive
Affected = q2
Carrier = 2pq
Non-affected = p2

X-Linked Recessive
Males: Affected = q
Non-affected = p
Females: Affected = q2
Carrier = 2pq
Non-affected = p2

Genetic Drift: In small populations, the number of off-springs and number of genotype variations don’t
balance out. This can lead to either fixation of a gene or extinction of a gene

Gene Flow: involves migration resulting in a gradual change in gene frequencies, high frequency in one
primary area and gradual decreases in gene frequency in areas further away from the primary area (Ex:
CCR5)

Founder’s Effect: Founder is a carrier of the allele which can get fixed because of genetic drift in a small
population (Ex: Huntington Disease)

Heterozygote Advantage: Heterozygotes show increased fitness, beneficial effect of a mutation in single
gene (Ex: Sickle Cell Anemia and Malaria)

13 – Linkage Analysis
Recombination frequency (ϴ) -> smaller the number the closer the two loci
Distance between two loci is measured in cM (centimorgan) -> 1 cM = 1 Million bp
LOD Score (Z) -> Measure of confidence in recombination. The likelihood the two loci are linked or
unlinked.
Z score between -2 to 3 = Inconclusive -> no conclusions can be made

Ex: Look for the highest Z score

 0.00 0.01 0.05 0.10 0.20 0.30 0.40
In this case: 25.85
Match the corresponding ϴ, signifies distance
Z - 23.4 25.85 24.6 19.5 12.85 5.5
In this case: 0.05 = 5 cM

So with odds 1025.85 we can say that these loci are linked, and are located 5 cM away

(Note: if Z values include |-3| -2.1| -5| -> the largest value is -2.1, and this means odds against linkage)

14 – Complex Traits
Complex traits -> more than one variable involved. Ex: genetic and environmental
Studied using Twin studies: Concordance rates
100% = trait solely genetic
Higher the rate = higher the genetic component
Adoption Studies -> disease frequency in biological vs adoptive family

Threshold model: A limit that has to be reached for a trait to

be expressed
If genetic -> increased family tendency or lowered threshold
for the family to express trait

1st degree relatives have the highest risk

2nd degree relatives have lower risk
3rd degree relatives have the lowest risk, resemble rest of
the population

Increasing risk factors can put an individual on the right side

(pass the threshold) Ex: A person has a family history of
heart disease and he starts smoking. He moves to the right

Examples of Multifactorial Diseases:

Neural Tube Defects
Mutation: MTHFR -> elevated homocysteine levels
Note: Folic acid supplementation can reduce risk

Alzheimer’s Disease
Early Onset:
Mutation: APP, PSEN1 and PSEN2
APP -> Amyloid plaques
PSEN1 and PSEN2 -> Beta and Gamma Secretases -> function to cleave APP
Mechanism: GSK -3 phosphorylates tau -> hyperphosphorylation -> Tangles in brain
Late Onset:
Allele: ApoE 4 -> associated with alzheimers
15-16 – Cancer and Apoptosis:

Cancer genes:
Proto-Oncogenes -> Oncogenes (activated via point mutations, translocation mutations)
Tumour Suppressor Genes (Two hit hypothesis -> both genes must be affected)
Apototic and Anti-Apoptotic Genes

Telomerase: makes telomeres so the cell can divide more, active in stem cells and tumour cells

Two Hit Model: Need two hits to get the tumour, 1st hit can be inherited (heterozygous individual) and
2nd hit could be due to spontaneous mutation in the individual -> Loss of Heterozygosity

Oncogenes: (gain of function mutation)

Ras, RET, myc, abl

Multiple Solid Tumours

Mutation: Point mutation in GTPase domain of the Ras gene -> always active
Phenotype: many solid tumours

Multiple Endocrine Neoplasia (MEN2A, MEN2B)

Mutation: Point mutation in RET gene (constitutive activation of the receptor tyrosine kinase)
Phenotype: Thyroid cancers and pheochromocytoma

Burkitt’s Lymphoma
Mutation: Translocation of myc (transcription factor) on the strongest promoter t(8, 14)
Phenotype: Cancer of the Jaw, may be associated with Epstein Barr Virus

Chronic Myeloid Leukemia (CML)

Mutation: Translocation of abl on bcr t(9, 22) -> Philadelphia Chromosome (fusion gene)
Phenotype:

Tumour Suppressor Genes: (Loss of function mutation)

Rb -----------------------------> Retinoblastoma
TP53 --------------------------> Li Fraumeni Syndrome
APC ---------------------------> Familial Polyposis Coli (PCC) -> Colon Cancer
BRCA1/BRCA2 --------------> Breast Cancer and Ovarian Cancer
WT1 ---------------------------> Wilm’s Tumour (Kidney tumour in babies)
NF1 ----------------------------> Neurofibromatoma
MLH/MSH --------------------> Hereditary Non Polyposis Colon Cancer (HNPCC)

Apoptotic Genes:
B Cell Lymphoma
Mutation: BCL-2 (anti-apoptotic gene) translocated on the strongest promoter t(14, 18)
Phenotype:

Apoptosis Mechanism:
Two main pathways -> Extrinsic: Fas ligand binds to Fas receptor activating Caspases
 -> Intrinsic: externalization of Cytochrome C from the mitochondria, which
activate Caspases
-> Cytotoxic T Cells: Secrete Granzymes via porins to activate Caspases

17 – Hemoglobinopathies

Genes located in clusters, alpha gene cluster (zeta, psi and alpha) and beta gene cluster (epsilon,
gamma, psi, delta and beta) -> present in order/timing of expression

Locus Control Region (LCR): An enhancer that controls the expression of the genes. If mutation in LCR
then none of the genes are expressed

HBS – Sickle Cell

Mode of Inheritance: Autosomal Recessive
Mutation: GAG -> GTG , Glu 6 Val, Single nucleotide substitution [beta gene]
Phenotype: Loss of negative charge, occlusion in low O2, sickle shape, splenomegaly, local
hypoxia, anemia and hemolysis

Thalasemias:
Alpha-Thalasemia
Mode of Inheritance: Autosomal Recessive
Mutation: Point mutation or In/Del -> cuz of large gene deletion (unequal crossover)
Genotype: --/-- -> Hydrops Fetalis (Hb Barts, lethal)
-α/-- -> Hemoglobin H Disease (microcytic hypochromic anemia)
-α/-α or αα/-- -> α Thalasemia Trait (Minimal anemia)
-α/αα -> Silent Carrier (no abnormality)

Beta-Thalasemia
Mode of Inheritance: Autosomal Recessive
Mutation: Point mutation -> splicing defect or In/Del
Phenotype: hypochromic microcytic anemia, huge skull to increase bone marrow, presentation
at 2yrs of age (thats when the beta chain begins its expression)

Hb Lepore is fusion of delta and beta genes due to unequal crossover

18 – Porphyria, Hemophilia and Transport Disorders

Porphyria (Don`t have to differentiate)

Mode of Inheritance: Autosomal Dominant
Phenotype: cutaneous or neurological, intermediates in urine (wine red urine)

Hemophilia Disorders:
Hemophilia A
Mode of Inheritance: X-Linked Recessive
Mutation: Factor VIII gene
Phenotype: Unable to clot blood, prolonged bleeding time
Treatment: Replacement therapy with Factor VIII
 Venous Thrombosis
Mutation: Factor V Leiden
Phenotype: increased clot/thrombus formation

Transport Disorders:
Wilson’s
Mode of Inheritance: Autosomal Recessive
Mutation: ATP7B (copper accumulation in the liver and brain)
Phenotype: kayser-fleischer ring

Hemochromatosis
Mode of Inheritance: Autosomal Recessive
Mutation: HFE gene
Phenotype: too much iron, liver failure/cirrhosis (depletion therapy - can use leeches)

Cystic Fibrosis
Mode of Inheritance: Autosomal Recessive
Mutation: [CFTR gene] 3 bp deletion at F508 -> at nucleotide binding domain [NBD1]
(most common/severe = class 1 [null allele])
Phenotype: Cl channel messed up, increased NaCl in sweat, pancreatic enzyme deficiency,
infertility (no vas deferens) [high among Caucasians]

Familial Hypercholesterolemia Type II

Mode of Inheritance: Autosomal Dominant
Mutation: LDL receptor mutation or ApoB-100 mutation and EGF homology domain (don’t
release LDL to lysosome and trapped within ER)
Heterozygotes: Decreased LDL receptors, LDL 2x normal, CHD later in life (Incidence 1/500)
Homozygotes: No functional LDL receptors, CHD in childhood
Phenotype: xanthomas, high cholesterol

19 – Aminoacidopathies
Hyperphenylalanemia: Demonstrates both Locus and Allelic Heterogeneity
Locus: Mutation in gene for PAH or gene for BH4 -> same phenotype
Allelic: many mutations -> 3 different types: Classic PKU (PKU I)
Variant PKU (PKU II)
Non-PKU Hyperphenylalanemia
Phenylketonuria (PKU I)
Mode of Inheritance: Autosomal Recessive
Mutation: PAH, PCD, DHPR, GTP-CH, 6-PTS -> Deficiency of phenylalanine hydoxylase (PAH)
Phenotype: high blood/urine phenylalanine (musty/mousy urine smell), neurological problems
Treatment: Diet restriction

Phenylketonuria (PKU II)

Mode of Inheritance: Autosomal Recessive
Mutation: BH4 deficiency
 Phenotype: high blood/urine phenylalanine, neurological problems and low levels of serotonin
and catecholamines
Treatment: Diet restriction and have to give them Serotonin and Catecholamines

Albinism
Mode of Inheritance: Autosomal Recessive
Mutation: Tyrosinase Deficiency
Phenotype: Lack of pigmentation, white skin, white hair, red eyes

Alkaptonuria (AKU)
Mode of Inheritance: Autosomal Recessive
Mutation: Homogentisic acid oxidase deficiency
Phenotype: dark color urine, deposits in joints -> arthritis, onchronosis

Homocystinuria
Mode of Inheritance: Autosomal Recessive
Mutation: Cystathione synthase deficiency or B6 deficiency
Phenotype: Marfan-like, dislocation of lens, mental retardation
Treatment: Megadoses of B6

Maple Syrup Urine Disease

Mode of Inheritance: Autosomal Recessive
Mutation: keto acid dehydrogenase – can’t breakdown branched amino acids
Phenotype: urine smells like burnt sugar

Lesch-Nyhan Syndrome
Mode of Inheritance: X-linked recessive
Mutation: HPRT1 gene -> HGPRTase deficiency (involved in salvage of purines)
Phenotype: increase in uric acid in the brain, self mutilation

ADA-SCID
Mode of Inheritance: Autosomal Recessive
Mutation: ADA gene -> adenosine deaminase deficiency
Phenotype: recurrent infections, autoimmune

X-SCID
Mode of Inheritance: X-linked Recessive
Mutation: IL2RG -> IL2 receptor
Phenotype: recurrent infections, autoimmune

Mitochondrial:
Leber’s Hereditary Optic Neuropathy (LHON)
Mode of Inheritance: Homoplasmy, mitochondrial
Mutation: deficiency of NADH dehydrogenase [OXPHOS gene]
Phenotype: bilateral loss of vision, any tissue can be affected (mainly OXPHOS)

Homoplasmy: Daughter cells receive a purely normal or purely mutant mitochondrial DNA
Heteroplasmy: Daughter cells receive a mixture of normal and mutant mitochondrial DNA. Basis
for heterogeneity, leading to reduced penetrance, variable expressivity or pleiotropy.

20 – Lysosomal Storage Diseases

Tay Sachs
Mode of Inheritance: Autosomal Recessive
Mutation: Hex A gene (alpha subunit) -> TATC insertion -> frameshift mutation (Hex A enzyme def)
Variable expressivity: Infantile: Severe -> Child dies with it
Adult: Mild -> Late onset
Phenotype: cherry red spot, accumulation of GM2 gangliosides (confirm using northern blot),
neurological deterioration. (Common in Ashkenazi Jews)

Gaucher Disease
Mode of Inheritance: Autosomal Recessive
Mutation: Glucocerebrosidase deficiency -> glucocerebroside build-up
Phenotype: wrinkled paper appearance of the cytoplasm, pain, fatigue, hepatosplenomegaly, mental
retardation, jaundice.

Niemann Pick Disease

Mode of Inheritance: Autosomal Recessive
Mutation: Sphingomyelinase deficiency -> sphingomyelin build-up
Phenotype: cherry red spot, hepatosplenomegaly, jaundice, mental retardation (first few years normal -
> takes time to build up)

Hunter
Mode of Inheritance: X-linked Recessive
Mutation: Iduronate sulfatase deficiency
Phenotype: no corneal clouding, mental retardation and physical deformity

Hurler’s (Schie) [variable expressivity]

Mode of Inheritance: Autosomal Recessive
Mutation: alpha-L-iduronidase deficiency
Phenotype: corneal clouding, coarse facies, mental retardation and physical deformity

I-Cell Disease
Mode of Inheritance: Autosomal Recessive
Mutation: N-Acetyglutasamine-1-Phosphotransferase deficiency
Phenotype: Lysosomal enzymes in the blood, coarse facial features, mental and growth retardation

Peroxisomal Disorders:
X-linked ALD (Adrenoleukodystrophy)
Mode of Inheritance: X-linked Recessive
Mutation: ABCD1 (ATPase) deficiency
Phenotype: destroys myelin sheath, neurological problems
 Refsum Disease
Mode of Inheritance: Autosomal Recessive
Mutation: PHYH -> phytanoyl-CoA dioxygenase -> accumulation of phytanic acid
Phenotype: Anosmia (loss of smell), neuropathy

Zellwegger Syndrome
Mode of Inheritance: Autosomal Recessive
Mutation: PEX gene
Phenotype: problems in prenatal development

21 – Blood Groups and Cytoskeletal Disorders

ABO blood group determined by ABO gene locus on Chr. 9 that codes for galactosyl transferase
Blood Type A: N-acetylgalcosyltransferase
Blood Type B: galactosyltransferase

Rh Incompatibility: Rh- mother has a Rh+ fetus, some amount of fetal blood comes into the maternal
circulation and the mother makes antibodies against it for the next exposure. In a subsequent pregnancy
if the mother has another Rh+ fetus then the antibodies will destroy all the fetal blood -> Hemolytic
disease of the newborn -> fetal death

Cytoskeletal Disorders:
Duchenne/Becker’s Muscular Dystrophy
Mode of Inheritance: X-linked Recessive
Mutation: Dystrophin (large deletions) -> no protein synthesis
2 hotspots: Actin binding domains and dystroglycan binding domains
Phenotype: weakness, mental retardation in duchenne, if some protein synthesis then Becker’s
(less severe) -> western blot to confirm
Mothers of Duchenne children can also present with muscle weakness -> Skewed X-Inactivation

Osteogenesis Imperfecta (Type 1)

Mode of Inheritance: Autosomal Dominant
Mutation: null allele -> decreased production of pro-alpha chains but normal structure
Phenotype: blue sclera, brittle bones, no bone deformity

Osteogenesis Imperfecta (Type 2)

Mode of Inheritance: Autosomal Dominant
Mutation: substitution of glycine with a bulky amino acid -> structural variant (also in Type 3/4)
Phenotype: Perinatal lethal, severe skeletal deformities, dark sclera

Ehlers Danlos Syndrome

Mode of Inheritance: Autosomal Dominant
Mutation: COL genes (many genes) -> Type 3 collagen effected
Phenotype: hyper extensible skin, hypermobile joints

Marfan’s Syndrome
Mode of Inheritance: Autosomal Dominant
Mutation: FBN1 gene -> codes for fibrillin
Phenotype: dilatation of the aorta, pectus excavatum, arachnodactyly, hyper-extensible joints
 Alpha-1-Antitrypsin Deficiency
Mode of Inheritance: Autosomal Recessive
Mutation: Z gene (M gene = normal allele)
Phenotype: more prone to COPD and emphysema and liver damage

22 – Pharmacogenetics
Phase I Drug Metabolization:
Uses CYP proteins coded by CYP genes
CYP genes-> involved in detoxification and metabolization of drugs and alcohol
-> Highly polymorphic (especially CYP2D6)
-> can increase of decrease the rate of metabolization
-> Poor metabolizers: Risk of toxification
-> Ultrafast metabolizers: need more of drug for same effect

Phase II Drug Metabolization:

Acetylation
Fast Acetylators: Need higher doses (rapid inactivation of drug)
Slow Acetylators: Need lower doses (slow inactivation of drug)

INH (Isoniazid) therapy for Tuberculosis -> Fast: Decreased serum [INH] -> under-treated
Slow: Increased serum [INH] -> neuropathy

50% of all Caucasian and African Americans are Slow Acetylators

G6PD Deficiency
Mode of Inheritance: X-Linked Recessive
Phenotype: Hemolytic Anemia
Precipitated by: High oxidant stress, Primaquine (anti-malarial), Fava Beans

Malignant Hyperthermia
Mode of Inheritance: Autosomal Dominant
Mutation: RYR1 gene mutated (encodes a intracellular Ca2+ channel)
Phenotype: life threatening fever, sustained muscle contraction
Precipitated by: Halothane, anesthetics, muscle relaxants

Warfarin Therapy -> Anticoagulant, works by blocking Vit K epoxide reductase -> VKORC1 gene
Vit K epoxide reductase: Works by reducing Vit K into active form which can then
glycosylate the glutamine residue on the coagulation factors and make them active
-> Dose varies in people, too much can cause excessive bleeding
-> Dose dependent upon allele
VKORC1 Haplotype A: need a smaller dose
VKORC1 Haplotype B: need normal dose
CYP2C9 deficiency: need a lower dose than normal
-> Double Homozygote: VKORC1 Haplotype A and CYP2C9 deficiency
-> Need 1/6th of normal dose for same effect
23 – Treatment
Types of Treatment: (examples are NOT important only types are)
Restriction Therapy: Galactosemia -> avoid all dairy products
Replacement Therapy: Provide the essential factor exogenously (Factor VIII in Hemophilia)
Diversion Therapy: Divert the harmful metabolite into a different pathway (Cholestryamine)
Inhibition Therapy: Decrease transport and inhibit catalysis (FH -> Inhibit cholesterol synthesis)
Depletion Therapy: Removal of compound from the body (Hemochromatosis -> remove iron)
Enzyme Replacement Therapy: replace the damaged enzyme, very expensive (Gaucher)
CoFactor Administration: Megadoses of cofactors (Homocysteinuria and vit B6)

Gene Transfer (for gene replacement therapy)

ExVivo: Gene taken from patient cultured in Petri dish and reintroduced after gene transfer
InVivo: The functional gene is packaged into a plasmid and directly injected into the patient
Plasmid/Vector: Very expensive to use but very effective

Stem Cells: Totipotent -> Ability to differentiate into anything, present before the blastocyst
Ex: Embryonic stem cells
Pluripotent -> Inner cell mass of the blastocyst, able to differentiate into all tissues
Ex: Embryonic germ cells, adult germ cells
Multipotent -> Give rise to cells that have a particular function (committed)
Ex: Skin stem cells or blood stem cells

Mesenchymal Stem Cells are multipotent adult stem cells which can differentiate into bone, cartilage
muscle and fat

Cloning:
2 Types:
Therapeutic: Grow the embryo to make a tissue or organ needed for transplant for DNA donor
Reproductive: Create a new animal with a same DNA as the donor

24 – Screening
Newborn Screening (Mandatory)
Criteria: Treatment must be available for that disease
Early treatment/care can reduce the severity of disease
Testing is required, can’t be determined by routine observation
Disease must be prevalent/common (justifies cost)
Diseases screened: (depends on state/province)
PKU
Galactosemia
Biotinidase Deficiency
Guidelines: Direct benefit to neonate
Cost-effective
Reliable test
System in place to deal with screening and follow-up

Heterozygote Screening (Optional)

Screening for carriers
Targeting specific ethnic groups
 Diseases Screened: Tay Sachs is Ashkenazi Jews
Sickle Cell in African Americans
Beta-Thalasemia
Criteria: High frequency of carriers
Inexpensive and dependable
Genetic counselling available
Availability of pre-natal diagnosis
Voluntary participation

Pre-Natal Screening
Common tests: Chromosomal analysis for Advanced Maternal Age
Alpha-fetoprotein levels (AFP)
Invasive (All have a risk of abortion)
Reasons: Advanced Maternal Age
Previous de novo mutation in child
Family history or mutation in one of the parents
Techniques:
Amniocentesis: Needle inserted transabdominally into amniotic cavity (15th - 16th week)
-> Fetal chromosomal analysis
-> Detect alpha-fetoprotein levels
-> High AFP Levels => Neural Tube Defects (NTD)
-> Low AFP Levels => Trisomies (13, 18 or 21)
Chorionic Villus Sampling (CVS): Needle inserted transcervically and transabdominally
into the chorionic villus (10th – 12th week)
-> Can detect major problems earlier
-> Can’t detect AFP levels
Cordocentesis: Fetal blood from umbilical cord (19th – 21st weeks)
-> Confirmatory test (clears any ambiguity)
-> Late Diagnosis
Non-Invasive
Maternal serum screen for alpha-fetoprotein (16 weeks)
Checking for Neural tube defects
Maternal Serum Screen for multiple markers
Triple Screen: Measure AFP -> Alpha feto-protein
uE3 -> Unconjugated Estriol
hCG -> Human Chorionic Gonadotropin

Quad Screen: Measure AFP -> Alpha feto-protein

uE3 -> Unconjugated Estriol
hCG -> Human Chorionic Gonadotropin
Inhibin-A (increased in down syndrome)
Ultrasonography: Able to identify major anomalies in the first trimester
Can detect: Chromosomal Aneuploidy
Single gene defects
Fetal sex and age
Multifactorial disorders (cleft lip, congenital heart defects, NTD)