SSN MM Block 3 - Genetics

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PATTERNS OF INHERITANCE
MOLECULAR BASIS OF DISEASE
Naralys Batista nb2738
Based on previous presentations by Alana Ganz, Emily Harris, Gabby Loeb, and Sarah Karinja and
slides/lecture given by Wendy Chung, MD, PhD.
OUTLINE
1. Important Terms
• Genotype, phenotype, penetrance, expressivity
• Allelic heterogeneity, locus heterogeneity, phenotypic heterogeneity, pleitropy
2. Pedigrees and Modes of Inheritance

• Autosomal dominant
• Autosomal recessive
• X-linked
• Mitochondrial
3. Molecular Basis of Disease

• GOF à dominant
• LOF à dominant, recessive, or dominant negative
DEFINITIONS
• Genotype = what is encoded in your DNA at a given location (allele) in the genome
• Phenotype = observable expression of genotype

• Can be observable or require lab test
• Sometimes must be provoked
• Penetrance = the probability that an individual carrying a specific genotype will express
any observable phenotype
• Can be complete (100%) or incomplete (<100%)
• Expressivity = to what degree and in what way the phenotype is apparent
Genotype
Expressivity Penetrance
Phenotype
GENOTYPE
Genotype = what is encoded by your DNA at a given location (allele) in the genome
Ex. sickle cell disease, Hbb = hemoglobin beta gene
• Hbb A17T = “nucleotide sequence has one A and one T at nucleotide position 17” = heterozygous
• Hbb Glu6Val = “amino acid sequence has one glutamic acid and one valine at amino acid position 6” =
heterozygous
• Hbb AS = “one copy of adult A allele, one copy of sickle cell S allele = heterozygous
All of these notations mean the same thing!

COMPLETE PENETRANCE
Complete penetrance – sickle cell disease
Genotype: Hbb SS
All patients with the genotype have the phenotype.

100% of patients with genotype have phenotype = Complete penetrance!
INCOMPLETE PENETRANCE
Incomplete penetrance – BRCA1 mutation
Genotype: BRCA1 carrier
ONLY SOME patients with the genotype have the phenotype.

80% of patients with genotype have phenotype = Incomplete penetrance!
WHY INCOMPLETE PENETRANCE?
• “Second hit” sometimes required

• Another gene mutation or environmental exposure required
in addition to the initial genotype
• Age
• Phenotype might not manifest until older age
• “Sex-limited”
• Ovarian cancer – will not develop in males
• Male-pattern baldness – will not develop in females
EXPRESSIVITY
• To what degree and in what way the phenotype manifests
Ex. Marfan syndrome – connective tissue disorder
-arachnodactyly = long fingers/toes (thumb sign, wrist sign)
-tall
-hyperflexibility of joints
-aortic dilatation -> dissection/aneurysm
-dislocation of lens of eye
These are all different phenotypic manifestations of

the same genetic disorder!
Different people with the same genotype

can have a different set of phenotypic
features. This is called variable expressivity.
There can be variability within a family or

between families
HETEROGENEITY
ALLELIC HETEROGENEITY
• different mutations in the same gene cause same (or similar)

phenotype.
Ex. Sickle Cell Disease
• Hbb S (Glu -> Val) = classic sickle cell disease

• Hbb C (Glu -> Lys) = less severe sickle cell disease
Someone with Hbb SC (one locus has S and the other has C) is called a “compound
heterozygote” and has less severe disease than someone with Hbb SS genotype
LOCUS HETEROGENEITY
• Mutations in different genes cause the same (or similar) phenotype

Ex. BRCA1 & BRCA2
• BRCA1 gene mutation can cause early onset breast cancer.
• BRCA2 gene mutation can also cause early onset breast cancer.
(different genes, same phenotype)
Ex. Osteogenesis imperfecta

• COL1A1 and COL1A2 are each collagen genes
• Mutations in COL1A1 can cause this disease. Mutations in COL1A2 can also cause this disease.
(Different genes mutated, same phenotype results)
It is important to consider ALL GENES within the differential diagnosis!

Look for multiple genes using a gene panel
PHENOTYPIC HETEROGENEITY
• Different mutations within the same gene cause different phenotypes
Ex. Hemoglobin beta gene

Hbb Val98Met -> hemolysis
Hbb Val67Glu -> cyanosis
Ex. RET mutations can cause Hirschsprung disease or MEN2

(multiple endocrine neoplasia).
HETEROGENEITY
Allelic Locus Phenotypic

• Same gene • DIFFERENT gene • SAME mutation
• DIFFERENT allele • Similar phenotype • DIFFERENT phenotype
• Similar phenotype
Hgbβ (S or C) BRCA1 BRCA2 RET
Hirschsprung Multiple
Sickle Cell Breast disease Endocrine
Anemia cancer Neoplasia 2
PLEIOTROPY
• One mutation in one gene has widespread effects in multiple organ

systems
• Ex. Marfan Syndrome (as discussed earlier)
DEFINITIONS
• Allelic heterogeneity – different mutations in the

same gene cause same (or similar) phenotype.
• Locus heterogeneity – different mutations in different

genes cause the same (or similar) phenotype.
• Phenotypic heterogeneity – different mutations in the

same gene cause different phenotypes.
• Pleiotropy – One mutation in one gene has effects in

multiple organ systems
Locus heterogeneity
Phenotypic heterogeneity
Allelic heterogeneity
Pleiotropy
MODES OF INHERITANCE
PEDIGREE
• Proband = patient/individual who initiated the encounter
PEDIGREE
• First degree relatives share 50% of genetic info

• All siblings, both parents, all children
• Second degree relatives share 25% of genetic info

• Nieces, Nephews, Grandparents, Grandchildren
• Usually includes three generations
• Monozygotic twins are genetically the same -> “one person”

AUTOSOMAL DOMINANT
• Every generation has affected individuals
• Affected individuals usually have one affected parent
• Carriers have 50/50 chance of passing it to children
• Can be transmitted by males or females
• M & F affected
• Males and females equally affected
• Does not skip generations
NOTE: Each child is an independent event!!!
It doesn’t matter if a carrier has
already had four kids without the
mutation, the likelihood of her next kid
inheriting the mutation is still 50%
AUTOSOMAL DOMINANT
Exceptions to the rules:

-new mutations acquired
-reduced penetrance
• people don’t know that they have the gene so it appears to “skip” a generation
-variable expressivity
• people don’t realize that they are expressing a manifestation of disease so they think
they are unaffected
-sex-limited traits
• Ex. male baldness
-germline mosaicism
• A mutation happens just within gonads - all sperm produced from that cell carry
mutation, but the individual in which the mutation occurred had no disease
AUTOSOMAL DOMINANT
De novo
germline
mutation!
AUTOSOMAL DOMINANT
Incomplete penetrance!
AUTOSOMAL DOMINANT
Sex-limited! e.g. Precocious puberty

MOSAICISM
AUTOSOMAL RECESSIVE
• Affected individuals usually born to unaffected parents • M & F affected
• Both parents are carriers -> ¼ chance of affected child • Can skip generations
• Observed more frequently in consanguineous marriages
• Affects either sex
X-LINKED RECESSIVE
• Gene on the x chromosome
• Usually M affected
• Dot = carrier female, asymptomatic • Can skip generations
• Usually affects males • No male-to-male transmission
• Affected males born to unaffected parents
• CANNOT HAVE MALE TO MALE TRANSMISSION!
X-LINKED RECESSIVE
Females can show signs of an x-linked
recessive disorder if…
-unfavorable lyonization (inactivate

normal copy of X chromosome)
-inherit two mutated chromosomes: one

mutated X from mom, another from dad
-chromosomal abnormality:
45 X (Turner Syndrome)
XY female
X-LINKED DOMINANT
• Heterozygous females affected • Does not skip generations

• No male-to-male transmission
• Males often more affected (but not always) • Can be male lethal
• Never male to male transmission!
NOTE: some x-linked disorders are male
lethal -> fewer males than females in
family
MITOCHONDRIAL INHERITANCE
• Mitochondria have their own genome

• Mitochondria are exclusively inherited from mom
• Each egg has a population of mitochondria, and only a subset of
mitochondria have the mutation
Some cells have lots of mutant mitochondria

Some cells have no mutant mitochondria
This is a random process!
-manifestations in different parts of body

depending on where these bad mitochondria
randomly end up
MITOCHONDRIAL INHERITANCE
• Notoriously hard to diagnose (diff. tissues in diff. family members)
• Tends to impact tissues w/ high energy requirements

• Myopathy
• Only maternal transmission
• Stroke
• Many children affected
• Vision loss
• Hearing loss
• Cardiomyopathy
DISEASES
Dominant Recessive
-Neurofibromatosis -Cystic fibrosis
-Marfan’s syndrome -Sickle cell disease
-Cancer predisposition -Hemochromatosis
Loss-of-function of tumor repressor genes (BRCA1/2, Rb, APC) -Deafness (usually)
-Huntington’s -Spinal muscular dystrophy
-Osteogenesis Imperfecta -Most metabolic disorders
-Maturity onset diabetes of youth (MODY) eg Phenylketonuria, α1 Antitrypsin Deficiency
-Long QT
-Cardiomyopathy
-Split-Hand / Split-Hoof
-Precocious puberty
-Acute intermittent porphyria
-Achondroplasia
-Hereditary angioedema X-linked Recessive
-Duchenne muscular dystrophy
X-linked Dominant -Becker muscular dystrophy
-Fragile X syndrome -Rett syndrome
-Craniofrontonasal dysplasia -Red-green color blindness
-Hemophilia
-Incontinentia pigmenti (male lethal)
Seriously
DISEASES Susceptible
Mom and
Dominant Dad
-Neurofibromatosis Recessive
-Marfan’s syndrome Sickle cell disease Have
-Cancer predisposition Spinal muscular dystrophy Child
Loss-of-function of tumor repressor genes (BRCA1/2, Rb, APC) Metabolic disorders (most)
-Huntington’s eg Phenylketonuria, α1 Antitrypsin Deficiency
-Osteogenesis Imperfecta Deafness (usually)
-Maturity onset diabetes of youth (MODY) Hemochromatosis
-Long QT
Cystic fibrosis
-Cardiomyopathy
-Split-Hand / Split-Hoof
-Acute intermittent porphyria
-Achondroplasia
-Precocious puberty
-Hereditary angioedema X-linked Recessive MaRCH
Muscular dystrophy (Duchenne, Becker)
X-linked Dominant a
Fragile X syndrome Rett syndrome
CraniofrontonasaL dysplasia Color blindness (red-green )
Incontinentia pigmenti (male lethal) Hemophelia
Mutation Inheritance
Gain of function (GOF)
mutations – protein is Dominant
overly expressed or gains
new function
Loss of function (LOF) Recessive

mutations – point,
Dominant
deletion, or nonsense
mutation à protein has Dominant negative
less or no function
AD GOF
• Huntington disease: CAG trinucleotide (polyglutamine) repeats à novel function of mutant protein à
neuron death & brain atrophy
• Age of onset depends on # of repeats. Repeat expansion causes anticipation (earlier onset in next
generation, more common in paternal transmission)
AD GOF
• Huntington disease: CAG trinucleotide (polyglutamine) repeats à novel function

of mutant protein à neuron death & brain atrophy
• Age of onset depends on # of repeats. Repeat expansion causes anticipation
(earlier onset in next generation, more common in paternal transmission)
• Myotonic dystrophy: maternally-transmitted CTG trinucleotide repeats in DMPKà
affect binding to RNA-binding proteinsà oral hypotonia
AD GOF
• Huntington disease: CAG trinucleotide repeats à novel function of mutant protein à neuron death & brain
atrophy
• Myotonic dystrophy: maternally-transmitted CTG trinucleotide repeats in DMPKà affect binding to RNA-
binding proteinsà oral hypotonia
• Fragile X syndrome: X-linked CGG trinucleotide repeat in FMR1 gene, phenotype depends on # of copies:
• 6-200 = carrier w/ tremor ataxia & premature ovarian failure
• >200 = silenced FMR1 à intellectual disability, long face
AD GOF
atrophy
• Achondroplasia: FGFR3 GOF inhibits chondrocyte proliferation à failed longitudinal bone growth
àdwarfism
AD GOF
atrophy
• Achondroplasia: FGFR3 GOF inhibits chondrocyte proliferation à failed longitudinal bone growth
àdwarfism
Mutation Inheritance
Gain of function (GOF)
mutations – protein is Dominant
overly expressed or gains
new function
Loss of function (LOF) Recessive

mutations – point,
Dominant
deletion, or nonsense
mutation à protein has Dominant negative
less or no function
INHERITANCE OF LOF MUTATIONS
Inheritance Why?
If 50% normal activity is sufficient,
Recessive then heterozygous individuals will be
asymptomatic.
If 50% abnormal ac5vity confers the

Dominant abnormal phenotype, then heterozygous
individuals will be symptoma;c.
If the abnormal protein poisons the

Dominant normal protein (ex. multimer), then
negative heterozygous individuals will be
symptomatic.
LOF: Recessive
If 50% normal activity is sufficient, then heterozygous individuals will be asymptomatic.
Inborn errors of metabolism (IEM): enzyme mutation à substrate accumulation, product

deficiency, or shunting of accumulated metabolites into other pathways à symptoms à
treated with dietary modification/restriction, vitamins/cofactors, controlled
production/removal of substrate, enzyme replacement
LOF: Recessive
If 50% normal activity is sufficient, then heterozygous individuals will be asymptomatic.
Inborn errors of metabolism (IEM): enzyme mutation à substrate accumulation, product

deficiency, or shunting of accumulated metabolites into other pathways à symptoms à
treated with dietary modification/restriction, vitamins/cofactors, controlled
production/removal of substrate, enzyme replacement
Cystic fibrosis (CF) – deletion in CFTR gene encoding ATP-gated Cl channel (secretes Cl in
lungs & GI; reabsorbs in sweat glands) à misfolded protein à thick mucous in lungs & GI
à frequent pulm infections
Inheritance Why?
asymptomatic.
If 50% abnormal activity confers the

individuals will be symptomatic.

negative heterozygous individuals will be
symptomatic.
LOF: Dominant
If 50% abnormal activity confers the abnormal phenotype, then heterozygous individuals will be symptomatic.
Maturity onset of diabetes in youth (MODY) : glucokinase mutation à predisposes individual to diabetes à loss
of sensitivity to gluten à hyperglycemia
LOF: Dominant
Acute intermittent porphyria (AIP) – mutation in porphobilinogen deaminase (enzyme involved in heme
production) à decreased heme à presents with Painful abdomen, Port wine-colored urine, Polyneuropathy,
Psych sx, Precipitated by drug use
LOF: Dominant
LDL-R deficiency aka Familial hypercholesterolemia – semi-dominant due to gene dosage effect
# missing copies of LDL-R ~ cholesterol levels (0 missing = normal, 1 missing = mild, 2 missing = worst)
LOF: Dominant
LDL-R deficiency aka Familial hypercholesterolemia – semi-dominant due to gene dosage effect
# missing copies of LDL-R ~ cholesterol levels (0 missing = normal, 1 missing = mild, 2 missing = worst)
Tumor suppressor mutations in hereditary cancer – AD inheritance but cellularly recessive

2-hit hypothesis: inherited genetic mutation + lifetime mutation of 2nd allele for phenotype (ex. BRCA1/2, Rb,
FAP)
Inheritance Why?
asymptomatic.
If 50% abnormal activity confers the

individuals will be symptomatic.

nega2ve heterozygous individuals will be
symptomatic.
LOF: Dominant Negative
If the abnormal protein poisons the normal protein (ex. multimer), then heterozygous individuals will be symptomatic.
• Osteogenesis Imperfecta (OI): missense mutation in glycine

à abnormal collagen à worse bone & worse prognosis
Unlike AD-inherited glycine deletion, which results in normal
collagen and is associated with a better prognosis
Questions?
2. Genes and Copying Errors
- Anatomy of the Gene (11/16/18 lecture by Dr. Chung)
- Meiotic & Mitotic Errors (11/13/18 lecture by Dr. Levy)
Anna Qian (lq2177)

Anatomy of the Gene
Anna Qian (lq2177)
Basics/Central Dogma Components of a Gene Organization of genes & DNA Mutations
Outline - Anatomy of the Gene

• Basic Concepts/Central Dogma
• Components of a gene
• Organization of genes & DNA
• Types of mutations
DNA vs RNA
DNA RNA
SUGAR Deoxy ribose Ribose
T or U Thymidine Uracil
Strand Double Single
Stability Stable (fossils!) Unstable &
short-lived
Pyrimidines
• A==T (or U); C≡≡G *stronger have “Y”
Flow of Genetic Information

• DNA à RNA à Protein
• Compartmentalization
transcription translation
• DNA RNA Protein
NUCLEUS CYTOPLASM
Components of a Gene
• Exons (expressed)
• Introns
• Promoter
• Enhancer, silencer, locus
control region, etc.
Control to transcribe or not to
transcribe, & how much
mRNA processing
• Add 5’ cap & 3‘ poly-A tail
• Stabilization
Splicing consensus sequences:

1. 5’ splice site 2. Branch site 3. 3’ splice site
-Every intron starts -An A in the middle -Variable # of pyrimidines
with GU somewhere -Ends with AG
mRNA processing
• Add 5’ cap & 3‘ poly-A tail
• Stabilization
• Cut out introns, aka splice
• 3 areas of very specific
sequences facilitate the
splicing process: splicing
consensus sequences
• GU—A—AG, same for all
introns in all genes
Exons & Translation

• Triplet code *Know how to read codon chart!
• AUG (ATG) = Met = Start codon

• Met always starts every polypeptide
• Met can also be in the middle of a
polypeptide
• Stop codons (UAA, UAG, UGA)
• Redundancy, mostly at 3rd position

Components of a Gene
• Summary:
• Exons
• Codons: AUG(Met)………………. UAA/UAG/UGA(Stop)
• Introns
• Splicing consensus sequences: GU----A----AG
• Regulatory regions:
• Promoter, enhancer, silencer, locus control region, etc
Organization of Genes & DNA

What’s in the genome?
• Coding (2%) • Non-Coding (98%)

Exons à proteins Regulatory things
- Enhancers, silencers, locus control regions
- microRNAs
- Chromatin structure regulators
- DNA methylation controllers
Repetitive seqseqsequences
- Satellites
- Transposable elements
Other things…
microRNAs
• miRNAs repress translation
• ~20 nucleotides
• Bind mRNA à load RNA-Induced Silencing Complex (RISC) à repress translation
Organization of DNA
• Histones
• Complicated 3D
structures
• Epigenetics…
Mutations
• Point mutations
• Silent
• Missense
• Nonsense
• Frameshift
• Splice mutation
• Transposable elements
• Expanded repeats
Silent mutation Missense mutation
Mutations No change in amino acid Change to different amino acid
Usually harmless, BUT Could be ok or bad.

• Point mutations • Might make new splice • Depends on how similar
site the new amino acid is to
• Silent • Might destroy splice the original
• Missense enhancers
• Nonsense
• Frameshift Nonsense mutation Frameshift mutation
Insert/delete non-
Change to premature triplet bases
STOP CODON à change reading
frame
Bad.
• Truncated protein Bad.
• Can cause mRNA to - Useless protein
be degraded sequence
- Premature STOP
codon
Mutations
• Point mutations
• Silent
• Missense
• Nonsense
• Frameshift
• Splice mutation Destroy or make a splice site à change intron/exon component of
mature mRNA à can change protein function.
Splicing mutations can be located within introns, exons, or at splice junctions. They
can lead to exon skipping or inclusion of novel sequence in the mRNA.
Sequences at splice junctions are highly conserved.
Mutations
• Point mutations
• Silent
• Missense
• Nonsense
• Frameshift
• Splice mutation
• Bits of DNA sandwiched by specific repeated sequences
• Cut
Hemophilia factor viiiat these sequences à past into another stretch of DNA
• Mix & match material from different genes/regulatory
regions à altered protein function.
• E.g. hemophilia
Mutations e.g. Huntington Disease:

CAG CAG CAG CAG CAG CAG CAG (7)
• Point mutations
• Silent Increased repeats = UNSTABLE at replication
• Missense
• Nonsense CAG CAG CAG CAG CAG CAG CAG CAG CAG (9)
• Frameshift
• Splice mutation
• Expanded repeats
However most trinucleoide repeats DO NOT cause disease.

Summary - Anatomy of the Gene

• Basic Concepts/Central Dogma
• DNA vs RNA
• DNA à RNA à Protein
• Components of a gene
• Exons, codons
• Introns, splicing consensus sequences
• Regulatory regions
• Organization of genes & DNA

• Non-coding = 98%, Coding = 2%
• miRNAs
• 3D organization of DNA
• Mutations
Meiotic and Mitotic Errors
Anna Qian (lq2177)
Adapted from Casey Wright & Henry Evans
Chromosomal Imbalances Mitosis and Meiosis Meiotic Errors Mitotic Errors
Outline – Mitosis and Meiosis

• Chromosomal imbalances
• Review mitosis and meiosis
• Meiotic errors
• Mitotic errors
Outline – Mitosis and Meiosis

• Meiotic errors
• Mitotic errors
Chromosomal Imbalances
• Aneuploidy: abnormal # of chromosomes in cell (normal = 46)
• Miscarriages
• Full monosomy = never viable
• Full trisomy = usually not viable (trisomies 16, 21, 22)
• Caused by non-dysjunction
• Female gametogenesis > male gametogenesis
• Meiosis I > Meiosis II
Mitosis
Purpose – replicate genetic material to make new somatic cells
NON-DISJUNCTION
Meiosis
• Diploid to haploid
• Gametes: n=23, 1 sister chromatid each
• Males
• 40 days, starting at puberty
• Spermatocytes replaced by mitosis
• 4 functional gametes
• Females
• Begins during development (14wk fetus),
arrested in prophase I
• Meiosis I completed after ovulation
• Meiosis II happens after fertilization
http://web2.mendelu.cz/af_291_projekty2/vseo/files/26/850.png • 1 functional gamete + 3 polar bodies
Cohesins
• Holds homologous pairs and sister chromatids together
• Recombination at chiasmata – crossing over
• Link between female aging and aneuploidy
• Oocyte arrested in prophase I
• Aging à cohesin depletion à unstable chiasmata, loss of association
between sister centromeres à anaphase I defects
Errors in Meiosis
• True non-dysjunction
• Achiasmatic non-dysjunction
• Premature separation of
sister chromatids (PSCC)
Meiosis I: True Non-Dysjunction
Errors in Meiosis
• Homologues travel together to
same pole
• Gametes: 2 disomic, 2 nullisomic Meiosis II:
Embryos: 2 trisomic, 2 monosomic
• Achiasmatic non-dysjunction
• Premature separation of sister

chromatids (PSCC)
Meiosis I: Achiasmatic Non-Dysjunction
Errors in Meiosis
• Achiasmatic non-dysjunction Meiosis II:

• Homologues fail to pair à travel
separately to same pole
• No recombination
• Gametes: 2 disomic, 2 nullisomic
• Embryos: 2 trisomic, 2 monsomic
chromatids (PSCC)
Meiosis I: Premature Separation of Sister Chromatids
Errors in Meiosis
• Achiasmatic non-dysjunction Meiosis II:

chromatids (PSCC)
• Chromatids separate instead of
homologues
• Gametes: 1 disomic, 2 normal, 1
nullisomic
• Embryos: 1 trisomic, 2 normal, 1
monosomic
• Main cause of Meiosis 1 errors
Errors in Mitosis
• Less common
• Early →birth defects
• Later →cancer
• Cause: disruption in amphitelic orientation of sister kinetochores
• Errors in mitotic chromosome segregation → aneuploidies mixed with

normal cell lineages →mosaicism
Amphitelic organization (or lack thereof)

Kinetochores of sister chromatids are lined up, attached
to microtubules coming from opposite poles of the cell
à checkpoint J à divide
Lack of tension à checkpoint L à mitotic arrest (usually)
Lack of tension à checkpoint L à mitotic arrest (usually)
Tension requirement satisfied à divide & make ERROR!

Anaphase lag --> sister chromatid (or homologous

chromosome) is not incorporated into either daughter cell
à lost à mosaicism

Kinetochores of sister chromatids are lined up, &
attached to microtubules coming from opposite
poles of the cell J
Lack of tension → mitotic arrest (usually)

• Mosaicism: 2 or 3 cell lineages (trisomy,
monosomy)
Disruption in amphitelic orientation
→ aneuploidies mixedLack
inofwith
tensionnormal
→ mitotic arrest (usually)
cell lineages → mosaicism
• Mosaicism: 2 or 3 cell lineages (trisomy,
monosomy)
Mosaicism
• Cells in same tissue w/ dif # of
chromosomes
• Can vary across tissues

• Affects phenotypes →difficult to counsel
patients prenatally
• Defined by percentage
• Count 20 cells in order to detect/define

Summary – Mitosis and Meiosis

• Aneuploidy, miscarriages, trisomy

• Cohesins & aging
• Meiotic errors
• True non-dysjunction, achiasmatic non-dysjunction, PSCC
• Mitotic errors
• Amphitelic organization, mosaicism
Cytogenetics
Eric Schweppe – eas2298
Ellen Myers – elm2202
(adapted from Casey Wright clw2168)
Basics Trisomy Sex Chromosomes Partial Aneuploidy Research Methods
Order of review
1. Basics
2. Trisomy
3. Sex Chromosome Aneuploidies
4. Partial Aneuploidy
5. Research Methods
Why care?
Cytogenetics – studying the structure

and function of chromosomes.
- Identify disorders
- Do something (often future tense)
Why care?
Cytogenetics – studying the structure

and function of chromosomes.
- Identify disorders
- Do something (often future tense)
Naming of Parts
Telomere
Short arm
Short arm p
p
Centromere
Long arm
q
Long arm Acrocentric
q
Telomere
Metacentric Sub-Metacentric
How do you identify chromosomes?

Mnemonic: Count to
Size 5 for Acrocentrics
Satellite
Banding pattern (ribosomal DNA)
Centromere Position Centromere

Stalk
Metacentric Sub-metacentric Acrocentric

13, 14, 15, 21, 22
How can you see a chromosome?

1. Grow cells
2. Add PHA – a mitogen - creates
active cell division (i.e. mitosis)
3. Halt mitosis in metaphase with
colchicine
4. Place cells in a hypotonic solution
to rupture nucleus and release
chromosomes
How can you see a chromosome?

1. Grow cells
2. Add PHA – a mitogen - creates
active cell division (i.e. mitosis)
3. Halt mitosis in metaphase with
colchicine
4. Place cells in a hypotonic solution
to rupture nucleus and release
chromosomes
5. Add a stain! E.g. with Giemsa (for
G banding)
Chromosomes gone wild
Ploidy – change in number of sets à lethal for sure

Tri-ploidy: 23x3 = 69
Mono-ploidy: 23x1 = 23
Aneuploidy – gain or loss of one chromosome

Trisomy 21 (47,XY,+21) – Down Syndrome
(In general, loss of a chromosome is more lethal than gaining one)

Mostly lethal with the exception of:
Monosomy – X can survive
Trisomy – 13, 18, and 21 can survive
Partial aneuploidy – +/- a piece of a chromosome

More likely to survive
“Classic” aneuploidy phenotype

• Developmental delay / 17.jpg
Down
Intellectual disability
Syndrome
Trisomy 18 – Edward Syndrome
• Facial morphogenetic
abnormality
• Growth delay
Trisomy 13
• Organ malformation (most
common = cardiac)
• Maternal nondisjunction!
• Age! COHESIN
What do we do when…
A child has congenital

abnormalities or unexplained
developmental delay?
Chromosomal
Microarray
Order of review
1. Basics
2. Trisomy
5. Research Methods
Down Syndrome (47, XX/XY, +21) 1.

Trisomy 21
•Epi: 1 in 700 live births, 95% caused by maternal
nondisjunction (meiosis 1)
•Signs: 2.
1. Simian line (single palm crease)
2. Brushfield spots
3. Epicanthal fold
Other: hypotonia (floppy baby), low-set ears, 3.
large tongue
•Medical problems: heart defects (40%); ↑
leukemia risk; frequent respiratory
infections
Edward Syndrome (47, XX/XY, +18)

Trisomy 18
2.
•Epi: 1 in 3,333 live births. Only 10%
alive after one year.
•Signs:
1. growth deficiency à small for 3.
gestational age
2. Rocker-bottom feet
3. Clenched hands
•Medical problems: heart defects *Mnemonic: Eddy turned 18, and
fist-pumped at his first rock show
(ventricular septal defect)
Trisomy 13 - Holoprosencephaly
Patau Syndrome (47, XX/XY, +13)
Trisomy 13
•Epi: 1 in 5,000 live births. Only 10%
alive after one year.
•Signs: Trisomy 13
1. Microcephaly
2. Holoprosencephaly
3. Polydactyly
•MOST TRISOMIES = SPONTANEOUSLY
ABORTED (even ”survivABLE”)
Detection methods
CVS (chorionic villus sampling)

@11-12 weeks
Amniocentesis @ 16 weeks
BOTH Invasive (risk of miscarriage)
https://www.pregnancyhealth.net/chorionic-villus-sampling-cvs-procedure-risks
Detection methods
Q. Why are fewer trisomy
mutations picked up on
amniocentesis?
http://clinicalgate.com/chromosome-disorders/
Detection methods
Q. Why are fewer trisomy
mutations picked up on
amniocentesis?
http://clinicalgate.com/chromosome-disorders/
A. Spontaneous pregnancy loss
Snap Review
Aneuploidy = gain or loss of a (whole/partial)
chromosome.
It is almost always (survivable/lethal).
Exceptions?
All the trisomies reviewed!
Down (21) Edward (18) Patau (13)
Order of review
1. Basics
2. Trisomy
5. Research Methods
Turner Syndrome (45, X0)

Epi: 1 in 5,000 female births; 99% of
embryos are aborted; 80% paternal X lost;
survivors? mosaic
Signs: triangular face; webbed neck; shield
chest; all have short stature
Medical problems: aortic coarctation;
kidney defects; ovarian dysgenesis à
infertility
Treatment: growth hormone and estrogen
Klinefelter Syndrome (47, XXY)

Epi: 1 in 1,000 male births
Signs: Tall and thin; small testes;
lower IQ (compared to sibs)
Low testosterone à gynecomastia
and poor development of
secondary sex characteristics;
sterility
XXXY, XXXXY à More Xs, more
problems
Triple X (47, XXX)

47, XXX
Epi: 1/1000 female births
g le im a ge
Signs: No physical signs! Learning Goo
r
search fo s!
disabilities; sometimes infertility. mor e d et ail
Won’t pass along extra Xs
47, XYY
Epi: 1/1000 male births
Signs: Tall, normal proportions,
lower IQ (compared to sibs)
NO increased aggression!!!
Aneuploidies – usually not survivable

Exceptions = 21, 18, 13, SEX
chromosome
Even then, most SPONTAENOUSLY
ABORT
Sex chromosome = less severe phenotypes
Advanced maternal age (meiosis 1) except XYY

and XO checks out – these are paternal (xo
= usually)
Order of review
1. Basics
2. Trisomy
5. Research Methods
What is partial aneuploidy?
Partial aneuploidies = a PIECE of chromosome =

more likely to lead to a viable fetus.
What is a translocation?
The genotype of offspring of
translocation carriers depends on
chromosome segregation during meiosis.
Balanced carriers à unbalanced
offspring
WAIT! Where are translocations
happening?
Anywhere cells are dividing.
Mitosis à mosaicism, cancer
Meiosis à genetic syndromes (mostly
Meiosis 1)
Robertsonian Translocation
Robertsonian translocation = long
arms of two acrocentric chromosomes
fuse at the centromere.
Acrosomes = (13, 14, 15, 21, 22)
Short arms are lost.
How do Robertsonian translocations

How many chromosomes does a
affect cells??? Robertsonian carrier have?
NO EFFECT, because ribosomal DNA is 45
redundant across acrocentric (Two chromosomes become one)
chromosomes.
Robertsonian Translocation
Remember!
Balanced carriers → unbalanced offspring
Carriers have an ODD number

of chromosomes (45) so
progeny can be monosomy or
trisomy
Inversions
Inversion = part of a single chromosome
breaks, flips, and is reinserted
Inversions
Type of Inversion What happens during meiosis? Outcome
Duplications/deletions à
Pericentric = Includes possible mono-or trisomy in
the centromere fetus
Paracentric = NOT From loop à dicentric bridge and acentric Nonfunctional

around the centromere fragment (lost) Gamete--
Preferable
b/c no option
for aneuploidy
in fetus.
Trisomy Rescue
Normal
Uni-Parental Disomy (UPD)

Ex. ch15
• Prader-Wili=paternal deletion (MM)
• Angelman – maternal deletion (PP)
M
Marker Chromosome
Try to identify where markers
come from
Deletion Syndromes There are MANY different syndromes associated with

genetic deletions. These are the two mentioned in this
lecture.
Cri du Chat Wolf-Hirschhorn
• Cri du Chat – 5p
• Cat-like cry, microcephaly.
Wolf-Hirschhorn – 4p
• Distinctive facial features.
• Two potential mechanisms:
87% de novo deletion
13% = unbalanced product of
parent chromosome carrying a
balanced translocation
Deletion Syndromes
• Reciprocal translocations usually lead to a ________ phenotype.
• Robertsonian translocations involve _____________ chromosomes, in which the _____

arms fuse and the _____ arms are lost. Carriers have _____ total chromosomes.
• Pericentric inversions ________ the centromere.
• ___________ inversions are “preferable” because they do not lead to aneuploidy in the
fetus.
Deletion Syndromes
normal phenotype.
• Reciprocal translocations usually lead to a ________
acrocentric
• Robertsonian translocations involve _____________ chromosomes, in which the _____
long
short arms are lost. Carriers have _____
arms fuse and the _____ 45 total chromosomes.
• Pericentric inversions ________

include the centromere.
• ___________
Paracentric inversions are “preferable” because they do not lead to aneuploidy in the
fetus.
Order of review
1. Basics
2. Trisomy
5. Research Methods
Methods
Technique How does it work? Resolution What is it used for?
G-banding PHA, colchicine, hypotonic, Giemsa Think BIG: trisomy, monosomy, big
karyotype → size, centromere, banding pattern 5 Mb translocations/deletions
DNA probe w/ fluorescent tag Microdeletions (<1Mbp), aneuploidy,

FISH → hybridizes to the DNA → 200-500 kb rearrangements. NB: we only have
look for fluorescence! probes for KNOWN genetic conditions.
SKY Karyotyping with many colors 5 Mb Easier to see translocations
Chromosomal Lots of FISH run simultaneously 200-500 kb Checking for presence of many
microarray genes in all ages, cancer, research
CGH Compare FISH results Identifies copy number variations (so can
between patient and sample 100 kb only identify unbalanced abnormalities)
DNA
NEW METHOD ALERT! SOMA

SOMA = SNP (single nucleotide
polymorphism) oligonucleotide
microarray analysis
Like chromosomal microarray but
with better resolution!
Picks up copy number variants
FISH vs. SOMA

What do you do when you suspect a child has a chromosomal
abnormality?
FISH – check for individual markers SOMA– run the whole panel
Size of microdeletion we can pick up

Guided by clinical phenotype depends on # of SNPs (500K-millions)
Good luck!
Eric Schweppe
Eas2298
Ellen Myers
elm2202
Genetic Variations
By Sonya Besagar (sb4054)
Slides adapted from Danielle Rome and Vicky Ro; review of lecture by Dr. Wendy
Chung
Outline
• What is genetic variation
• Polymorphisms
• Mutations
• Hardy Weinberg & allele frequency

Genetic variation
• We’re all the same person! (99.9%)
• That 0.1% = POLYMORPHISMS
• Offspring: 100 de novo variations
• Polymorphism: Variant in ≥1% of population

• i.e. normal variant
• Rare mutation: Variant in <1% of population
• More likely deleterious
• Mutation: Pathogenic variation (associated with disease)
Outline
• Polymorphisms
• Mutations

Polymorphisms: Normal variation
• In coding OR non-coding regions
• Most are NOT associated with functional

difference or any disease
Polymorphisms: Types
Polymorphism Definition Example
SNP (single nucleotide Single nucleotide change CAGàCAA

polymorphism)
Tandem repeat Short repeats of the same CAGATT CAGATT etc

sequence
Microsatellite Type of tandem repeat (2- CAG CAG CAG

4 bp)
Copy number variant Deletion/Duplication of

large sequence
Polymorphisms: BLOOOOOOD
• ABO blood type

• Glycosylations on RBC surface (chr
9)
• A and B are co-dominant
• O is recessive
• Rh factor
• Rh is dominant (chr 1)
• Rh+ means you express Rh-D
antigen
ABO Blood type
Type Genotype RBC Antigen on Antibody in Donate to Receives from

RBC plasma
surface
A AA A Anti-B A A
AO AB O
B BB B Anti-A B B
BO AB O
AB AB A and B Nothing! AB All

-Universal recipient
O OO Nothing! Anti-A and B ALL O

-Universal
donor
Rh factor
Type Antigen Antibody Gives to Receives from
Rh+ Rh-D None! Rh+ BOTH
Rh- None! Anti-D BOTH Rh-
This is important?!
If Mom is Rh NEGATIVE but
carrying Rh POSITIVE kiddo*
Mom will make Anti-D antibodies and start

attacking the fetus L
PREVENT WITH RhoGam (Rh immune globulin)
*Note: the first Rh+ baby won’t be affected

Only if it’s the 2nd or later Rh+baby
Outline
• Polymorphisms
• Mutations

Mutations
• Associated with disease
• Mostly RARE (<1%)
• Types
• Germline (parents à kiddos)
• Soma?c (acquired over life?me but NOT passed)
• Dominant fatal condi?ons almost always de novo (aka spontaneous)

• Usually de novo muta?ons occur from father (⬆ with advanced paternal age)
Mutations: types
Point mutation:
Achondroplasia
G à A or G à C
Autosomal dominant,
FGFR3 Gain of Function
mutation
Mutations: types
Deletions/duplications:
Thalassemias
Mutations: types
Intragenic recombination à Inversions:

Hemophilia A
Gene folds over on itself and recombines
Outline
• Polymorphisms
• Mutations

Hardy Weinberg Equilibrium
Handy tool for calculating allele frequency…
p2+2pq + q2 = 1
p+q=1
p = frequency of dominant allele (A)

q = frequency of recessive allele (a)
p2 =% of homozygous dominant (AA)
2pq = % of heterozygotes (Aa) *Carriers
q2 = % of homozygous recessive (aa) *have disease
Allele frequencies are constant from generation to generation as

long as the following conditions are met:
1. Large popula:on
2. Random ma:ng
3. No selec:on
4. Constant muta:on rate
5. No immigra:on/emigra:on
1. Large population
1. IRL: geographically/culturally isolated
communities
2. Random mating
3. No selection
4. Constant mutation rate
5. No immigration/emigration
1. Large population
2. Random mating
1. IRL: Non-assortative mating à certain traits
are more frequent
Dwarfism, deafness, CF
3. No selection
1. Large population
2. Random mating
3. No selection
1. IRL: fitness is NOT neutral
Sickle cell trait à resistance to malaria
1. Large popula-on
2. Random ma-ng
3. No selec-on
4. Constant muta-on rate
1. IRL: Environment/reproduc-ve age affects muta-on rate
5. No immigra-on/emigra-on
1. Large population
2. Random mating
3. No selection
1. IRL: People are global!
Why does it matter?!
• Genetic counseling to estimate carrier risk
Population Screening
By Sonya Besagar (sb4054)
Slides adapted from Run Banlengchit; review of lecture by Dr. Wendy
Chung
Screening:
Things to consider
• 1. High frequency/morbidity/mortality
• 2. Cost
• 3. Good test (sensi>vity & specificity)
• 4. Accepted treatment
• 5. Counseling: help people understand the results and make informed
choices
• 6. Acceptance by popula>on
Ashkenazi Jewish Carrier Screening
• Some diseases (e.g. CF) have more than ONE causative mutations
• Tests are not 100% sensitive
CF Screening
• Standard of care
• Carrier frequency varies by population: 1/22 in Caucasians vs 1/90 in
Asians
• Different sensitivity: 97% for Ashkenazi Jews vs 30% for Asians
• Counseling issues in general
• Careful interpretation of negative results (residual risk)
• Genotype-phenotype correlation
• General prognosis
• Variants of Uncertain Significance (VUS)
Aneuploidy Screening
• Amniocentesis • Biopsy of chorionic tissue

• Fetal tissue in amniotic fluid • 10th-12th week
• 16th-20th week • 1% risk of miscarriage
• 0.5% risk of miscarriage
• CVS
Other options: Cell free fetal DNA (non-invasive!), Preimplantation genetic
dx (very expensive with small chance of conception!)
Newborn screening
• All newborns • Sensitivity = test +, given disease+
• PKU • Specificity = test -, given disease -
• New technologies • Lower the threshold = increase
• Tandem mass spec sensitivity but decreased
• DNA confirmation (second-tier) specificity
sensitivity
• Sensitivity = True Positive/ (True Positive + False Negative)
• Aka how many people with the disease had a positive test result
• Aka how SENSITIVE was the test in picking up people with the disease
specificity
• Specificity = True Negative/ (True Negative + False Positive)
• Aka how many people who don’t have the disease had a negative
result
• Goal: minimizing false positives
Variant interpretation
Slides adapted from Lia Boyle, Manish Mehta;
review of lecture by Dr. Wendy Chung
Variant Classifica-on
• Pathogenic (aka, bad)
• VEP: Variant, expected pathogenic
• VUS: Variant of Unknown Significance
• VLB: Variant, likely benign
• Benign (negative, aka, good - usually)
Variant Classification
• Pathogenic (positive aka bad)
• Benign (negative aka good)
Variant Classification
• Pathogenic (positive aka bad)
• Benign (negative aka good)
Factors to consider
• Published literature
• Functional assays
• Case-control studies
• Cosegregation studies
• Case study/ case series
• Segregation information
• Population data
• In silico models
• Lowest level of evidence but used
most commonly!
Published literature
• Functional assays: see how the protein itself works

• Case-control studies: match affected patients with unaffected
people to determine relative risk
• Cosegregation studies: determine if variant correlates with
disease phenotype in large families; if de novo, confirm
maternity and paternity
• Consider: incomplete penetrance, age of onset, phenocopies
• Aka Do family members with variant have the disease? Are family
members without variants disease-free?
• Case study/case series: comparing groups of patients,
variants, and phenotypes (not super useful!)
Population Data
• Probably not that bad:
• The specific variant has been seen many times in the (presumably) ‘normal’
population databases
• Probably bad:
• The specific variant has almost never been seen in the ’normal’ population
databases
• Limitation:
• Who is in these ‘normal’ databases?
• Reduced penetrance
Analysis: In Silico
• Amino acid conservation

• Probably bad: Variant amino acid differs from original
• Probably benign: Variant amino acid similar to original
• Evolutionary conservation
• Probably bad: Amino acid well-preserved across species
• Probably benign: Amino acid not well-preserved across species
• Protein domain
• Predicted effect on known domain may suggest variant effect
on whole protein
• Splice algorithms/protein models
• Computational models predict effect of variant on splice site
Questions?
10 minute break
Breathe
Stretch
Give yourself a pep-talk
FILL OUT TEACHER EVALS!!!

hCps://goo.gl/forms/fqnZg0MrSBSiUcmY2
5 – Molecular Genetics and
Epigenetics
Etoroabasi Ekpe (eee2119)
SSN Genetics 2018
Outline
1. Molecular Biochemistry
2. Epigenetics
3. Pharmacogenetics
1. Molecular Biochemistry
Molecular Basis of Disease
Normal/ Pathophysiology Treatment
• DNA à mRNA à protein (enzymes) à • Dietary modification (restriction or avoidance)
metabolism • Control substrate production
• Muta8ons à deficient, non-func8onal, or
• Vitamins/ cofactors
missing enzymes
• Enzyme replacement
• metabolites: lack products, accumulate
substrates, shunt metabolites to other • Transplant
pathways, etc.
Mutated Gene Phenotype Example

Allelic Heterogeneity Same Similar SCD, CF
Locus Heterogeneity Different Similar BRCA, PKU (PAH v. BH4)
Phenotypic Heterogeneity Same Different PKU, A1AT, DMD v. BMD
Types of Mutations
• Gain of function (GOF) mutations
• Loss of function (LOF) mutations
§ Recessive (AR or XR)
§ Tumor Suppressor Mutations
§ Dominant (AD)
§ Dominant negative (D-)
Gain of function (GOF) mutations
• Overexpression/ gain new function à
autosomal dominant (AD) inheritance
• Achondroplasia
• FGFR3 GOF à severe limitation of bone growth
• Triple Repeat Disorders
• Huntington’s disease (CAG)
• paternally transmitted CAG repeats à brain
atrophy
• MORE repeats = EARLIER age onset of disease
(anticipation)
• Myotonic dystrophy (CTG)
• maternally transmitted CTG repeat à muscle
wasting, heart block, myotonia, oral hypotonia
(fish mouth)
• Fragile X Syndrome (CGG)
Don’t leave
• CGG repeat on 5’UTR end of X-chromosome
me, Bey
• >200 copies = silenced FMR1 à intellectual
disability
Loss of func)on (LOF) muta)ons
• Recessive (AR or XR) = • Dominant (AD) = haploinsufficiency;
haplosufficient; need 2 bad copies; 1 bad copy enough
carriers are asymptomatic; • Maturity onset of diabetes of youth
• Inborn Errors of Metabolism: ex PKU (MODY)
• Cystic Fibrosis • Acute Intermittent Porphyria
• Alpha-1-antitrypsin (A1AT) • LDL-R deficiency: Dose Effect
Deficiency • Dominant negative (D-) = “poisons”
• Muscular Dystrophy: DMD v. BMD normal protein (ex. multimer)
• Tumor Suppressor Mutations (AR/ • Osteogenesis Imperfecta - glycine
AD) = 2nd hit mutations mutation (no tight turns in collagen) à
brittle bone disease
• BRCA1/2 à breast/ ovarian cancer • Missense (qualitative problem)
• APC à Familial Adenomatous • Deletion (quantitative problem)
Polyposis (colorectal cancer)
• RB à retinoblastoma
2. Epigenetics
Epigenetics v. Genetics
• Genetics
• Heritable modifications of the DNA (ex. ACGTCAGCT) à determines mRNA
sequence
• Mutations: changes of the DNA nucleotide sequence
• Epigenetics
• Heritable modifications of chromatin (DNA, histones, etc.) à determines
mRNA “dosage”
• Does NOT change the DNA sequence
Epigenetic Changes
• Covalent modification of histone tails
• Histone methylation à tighter DNA à ↓ DNA transcription
(silencing)
• Histone acetylation àlooser DNA à ↑ DNA transcription
(expression)
• Covalent modifications of DNA (via methylation of CG
dinucleotides)
• hyper-methylated promoters recruit proteins that block
transcription factor
• Non-coding RNA binding: transcribed but not
translated
• bind DNA à DNA & histone tail covalent modifications à
silencing
• Importance: X-Inactivation and Imprinting

X-Inac'va'on
• Random inactivation of a single X chromosome in most female cells
• Mechanisms (silencing):
• Histone hypo-acetylation & hyper-methylation
• DNA methylation of all promoters (except Xist)
• Xist non-coding RNA coats chromosome
• Mutations
• Non-random X-inactivation aka “phenotypic rescue” à selective pressure for silent X
• X-linked Diseases in women: no selective pressure à mosaic X expression (mild disease)
• X-linked agammaglobulinemia (XLA)
• Duchenne’s muscular dystrophy (DMD)
• Rett syndrome
Imprinting
• Non-random inactivation of 1 of 2
alleles of a gene in all cells according
to allele’s parental origin (corrects for
protein dosage problem)
• Paternally imprinted (paternal gene
silenced, maternal gene expressed)
• Maternally imprinted (maternal gene
silenced, paternal gene expressed)
Diseases Related to Imprinting
• Haig Hypothesis (HH): “mother-father conflict” – mom wants to
survive (“keep resources”) while dad wants baby to grow (“steal
resources”)
• EPIMUTATIONS on chromosome 11
• Beckwith-Wiedemann Syndrome (BWS): GOF methylated maternal DMR
à ↑ IGF2 à big baby
• Silver Russel Syndrome (SRS): LOF demethylated paternal DMR à no
IGF2 à small baby
• MUTATIONS of imprinted genes on chromosome 15q11-13
• Prader-Willi Syndrome (PWS): paternal deletion, maternal imprint
(silenced) à infant hypotonia & poor feeding, adult obesity & obsessive
eating
• Angelman Syndrome (AS): maternal deletion, paternal imprint
(silenced)à severe mental delay, “happy puppets”
3. Pharmacogenetics
Definitions
• Pharmacodynamics: what drug does to body
• Pharmacokine/cs: what body does to drug (ADME)
• Pharmacogenomics: can’t pick your parents
• Pharmacogene/cs: gene<cs + environmental effects on drug’s
efficacy
Polymorphisms and Drug Metabolism
• SNPs – single nucleotide polymorphisms • Metabolism:
• Cytochrome P450 enzymes (CYPs), • Poor metabolizers (PM): susceptible to
• Phase II conjugative enzymes (e.g. UGT, GST, drug toxicity
SULT, MT, EH) • Intermediate metabolizers (IM): not quite
• Drug transporters (PGP – efflux, OATP and “normal”
OCTP – influx) • Extensive metabolizers (EM): "wild-type"
• CYP450 enzymes: CYP3A4/5 > CYP2D6 > • Ultra-rapid metabolizers (URM): may need
higher dose
CYP1A1/2
• Located in every tissue of body (esp. LIVER) • Ethnic differences
• Metabolize, activate, detoxify, non-toxic --> • CYP2C19*2 or *3: none produced in 13-
toxic (pro-carcinogen --> carcinogen) 20% of Asians (ex. omeprazole)
• Intra-subject v. Inter-subject variability • CYP2D6*2xN: 30% of Ethiopian/Saudis have
>2 alleles (UM need higher doses)
• CYP2D6*10: reduced activity in 70% of
Asians
• CYP2A6del: deletion in 15% of Asians (ex.
nicotine)
Drug-Drug Interactions Infectio
nl
metabo owers drug
lism: as
infection
/v
subsides iral load
• Genetic Testing to Predict Drug Rxn metabo
, drug
lism incr
• Warfarin (blood thinner; hemorrhage/ bruising) eases
• Atomoxetine (SNRI, non-stimulant)
• 6MP/azathioprine (immunosuppressive)
• Tamoxifen (breast cancer drug; interacts w/ SSRIs)
• Abacavir (HIV antiviral; hypersensitivity reaction)
• Trastuzumab (chemotherapy; cardotoxicty)
• DDI
• can only be predicted qualitatively
• effect is GREATER in extensive & ultra-rapid metabolizers
• effect is LESS in poor metabolizers
Thank you!
Questions?
Etoroabasi Ekpe
SSN Gene1cs 2018
Complex Genetic Traits
Aleksandar Obradovic
with credit to Megan Liu
Outline
• Monogenic vs. Polygenic
• Studying Polygenic
Disorders
• Environment vs. Genes
• Enemies of Genetic
Analysis
Monogenic < Oligogenic < Polygenic
Environment still matters for monogenic disorders!

e.g. PKU genotype but no phenylalanine = no disease
phenotype
Outline
Disorders GWAS
Analysis
Fam Extreme Linkage

Twin Studies GWAS
Cosegreg Trait Diseq
Twin Studies
Heritability =
2*(concordance between monozygotic twins – concordance between dizygotic twins)
Fam Extreme Linkage

Twin Studies GWAS
GWAS
For each SNP variant in a population, test how common the variant is in
disease population vs healthy subpopulation
Common disease, common variant
Can only reliably detect variants with >5% prevalence
Fam Extreme Linkage

Twin Studies GWAS
GWAS – T1DM implicated genes
• HLA
• DR3/4 alleles in HLA2 locus
(antigen-presenting)
• Affect relative risk differently for

different diseases
• Insulin
• Not produced at right time → not HLA affects many disease phenotypes
(basically every autoimmune disease, viral
recognized as self diseases, etc.)
Fam Extreme Linkage

Twin Studies GWAS
GWAS – Problem
• Statistically significant genes each e.g. Human height is ~80%
contribute only a small amount to heritable, but top 54 gene loci
disease risk (commonly 1.1-1.5 times only explain 5% of heritability
increased risk)
• BUT Family history is currently more
• Additive gene effects do not explain useful than GWAS for
enough predicting height and T2DM
Fam Extreme Linkage

Twin Studies GWAS
GWAS – What are we missing?
• Rare variants (<5% threshold) need more people to power such
studies
• Current technology misses certain mutations or deletions (e.g. in non-

coding regions)
• Not enough power for gene-gene interactions
• Commonly missing rare variants with huge effect, de novo mutations

Fam Extreme Linkage
Twin Studies GWAS
GWAS – What are we missing?
Rare variants = more
likely to be
pathogenic. Less
time for negative
selection.
Common variants =
inherited from ancient
ancestors, less likely to
be pathogenic, due to
negative selection
Fam Extreme Linkage

Twin Studies GWAS
Familial Cosegregation – A solution?
Fam Extreme Linkage

Twin Studies GWAS
Familial Cosegregation
• 1. Find patients with phenotype (e.g. wings)
• 2. Sequence family members with wings
• 3. Find genotype variants present in all of wings and

none of wingless
• 4. Examine general population for these genotypes
Fam Extreme Linkage

Twin Studies GWAS
Extreme Trait Sequencing – Another solution?
Fam. Extreme Linkage

Twin Studies GWAS
Cosegreg Trait Diseq.
Extreme Trait Sequencing
• 1. Find most extreme phenotype (e.g. biggest
wings) in general population
• 2. Sequence genomes of biggest winged people
• 3. Examine general population for these rare

variants

Twin Studies GWAS
Linkage Disequilibrium
• Adjacent genes tend to segregate
together in crossing over
• Probability of gene combination no

longer independent
1 1
2 2
3
• Can use one SNP to track larger 3
region
• e.g. use 2 to track 1-2-3

Twin Studies GWAS
Outline
Disorders
Analysis
Environment Modifies Genetic Risk
BOTH MATTER!!!
Common non-genetic risk factors: diet, income, education
Outline
Disorders
Analysis
Enemies of Genetic Analysis
• Phenocopies
• Same phenotype but different genotype
• E.g. Born without wisdom teeth vs had wisdom teeth removed
• Genetic heterogeneity
• Similar phenotype produced by variants in different genes
• E.g. 3 different genes contribute to early-onset Alzheimer’s (APP, Presenilin1,
Presenilin2), in Bardet-Biedl Syndrome many genes affect cilia structure
• Allelic heterogeneity
• Different mutations in the same gene can produce the same phenotype (even
for monogenic disorders the mutation is not always the same)
• E.g. for Cystic fibrosis >600 pathogenic mutant alleles have been identified in
the same gene
• Many genes of small effect

• Difficult to sample every single relevant gene if there is no single over-riding
gene contributing to disease phenotype.
SIDENOTE
Many of the alleles present at high-frequency in the
population today may have had advantageous effects in
the past but are pathogenic in the current environment
GOOD LUCK!!!!!!
Treatment and
Prevention & Gene
Therapy
Hannah Ford, hrf2110
Treatment & Prevention of
Genetic Diseases
Big Picture à Metabolism Manipulation à Target Proteins à Transplant à Future Directions

Big Picture
• Treatment is based off the nature of
the problem
• Too much? Take some out!
• Too little? Add some!
• Protein working too slow? Speed it up!
• Single organ dysfunction? Replace it!

Big Picture
• Treatment is based off the nature of
the problem
Big Picture à Metabolism Manipula4on à Target Proteins à Transplant à Future Direc4ons

Avoidance/Dietary Restriction
Disease Avoid/restrict ______
Phenylketonuria Phenylalanine

Hereditary Fructose Intolerance Fructose

G6PD deficiency Antimalarials, sulfa drugs, fava
beans, etc.

G6PD deficiency Antimalarials, sulfa drugs, fava
beans, etc.
Acute Intermittent Porphyria Barbiturates
Big Picture à Metabolism Manipula7on à Target Proteins à Transplant à Future DirecCons

Diversion
Urea Cycle Defects • Familial
◦Treatment: Sodium benzoate Hypercholesterolemia
• Treatment: Cholestyramine

Cofactor Supplementation
• Phenylketonuria
• Treatment: BH4
• B12-responsive
methylmalonic
aciduria
• Treatment: B12

Replacement
• Protein replacement Enzyme Replacement
• Most applicable for ◦Storage disorders
extracellular proteins ◦i.e. Gaucher’s disease: replace
• i.e. Hemophilia A: glucocerebrosidase
replacement of Factor VIII

Transplant
• Bone Marrow Transplant Tissue Transplant
• Thalassemias and Sickle Cell ◦Alpha-1 antitrypsin deficiency,
Disease, inherited urea cycle defects
immunodeficiency, storage
disorders

Gene$c Manipula$on
• Target the actual mutation
• i.e. Spinal Muscular Atrophy
(SMA), Cystic Fibrosis

SMA
• Normal: SMN1 provides
90% transcript of full
gene, SNM2 provides 10%
• SMA: no SMN1
• Treatment: use
oligonucleotides to
increase functional SMN2
• Downside: spinal
injections, $300k/year

Cystic Fibrosis
• Treatment: increase the activity of the defective receptor
• Kalydeco/ivacaftor for G551D mutation (4% of patients)
• With advances, can treat approximately 50% of patients
• Downside: $300K/year
Big Picture à Metabolism ManipulaJon à Target Proteins à Transplant à Future Direc2ons

Summary
• Treatment is based off
the nature of the
problem
• Know each method of
treatment and one or
two diseases for each

Human Gene Therapy
Mechanics of Gene Therapy à Clinical Applications à Future Directions

Gene Therapy
• Transfer of genes into cells
• Why?
• To correct a defect
• To provide a new function
• How?
• Gene replacement vs. gene addition
Mechanics of Gene Therapy à Clinical Applica;ons à Future Direc;ons

Gene Replacement
• Homologous recombination
• Swap a good copy of the gene for the bad one at specific location
• Theoretically great à not practical yet

• Possible future direction of gene therapy

Gene Addition
• Add a normal, exogenous gene to cells via a vector
• Vectors: naked DNA, DNA in lipid complexes, viruses
• Viruses:
• Adenovirus and adenovirus-associated viruses (DNA): stay in cytoplasm
• Lentivirus and oncoretrovirus (RNA + reverse transcriptase): do not
require cell division
• In vivo vs Ex vivo:
• In vivo: deliver vector directly into body
• Ex vivo: take cells out of the body, change them, and put them back

Viral Vector Mechanism
• Replace the viral genome with the
gene of interest
• Keep its ability to infect cells but
remove its ability to replicate
• Gene of interest inserts into host
genome randomly

Target Cells
• Within the
hematopoietic stem cell
lineage, progenitor cells
make better targets

Clinical Applications: Single Gene Defects
• Beta-thalassemia/globin gene disorders
• X-linked Severe Combined
Immunodeficiency (X-SCID)
• Adrenoleukodystrophy (ALD)
• Allogeneic bone marrow transplant
• Leber Congenital Amaurosis
• RPE65
• Direct injection into retina

Autotransplanta+on
Stem cells from
bone marrow
Use viral vector

to add normal
functioning gene
Attenuated
chemo to
partially ablate
endogenous
bone marrow
Transfuse cells with normal
functioning gene back to patient

Adverse Consequences
• Insertional mutagenesis:
since the gene of interest can
insert anywhere, it can have
unwanted effects
• Near an oncogene à cancer
• Clonal proliferation
• Autonomous or leukemic
clones
Mechanics of Gene Therapy à Clinical Applica4ons à Future Direc@ons

CRISPR/Cas9
• General mechanism:
induction of double
stranded DNA breaks
à new DNA sequence
edited in à repair
double stranded breaks
• Very precise

Summary
• Goals of gene therapy:
• Get gene to the right target
• Long lasting positive effects
• Limited side effects (safety!)
• Currently: limited clinical use
• Future: great potential for single gene
defects; use of induced-pluripotent
stem cells

Thank you!
• Feel free to send any ques0ons to hrf2110@columbia.edu!
Good luck, Happy Holidays!!!
Have questions? Email your teachers!
Let us know how we can be better:
FILL OUT TEACHER EVALS!!!

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SSN MM Block 3 - Genetics

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MM Block 3

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FILL OUT TEACHER

2. Pedigrees and Modes of Inheritance

3. Molecular Basis of Disease

• Phenotype = observable expression of genotype

• Expressivity = to what degree and in what way the phenotype is apparent

All of these notations mean the same thing!

All patients with the genotype have the phenotype.

ONLY SOME patients with the genotype have the phenotype.

• “Second hit” sometimes required

These are all different phenotypic manifestations of

Different people with the same genotype

There can be variability within a family or

• different mutations in the same gene cause same (or similar)

• Hbb S (Glu -> Val) = classic sickle cell disease

• Mutations in different genes cause the same (or similar) phenotype

Ex. Osteogenesis imperfecta

It is important to consider ALL GENES within the differential diagnosis!

Ex. Hemoglobin beta gene

Hbb Val67Glu -> cyanosis

Ex. RET mutations can cause Hirschsprung disease or MEN2

Allelic Locus Phenotypic

• DIFFERENT allele • Similar phenotype • DIFFERENT phenotype

Hgbβ (S or C) BRCA1 BRCA2 RET

• One mutation in one gene has widespread effects in multiple organ

• Allelic heterogeneity – different mutations in the

• Locus heterogeneity – different mutations in different

• Phenotypic heterogeneity – different mutations in the

• Pleiotropy – One mutation in one gene has effects in

• First degree relatives share 50% of genetic info

• Second degree relatives share 25% of genetic info

• Usually includes three generations

• Monozygotic twins are genetically the same -> “one person”

Exceptions to the rules:

Sex-limited! e.g. Precocious puberty

-unfavorable lyonization (inactivate

-inherit two mutated chromosomes: one

• Heterozygous females affected • Does not skip generations

• Mitochondria have their own genome

Some cells have lots of mutant mitochondria

-manifestations in different parts of body

• Notoriously hard to diagnose (diff. tissues in diff. family members)

• Tends to impact tissues w/ high energy requirements

Loss of function (LOF) Recessive

• Huntington disease: CAG trinucleotide (polyglutamine) repeats à novel function

Loss of function (LOF) Recessive

If 50% abnormal ac5vity confers the

If the abnormal protein poisons the

Inborn errors of metabolism (IEM): enzyme mutation à substrate accumulation, product

Inborn errors of metabolism (IEM): enzyme mutation à substrate accumulation, product

If 50% abnormal activity confers the

If the abnormal protein poisons the

Tumor suppressor mutations in hereditary cancer – AD inheritance but cellularly recessive

If 50% abnormal activity confers the

If the abnormal protein poisons the

• Osteogenesis Imperfecta (OI): missense mutation in glycine

Anna Qian (lq2177)

Outline - Anatomy of the Gene

• Organization of genes & DNA

Flow of Genetic Information

Splicing consensus sequences:

Exons & Translation

• Robertsonian translocations involve _________ chromosomes, in which the _