DATE: October 25, 2018
tumor
Diagnosis
4. Genetic testing
- Testing for the presence of
specific mutations in onco- or
tumor-suppressor Genes
- In 2002: eight (8) ovarian cancer-
related SNP alleles
5. Imaging techniques
- Determine imagine of tumor
through:
- X- rays for mammogram
- MRI (magnetic resonance
imaging)
- CT scan (computerized
tomography)
Refer to HAND OUT
6. Detection of Tumor Markers
- Detection of antigens produced
by cancer cells. Examples:
- PSA - prostate specific
antigen
- CA 125 - tumor cell-
surface glycoprotein;
tumor-associated protein
(does not indicate ovarian
cancer all the time)
Treatment /there is no just one choice/
1) Surgery - removal of primary
2) Radiation therapy - kills cells at S
or M phase
Cobalt and Cesium (burn
skin)
3) Immunotherapy - stimulation of a
person’s immune system to fight
cancer cells
4) Chemotherapy - use of anti-
cancer drugs
5) Angiogenesis control
6) Gene Therapy
Ways to lower risk :) /fun facts/
● Eat plenty of fiber
● Do not smoke
● Drink alcohol in moderation or not
at all
● Exercise regularly
● Do not become overweight
● Limit dietary fat
● Limit sun exposure or use
sunscreen
● Learn to recognize the warning
signs of cancer
End of Lecture on Cancer Genetics
Coverage of Exam 2
EXAM THREE
The Molecular Genetics of
Neurological Disorders & Behavior
Behavioral Traits (Lewis, 5th ed. Human
Genetics)
❏ Related to psychology ~ memory,
intelligence, personality,
emotions
❏ Also related to neurology ~
nervous system function and
diseases
❏ Are heritable traits which can be
multifactorial (polygenic) with a
high environmental influence
❏ Some questions:
❏ What portion of a behavior
results from the action of
genes?
❏ What portion of a behavior
is learned?
❏ Behavioral Genetics is the study
of the genes that govern & genes
involved in the development and
regulation of the nervous system.
Some common behavioral traits /ADD
ON/
Condition: Alzheimer Disease, Anxiety,
ADHD, Autism
Most behavioral traits are multifactorial
❏ Attention deficit disorder (ADD) or
Attention deficit/ Hyperactivity
disorder (ADHD)
❏ Siblings of affected child
show 3-5x greater risk
than those without an
affected sibling.
❏ Twins studies indicate
~80% heritability.
❏ Linkage studies indicated
dopamine pathway may be
involved in ADHD/ADD
Examples of Eating Disorders
❏ Anorexia nervosa
❏ Psychological perception
of obesity and intentional
starvation
❏ 10% of cases are males
❏ Heritability of 0.5-0.8
e.g. 9/16 MZ twins
concordant versus
1/14 DZ twins
❏ Bulimia
❏ Psychological perception
of obesity and intentional
vomiting
❏ Muscle dysmorphia
❏ Results from steroid
consumption to develop
enlarged musculature
(perception of inadequate
muscles)
Sleeping Disorder
❏ Function of sleep remains
unclear but without sleep,
animals die.
❏ Genetic contributions based on:
heritability among families and
identification of genes in model
systems.
❏ Environment influence is great
❏ Sleep-wake cycles are regulated
in part by light via the
suprachiasmatic nucleus in the
brain.
Narcolepsy with cataplexy
❏ Daytime sleepiness with
tendency to rapidly fall asleep
(narcolepsy) and periods of
muscle weakness (cataplexy)
 ❏ 1-2 % risk with first degree
relative
25-31% concordance among MZ
twins
❏ Model of narcolepsy in dogs:
Fully penetrant autosomal
recessive trait due to allele
at gene canarc-1
Drug addiction
❏ Tolerance
The need to take more of
a drug to achieve the
same effect
❏ Dependence
The onset of withdrawal
symptoms with cessation
of drug
● Drug addiction produces stable
(not transient) changes in the
brain
● Heritability is 0.4-0.6
● Twin and adoption studies
support role of genes in drug
addiction
Mechanism of Drug Action
❏ Biosynthetic pathways of
neurotransmitters in
presynaptic neuron
❏ Reuptake transporters
❏ Cell surface receptors
❏ Signal transduction
pathway in post synaptic
neuron
11/6/18
Narcolepsy with cataplexy
l Drug addiction produces
stable( not transient) changes in
the brain
l Heritability is 04-0.6
l Twin and adoption studies support
role of genes in drug addiction
Brain
- neurons ~ 100 billion
- neuroglia ~ at least 1 trillion (NS cells
that support and provide nourishment to
neurons)
Drug addiction
- Tolerance
The need to take more of a drug
to achieve the same effect
- dependence
The onset of withdrawal
symptoms with cessation of drug
*Drugs affect post synaptic neuron
Mechanism of drug action
- Biosynthetic pathway of
neurotransmitters in presynaptic neuron
- reuptake transporters (presynaptic
neurons)
- cell surface receptors (post synaptic)
- signal transduction pathway in post
synaptic neuron
*Prefrontal cortex, Nucleus accumbens
and ventral tegmental area
associated with drug addiction - limbic
system
NA- activated by cocaine
PFC- affected by alcohol
Cocaine, opium, THC ~ Endorphins,
enkephalins
LSD - Lysergic acid diethylamide
--> bind receptors for trace amines (low
level) ---> hallucination ~~ SCZ
schizophrenia
Effects of nicotine at the cellular level
*see picture
1) Nicotine binds to the receptor (which
also binds acetylcholine).
2) This triggers release of dopamine
from vesicle and into the synapse
3) Some dopamine bind receptors on
postsynaptic neuron
4) Some re-enter the presynaptic
neuron via dopamine transporter
5) Uptake of dopamine in postsynaptic
neuron triggers the -pleasurable feeling
associated with smoking
Mood disorders
❏ Represents the extremes of
normal behavior
Major depressive disorder (MDD)
Marked by unexplained lethargy
and sadness and chronic
depression
Bipolar disorder (BPD) or manic-
depression
Marked by depression
interspersed with mania
(euphoria~excessive
cheerfulness)
Mood disorders: examples of molecular
basis
❏ Serotonin, a neurotransmitter,
can affect mood, emotion,
appetite, sleep, and learning
❏ Many antidepressive drugs are
serotonin reuptake inhibitors
(SSRIs) including Prozac, Paxil,
and Zoloft.
Schizophrenia
❏ 1% of the world population
❏ Onset: 17-27 in males; 20-37 in
females
❏ A mental disorder
❏ Loss of the ability to organize
thoughts and perceptions
❏ Leading to withdrawal from reality
Progression of disorder:
❏ Difficulty paying attention
 ❏ Memory and learning skills
affected
❏ Psychosis - loss of contact with
reality; paranoia
❏ Delusion - false belief of
persecution, power etc.
❏ Hallucinations - false perception
of something not really there ~
visual, auditory, tactile, gustatory,
olfactory
Schizophrenia is a multifactorial
trait:
Inheritance patterns suggest a genetic
component
Genetic component
❏ Biochemical pathways associated
with two neurotransmitters (NTs):
❏ a) Dopamine - governs
motivation, pleasure, arousal,
motor responses
❏ b) Glutamate (aa) - general
excitatory NT
❏ (aa = amino acid)
❏ Problem in membrane transport
of these two NTs
❏ Seven candidate genes as of
2007
❏ Located in chromosome 6 and
22; possibly in other chrom.
❏ Also chromosomal aberrations:
deletions & translocations
Association studies indicate an
environmental component
Risk factors for schizophrenia
Maternal malnutrition
Infection by Boyna virus
Fetal oxygen deprivation
Obstetric or birth complication
Psychoactive drug use (PCP)
Traumatic brain injury
Herpes infection at time of birth
Other Neurologic Disorders
Huntington disease (HD)
Fragile X syndrome (FRAXA)
Myotonic dystrophy (DM)
^(above)Look up on expansion that
happens on what gene
What are the trinucleotide repeat
Copy number variation (CNV)
It’s possible for a gene..
Trinucleotide repeat would be less than
20 (10-20) normal but if exceed to 80
then you would be expressing said ❏ May involve any of the
disorder major metabolic pathways
for proteins, CHOs, lipids,
nucleotides, sterols,
among others

Classification of IEMS
1. Disorders of Amino Acid and
Peptide Metabolism
2. Disorders of Carbohydrate
Metabolism
3. Disorders of Fatty Acid and
Ketone Body Metabolism
4. Disorders of Energy Metabolism
(some Mitochondrial)
5. Disorders of Purine/Pyrimidine/
Metabolism
6. Disorders of Sterol Metabolism
7. Disorders of Porphyrin and Heme
Metabolism
8. Disorders of Lipid and Lipoprotein
Metabolism
9. Disorders of Protein Metabolism
THE END & Protein Glycosylation
10. Lysosomal & Peroxisomal
November 15, 2018 Disorders
11. Others: neurotransmitter,
INBORN ERRORS OF METABOLISM Vitamins, Cofactors, Trace
❏ Definition of IEM Elements, Metals, Xenobiotics
❏ Disorders that are caused
by a deficiency of enzyme Definition
catalysis or an enzyme IEMS are defined by:
that facilitates the - Their clinical features
transport of biological - Specific enzyme affected (gene
substances locus)
❏ Coined by Garrod AE in - Their pattern of inheritance
1908
❏ A genetic defect in paty of Xenobiotic- a chem substance not
the metabolic pathways naturally produced or present within an
since birth org.
Epidemiology
 ● Most are very rare but collectively
they are very common
● Frequencies for each individual
IEM vary
- Affected by geographical
and ethnic composition of
the population
Philippines, National Screening Program
- 21 hospitals from Sep 2001-
2003
- DOH exerting efforts for national
implementation
Newborn screening in the Philipines
currently includes screening of six
disorders
1. Congenital hypothyroidism (CH)
2. Congenital adrenal hyperplasia
(CAH)
3. Phenylketonuria (PKU)
4. Glucose-6-phosphate
dehydrogenase (G6PD)
deficiency
5. Galactosemia (GAL) and
6. Maple syrup urine disease
(MSUD)
● Current program (2014) includes
neither hemoglobinopathy
screening nor expanded
metabolic screenings which
may decrease morbidity and
mortality. However, these
screenings are included in the
standard care across the globe.
Medium Chain Acyl CoA
dehydrogenase deficiency (MCCDD)
VLC - very long chain dehydrogenase
deficiency (VLCAD)

● In the Philippines, NBS was
implemented through the
enactment of Republic Act 9288
or Newborn Screening Act of
2004
● The Act ensures that sustainable
NBS system is employed as part
of the public delivery health
system and every baby born in
the Philippines is offered NBS.
● The DOH is the lead
implementing agency along with
its field implementers: Centers for
Health Development (CHD) and
Newborn Screening Reference
Center (NSRC).
● Four infants can be saved every
hour from mental retardation or
death as a result of newborn
screening (DOH).
● metabolic pathway
● Dr. Carmencita Padilla
Mortality/Morbidity
● IEMs can affect any organ
system and usually affect multiple
organ systems
● Manifestations vary from acute
life-threatening to subacutte
progressive degenerative
● Progressions may be:
- Unrelenting with rapid life-
threatening deterioration
over hours
- Episodic with intermittent
decompensations and
asymptomatic intervals
- Insidious with slow
degeneration over
decades
Pattern of Inheritance
● Majority are autosomal recessive
● Many IEMs have multiple forms
that differ in their mode of action
● Male: Female ratio is usually 1:1
- Autosomal recessive
- Autosomal dominant
- X-linked dominant
Pathophysiology
● Single gene defects result in
abnormalities in the synthesis or
catabolism of proteins, CHOs, or
fats
- Most due to defect in
enzyme of transport
protein that disrupts
● Toxic accumulation
of
substrate/intermedi
ates
● Defects in energy
production/
utilization
● Nearly every metabolic disease
has several forms that vary in
 age of onset, clinical severity and - Some porphyrias result in
often, mode of inheritance abdominal pain and liver
damage

*see handout: amino acids, Evaluation

phenylketonuria 1. Personal and Family History
- Features that arouse
Continuation at google docs suspicion
2. Physical Examination
B-Thalassemia - Facial dysmorphism, cataracts,
C-Autosomal recesive diorder retinopathy, structural brain
D-Mutation in the B-glocin gene and its anomalies, hypertrophic or
regularory sequence dilated cardiomyopathy,
E-May require blood transfusion and hepatomegaly, multicystic
iron-chelation therapy dysplastic kidneys, myopathy
3. Initial Screening Tests
Porphyrias - Progressive-
● Porphyrias are caused by 4. Advanced Screening tests
deficiency of enzymes involved in - Biomarkers, MRI, MR
the biosynthesis of heme: Spectroscopy of the brain,
- The result is a deficiency Tandem metabolic
or inactivity o specific screening
enzyme in the heme
production process, with
resulting accumulation of
heme precursors.
- Some porphyrias result in
photosensitivity, because
certain porphyrins are
deposited in the skin.
- When exposed to light and
oxygen these porphyrins
can generate a charged,
unstable form of oxygen,
capable of damaging the
skin.
- Nerve damaging, leading
to pain and even paralysis,
can also occur in some
porphyrias

Medium chain acyl CoA DH deficiency
(MCAD)
Examples
Phenylketonuria
● Mental Retardation
● Neurological problems
● Strange urine odor (musty)
● High urine phenylacetic acid
● Unable to convert phenylalanine
to tyrosine in the liver
● Inherited defect in phenylalanine
hydroxylase
● Incidence- 1:16 - 10K
● If untreated, can cause
Galactosemia
● Unable to metabolize galactose
● Due to deficiency in galactose-1-
phosphouridyl transferase
● Incidence - ~1.60K
● Untreated infants present with
- Vomiting, diarrhea, failure
to thrive, jaundice, livery
dysfunction and
hepatomegaly,
hyperglycemia, abnormal
clotting, MR, cataracts
● Treatment
- Elimination of dietery
galactose (from lactose in
milk, medications)
● Most common IEM of faty acid
oxidation
● Incidence - ~1:10K
● Lipid metabolism is important
during fasting periods
- Lipid lipolysis -> fats (𝞫-
oxidation) -> energy
- 𝞫-oxidation defective in
MCAD
● Typical signs and symptoms
- Recurrent hypoketotic
hypoglycemia
- Reye’s syndrome-like
illness (vomiting, lethargy,
delirium, coma, and
convulsions)
 - Liver dysfunction 𝞫-Thalasemia alleles
- Accumulated medium-
chain acyl CoA esters bind
to carnitine and are
exerted in urine ->
secondary carnitine
deficiency (muscle
weakness, hypotonia)
● Treatment
- Administration of IV
glucose - to correct
hypoglycemia and provide
energy
- Carnitine administration
during crisis treat
deficiency and promote
excretion of excess esters
- Avoid prolonged periods of
fasting and treat signs of
hypoglycemia early
● Attacks become less frequent
during childhood and fasting
tolerance improves with
increasing body mass

● More than 200 known mutations

● Mutations affecting transcription
Promoter mutations
● mRNA processing defect
 ● Mutations affecting translation
Cap site mutation
● In-frame indels, frameshift, large
deletions due to unequal
crossing-over
Significance of the Study
● Initial attempt at characterization
of 𝞫-globin gene mutations in 𝞫-
thalassemia patients in the
Philippines
● Elucidation of the 𝞫-thalassemia
mutations in Filipinos will be
useful for the development of
diagnostic tests - useful for future
screening programs
Polymerase chain reaction
November 27, 2018
Human Microbiota
● Microbiota: “ecological
community of commensalism
symbiotic and pathogenic
microorganisms”
● Microbiome: collective genomes
of microorganism
● Larger and more diverse than the
human genome
● Plays an important role in health
and disease by interacting with
human genes
● Partly heritable, and correlates
with ethnicity, geography, and
mode of subsistence
The Human Microbiome Project
242 healthy US volunteers
>5,000 samples were collected
Findings
The microbiome can change over time,
and is affected by your disease state
and medication
The human microbiome outnumber cells
in the human body by 10 to 1 microbes
It contributes more genes responsible
for human survival than humans’ own
genes.
Ex. Nature magazine: Our ‘other’
genome - Metagenomics of the HUman
Intestinal Tract
16S rRNA gene

Function of the microbiome:

Extracting energy from a wide array of
host-indigestible carbohydrates
Producing vitamins
Promoting homeostasis
Preventing colonization of the gut by Dysbiosis: individual and context-
pathogens specific taxonomic and functional
changes to the composition of the
The gut microbiome is the most diverse: microbiome that result in a disease
150 genera state.

The vaginal microbiome IBD- irritable bowl disorder

The human microbiome changes with

age.
Condition of the host can affect the
microbiome that is present
Plays an important role in health and Maternal for microbiota influence child's
disease by interacting with human gut microbiota.
Gene's

Host genetics define the chemical and

physical landscape inhibited by the gut
microbiome.

Metabilike or phenome.

PLDI cancer

Partly heheritable
Bacteriodacea and Bifidibacteriacaea
xo-speciate with great ape hosts.

Nov. 29
IV. Issues and Applications
A. Genetic Screening
Involves history taking, physical
examination, conventional tests:
x-rays, biochemical, cytogenetic ,
molecular tests
Health professional team
- Clinical geneticists
- Medical specialists
- Genetic counselor
- Social worker
B. Biochemical Detection
Involves measurement r detection of:
1. Enzyme activity e.g. G6PDH
activity
2. Level of metabolites e.g. alpha-
keto acids in MSUD
3. Size or quantity of protein
4. Defective structural protein e.g. in
haemophilia and thalassemia
Samples:
- Blood, urine, amniotic fluid, or
cerebrospinal fluid
- Note: proteins are unstable and
degrade easily
- Recall in newborn screening:
tests on the dried blood spot
(BBS) filter cards must be done
immediately
Detection methods (examples):
- Color reaction
- Spectrophotometry
- HPLC Analysis
- immunotechniques
9
Defective enzymes in maple syrup urine
disease (MSUD)
- Accumulation of alpha- keto acids
produced by transamination
- Excreted in urine → smells like
maple syrup or burnt sugar
C. DNA-based detection
1. Direct PCR Analysis of deletions
- Differently sized-DNA
bands
2. Allele-specific oligonucleotide (probe)
hybridization
Wt probe + wt DNA = hybridize
Wt probe + mut DNA = not hybridize
Mut probe + mut DNA = hybridize
ddNTP - will stop since it is very specific
D. Gene therapy: Classical Approach-
provide correct genes
E. Genetic Counseling
❏ Communication process between
the health professional and the
patient
~regarding a genetic disorder in
the family
❏ Occurrence
❏ Possible transmission
❏ Manifestations and severity
Combined
Genetic counseling also helps the family
to:
a) Understand the following
b) Choose the appropriate action to
take
c) Adjust the psychosocial impact of
the genetic condition
FORENSIC GENETICS
Forensic Science is the application of
genetics to human and on human
material for the resolution of legal
conflicts
DNA fingerprints follow mendelian
inheritance
What revolutionized forensic genetics?
- Discovery of DNA fingerprints
- Invention of
Genetic markers: Factors to consider
● Mode of inheritance
● Sex-specificity
● Mutation Rates
● Copy number per cell
● Genotyping
● Stability
 ● Diversity ● Ethics review board approval

Commonly used DNA markers PCHRD-DOST Guidelines

● Short tandem repeats National Guidelines on the conduct of
● Single nucleotide polymorphisms Biomedical Research
● mtDNA HVI/HV2
● Insertion deletion polymorphisms Informed Consent
● “Similar to a contract”
Autosomal short tandem repeats
Recruitment of study participants:
Sample collection & Storage INCLUSION CRITERIA example
Body fluid identification 1) Clinical diagnosis established
DNA extraction
DNA Quantification The end.
“How much amplifiable human
DNA is present?”
“What is the male:female DNA
ratio?”
PCR Amplification
Separation and Detection of Fragments
Data Interpretation
Statistical Interpretation

1 in 1/0.00014 or 1 in 7,143
Combined Matching Probability
1 in 3.996x10^(25)

G. Ethics and etc.

Genetic Privacy
● Confidentiality is an absolute right
(only the patient can waive the
right)
● Information should be disclosed
to patient or legal guardian
● Can be breached ONLY if there
is a risk to harm others
Ethics in research involving human
subjects
● Ethical guidelines of the
declaration of helsinki (1975)
● Minor revisions followed