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Learning Objective
• Chromosome and chromosomal abnormalities
FUNDAMENTAL MEDICAL SCIENCE 1 • Principles of Inheritance in Genetics in Medicine
• The cause and inheritance of genetic disorder
Genetics in Medicine • Clinical Genetics
• Trend in Genetics in Medicine

Lecturer : Ivet Suriapranata

Mochtar Riady Institute for Nanotechnology
ivet.suriapranata@mrinstitute.org

Autosomal recessive inheritance

Topics which will be covered in week 3
Example: Cystic Fibrosis
• Review Cell Division, DNA, Genes and Chromosomes,
Mutation and DNA Repair • mutation in Cystic Fibrosis Transmembrane
Conductance Regulator (CFTR) gene
• Definition, Type, Cause, Mechanisms of chromosome • chloride channel
abnormalities • controls the regulation of
transport pathways
• Methods of Chromosomal Analysis
• Review of Mendelian Law, Variations of Mendelian
Inheritance
• Polygenic and Multifactorial Inheritance
• Genetic Disorder and its Inheritance
• Trend in Genetics in Medicine

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Cystic Fibrosis Examples of autosomal recessive inheritance

Over 300 CFTR variations
have been identified
Disorder or Abnormality Main Symptoms
most common: deletion
of amino acid Phenylalanine Albinism Absence of pigmentation
at position 508 (F508) Cystic fibrosis Excessive glandular secretions leading to tissue, organ damage
Ellis–van Creveld syndrome Extra fingers, toes, short limbs
Fanconi anemia Physical abnormalities, bone marrow failure
Galactosemia Brain, liver, eye damage
Phenylketonuria (PKU) Mental impairment
Mutations can cause:
Sickle-cell anemia Adverse pleiotropic effects on organs throughout body
• reduction of synthesis
• prevention of the protein from
reaching the plasma membrane
• incorrect function at the
membrane

X-linked dominant inheritance

Mendelian disorders

Mom
XA X
 Autosomal dominant inheritance X XX
A
XX
Dad
 Autosomal recessive inheritance Y A
X Y XY

 X-linked dominant inheritance

 X-linked recessive inheritance

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X-linked dominant inheritance X-linked dominant inheritance

 males and females may be

affected
Mom
 both sons and daughters
X X of affected women have
A A 50% risk of being affected
XA X X X X
Dad  all daughters of affected male will
be affected
Y XY XY  no male to male transmission
 affected women have milder
phenotype than affected men

X-linked dominant inheritance

Ornithin Transcarbamylase
Deficiency (OTCD)

• Urea Cycle disorder

• 1 in 80,000 births
• caused by a number of
different mutations in OTC
gene

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Examples of X-linked dominant inheritance

How are changes in the OTC gene related to
health conditions? Disorder or Abnormality Main Symptoms

Hyphosphotamic rickets the bones become painfully soft and bend easily
X because the blood contains low levels of
Missing or misshapen enzyme affects the phosphate

urea cycle. Excess nitrogen is not Microphtalmia with linear skin defects small or poorly developed eyes
converted to urea for excretion, and
Oral facial digital type I syndrome malformations of the face, oral cavity, hands and
ammonia accumulates in the body. feet.

Ammonia is toxic, especially to the nervous system, so this accumulation causes

neurological problems and other signs and symptoms of OTC deficiency

X-linked recessive inheritance

Mendelian disorders

Mom
XA X
 Autosomal dominant inheritance A
X XX XX
Dad
 Autosomal recessive inheritance Y A
X Y XY
 X-linked dominant inheritance
 X-linked recessive inheritance

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X-linked recessive inheritance X-linked recessive inheritance

Mom  trait more frequent in males

X X than females
 no male to male transmission
XA XAX XAX
Dad  all daughters of affected male
Y are carriers
XY XY

X-linked recessive inheritance X-linked recessive inheritance

Hemophilia X linked Severe Combined

mutation in blood coagulation Factor VIII or Factor IX Immunodeficiency (SCID)
 occurs almost exclusively in males
 mutations in ILR2 gene, which is
necessary for growth and maturation
of lymphocytes
 prone to recurrent and persistent
infections
 grow more slowly than other children.
 usually do not live beyond infancy if
untreated

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Examples of X-linked recessive inheritance

Disorder or Abnormality Main Symptoms

Androgen insensitivity
syndrome

Color blindness
XY individual but having some
female traits; sterility

Inability to distinguish among some or all colors

X
Fragile X syndrome

Hemophilia
Mental impairment

Impaired blood-clotting ability

Y
Muscular dystrophies Progressive loss of muscle function

The Y Chromosome Non-Mendelian Inheritance

• Fewer than two dozen genes identified

• One is the master gene for male sex
Some pedigrees cannot be explained by typical
determination Mendelian inheritance of nuclear genes
– SRY gene (sex-determining region of Y)
• SRY present, testes form
• SRY absent, ovaries form
• Genes in Y are mainly involved in male fertility

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mtDNA Mitochondrial Inheritance

• 16,500 bp
• due to mutation in mtDNA
• contain 37 genes
• maternal inheritance pattern
• all essential for normal
• males and females
mitochondria function affected
• prone to mutation • variable age at onset and
expression of disease

Mitochondrial Inheritance Examples of Mitochondrial Inheritance

Leber Hereditary Optic Neuropathy (LHON)

 acute and subacute loss of

central vision
 mutations in genes encoding
subunits of Complex I

Myoclonic Epilepsy and Ragged Red Fibres

(MERRF)
a multisystem disorder characterized by myoclonus, which is often
the first symptom, followed by generalized epilepsy, ataxia, weakness, and
dementia. Onset is usually in childhood, occurring after normal early
development

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Genetic susceptibility to common disease

Types of genetic approach to the common diseases Hypertension

Population/ migration studies  10% to 25% of the population

is hypertensive
Family studies  leads to a greater risk of stroke,
coronary artery and renal
Twin studies disease

Adoption studies
Essential hypertension
Polymorphism association •more common
• begins in middle age
Biochemical studies • no recognized cause

Animal models

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Importance of genetic factors in hypertension Candidate genes for Hypertension

Recurrence Risks for hypertension There is not one single mutation

or one single gene that contributes
Result from twin and familial studies to hypertension just as there is
Group % not one single environmental factor
Population 5
More than 50 genes involved
2 Normotensive parents 4 in the biological
control of blood pressure
1 Hypertensive parent 8-26%

2 Hypertensive parents 25-45%

more studies are still needed !!

Diabetes Mellitus Importance of genetic risk factors

in T1DM and T2DM

 identical twins are more likely to have T1DM or T2DM

than non identical twins
 increased risk for 1st degree relatives

Type 1DM Type 2DM

 insulin dependent
 5-10% of diabetes
 peak age of onset in adolescence
 regular injection of insulin
 more common
 usually affects older persons
 may respond to restriction of
carbohydrate intake, oral
medication or insulin

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Genes related to T1DM Genes related to T2DM Finding Genes for T2DM

IDDM1 NIDDM1
 Candidates selected because they are involved in
Human Leukocyte Antigen (HLA)
intracellular Ca-dependent protease  Pancreatic beta cell function
IDDM2 involves in insulin secretion and resistance  Insulin action/ glucose metabolism
Insulin gene  Energy intake/ expenditure
PPAR
 Lipid metabolism
CTLA4 Peroxisome proliferator-activated receptor 
T cell receptor associated with insulin sensitivity
 Genome wide association studies
ABCC8 and KCNJ11  Current approach based on thousands of cases
and controls
part of ATP-sensitive potassium channel
plays a key role in regulating insulin
and glucagon release
Challenges ?? Many !!
etc. etc.

Lecture 3
The Trend in Genetics in Medicine Single Nucleotide Polymorphisms (SNPs)

 Single Nucleotide Polymorphisms (SNPs)

Disease Susceptibility
Pharmacogenomics (Personalized Medicine)
 Gene Therapy
Principles of Gene Therapy
Technology of Gene Therapy

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Structure of DNA Structure of DNA

 DNA has four bases
 Adenine (A), Guanine (G), Cytosine (C), Thymine (T)
Base
Phosphate  A and G are purines, C and T are pyrimidines
 Purines are double ring bases
 Pyrimidines are single ring bases.
N O
N C N C N O
N C N C
O O
C C N C C
Sugar N
N C
N C C C C
N C
C N C N C
N C N
Adenine Guanine Cytosine Thymine

C>T exchange in the sequence SNPs

 Occur when a single nucleotide (A,T,C,or G) in the
genome sequence is altered, e.g., AAGGCTAA to
ATGGCTAA
 A nucleotide change must be present in > 1% of
the population to be called a SNP.
 Comprise 90% of all human genetic variation
 Exist every 100 to 300 bases along the 3-billion-base
human genome
 Found in both coding (i.e., gene) and noncoding
regions of the genome.
 Usually have no effect on cell function, but some could
predispose people to disease or influence their
response to a drug

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Where are the SNPs? The Central Dogma

GENE

Humans: ~ 5% of genome encodes gene product

Introns

Regulatory sequence 95% Sequence variation

Noncoding sequence

SNPs in intergenic regions SNPs in coding regions

may change the codon of an amino acid

may …
1. synonymously
 have no effect TTT = Phenylalanine
 affect regulatory signals TTC = Phenylalanine
 interfere with splice sites
2. non-synonymously
TTT = Phenylalanine
TAT = Tyrosine

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non-synonymous AA replacement

 conservative exchange
 an amino acid is replaced with another amino
acid of similar chemical structure
 may have no affect on protein function

 non-conservative exhange
 an amino acid is replaced with another amino
acid of different chemical structure
 affect protein function

Disease resistant population Disease susceptible population

Disease Susceptibility
Genotype all individuals for thousands of SNPs

ATGATTATAG geneX ATGTTTATAG

Resistant people all have an ‘A’ at position 4 in geneX, while susceptible people have a ‘T’

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SNP genotype
Experimental design
• We inherit two copies of each chromosome
(one from each parent)
• For a given SNP, the genotype defines the type of alleles we carry • Pick random humans with and without disease
• for the SNP A/G one’s genotype may be
– AA if both copies of the chromosome have A • Perform SNP genotyping on candidate genes
– GG if both copies of the chromosome have G
– AG or GA if one copy has A and the other has G • Evaluate the association of SNPs with
– The first two cases are called homozygous and latter two are the disease by biostatistical analysis
heterozygous

DNA Amplification using Polymerase Chain Reaction (PCR)

SNPs for Disease Susceptibility

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ApoE genotyping is sometimes used as an adjunct test

Late-onset Alzheimer’s Disease to help in the diagnosis of probable late onset Alzheimer’s disease (AD) in symptomatic
adults.
develops after age 60.
It is called susceptibility or risk factor testing because it indicates whether there is an
In 1992, researchers found that three increased risk of AD but is not specifically diagnostic of AD
forms, or alleles, of a gene called
Apolipoprotein E (APOE) can influence the
risk of late-onset AD:
* APOE ε2, a rarely occurring form, may
provide some protection against AD.
* APOE ε3, the most common form, plays
a neutral role, neither increasing nor
decreasing risk.
Mean age of onset of
* APOE ε4, which occurs in about 40 Alzheimer disease as a
percent of all people who develop late- function of the
onset AD and is present in about 25 to 30 inheritance of the
percent of the population, increases risk by common APOE
lowering the age of onset. genotypes

Impact of Test
• Prevention: Preventative drugs or supplements for
avoiding disease occurrence

• Early Detection: Screening methods for high risk

individuals Pharmacogenomics
• Lifestyle Changes: Major factor in preventing/beating
the disease

• Low-Risk individuals “peace-of-mind”

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Due to individual variation…

Same symptoms
Same findings Different
Same disease? patients

Same drug
Same dose  20-40% of patients benefit from an approved drug
 70-80% of drug candidates fail in clinical trials
 Many approved drugs removed from the market due to
adverse drug effects
Genetic
Differences
Ethnicity
Different
G Age
Pregnancy
Effects
Genetic factors
A Possible Reasons:
Disease
Drug interactions Individual variation

Drug Metabolism
Why Pharmacogenomics ?

The use of DNA sequence information to measure Adverse drug reactions are a
and predict the reaction of individuals to drugs enable major cause of morbidity and
mortality
 Personalized drugs
 Faster clinical trials Individual differences in response
 Less drug side effects to drugs in humans are, however,
often genetically determined

Pharmacogenomics
The study of variations in genes that determine an individual’s response to drug therapy.

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Examples of pharmacogenomic markers

Potential Target Genes for drug responses

Gene Drug Pharmacogenomic effect

TPMT 6-Mercaptopurine Myelosuppression in poor metabolizers
 Drug-metabolizing enzymes Azathioprine Nonresponder in fast metabolizers
CETP Pravastatin Responder with TaqB1 genotype
 Drug Transporters Nonresponder with TaqB2 genotype
5-
 Drug Targets lipoxygenase Zileuton Responder with wild-type 5-LO promoter
Nonresponder with variant 5-LO promoter
Her2/neu Herceptin Responder for Her2 positive
IL28B Interferon Sustained Viral Response for CC genotype

SNPs Use in Medicine

• Prediction of Disease Susceptibility
Individuals with certain genetic variations are
predisposed to particular disease
• Pharmacogenomics Gene Therapy
Individuals with certain genetic variations might Principles and Technology
respond differently to particular treatment

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Choosing the right targets

How do you know

whether a disorder is
a good candidate for gene
therapy?

1. Does the condition result from mutations in one or more genes?

2. Which genes are involved ?
3. What do you know about the biology of the disorder?
4. Will adding a normal copy of the gene fix the problem in the affected tissue ?
5. Can you deliver the gene to cells of the affected tissue ?

Gene Delivery: The Key to Gene Therapy

• Genes are made of DNA

• Successful gene delivery requires an efficient
way to get the DNA into cells and to make it work
• Scientists refer to these DNA delivery "vehicles"
as vectors
Types of vectors Gene Therapy
Viral vectors
General advantages : for inherited disorders
* very good at targeting and entering cells.
* can be engineered to target specific types of cells.
* can be modified so that they can not replicate and
destroy the cell.
Non-Viral Vectors
typically circular DNA molecules, also known as plasmids.
In nature, bacteria use plasmids to transfer genes from cell
to cell.

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Gene Therapy Case Study: Cystic Fibrosis Reference

• Books:
– Tom Strachan and Andrew Read: Human Molecular Genetics,
1. Understanding The Problem Garland Science. The second edition in available online at NC
BI Books (http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=h
mg)
2. Is Cystic Fibrosis a Good Candidate? – Robert F. Mueller, Ian D. Young:
Emery's Elements of Medical Genetics, Churchill Livingstone
• Websites:
3. Choosing a Vector for CF Gene Therapy – http://www.dnaftb.org
– http://www.dnalc.org
– http://www.ncbi.nlm.nih.gov/disease/
4. Build and Test a CF Gene Therapy Vector – http://ghr.nlm.nih.gov/
– http://ornl.gov
– http://www.cellsalive.com

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