cracking the code: a journey through genetics
TRANSCRIPT
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Cracking the Code:
A Journey through Genetics
Amanda Cocca & Anna Haasen
Clinical Genetics MLTs
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Learning Objectives
•Describe the basic structure of the genetic code
and how genetic variation relates to disease.
•Differentiate between inherited (constitutional) and
acquired (malignant) genetic changes.
•Give examples of the application of molecular
genetics in the medical community.
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DNA: The Blueprint of Life
• DNA =
deoxyribonucleic acid
• Contains instructions
for living organism
• Most DNA in nucleus
46 chromosomes
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DNA: The Blueprint of Life • 1953: Watson & Crick DNA double helix
• Banister = sugar-phosphate backbone
• Stairs = Hydrogen bonding between base pairs
One nucleotide
“A” “T”
“C” “G”
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What is a “Gene”?
• Defined section of DNA
• Instructions for how to make a protein
• Gene = introns + exons + untranslated regions
T A A T G G G C T A G C G T A T A C G A T G G G C A A T A T T G A C C A C A T T A A T T A
eg. BRCA1 gene has 24 exons coding for one protein
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The Central Dogma
DNA
translation
RNA
PROTEIN
transcription
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• Normal cell division
• Typical of ordinary tissue
growth
• Result: two daughter cells
each with the same number
and kind of chromosomes as
the parent cells
Mitosis
• Creates all cells of the body
(except germ cells; eggs and sperm)
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Mitosis
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Mitosis
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Mitosis
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Mitosis
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Mitosis
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Mitosis
END RESULT:
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Metaphase
8
8
46,XX
20
20
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Meiosis
END RESULT:
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Sex Determination
Zygotes
(offspring)
44+
XX
44+
XY
22+
X
22+
Y
22+
X
Egg
Sperm
♀
♂
44+
XX ♀
44+
XY ♂
Female: 46,XX
Male: 46,XY
END PRODUCT
OF MEIOSIS
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Non-Disjunction
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Non-Disjunction Example: Down Syndrome (Trisomy 21)
Extra chromosomal material
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Non-Disjunction Example: Turner Syndrome (45,X)
•Missing chromosomal material
•Webbed neck, short stature,
delayed growth
•Unable to conceive without
fertility treatments
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Constitutional Genetic Changes • Inherited or de novo
• Blood, tissue, saliva, products of
conception, cheek swabs
• Diagnosis, management, recurrence risk
assessment
• Testing:
• Chromosome analysis (karyotype)
• Chromosome microarray
• Exome sequencing
• Testing for single gene disorders by molecular
techniques
• Next generation sequencing (NGS) panels
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• Mutations in somatic cells
(cells other than sperm and
egg)
• Can occur at any time in a
person’s life
• Caused by environmental
factors
• Changes cannot be passed
along to the next generation
Acquired Genetic Changes
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1. Disease Classification
2. Disease Sub-type
3. Drugs that will target the
genetic mutations
4. Prognosis
5. Long term treatment
Acquired Genetic Changes
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Disease Classification and Subtype
• t(15;17)APL/AML-M3
Drug treatment
• ATRA (all-trans-retinoic acid)
Prognosis
• Remission rates of 80-90%
• Long term survival > 75%
Long term treatment
• Track molecular level of t(15;17) by PCR-based assays
• Eligibility for stem cell transplant
Example: Acute Myeloid Leukemia (AML)
Acquired Genetic Changes
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•Single Nucleotide Polymorphisms (SNPs)
– No effect on health
– ~10 million SNPs in the human genome
Genetic Variation
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•Variant of Uncertain
Significance (VUS) – Suspected benign
– Significance unknown
– Suspected pathogenic
Genetic Variation
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•Cleft palate order CMA
•Small deletion weakly linked
to autism (VUS), unrelated to
original indication for testing
•Pre and post test counselling
Case study of VUS
Genetic Variation
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HGVS nomenclature
• Human Genome Variation Society
• A universal “genetic” language
BRCA1 c.230 C>T (DNA-level)
The nucleotide at base pair 230 in the BRCA1 gene changed
from cytosine to thymine.
BRCA1 p.Pro1430Ser (Protein-level)
The amino acid at position 1430 in the BRCA1 gene changed
from a proline to a serine.
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Modes of Inheritance Autosomal Dominant
•Disease phenotype in
individuals with one
copy of the mutated
allele (gene)
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Modes of Inheritance
•Affected individual
must have two copies
of recessive allele to
show phenotype
•Carriers have one
dominant and one
recessive copy
Autosomal Recessive
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Pedigrees
Eg. Huntington Disease - Autosomal dominant disease
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Single Gene diseases • A change in sequence (“mutation”) in one gene causes
the disease
• Defined pattern of inheritance
Example: Phenylketonuria (PKU) in PAH gene
T A A T G C T C G G C
Normal
protein
Normal
enzyme
function
T A A T G C T A G G C
Altered
protein
Non-functional
enzyme =
phenylalanine
build-up in the brain
NORMAL
ABNORMAL
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Multifactorial diseases
Genetic Variation
• Copy number variation
• Mutations in specific genes
• Polymorphisms
Environment
• Pathogens
• Smoking
• Diet
• Sun exposure
• Combination of genetic variation at multiple loci in the
genome and environmental factors
• No clear pattern of inheritance
eg. Mutation in BRCA1 or BRCA2 gene indicates an
increased risk of developing breast or ovarian cancer
in the individual’s lifetime.
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Applications of Molecular Genetics
1. Forensics
2. Diagnosis and prognosis of disease
3. Pharmacogenetics
4. Monitoring response to treatment
5. Predictive testing for disease risk
6. Prenatal genetic testing
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FORENSICS •DNA evidence important in court of law
•Compare human identity profiles to
identify victims or suspects
DNA FOUND UNDER
VICTIM’S FINGERNAILS
SUSPECT #2
WE FOUND
A MATCH!! SUSPECT #1
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DIAGNOSIS AND PROGNOSIS
OF DISEASE PML-RARa (subtype M3) AML1-ETO (subtype M2)
POSITIVE
FOR
AML1-ETO
AML
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PHARMACOGENETICS
•Variants in an individual’s genome
may affect their response to a
particular drug
– Absorption
– Activation
– Target response
– Catabolism and excretion
• Tailor the dosage based on
patient’s genetic make-up
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MONITORING RESPONSE TO
TREATMENT
• Determine how well patient is responding to treatment
by quantifying abnormal RNA/DNA in body fluid
Decreasing quantity of abnormal nucleic acid
CML
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PREDICTIVE TESTING
•Determine a family member’s susceptibility to
developing a disease (single-gene vs. multifactorial)
• Recurrence risks
Eg. Hereditary Hemochromatosis - Autosomal recessive disease
NORMAL SEQUENCE
ABNORMAL SEQUENCE
A>G
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PRENATAL GENETIC TESTING Before Conception
• To identify reasons for infertility or recurrent miscarriage
(chromosome studies)
• To screen embryo prior to implantation in assisted
reproductive technologies
During Pregnancy
• To identify aneuploidy during pregnancy
• To predict whether baby carries known familial disease
After Delivery
• To investigate unusual phenotypes (microarray)
• To confirm results of Newborn Screening program
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ETHICS & GENETICS Entering uncharted territory…
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