GENETICS Part 1

Catherine Joy Agustin-Enciso, MD, DPPS

General Pediatrics
 DISCLAIMER

Slides contain images grabbed from the web and not my

personal patients. No copyright infringement intended. Slides
are used solely for classroom lecture purposes and not for
purposes of reproduction.

References:
Nelson’s Textbook of Pediatrics 20th Edition
UP National Institutes of Health
Google search (for some images)
Learning Objectives
01 Realize the burden of genetic disorders in childhood

02 Recognize the role of genetic factors in health and disease

03 Elicit a comprehensive history, family medical history

04 Perform a thorough physical examination

Identify patients with strong inherited predispositions to
05 common disease and facilitate appropriate assessment of
other at-risk family members

06 Select appropriate diagnostic tests

07 Discuss ways to prevent genetic disorders

08 Outline appropriate management of genetic conditions

 Genetic disorders in childhood
Ongoing genetic research
79/1,000* groups
Estimated disease with - Autism
important genetic - Bipolar disorder
component including
congenital malformations
- Birth defects
- Cancer genetics
*Nelsons Pediatrics 20th - Cardiovascular genetics
Edition - Clefting genetics
- Diabetes
- Kawasaki disease
- Nutrigenomics
- Oral cleft
- Schizophrenia
- SSPE
- Thalassemia
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 ECONOMIC
BURDEN
GENETIC
DISEASE

Hidden costs of Rare Diseases: A Feasibility

Study. Genetic Alliance UK. September 2016.
Philippine Republic Act 10747, Rare Diseases Act
Signed into a law last March 2016
Milestones Law aims to:

improve rare disease patients’

access to comprehensive medical
care

set up a Rare Disease Registry to

inform policy making

identify interventions, and design

research studies on rare diseases

promote public awareness on rare

diseases, among others

designate persons with rare

diseases as persons with disabilities
Philippines: Institute of Human Genetics

25th
Objectives Laboratories 29
February
and Units February
1999

Institute of - Provide services for - Biochemical Genetics

Human diagnosis and early
- Clinical Genetics and Rare
Genetics detection Research Disease
formed - Promote health by - Cytogenetics
- Hemoglobinopathy Day
Promote clinical understanding genetic
researches and basis of common Reference Unit
increase - Microarray Core
diseases
awareness on - Propagate awareness Laboratory
genetic - Provide technical - Molecular Genetics
disorders information Unit Source: National Institutes of Health – University
of the Philippines Manila (
- Newborn Screening http://nih.upm.edu.ph/institute/institute-human-geneti
Center-NIH cs
Human Genome
Human Genome

25,000 Approximate number of genes that

encode various proteins in the body

 46 chromosomes: 22 pairs of autosomes (nonsex

chromosomes) and 1 pair of sex chromosomes (XY in male,
XX in female)
 Most genetic material found in cell nucleus
 Mitochondrial chromosome – either endogenous or
exogenous; exclusively maternally derived
• Nuclear DNA is transcribed into mRNA 
transported to cytoplasm  translated into
protein
• DNA: pair of chains of sugar-phosphate
backbone linked by pyrimidine (cytosine and
thymine) and purine (guanine and adenine)
bases
• Bases are paired with H bonds
• A with T
• G with C
• Each stand has polarity with the 2 strands
oriented in opposite polarities in double helix
DNA Replication
• Nuclear DNA is transcribed into
mRNA  transported to
cytoplasm  mRNA binds to
ribosomes  translated into
protein
• Initiated by attachment of RNA
polymerase
• Gene regulation
• Regulatory proteins
(transcriptions factors)
• Methylation of cytosine bases
(epigenetic change)
• Flexible and responsive
 Transcribed from DNA but are not
translated to proteins

Noncoding
RNAs Function: mediates splicing, processing
of coding RNAs,, translation of coding
RNAs in ribosomes; regulation of gene
expression (e.g. microRNAs or
miRNAs)
Genetic Variation
 •Loss-of-function
• Reduction in the level of protein function
due to decreased expression or ineffective
protein production

•Gain-of-function

Mutation • Protein molecule with increased ability to

perform normal function

effects • E.g. Achondroplasia – mutated fibroblast

growth factor receptor 3 gene (FGFR3);
leads to receptor activation
• E.g. Sickle cell disease – sickle Hgb
chains aggregate under conditions of
deoxygenation, leading to formation of
fibers and deforming RBCs
• E.g. Oncogenes
 Terminologies:

•Genotype – internally coded,

heritable individual information
Genotype-
phenotype •Allele – alternative version of gene

correlations in •Locus – location of gene in

genetic chromosome
disease
•Phenotype – observed structural,
biochemical, and physiologic
characteristics of an individual
• Determined by genotype
Long QT Syndrome

• Genetically heterogenous
• KCNQ1 gene: increased cardiac events (63%), noted more during
exercise and rarely during rest or sleep
• KCNH2 gene and SCN5A gene: increased cardiac events (46% and 18%,
respectively) but more during rest or sleep

Marfan syndrome

• Gene: fibrillin-1
• Skeletal, ocular, and aortic manifestations (aortic dissection and sudden
death)
• Fibrillin-1 gene has 65 exons, almost all are mutated BUT location matters
• Neonatal Marfan syndrome: exons 24-27 and exons 31 and 32
• milder forms: exons 59-65 and exons 37 and 41
Cystic Fibrosis

• Multisystem disorder: epithelia of the respiratory tract (most

common cause of morbidity and mortality), exocrine pancreas,
intestine, male genital tract, hepatobiliary system, and exocrine
sweat glands

• Gene: CF transmembrane conductance regulator (CFTR) gene

• >1,600 different mutations

• most common: ΔF508 mutation (approx. 70%)
• Pancreatic sufficiency generally determined by genotype-
phenotype correlation (dominant 1 or 2 pancreatic-sufficient
alleles) while the correlation is weaker in pulmonary disease
(varied severity among persons with identical genotypes), the
latter being affected by genetic modifiers or environmental
factors
• Other phenotypic changes:
• changes in the other allele of the same gene
• changes in specific modifier genes
• variations in a number of unspecified genes (genetic background)

• Sickle cell anemia

• Sickle cell + hereditary FHb persistence  less severe sickle cell
phenotypic expression

• Cystic Fibrosis
• Modifier genes can influence the development of congenital meconium
ileus, or colonization with Pseudomonas aeruginosa

• (+) modifier genes can also affect disease manifestations of Hirschsprung

disease, neurofibromatosis type 2, craniosynostosis, and congenital adrenal
hyperplasia
 Patterns of Genetic Transmission
• Detailed family history
• Identify risk for development of diseases
• Identify common environmental and behavioral factors
• Use of pedigree
• graphic depiction of a family’s structure and medical history
• 3 to 4–generation pedigree
• can provide clues to the inheritance pattern and can aid clinician in
determining the risk to the proband and other family members
• The closer the relationship, the greater is the shared genetic
complement
• First-degree relatives: parent, full sibling, or child
• share ½ their genetic information on average
Common pedigree symbols,
definitions and abbreviations
Source: Nelson’s Textbook of Pediatrics 20th Edition
Pedigree line definitions
Source: Nelson’s Textbook of Pediatrics 20th Edition
 Inheritance

Mendelian Inheritance
- Classic forms of genetic inheritance
- After George Mendel, 19th century monk whose experiments led to
the laws of segregation of characteristics, dominance, and
independent assortment

Autosomal Autosomal
X-linked
Dominant Recessive
Autosomal Dominant
inheritance
• (+) 1 abnormal gene on 1 of the
autosomes (chromosomes 1-22)
• change in 1 of the paired genes
influences the phenotype (physical
manifestations, behavioral
characteristics)
• Vertical (parent-to-child) pattern and can
appear in multiple generations
• affected individual has 50% chance of
passing on the deleterious gene in each
pregnancy (aka recurrence risk for the
disorder)
• Unaffected individuals do not pass the
disorder
• Males and females equally affected
Autosomal Dominant
inheritance
Sometimes, there is (-) FHx due to:
• New mutation in DNA of egg or sperm
• incomplete penetrance, not all
individuals have phenotypic
manifestations (skipped generation)
• modifier genes, environmental
factors, gender, and age
• Varied degrees of manifestation
(variable expression)
• spontaneous genetic mutations in cell of
developing embryo (somatic
mutations)  mosaic
Autosomal
Recessive
• Mutations in both copies of a gene
• Example: CF and sickle cell
• horizontal transmission
• Multiple affected members in same
generation, but no affected members in
other generations
• recurrence risk: 25% for parents with a
previous affected child
• males = females, some traits exhibit different
expression (in consanguineous parents)
• Consanguinity – increases chance parents
carry identical mutated gene
• RR of genetic disorder in first-cousin
marriage: 6-8%
• General population: 3-4%
Autosomal
Recessive
• EVERYBODY may have several rare, harmful, recessive mutation!

• Genetic isolates: have rare recessive mutations more common than general
population
• E.g. Ashkenazi Jews: prenatal or preconception screening
• Gaucher disease type 1 (carrier rate 1:14) - cystic fibrosis (1:25)
• Tay-Sachs disease (1:25) - familial dysautonomia (1:30)
• Glycogen storage disease type 1A (1:71) - Bloom syndrome (1:100)
• maple syrup urine disease (1:81) - Canavan disease (1:40)
• Fanconi anemia type C (1:89) - mucolipidosis IV (1:120)
• Niemann-Pick disease type A (1:90)
• possibly neonatal familial hyperinsulinemic hypoglycemia
Autosomal
Recessive
• African population: increased frequencies of sickle cell carrier state

• Northern European population: increased CF

• Heterozygous carriers: advantage

• Sickle cell carrier: some resistance to malaria
• CF carrier: resistance to cholera or enteropathogenic Escherichia
coli

• Screening recommended for high risk population

Pseudodominant
Inheritance
• apparent dominant transmission of a
known autosomal recessive disorder

• homozygous affected individual +

heterozygous carrier

• E.g. Sickle cell anemia or

nonsyndromic autosomal recessive
hearing loss (mutated GJB2, the gene
that encodes Connexin 26)
X-Linked
Inheritance
• Characteristics:
• Males: more commonly and more severely
affected
• Female: carriers, unaffected, or mildly affected
• Female carriers:
• 25% risk of having affected son
• 25% risk for carrier daughter
• 50% chance of no inheritance
• Affected males: carrier daughters (X chrom),
unaffected sons (Y chrom)
• Female can exhibit X-linked trait
• homozygosity for X-linked trait
• presence of a sex chromosome abnormality
(45,X or 46,XY female)
• skewed or nonrandom X chromosome
inactivation
X-Linked
Inheritance
X chromosome
inactivation
• Inactivation in SAME X
chromosome
phenotypic expression
of X-linked mutation
• Due to chance, cells
inactivating X
chromosome with normal
gene, or X chromosome
abnormalities that
inactivate X
chromosome with normal
gene
X-Linked
Inheritance
X-linked dominant
• Female carriers manifest
abnormal findings

• An affected man = affected

daughters and unaffected sons,
50% of offspring of an affected
woman will be affected

• Some are lethal (incontinentia

pigmenti)
• 2:1 F:M ratio with
increased miscarriages
Y-Linked
Inheritance
• male-to-male transmission ONLY
• ONLY males are affected

• Most are related to male sex determination and

reproduction, associated with infertility hence rare
to see familial transmission

• Leri-Weill dyschondrosteosis
• rare skeletal dysplasia (bowing of both
forearms with dislocations of ulna at the wrist
and generalized short stature)
• Heterozygous SHOX mutation; SHOX gene is
one of few genes residing in pseudoautosomal
regions on the Y chromosome
• Langer mesomelic dwarfism
• Homozygous mutations; more severe
Digenic Inheritance
• exhibit characteristics of both AD
(vertical transmission) and AR (1 in 4
recurrence risk)

• E.g. Retinitis pigmentosa (RP)

• Mutation: RP gene in carrier
parents
• Both parents have normal vision
but offspring who are double
heterozygotes develop RP
Pseudogenetic
Inheritance and
Familial Clustering
• nongenetic reasons for occurrence of disease in multiple family members

• nongenetic factors:
• environmental factors
• teratogenic exposures
• Undetermined and/or undefined

• E.g. multiple siblings with asthma resulting from exposure to cigarette smoke
• E.g. Fetal alcohol syndrome: FTT, developmental delay, and unusual facies

• Disease is sufficiently common in general population; clustering is by chance

• E.g. Breast cancer affects 11% of all women, its possible to develop even without genetic
predisposition. However, genetic mutations in BRCA1 and BRCA2 should be suspected in those with
breast cancer with onset <50 yrs old, early-onset breast and ovarian cancer at any age, bilateral or
multifocal breast cancer, a family history of breast cancer or breast and ovarian cancer consistent with
autosomal dominant inheritance, and/or a personal or family history of male breast cancer
 Inheritance

Nontraditional Inheritance
- Inheritance not following Mendelian pattern

Mitochondrial Triple repeat

Inheritance expansion diseases

Imprinting
defects
Mitochondrial
Inheritance
• mitochondrial genome is entirely
derived from the mother

• Affected mother = affected offspring

of either sex
• Affected father = no penetrance

• often deletions or point mutations;

1:400 overall

• Distinguish from autosomal

dominant or X-linked inheritance
Mitochondrial
Inheritance
• Mitochondria: cell powerhouse
• Organs affected: greatest energy requirements (brain, muscle, heart, and liver)
• Common manifestations:
• Developmental delay
• Seizures
• Cardiac dysfunction
• Decreased muscle strength and tone
• Hearing and vision problems

• Highly variable in clinical manifestation due to multiple mitochondria in cells

(heteroplasmy – mix of normal and abnormal)  variable degrees of affectation

• DNA analysis: test affected tissues such as muscle

Triple Repeat
Expansion Diseases
• caused by expansion in the number of 3-bp repeats

• Examples:
• Fragile X syndrome – fragile X gene (FMR1); 41 to 58 repeats or permutation level (59-200 repeats;
normal: 5-40 CGG triplets)
• Male carriers of permutation develop fragile X–associated tremor/ataxia syndrome (FXTAS),
females develop fragile X-associated primary ovarian insufficiency (FXPOI)
• Myotonic dystrophy
• Huntington disease
• Spinocerebellar ataxias

• Those with a premutation are at risk for having gene expand further  full mutation in offspring

• Fragile X: threshold for clinical diagnosis is >200 repeats; FMR1 gene becomes hypermethylated, and
protein production is lost
• Huntington disease: expansion causes new, toxic effect on the neurons of the basal ganglia
Triple Repeat
Expansion Diseases
• Clinical correlation to the size of expansion: greater
expansion equals more severe symptoms and/or
earlier onset

• Genetic anticipation – observation of increasing

severity of disease and early age at onset in
subsequent generations
Genetic Imprinting
• Normal: 2 copies of most autosomal genes are functionally equivalent
• 1 copy of a gene is transcribed and the other is silenced  DNA methylation
• epigenetic modification – no change in DNA nucleotide sequence

• Result from an imbalance of active copies of a given gene

• Prader-Willi and Angelman syndromes, caused by microdeletions of chromosome 15q11-12

• Prader-Willi syndrome: paternally derived chromosome 15 deletion

• Angelman syndrome: maternally derived UBE3A gene deletion

• paternal copy of UBE3A is transcriptionally silenced, maternal copy transcribed
• maternal copy is deleted  insufficient amount of UBE3A protein in the brain  neurologic
deficits
Genetic Imprinting
• Uniparental disomy (UPD)
• rare occurrence
• child inherits BOTH copies of a chromosome from the SAME parent
• Maternal UPD15 accounts for ~30% of PWS cases, 3% of Angelman syndrome caused by
paternal UPD15

• Mutation in an imprinted gene

• ~ 11% of patients with Angelman syndrome; also result in familial transmission
• most uncommon cause: mutation in imprinting center  unable to correctly imprint UBE3A
• Female: 50% risk of passing gene

• Other regions of clinical interest: short arm of chromosome 11 (Beckwith-Wiedemann syndrome

and nesidioblastosis map) and long arm of chromosome 7 with maternal UPD of 7q (idiopathic
short stature and Russell-Silver syndrome)
Multifactorial and
Polygenetic inheritance
• traits caused by a combination of: inherited, environmental, and stochastic factors
• segregate within families but do not exhibit a consistent or recognizable inheritance
pattern
• Characteristics:
• similar rate of recurrence among all 1st-degree relatives, risk is unusually to
found in distant relatives
• risk of recurrence is related to incidence
• sex predilection; E.g. Pyloric stenosis (PS): M>F; Congenital dislocation of the
hips: F>M
• Relative risk is inverse to sex of index case
• E.g. Son of affected female with infantile PS has 18% risk, while son of
affected male has 5% risk
Multifactorial and
Polygenetic inheritance
• Identical twins may not always share fully penetrant genetic disorders
(<100%; as opposed to mendelian inheritance)
• Multiple family members affected = increased risk of recurrence
• E.g. Unilateral cleft lip and palate: 4% if with 1 child, 9% if with 2 affected
children
• Recurrence risk is greater when disorder is more severe
• E.g. Infant with long-segment Hirschsprung disease has a greater chance
of having an affected sibling than the infant who has short-segment
Hirschsprung disease
Multifactorial and
Polygenetic inheritance
• 2 types
• One exhibits continuous variation, within “normal” limits
• “Abnormals”, falling outside normal range
• E.g. intelligence, BP, height, and head circumference
• Can also be based on the presence or absence of a particular
trait
• E.g. PS, NTDs, CHDs, and cleft lip and cleft palate
• Threshold model – those who exceed a threshold
liability develop the trait, and those below the threshold
do not
• In NTDs:
• (+) genetic factors but with recurrence risk of 3%
• (+) nongenetic environmental factors: recurrence risk can
be lowered by up to 87% if the mother-to-be takes 4 mg
of folic acid per day starting 3 months before conception.
• Adult-onset diseases: Diabetes, CAD, and schizophrenia
Cytogenetics
Insert the Sub Title of Your Presentation
• Study of chromosomes: their structure, function, inheritance, and
abnormalities

• Occurrence rate: ~1-2% of live births, 5% of stillbirths, and 50% of

early fetal losses in 1st trimester

• More common among persons with intellectual disability and

neoplasias
Indications for chromosomal analysis:

• multiple congenital anomalies, dysmorphism, and/or intellectual disability

• Advanced maternal age (>35 yr) or multiple abnormalities on fetal ultrasound,
multiple congenital anomalies, unexplained IUGR or postnatal growth and
development problems
• ambiguous genitalia
• unexplained intellectual disability with/without associated anatomic
abnormalities
• primary amenorrhea or infertility
• recurrent miscarriages (≥3) or prior history of stillbirths and neonatal deaths
• FHx: 1st-degree relative with a known or suspected structural chromosome
abnormality
• clinical findings consistent with a known anomaly, some malignancies, and
chromosome breakage syndromes (e.g., Bloom syndrome, Fanconi anemia).
 Methods of
Chromosomal Analysis
• Specimens:
• Peripheral blood lymphocytes
• Prenatal: amniotic fluid, chorionic villus tissue,
and fetal blood
• Bone marrow (tumor surveillance)

• Types of cell division:

• Mitosis – occurs in somatic cells

• Meiosis – limited to germ cells
• Mitosis

• Single parent cell = 2 daughter cells

• DNA duplication has already occurred during interphase
• 2 double DNA strands joined at centromere (sister
chromatids)
• 4 stages: prophase, metaphase, anaphase, and
telophase
• Meiosis

• begins in female oocyte during fetal life, completed years to

decades later
• Males: begins in spermatogonial cell between adolescence
and adult life, completed in a few days
• preceded by DNA replication hence 46 chromosomes
consists of 2 chromatids
• diploid cell (2n = 46 chromosomes) divides to form haploid
cells (n = 23 chromosomes)
• Role: reduces the chromosome from diploid to haploid to
allow genetic recombination during fertilization
• Errors of cell division

• Nondisjunction: 2
chromosomes fail to
separate during
meiosis  1 cell has
2 copies, another cell
has none

• Anaphase lag:
chromatid or
chromosome is lost
during mitosis
because it fails to
move quickly during
anaphase
 Methods of
Chromosomal Analysis
• cells are cultured, with or without stimulation
• Artificially arrested in mitosis during metaphase (or prometaphase)
• + hypotonic solution  nuclear cell membrane disruption  dispersion of the
chromosomes
• Fixed, banded, and stained
• GTG banding (G-bands trypsin Giemsa) – most commonly used banding
and staining method
• aka G banding
• dark (G-positive) and light (G-negative) bands that permits recognition of
all individual 23 chromosome pairs
• Q-banding – uses quinacrine
• reverse banding (R-banding) – uses acridine orange
• C-banding (constitutive heterochromatin) – uses barium hydroxide
 Methods of
Chromosomal Analysis
• Metaphase chromosome spreads and evaluated microscopically, photo or
video capture, stored, later analyzed

• homologous chromosomes arranged systematically to assemble a karyotype

(based on standards set by International System for Human Cytogenetic
Nomenclature or ISCN)
• Largest: chromosome 1; smallest: chromosome 22
• Nomenclature: total number of chromosomes followed by the sex
chromosome constitution (46,XX for females and 46,XY for males)
• Abnormalities noted after the sex chromosome complement
• Position of centromere relative to the ends of chromosome
• short arm: p arm; long arm: q arm
• + or – indicates extra or missing chromosome
 Methods of
Chromosomal Analysis
• FISH
• used to identify the presence, absence, or rearrangement of specific DNA
segments
• uses gene- or region-specific DNA probes
• DNA sequence or probe is labeled with a fluorescent dye, examined
microscopically
• (+) fluorescence when the probe pairs with its complementary DNA sequence
• Can document exact chromosomal location, number of copies (deletions,
duplications) even deletions as small as 50-200 kb of DNA
• useful in chromosomes 13, 18, and 21 and for the sex pair X and Y
• no longer the first line of testing
 Methods of
Chromosomal Analysis
• Spectral karyotyping and multicolor FISH
• Also uses probes and 5 fluorochromes
• Studies different wavelengths emitted by 22 chromosomes and X
and Y
• especially useful for identifying the complex chromosome
rearrangements found in many tumors
• Costly
 Methods of
Chromosomal Analysis
• Array comparative genomic hybridization studies (conventional CGH and
array CGH [aCGH])
• Conventional CGH
• molecular-based technique
• Uses green fluorescent dye to label DNA, normal reference DNA labelled
with red fluorescent dye
• ratio of green : red fluorescence is measured
• Abnormal: more green fluorescence; normal: green : red ratio is 1 : 1 and
chromosomes appear yellow
 Methods of
Chromosomal Analysis
• Array CGH (aCGH)
• uses DNA spotted onto a slide or microarray grid
• short DNA segments distributed in a microarray that resembles the
chromosomes in a metaphase
• Advantages:
• can test all critical disease causing regions in the genome at once;
FISH requires the clinical knowledge and tests only 1 area at a time
• can detect duplications and deletions (not recognized as disease
causing by FISH)
• detects single and contiguous gene deletion syndromes
• does not always require cell culture to generate sufficient DNA
• Disadvantages: does not detect balanced translocations, inversions, or
very low-levels of mosaicism
aCGH Types:

• Targeted aCGH
• effective and efficient technique to detecting clinically known cryptic
chromosomal aberrations, which are typically associated with known disease
phenotypes

• Whole-genome arrays
• target entire genome
• Advantage: allows better and denser coverage of the entire genome
• Disadvantage: interpretation may be difficult if involving areas not previously
known to be involved

• Single nucleotide polymorphism (SNP) array

• Polymorphic variations between 2 nucleotides analyzed in massive parallel
fashion
• help with the detection of uniparental disomies as well as consanguinity