Human genetic architecture
- 20,000-50,000 genes that code for proteins
- 2 MC forms of DNA variations are
o single nucleotide polymorphisms (SNPs)
o copy number variations (CNVs)
- SNPs
o <1% occur in coding regions
o marker that is co-inherited w/ diseaseassoc. gene due to close proximity
o SNP & causative genetic factor are in
linkage disequilibrium
- CNVs
o 50% involve gene-coding regions
- epigenetics = heritable changes in gene
expression that are not caused by alterations in
DNA sequence
- many genes don’t encode proteins but play
regulatory functions
- miRNAs don’t encode proteins but inhibit gene
expression
- siRNAs are similar to miRNAs but siRNA
precursors are introduced by investigators into
the cell
Genes and human diseases
Human genetic disorders can be classified into 3
groups:
- mutations in single genes w/ large effects
o usually follow classic Mendelian pattern of
inheritance
o aka Mendelian disorders
- chromosomal disorders
- complex multigenic disorders
o interactions between multiple variant
forms of genes & environmental factors
o polymorphisms = variations in genes
common in the population
o examples = DM, HTN, autoimmune dz
Transmission patterns of single-gene disorders
Autosomal dominant disorders
- affected individual’s children have a ½ chance of
getting dz
- incomplete penetrance = some pts inherit
mutant gene but are phenotypically normal
- variable expressivity = trait is seen in all
individuals with mutant gene but expressed
differently
- if mutation affects enzyme protein,
heterozygotes are usually normal
- 2 major groups of nonenzyme proteins affected
in AD disorders:
o regulation of complex metabolic pathways
that are subject to feedback inhibition
o key structural proteins such as collagen,
cytoskeletal elements of RBC membrane
(spectrin)
- dominant negative = when mutant allele impairs
the function of a normal allele
- GOF mutations less common
o often endow normal proteins w/ toxic
properties
o or rarely  normal activity
Biochemical & molecular basis of single-gene
disorders
Enzyme defects and their consequences
3 major consequences:
- accumulation of substrate
o excessive accumulation of complex
substrates w/in lysosomes from deficiency
of degradative enzymes
o ex = lysosomal storage diseases
- enzyme defect  metabolic block and  end
product necessary for normal function
- failure to inactivate a tissue-damaging substrate
Autosomal recessive disorders
- expression of defect is more uniform than AD
disorders
- complete penetrance common
- onset frequently early in life
- many of the mutated genes encode enzymes
Genetically determined adverse rxn to drugs
- enzyme deficiencies that only unmask after
exposure to certain drugs
- pharmacogenetics
- classic example is G6PD deficiency
o primaquine causes severe hemolytic
anemia
X-linked disorders
- almost all X-linked disorders are recessive
- Y-linked genes are usually infertile (no Y-linked
inheritance)
- males are hemizygous for X-linked mutant genes
- females have variable proportion of cells in
which mutant X chromosome is active
o heterozygous female express the disorder
partially
- example = G6PD deficiency
- vit D resistant rickets is only X-linked dom.
Defects in receptors & transport systems
- defect in:
o receptor mediated endocytosis, or
o transport protein
- familial hypercholesterolemia = reduced
synthesis of LDL receptors  defective transport
of LDL into cells
- cystic fibrosis
Alterations in structure, function, or quantity
of nonenzyme proteins
‘
Disorders associated w/ defects in structural
proteins
Marfan syndrome
- disorder of CTs
- changes in skeleton, eyes, cardiovascular system
- 70-85% familial AD
- inherited defect in extracellular glycoprotein
fibrillin-1
- abnormal and excessive activation of TGF-β
- fibrillin = major component of microfibrils in
ECM
o provide scaffold
o tropoelastin deposits on to form elastic
fibers
o microfibrils abundant in aorta, ligaments,
ciliary zonules supporting the lens
o FBN1 gene
- congenital contractural arachnodactyly =
mutation in fibrillin-2; causes skeletal
abnormalities
- morphology:
o skeletal abnormalities
 unusually tall w/ long extremities
 long tapering fingers & toes
 joint ligaments in hands & feet are lax
 dolichocephalic (long-headed) w/
bossing of frontal eminences &
prominent supraorbital ridges
 kyphosis, scoliosis, or
rotation/slipping of dorsal or lumbar
vertebrae
 pectus excavatum or pigeon-breast
deformity
o ocular changes
 B/L subluxation or ectopia lentis
(dislocation of lens)
o cardiovascular lesions
 MC = mitral valve prolapse
 dilation of ascending aorta due to
cystic medionecrosis
 weakening of media  predisposes to
intimal tear  aortic dissection
- clinical:
o loss of CT support in mitral valve leaflets
make them soft and billowy (floppy valve)
o mitral regurgitation
o echocardiograph very helpful in Dx of
Marfan’s
o MC cause of death = rupture of aortic
dissection
Ehler’s-Danlos syndromes (EDS)
- defect in synthesis or structure of fibrillar
collagen
- clinically variable disorder; several patterns of
inheritance
- 6 variants:
o classical (I/II)
o hypermobility (III)
o vascular (IV)
o kyphoscoliosis (VI)
o arthrochalasia (VIIa, b)
o dermatosparaxis (VIIc)
- tissues rich in collagen (skin, ligaments, joints)
frequently involved
- skin = hyperextensible, stretchable, extremely
fragile, vulnerable to trauma
- joints = hypermobile; predisposed to dislocation
- serious internal complications:
o rupture of colon or large arteries (vascular
EDS)
o ocular fragility, rupture of cornea, retinal
detachment (kyphoscoliosis EDS)
o diaphragmatic hernia (classical EDS)
- kyphoscoliosis type
o MC AR EDS
o mutation in lysyl hydroxylase (essential for
collagen cross-linking)
o collagen lacks structural stability
- vascular type
o abnormality in type III collagen
o mutation in structural protein
o AD pattern
o severe defects (spontaneous rupture)
- arthrochalasia & dermatosparaxis type
o defect in conversion of type I procollagen
to collagen
o arthrochalasia
 mutation in one of the type I collagen
genes (COL1A1 or COL1A2) that is
resistant to cleavage
 protein mutation; AD
o dermatosparaxis
 mutation in procollagen-N-peptidase
genes, essential for cleavage of
collagens
 enzyme deficiency; AR
- classical type
o genes other than collagen involved
o usually type V collagen
Disorders associated w/ defects in receptor
proteins
Familial hypercholesterolemia
- mutation in gene encoding receptor for LDL
- one of MC mendelian disorders
- homozygotes are much more severely affected
o 5 to 6-fold elevation in plasma cholesterol
lvls
o skin xanthomas
o coronary, cerebral, peripheral vascular
atherosclerosis in early age
- cholesterol metabolism
o IDL is immediate & major source of plasma
LDL
o 70% of plasma LDL is cleared by the liver
(rest by scavengers)
o LDL binds to receptor then endocytosed by
coated pits
o lysosomes degrade LDL  free cholesterol
o cholesterol exits lysosome through NPC1
and NPC2
- cholesterol’s effects in the cell cytoplasm
o inhibits HMG CoA reductase ( synthesis)
o activates acyl-coenzyme A ( esterification
& storage of excess cholesterol)
o suppress synthesis of LDL receptor (
accumulation)
- scavengers
o monocytes & macrophages have receptors
for oxidized or acetylated LDL
o in hypercholesterolemia, marked  in
scavenger-mediated traffic of LDL
cholesterol into cells of mononuclear
phagocyte system
- 5 groups of mutations:
o class I = uncommon; complete failure of
synthesis of receptor protein (null allele)
o class II = fairly common; encode receptors
that accumulate in the ER due to folding
defects
o class III = affect LDL-binding domain; reach
cell surface but fail to bind LDL
o class IV = bind LDL but fail to localize in
coated pits
o class V = pH dependent dissociation of
receptor and bound LDL fail to occur
- statins suppress intracellular cholesterol
synthesis by blocking HMG CoA reductase  
synthesis of LDL receptors
Disorders associated with defects in enzymes
Lysosomal storage diseases
- lysosomal enzymes undergo post-translational
modifications
o attachment of terminal mannose-6phosphate groups to some of the
oligosaccharide side chains
o recognized by receptors on inner surface of
Golgi membrane
o pinched off and shuttled to lysosomes
- lysosomal storage diseases can result from:
o lack of enzyme activator or protector
protein
o lack of substrate activator protein
o lack of transport protein required for
egress of the digested material from the
lysosomes
Tay-Sachs disease
- GM2 gangliosidosis includes 3 diseases
o Tay-Sachs = hexosaminidase α-subunit
deficiency
o Sandhoff = hexosaminidase β-subunit
deficiency
o GM2 gangliosidosis variant AB = ganglioside
activator protein deficiency
- all have accumulation of GM2 gangliosides
- Tay-Sachs is MC form of GM2 gangliosidosis
- severe deficiency of hexoaminidase A
- prevalent in Ashkenazic Jews
- morphology:
o involvement of neurons in CNS, ANS, retina
o neurons ballooned w/ cytoplasmic
vacuoles
o oil stains (red O & Sudan black B) positive
o cytoplasmic inclusions = whorled
configurations w/in lysosomes composed
of onion-skin layers of membranes
o cherry-red spot
 ganglion cells in retina are swollen w/
GM2 ganglioside, esp at margins of
macula
 pallor surrounding spot in contrast to
the normal color of the spot
- clinical:
o symptoms appear ~6 mo.
o motor & mental deterioration
o muscular flaccidity, blindness,  dementia
o vegetative state within 1-2 years
o death at 2-3 years
Neiman-Pick disease type A & B
- lysosoal accumulation of sphingomyelin
- inherited deficiency of sphinogmyelinase
- more common in Ashkenazi Jews
- imprinted gene preferentially expressed from
maternal chromosome
- type A
o severe infantile form; complete enzyme
deficiency
o extensive neurologic involvement
o marked visceral accumulations of
sphingomyelin,
o protuberant abdomen from
hepatosplenomegaly
o progressive FTT, vomiting, fever,
lymphadenopathy, progressive
deterioration of psychomotor function
o early death w/in 3 years of life
- morphology:
o lipid accumulation in lysosomes (esp.
mononuclear phagocyte system)
o foamy cytoplasm (innumerable small
vacuoles)
o stain positively for fat
o vacuoles = engorged lysosomes with
membranous cytoplasmic bodies; “zebra
bodies”
o lipid-laden phagocytic foam cells in spleen,
liver, lymph nodes, bone marrow, tonsils,
GI tract, and lungs
o massive splenomegaly
o brain and gyri shrunken, sulci widened
o vacuolation and ballooning of neurons
o cherry-red spot in macula seen in ⅓-½ of
cases
- type B
o organomegaly but no CNS involvement
o survive into adulthood
Niemann-Pick disease type C
- more common than A + B combined
- mutations in 2 genes can give rise to it (NPC1,
NPC2)
- NPC1 mutation = 95% of cases
- due to 1 defect in lipid transport
- MC form presents in childhood
- ataxia, vertical supranuclear gaze palsy,
dystonia, dysarthria, psychomotor regression
Gaucher disease
- group of AR disorders from mutation in
glucocerebrosidase
- MC lysosomal storage disorder
- glucocerebroside accumulates mostly in
phagocytes (some subtypes in CNS)
- 3 clinical subtypes:
o type 1 = chronic non-neuronopathic form
 splenic & skeletal involvement
 Jews of European stock
 reduced but detectable lvls of
glucocerebrosidase activity
 longevity shortened
o type II = acute neuronopathic form
 infantile acute cerebral pattern
 no predilection for Jews
 no detectable glucocerebrosidase
activity
 hepatosplenomegaly
 progressive CNS involvement  early
death
o type III = intermediate form
- morphology:
o Gaucher cells
 distended phagocytic cells
 in spleen, liver, bone marrow, lymph
nodes, tonsils, thymus, Peyer’s
patches
 have fibrillary cytoplasm = crumpled
tissue paper
 enlarged with 1+ dark eccentrically
placed nuclei
 strongly PAS +
o type I disease
 splenomegaly
 mild lymphadenopathy
 Gaucher cells in bone marrow  bone
erosion  pathologic fractures
o if CNS involvement:
 Gaucher cells in Virchow-Robin
spaces
 arterioles surrounded by swollen
adventitial cells
 no storage of lipids in neurons
 neurons appear shriveled 
progressive destruction
- clinical:
o type I disease
 symptoms begin in adulthood
 splenomegaly or bone involvement
 pancytopenia or thrombocytopenia 2
to hypersplenism
 may have pathologic fractures
o type II and III
 CNS dysfunction
 convulsions
 progressive mental deterioration
dominate
- treatment = recombinant therapy w/
recombinant enzymes (extremely expensive)
Mucopolysaccharidoses (MPSs)
- deficiencies of lysosomal enzymes involved in
degradation of mucopolysaccharides
(glycosaminoglycans)
- abundant in the ground substance of CT
- glycosaminoglycans that accumulate in MPSs =
dermatan sulfate, heparin sulfate, keratin sulfate,
chondroitin sulfate
- all MPSs except one are AR
- Hunter syndrome is X-linked recessive
- progressive disorder
- coarse facial features, clouding of cornea, joint
stiffness, mental retardation
-  urinary excretion of mucopolysaccharides
- morphology:
o accumulations in mononuclear phagocytic
cells, endothelial cells, intimal smooth
muscle cells, and fibroblasts throughout
the body
o common sites are spleen, liver, bone
marrow, lymph nodes, BVs, and heart
o balloon cells (distended cells with clearing
of cytoplasm)
o lysosomes replaced by lamellated zebra
bodies
o hepatosplenomegaly, skeletal deformities,
valvular lesions, subendothelial arterial
deposits (esp. in coronary arteries), and
lesions in brain
o MI & cardiac decompensation = important
causes of death
- clinical:
o Hurler syndrome (MPS I-H)
 deficiency of α-1-iduronidase
 most severe form of MPS
 hepatosplenomegaly by 6-24 mo.
 growth retardation
 coarse facial features
 skeletal deformities
 death by age 6-10 due to CV problems
o Hunter syndrome (MPS II)
 X-linked
 absence of corneal clouding
 milder clinical course
Glycogen storage diseases (glycogenoses)
- deficiency in any of the enzymes that break
down glycogen
- glycogen is a storage form of glucose
- 3 major subgroups:
o hepatic forms
 deficiency in hepatic enzymes
involved in glycogen degradation
 hepatomegaly +  blood [glucose]
 type 1 (von Gierke dz) = glucose-6phosphatase
o myopathic forms
 glycolytic pathway can’t be used for
energy
 muscle weakness from impaired
energy production
 muscle cramps after exercise &
lactate lvls in blood fail to rise after
exercise due to block in glycolysis
 type V (McArdle dz) = muscle
phosphorylase deficiency
 type VII = muscle
phosphofructokinase
o deficiency in α-glucosidase (acid
maltase) & lack of branching enzyme
 glycogen storage in many organs
 death early in life
 type II (Pompe) = deficiency in acid
maltase (also lysosomal enzyme);
cardiomegaly; glycogen storage in all
organs
Alkaptonuria (Ochronosis)
- AR; 1st discovered inborn error of metab.
- lack of homogentisic oxidase (converts
homogentisic acid  methylacetoacetic acid in
tyrosine degradation pathway)
- homogentisic acid accumulates in body
- large amt excreted = urine becomes black when
oxidated
- morphology:
o blue-black pigmentation (onchronosis) of
collagen in CT, tissues, tendons, cartilage
o ears, nose, cheeks
o pigment may deposit in articular cartilage
of joints  brittle & fibrillated
o intervertebral disc attacked commonly
o knees, shoulders, hips later affected
- clinical:
o degenerative arthropathy develops slowly
o not clinically evident until 30s
o arthropathy may become severe
Chromosomal disorders
Normal karyotype
- G banding = commonly used (Giemsa stain) to
identify individual chromosomes on basis of
alternating light and dark band pattern
Structural abnormalities of chromosomes
- euploid = any exact multiple of haploid number
- aneuploidy = error occurs in meiosis or mitosis,
cell acquires a chromosome complement that's
not exact multiple of 23
o MC causes = nondisjunction & anaphase lag
- monosomy of an autosome = too much loss of
genetic info (non viable)
- some autosomal trisomies permit survival
(trisomy 21)
- mosaicism = mitotic errors in early development
 2+ populations of cells w/ different
chromosomal complement
o mosaicism of sex chromosomes is pretty
common
- deletion = loss of portion of chromosome; mostly
interstitial (terminal deletions are rare)
- ring chromosome = break at both ends of a
chromosome  fusion of damaged ends
o may be expressed as 46,XY,r(14)
- inversion = rearrangement w/ 2 breaks in a
single chromosome w/ reincorporation of
inverted segment; fully compatible w/ normal
development
o paracentric = involves only 1 arm
o pericentric = breaks on opposite sides of
centromere
- isochromosome – 1 arm of chromosome is lost
and remaining arm is duplicated; 2 long arms or
2 short arms
o MC isochromosome is long arm of X =
i(X)(q10)
- translocation = segment of chromosome is
transferred to another
- balanced reciprocal translocation = single breaks
in each of 2 chromosomes  exchange of
material; usually phenotypically normal;  risk
of abnormal gametes
- robertsonian translocation = aka centric fusion;
translocation btwn 2 acrocentric chromosomes
 1 large chromosome and 1 small chromosome
that becomes lost; usually compatible with
normal life
Cytogenic disorders of autosomes
Trisomy 21 (Down syndrome)
- MC chromosomal disorder
- major cause of mental retardation
- MC cause of trisomy = meiotic nondisjunction
- maternal age important
- 95% cases extra chromosome is maternal
- 4% cases due to robertsonian translocation of
long arm of 21 (frequently familial)
- 1% of Downs are mosaics (from mitotic
nondisjunction in early embryogenesis)
- clinical features:
o flat facial profile
o hypotonia
o oblique palpebral fissures
o epicanthic folds
o severe mental retardation
o gentle, shy manner
o 40% have congenital heart dz (MC
endocardial cushion defect – ostium
primum, ASD, atrioventricular valve
malformation, VSD)
o 10-20 fold  risk of acute leukemia
 MC acute megakaryoblastic leukemia
o all pts >40 develop neuro changes like
Alzheimers
o abnormal immune response  risk for
serious infections (lungs) and thyroid
autoimmunity
Other trisomies
- trisomy 18 = Edwards syndrome
o micrognathia
- trisomy 13 = Patau syndrome
o cleft lip
- both have rocker bottom feet, mental
retardation, heart, and kidney problems
- most cases meiotic nondisjunction
-  maternal age = risk factor
- most succumb few weeks after birth
Chromosome 22q11.2 deletion syndrome
- spectrum of disorders including:
o congenital heart defects
o abnormalities of the palate
o facial dysmorphism
o developmental delay
o variable degrees of T-cell
immunodeficiency
o hypocalcemia
- DiGeorge syndrome
o thymic hypoplasia  immunodeficiency
o parathyroid hypoplasia  hypocalcemia
o cardiac malformations of outflow tract
o mild facial anomalies
- velocardiofacial syndrome
o facial dysmorphism (prominent nose,
retrognathia)
o cleft palate
o cardiovascular anomalies
o learning disabilities
o immunodeficiency less common
-  risk for psychotic illness (schizo & bipolar)
- ADHD in 30-35%
- dx by detection of deletion by FISH
- some pts only have conotruncal cardiac defects
Cytogenic disorders of sex chromosomes
- Lyon hypothesis
o only 1 X chromosome is genetically active
o other X undergoes heteropyknosis
(rendered inactive)
o inactivation of either X occurs at random to
all cells of blastocyst ~16th day of embryo
o inactivation of same X chromosome in all
cells derived from precursor cell
Klinefelter syndrome
- male hypogonadism due to 2+ X chromosomes
and 1+ Y chromosomes
- 1 of MC forms of genetic dz of sex chromosomes
- MC cause of hypogonadism in male
- rarely Dxed before puberty
-  length btwn soles & pubic bone (elongated
body)
- eunuchoid body habitus w/ abnormally long legs
- small atrophic testes; small penis
- mean IQ lower but no mental retardation
-  incidence of type 2 DM
- mitral valve prolapse in 50%
-  FSH (constant)
-  testosterone (variable)
- reduced spermatogenesis
- male infertiligy
-  risk for breast CA, extragonadal germ cell
tumors, autoimmune dz (SLE)
- 90% 47, XXY
Turner syndrome
- complete or partial monosomy of X
chromosomes
- hypogonadism in phenotypic females
- MC sex chromosome abnormality in females
- 57% missing entire X chromosome
- 14% structural abnormality of X
- 29% mosaics
- may present as 1 amenorrhea
- most severe pts:
o present in infancy
o edema of dorsum of hand & foot from
lymph stasis
o swelling of nape of neck (cystic hygroma)
o may cause B/L neck webbing
o congenital heart disease
 L-sided
 preductal coarctation of aorta
 bicuspid aortic valve
 most important cause of  mortality
in children w/ Turner’s
- puberty = failure to develop normal 2 sex
characteristics
- mental status = subtle defects in nonverbal,
visual-spatial information processing
- clinical:
o short stature
o Turner’s = single most important cause of
1 amenorrhea
o hypothyroidism
o glucose intolerance
o obesity
o insulin resistance
o accelerated loss of oocytes  streak
ovaries
Hemaphroditism & pseudohermaphroditism
- true hermaphrodite = presence of ovarian &
testicular tissue
- pseudohermaphrodite = disagreement btwn
phenotypic & gonadal sex
- female pseudohermaphroditism
o genetic sex is XX
o gonad & internal genitalia development
normal
o external genitalia ambiguous or virilized
o excessive exposure to androgenic steroids
in early gestation
o congenital adrenal hyperplasia (AR)
- male pseudohermaphroditism
o possess Y chromosome
o gonads are testes
o genital ducts or external genitalia are
incompletely differentiated along male
phenotype
o many causes
o MC form = complete androgen insensitivity
syndrome (testicular feminization);
mutation in androgen receptor
Single gene disorders w/ nonclassic inheritance
Dzes caused by trinucleotide repeat mutations
- mutations = expansion trinucleotide repeats
- usually share G & C
- DNA is unstable
- tendency to expand depends on sex of
transmitting parent
o fragile-X expansion occurs in oogenesis
o Huntington occurs in spermatogenesis
- repeats can occur in noncoding regions (fragileX & myotonic dystrophy) or coding regions
(Huntington’s)
- mutations in coding regions
o involve CAG repeats (polyglutamine dzes)
o progressive neurodegeneration
o striking in midlife
o lead to toxic GOF
o accumulation of aggregated mutant
proteins in large intranuclear inclusions
- mutations in noncoding regions
o LOF type
o affect many systems
o intermediate-size expansions or
premutations that expand to full
mutations in germ cells
Fragile-X syndrome
- prototype of trinucleotide repeat disease
- 2nd MC genetic cause of mental retardation
- unusual mutation w/in familial mental
retardation-1 (FMR1) gene
- clinical:
o affected males are mentally retarded (but
more females have dz)
o long face w/ large mandible
o large everted ears
o macroorchidism (most distinctive
feature)
o hyperextensible joints
o high arched palate
o mitral valve prolapse
o mimic CT disorder
- FMR1 gene has multiple tandem repeats of CGG
in 5’ untranslated region
- premutations are converted to mutations by
triplet-repeat amplification during oogenesis
(not spermatogenesis)
- 30% of females carrying premutation have
premature ovarian failure (before 40)
- 1/3 of premutation-carrying males have
progressive neurodegenerative syndrome
starting in 6th decade called fragile-X assoc.
tremor/ataxia
o intention tremors
o cerebellar ataxia
o progress to parkinsonism
- mental retardation due to LOF of FMRP
o  in FMRP 
o  translation of bound mRNAs at synaptic
junctions 
o permanent changes in synaptic activity 
o mental retardation
- FMRP most abundant in brain & testis
- anticipation
- Dx = PCR based detection of repeats
Mutations in mitochondrial genes
- mtDNA has maternal inheritance
- mutations in mtDNA affect organs most
dependent on oxidative phosphorylation (CNS,
skeletal & cardiac muscle, liver, kidneys)
- “threshold effect” = minimum # of mutant
mtDNA must be present in a cell or tissue before
oxidative dysfunction gives rise to dz
- most diseases of mtDNA inheritance affect
neuromuscular system
- Leber hereditary optic neuropathy
o prototype mtDNA disorder
o neurodegenerative dz
o progressive BL loss of central vision
o visual impairment starts at 15-35 yrs
o eventual blindness
o cardiac conduction defects
o minor neuro manifestations
Genomic imprinting
- imprinting selectively inactivates either the
maternal or paternal allele
- occurs in the ovum or sperm before fertilization
- methods of imprinting:
o differential patterns of DNA methylation at
CG nucleotides
o histone H4 deacetylation & methylation
Prader-Willi syndrome & Angelman syndrome
Prader-Willi syndrome
- mental retardeation
- short stature
- hypotonia
- profound hyperphagia
- obesity
- small hands and feet
- hypogonadism
- interstitial deletion of band q12 in long arm of
chromosome 15
- deletion in paternally derived chromosome 15
Angelman syndrome
- mentally retarded
- ataxic gait
- seizures
- inappropriate laughter
- “happy puppets”
- affected gene is UBE3A which is imprinted on
paternal chromosome
Gonadal (germ line)mosaicism
- mutation that occurs postzygotically during
early (embryonic) development
- mutation affects only cells destined to form the
gonads  gametes carry mutation but somatic
ccells are completely normal
- phenotypically normal parent w/ germ line
mosaicism can transmit the dz-causing mutation
to the offspring through the mutant gene
Molecular diagnosis of genetic diseases
Indications for analysis of germ line genetic
alterations
Prenatal genetic analysis
- can be done by amniocentesis, chorionic villus
biopsy material, or umbilical cord blood
- indications for prenatal genetic analysis:
o mother >35 yrs old
o parent who is a carrier of balanced
reciprocal translocation, robertsonian
translocation, or inversion
o previous child with chromosomal
abnormality
o fetus with ultrasound detected
abnormalities
o parent with X-linked genetic disorder
o abnormal lvls of AFP, βHCG, and estradiol
Postnatal genetic analysis
- usually performed on peripheral blood
lymphocytes
- indications for postnatal genetic analysis:
o multiple congenital anomalies
o unexplained mental retardation and/or
developmental delay
o suspected anomaly (features of Downs)
o suspected unbalanced autosome (PraderWilli)
o suspected sex chromosomal abnormality
(Turner)
o suspected fragile-X syndrome
o infertiligy (to rule out sex chromosomal
abnormality)
o multiple spontaneous abortions (rule out
parents as carriers of balanced
translocation)
Polymorphic markers & molecular diagnosis
Polymorphisms
- naturally occurring variations in DNA sequences
- used as marker loci in linkage studies
- 2 types:
o SNPs
 occur in 1 NT per stretch of ~100 BPs
 used in linkage analysis for
identifying haplotypes assoc. w/ dz
o minisatellites & microsatellites
 repeat length polymorphisms
 microsatellites are <1 kilobase;
repeats of 2-6 BPs
 minisatellites are 1-3 kilobases;
repeats of 15-70 BPs
 extremely variable in a population
- microsatellite marker PCR assays routinely used
for paternity tests and criminal investigations
Indications for analysis of acquired genetic
alterations
Diagnosis and management of cancer
- detection of tumor-specific acquired mutations
& cytogenic alterations that are the hallmarks of
specific tumors (BCR-ABL1 in CML)
- determination of clonality as indicator of
neoplastic condition
- direct therapeutic choices (HER2/Neu in breast
CA or EGFR in lung CA)
- determination of tx efficacy
- detection of Gleevec-resistant forms of CML and
GI stromal tumors
Genome-wide association studies (GWAS)
- powerful method of identifying genetic variants
assoc. w/  risk of developing a dz
- such variants may be causative or be in linkage
disequilibrium w/ other genetic variants
responsible for  risk
Diagnosis and management of infectious disease
- detect microorganism genetic material
- ID genetic alterations of microbes associated
with drug resistance
- determination of tx efficacy (assess viral loads)
PCR & detection of DNA sequence alterations
- indirect & direct detection methods for
mutations
- direct methods obtain a specific readout of order
of nucleotides
- indirect methods detect different sizes of
sequences or identifying mutations at specific
locations
Molecular analysis of genomic alterations
Southern blotting
- can detect changes in specific loci
- hybridization of radiolabeled sequence-specific
probes to genomic DNA that's been 1st digested
w/ restriction enzyme and separated by a gel
electrophoresis
- probe detects 1 germ line band in normal pts
- useful in detection of large-trinucelotideexpansion dz (fragile-X syndrome); also
detection of clonal Ig gene rearrangements in dx
of lymphoma
Fluorescence in situ hybridization
- uses DNA probes that recognize sequences
specific to particular chromosomal regions
- DNA clones labeled w/ fluorescent dyes &
applied to metaphase spreads or interphase
nuclei
- probe hybridizes to its homologous genomic
sequence & labels a specific chromosomal region
(visualized under fluorescent microscope)
- can be performed on prenatal samples,
peripheral blood lymphocytes, touch
preparations from CA biopsies, & archival tissue
sections
Array-based comparative genomic
hybridization (Array CGH)
- test DNA and reference (normal) DNA are
labeled w/ 2 different fluorescent dyes
o MC dyes = Cy5 (red) and Cy3 (green)
- differently labeled samples hybridized to glass
slide spotted w/ DNA probes that span human
genome at regularly spaced intervals
- if contributions of both samples are equal for a
given region (test sample is diploid), all spots on
array will fluoresce yellow (red + green)
- if test sample shows excess of DNA an any given
chromosomal region (due to amplification) there
will be corresponding excess of signal from dye
w/ which this sample was labeled
- reverse will be true for a deletion, w/ excess of
signal used for labeling reference sample
Epigenetic alterations
- epigenetics = study of heritable chemical
modification of DNA or chromatin that doesn’t
alter DNA sequence itself
- methylation of DNA
- methylation and acetylation of histones
- methylation usually occur in cytosines
(specifically in the CG dinucleotide-rich
promoter regions, CpG islands)
-  methylation =  gene expression
- to detect methylation, treat genomic DNA with
sodium bisulfite  changes unmethylated
cytosines to uracil, while methylated cytosines
are protected from modification
RNA analysis
- most important application = detection &
quantification of RNA viruses such as HIV and
hepatitis C virus
- mRNA expression profiling rapidly becoming
important tool for molecular stratification of
tumors