Genetics

• Doubles in size every 18 months
• Database of sequences

• Used to predict patterns
• Can find frequency by population

• Mapped variations and tagged them with specific number
• Hyperlinks to more information
• Can look at all coding SNPs

• Almost complete human sequence
• Location and structure of most genes
• Identification of most of major variants

• Encyclopedia of DNA elements
• Complete characterization of 1% of human genome to start
• Trying to understand regulatory code
• Showed that alternative splicing is more than an artifact
• Many splice variants for UDP-Glucosyltransferase (UGT1A) - 1 gene but 9 variants in different substrates

• 2 genes at same locus (intron, overlapping sequences, distant regulatory elements)
• Structural variation (mobile elements, copy-number variants, alternative splicing, RNA editing, pseudogenes)
• Non-translated genes (miRNA, antisense RNA)

• Creates public databases
• Conducts research
• Develops software
• Disseminates biomedical information

Has common variants

Catalog of genetic diseases

• Lysis of RBCs
• Centrifugation of WBCs
• Lysis of WBCs
• Extraction of proteins (salt)
• Extraction of DNA (alcohol)
• Quantitiation of DNA

for measuring DNA

• Genomic DNA
• Forward primer
• Reverse primer
• Taq DNA polymerase buffer
• Taq DNA polymerase
• Thermocycler for amplification of DNA
• Gel Electrophoresis

• Acts like a probe for a specific sequence of DNA
• Contains a radioactive, enzymatic, or fluorescent tag
• Can be used to detect differences as small as SNPs
• 5' end label primers with T4 kinase and 32p-gamma dATP
• Specific alleles fluoresce at different wavelengths - can determine how frequently an allele is present

• Probe for a single SNP
• Can determine genotypes based on color squares
• Colors specific for A, C, G, and T
• For looking at SNPs

• Important for looking at tumors
• Karyotyping
• Adds dyes to chromosomes
• Easy to identify translocation
• Used to ID leukemia, steroid sulfatase deficiency, and HER2

For large insertions and deletions

Study of chromosomes

• Number and structure of chromosomes can be analyzed
• Can't detect single gene deletion

• Peripheral blood (lymphocytes)
• Skin (Fibroblasts)
• Bone marrow
• Chorionic villi
• Amniotic fluid
• In mitosis, capable of rapid growth and division

Structure where spindle fibers are attached

6bp sequence that repeasts at ends of chromosomes

Both their length and location of centromere

• Routine diagnostic procedure
• Problems of early growth and development
• Still birth and neonatal death
• Fertility problems
• Family hx
• Neoplasia
• Pregnancy in women with advanced age

• Exact multiple of haploid number
• Ex: 23, 46, 69
• Triploidy = 3n
• Tetraploidy= 4n

Any chromosome number other than 46

• Extra OR missing chromosome (+1 or -1)
• Most common and clinically significant chromosomal abnormality
• Occurs in 5% of all clinically recogniezd pregnancies
• Trisomy= 3 rather than 2 of chromosome
• Monosomy= 1 rather than 2 of chromosome
• Most common is Trisomy 21, Trisomy 18, and Trisomy 13

• Meiotic nondisjunction - failure of choromosomes to disjoin properly during meiosis I
• Most common reason for trisomy
• Can be detected with FISH staining

• Normal complement of chromosome material just in different places
• Usually no phenotypic effect
• Threat to subsequent generations
• Inversion - Paracentric (one arm w/o centromere) and Pericentric (one arm w/centromere)

• Addition or missing material
• Usually deletion, duplication, or both
• Will lead to partial trisomy or partial monosomy
• Isochromasomes - one arm is missing and the other is duplicated (Turner Syndrome - long arm of X chromosome)

Functional centromere and 2 telomeres

• Reciprocal - breakage of nonhomologous chromosomes, relatively common, usually harmless
• Robertsonian - 2 acrocentric chromosomes fuse near centromere region with loss of short arms (13, 14, 15, 1, and 22) - resulting karyotyping only has 45 chromosomes including translocation chromosome whihc is long arms of 2 different chromosomes
• Insertion - nonreciprocal, segment removed and inserted into a different chromosome either inverted or normal orientation

• Two or more different chromosome complements present in an individual
• Usually numerical but sometimes structural
• Typically detected by conventional karyotype
• Common cause is nondisjunction

• Autodomal Dominant
• Trisomy 21
• Single most common genetic cause of mental retardation
• Hypotonia (reduced muscle tone)
• Characteristic facial features
• Short
• Brachycephaly, flat occiput
• Short neck w/extra skin
• Flat nasal bridge
• Low set folded ears
• Open mouth - furrowed protruding tongue (Macroglossia)
• Upslanting palpebral features
• Tiny white spots on iris (brushfield spots)
• Short hands - incurved 5th digid
• Single transverse palmar crease
• Wide gap between 1st and 2nd toes
• Mental retardation (IQ=30-60)
• Some have congenital heart disease (1/3), respiratory infections, GI tract anomalies, leukemia, Alzheimers
• Cause is meiotic nondisjunction (95%), Robertsonian translocation (5%), Mosaicism (1%)
• Cause of defect unknown
• Can be detected prenatally with CGH analysis
• Risk of recurrence is ~1%

• Mental retardation
• Failure to thrive
• Malformation of heart
• Hypertonia
• Large head w/prominent occiput
• Receding jaw
• Low, malformed ears
• Short sternum
• Fists clench (2nd and 5th digits overlap 3 and 4)
• Feet have prominent calcanei
• Single creases on palms, arch patterns on most digits

• Mental and growth retardation
• Cleft lip/palate and other significant facial features
• Ocular defects
• Polydactyly
• Clenched fists
• Rocker-bottom feet

One or other X is chosen at random to become future inactive X (barr body) in interphase nuclei

• drug that blocks ATP from binding ABL component of BCR-ABL oncoprotein
• Keeps cell from being turned on all the time
• Part of Philedelphia chromosome is BCR-ABL
• Leads to chronic myelogenous leukemia

Leads to amino acid change

Leads to stop codon

Addition of nucleotides, leads to frameshift

Deletion of nucleotides, can lead to frameshift

changes in RNA splicing

• Missense
• Nonsense
• Insertion
• Deletion
• Splice site
• Expansion of repeat units

• Transition: pyr--> pyr
• Tranversion: pyr--> pur

• C frequently methylated
• Spontaneous deamination to T
• "hotspot" mutation area
• 8.5x more likely to change than any other dinucleotide pair

Caused by deletion F508

• Silent - "wobble"
• Nonsense - AA to "stop"
• Missense - can be conservative (changes aa to same or similar) or nonconservative (changes aa by function or charge)

• Whole gene deletions or duplications - often due to repeated sequences and mispairing in replications
• Portion of gene deleted or fragment inserted- often due to aberrant splicing

• Promoter/enhancer element
• Trinucleotide repeats in 5' and 3' untranslated regions of genes or within coding regions
• Splice sites

• Loss of function
• No gene product

Decreased amount/activity

Increased amount/activity

Antagonizes normal product

Novel activity of product

• Silent= polymorphism - we have 1,000s of these
• Manifesting= mutation - we all carry 7-10 gene mutations

• Males and females affected equally
• 1 in 2 chance of being affected from affected parent
• Male to male transmission

• AD
• 100% penetrance
• Most common genetic dwarfism
• 80% new mutations in FGFR3 gene - activating mutation
• Short upper arms and thighs
• Large head
• Lower spine curves out
• Small foramen magnum
• Intact intellect
• G-->A at nt1138 causes gly380arg

• One gene, many effects on different systems
• Ex: Marfan syndrome - disproportionate long bone growth, tall stature, dislocated eye lenses, heart has dilation of aortic arch

• Cancer due to mutations are early in onset and often bilateral
• Phenotype inherited as dominant trait but recessive at cellular level - 2 abnormal alleles required for manifestation = 2 hit hypothesis

Recessive state in the cell inherited as AD trait

• Males and females equally affected
• Condition seen in siblings but usually not other relatives
• Risk of recurrence in siblings is 25%
• 2/3 of unaffected siblings are carriers
• Consanguinity increases risk

• Likely when point mutations give the same phenotype as deletion of an allele
• Loss of function and gain of function mutations in same gene will cause different diseases
• Inherited as recessive traits when 50% of expression is sufficient for normal phenotype

• Degradation of mucopolysaccharides requires a series of lysozomal enzymes
• Abnormalities in any of these enzymes can cause a similar phenotype
• Coarse facies, enlarged organs, skeletal abnormalities
• MPS Disease= alphaL iduronidase deficiency
• Severe mutations = Hurler
• Milder mutations = Scheie
• Phenotype is dependent on nature of mutation in alleles

• AR
• Absent or reduced pigment in melanosomes
• Reduced visual acuity - many pts can't drive, optic nerve misrouting, foveal hypoplasia, nystagmus, strabismus
• Tyrosinase--> DOPAquinone-->Phenomelanin or Eumelanin - if you have a tyrosinase gene mutation --> no enzyme activity or resinual enzyme activity
• 4 autosomal genes involved in separate albanism conditions: TYR (tyrosinase), P locus, TRP1 (tyrosinase protein 1), and MATP

• Single allele change gives disease:
• - Genes on X (X linked)
• - AD
• Mutation in both alleles required for disease
• - AR
• - Female homozygote for X linked

• Primarily males affected
• Females typically unaffected but can be if born to affected father and carrier mother
• Females can be affected if they have very skewed lyonization
• No male to male transmission
• Males born to carrier mother have 50% risk of inheriting gene
• Ex: Muscular Dystrophy

• Male surviving - either sex affected, males more severely
• Male lethal - only females seen with disease, mosaic patterns of expression
• Affected males will only have affected daughters and unaffected sons
• No male to male transmission
• Ex: Inconinentia Pigmenti

• Mutation in dystrophin gene
• Duchenne - frameshift, more severe, no protein product, elevated creatinine kinase, onset before age 5, calf pseudohypertrophy, severe muscle wasting, affects respiratory and cardiac muscle,
• Becker - no frameshift so milder, shortened protein

• Male lethal
• Linear blisters in newborn girls
• "Crops" followed by scarring
• Small teeth
• Eye abnormalities
• Patchy hair loss
• Only girls affected, males typically unaffected
• Linear erosions on soles

• Good at identifying highly penetrant rare alleles associated with disease but the majority of complex (common) diseases are most liekly not caused by highly penetrant rare genes
• +3= linked
• -2 or less= not linked
• Q= % of recombination

• Odds ratio gives indication of the effect size a given allele has on the phenotype or the odds an individual will get the disease having inherited the risk allele
• Some individuals who inherit the risk allele won't have the phenotype and some without the risk allele will get the disease
• OR of 2 means they are 2x more likely to get disease then someone without it

• Need large sample group
• Fast
• Bonferroni correction
• Generally designed to include 2 populations - one with and one without condition of interest

• Non-random association of two or more alleles
• Ancestral DNA segment that contains a disease producing mutation that is in the same segment

• Mutation
• Loss of heterozygosity
• Deletion
• Epigenetic modification such as DNA methylation or chromatin remodeling

• Amplification
• Increased transcription
• Changes in structure due to mutations that lead to increased transforming activity

• Tumor suppressor genes
• Oncogenes
• DNA damage response genes

• 3-12 weeks
• 5-7 weeks = lip formation
• 7-12 = palate formation

• Sporadic (isolated) - 75%
• Familial = 25%

• CHARGE syndrome
• Opitz G/BBB syndrome
• Gorlin syndrome
• Trisomy 13

• Velocardiofacial syndrome
• Stickler syndrome
• Kabuki syndrome
• Smith-Lemli-Opitz syndrome

• AD
• 92% penetrance
• Paramedian lower lip pits
• Hypodontia
• Cleft lip/palate, cleft palate
• Chromosome 1q32 IRF6
• Variable clefting
• Mutations in 60-85% of families

• Small jaw
• Cleft palate in a lot of cases

• CPO
• Small jaw
• Glasses

• 1 in every 4000 newborns
• 8% of all cleft palate patients
• AD
• Hemizygous microdeletion shared with DiGeorge Sequence at 22q11.2
• Cleft palate
• Congenital heart disease
• Chasracteristic facies
• Hypernasal speech
• Learning disabilities

• CLP> either defect alone
• Men> women
• Unilateral > bilateral
• Left> right sided involvement

• 50% nonsyndromic
• More common in females
• Families with AD and x-linked recessive

• Alcohol
• Dilantin
• Retinoic Acid
• Smoking
• Agricultural Chemicals

• 4% if 1 child affected
• 9% if 2 kids affected
• 17% if 1 child and 1 parent affected

• Chediak-Higashi syndrome
• Neutropenia
• Ehler-Danlos syndrome
• Histiocytosis X
• HypophosphtSi
• Papillon-LeFevre Syndrome

• favors AD inheritance
• Frequency of disease higher in blacks than whites
• Highlights genetic heterogeneity

• Approximately 50% of population variance for attachment loss and probing depth is attributed to genetic variance
• Genetic factors don't significantly influence levels of plaque or calculus or presence of specific bacteria

• Lysosomal protease present in neutrophils and macrophages
• 11q14.1-q14.3
• Gene spans 46kb region and has 7 exons

• Cytokines, inlcuding interleukin-1
• Vitamin D receptor
• N-formyl peptide receptor
• Class II HLA antigens
• Cathepsins
• Toll-like receptors
• MMPs

• Familial
• AD disorder
• Complex inheritance pattern
• Strong environmental component
• No major gene IDed
• Genetrically heterogenous

• Bone disease
• AR
• Cathepsin C gene mutation
• Hyperkeratosis of palms and feet
• Periodontitis --> floating teeth
• Teeth erupt in normal sequence at normal time and position
• Teeth are lost in sequence they erupt
• Permanent teeth lost before 14 years
• Peripheral neutrophil is depressed
• Retinoid therapy improves skin condition but not periodontal condition

• Bone disorder
• Autosomal Dominant2-5 years of age
• Typically progresses until puberty
• Bilateral involvement of posterior mandible - expanded
• Eyes upturned
• Marked widening and distortion of alveolar ridges
• Tooth displacement and eruption failure
• Teeth randomly distributed
• Lesions exhibit "ground glass" appearance
• Similar to giant cell granuloma
• Vascular fibrous tissue and giant cells
• Eosinophilic cuffing around blood vessels
• Prognosis unpredictable

• defect in Cbfa1/Runx2
• Autosomal Dominant
• Clavicles are absent
• Short stature; large heads
• Broad base of nose, depressed nasal bridge
• Parietal bossing
• Skull sutures show delayed closure
• Narrow, high arched palate
• Increased prevalence of cleft palate
• Unerupted permanent and supernumerary teeth
• Prolonged retention of deciduous teeth, delay or failure of eruption of permanent teeth
• Unerupted permement teeth lack 2ndary cementum
• No treatment

• Autosomal Dominant
• FGFR2
• Craniosynostosis: premature closing of sutures
• ocular proptosis: blindness and hearing deficit
• headaches
• normal intelligence
• underdeveloped maxilla, crowding of maxillary teeth, bifid uvula
• "Beaten metal" skull in radiographs
• Surgical tx

• Autosomal Dominant
• FGFR2
• Bone disorder
• Craniosynostosis
• Tower skull
• Ocular proptosis, vision loss, "beaten metal" radiographs
• V shaped arch, open mouth feature, hearing loss
• Syndactyly of 2nd, 3rd, and 4th digits
• Mental retardation
• Pseudo cleft palate due to swellings, crowding of max. teeth, bifid uvula
• Surgery

• Autosomal Dominant
• TCOF1 gene
• Bone disorder
• 60% new mutations
• Defects of 1st and 2nd branchial arches
• Narrow face, depressed cheeks, downward slanting palpebral fissures
• Coloboma (notch) at outer portion of lower eyelid
• Deformed pinnae, extra ear tags, middle ear ossicle defects (hearing loss)
• Underdeveloped mandible
• Condyle and coronoid hypoplasia
• Lateral facial clefting and cleft palate
• No tx or cosmetic surgery

• Autosomal Dominant
• Chromosome 9
• Bone disorder
• High penetrance
• Multiple basal cell carcinomas
• Odontogenic keratocysts
• Epidermal cysts
• Palmar/plantar pits
• Calcified falx cerebri
• Rib anomalies
• Hypertelorism
• Frontal and temporoparietal bossing
• Mild mandibular prognathism
• Bifid ribs, kyphoscoliosis

• Bone disorder
• Autosomal recessive for infants; Autosomal dominant for adults
• Infantile: osteosclerosis, hematologic, neurologic, die before 20, anemia, tooth eruption delayed, narrowing of cranial nerve foramina (blindness, deafness, facial paralysis), broad face, hypertelorism, snub face, frontal bossing, dense bones, osteomylitis of jaw, distinction between cortical and cancellous bone is lost
• Adult: more common, manifestations usually mild, fractures are uncommon

• Skin disorder
• NF1 - Chromosome 17
• Autosomal dominant
• 50% new mutations
• 6 or more cafe au lait macules
• Axillary freckles
• Optic glioma
• Lisch nodules - brown spots on iris
• Distinct osseous lesions (thinning of long bone cortex)
• Enlargement of fungiform papilla, mandibular foramen, and mandibular canal

• Skin disorder
• Autosomal dominant
• Chromosome 10
• 50% new mutations
• Marfanoid
• Narrow face, big lips, everted upper eyelid
• Neuromas on conjunctiva, eyelid margin, or cornea
• Oral lesions may be first sign
• Secretion of catecholamines - sweating, diarrhea, headaches, flushing, heart palpitations, hypertension
• Calcitonin production
• Highly metastatic

• Autosomal dominant
• Melanotic macules
• Intestinal polyps
• Abdominal pain, rectal bleeding, diarrhea

• Hypoplastic type: inadequate deposition of organic matrix, normal mineralization
• - Generalized pitted
• - Diffuse smooth
• Hypomaturation type: defect in maturation of enamel crystals
• - Diffuse pigmented (AD)
• - Snow Capped Teeth (AD, Xlinked?)
• Hypocalcified type: no significant mineralization (AD or AR)

• Mutations of type I collagen
• Autosomal dominant, Autosomal recessive hereditary/sporadic
• Most common type of inherited bone disease
• Weak bones, blue sclera, altered teeth, hearing loss, long bone and spinal deformity, joint hyperextension
• Shell teeth
• Premature pulpal obliteration
• Opalescent teeth
• Maxillary hypoplasia
• Types 1-4 (1 is most common, mildest; 2 is most severe, lethal, 3 is most severe survivable; 4 is mild to moderate)
• No treatment
• Varied prognosis

• Autosomal recessive
• Decreased alkaline phosphatase
• Similar to rickets
• Increased blood/urinary phophoethanolamine
• Premature loss of primary teeth
• No cementum on teeth
• Perinatal: most severe
• Infantile: normal till 6 months, failure to grow after that (severe)
• Childhood: teeth defects with enlarged pulp chambers, premature fusion of cranial sutures
• Adult: mild

• X linked, AD?
• Zone of white opaque enamel on incisal and occlusal surface

• AD or AR
• No significant mineralization
• Teeth normally shaped at eruption
• Enamel very thin and easily lost
• Yellow or brown color
• Calculus
• Open bite
• Tx is restorations, veneers, dentures

• AD
• Pinpoint/head pits in rows
• Normal enamel in between
• Across the surface
• Doesn't correlate with pattern of environmental damage

• AD
• Like crown preparations, open bite
• Opaque white to brown
• Peripheral thin enamel outline
• Unerupted exhibit resorption

• AD
• Chippin from dentin with an explorer
• Very uncommon anterior open bite
• Soft similar to hypocalcified
• Calculus

• Diffuse pigmented and Snow Capped
• Defect in maturation of enamel crystals
• Normal shape
• Mottled appearance
• White, yellow, or brown
• Enamel is soft
• Radiodensity similar to dentin