Genetics in Medicine
Nathaniel H. Robin, MD
Department of Genetics
University Alabama at Birmingham
Overview
• Genetic evaluation
• Structural anomalies
– Malformation, deformation, dysplasia, disruption
• Multiple anomaly groupings
– Syndrome, association, sequence
• Examples of genetic disorders
– Chromosomal disorders
– Single gene disorders
• Genetic testing: past, present, and future
Dysmorphology
vs.
Genomic Medicine
Genomic Medicine
“ … the routine use of genotypic analysis, usually in
the form of DNA testing, to enhance the quality of
medical care.”
- A. Beaudet, 1998 ASHG Presidential Address (AJHG 64:1-13 1999)
Examples
- Inherited cancer (eg, BRCA1 and 2)
- Asthma
- Pharmacogenetics
- Warfarin, etc.
Family history
MI
MI
“female” cancer
45 yr
68yr
28yr
35 yr
28 yr
29 yr
88 yr
40 yr
87 yrs
2 wks
SIDS
Breast cancer
5 yr
3 yr
10 mo
‘Traditional’ genetics
Dysmorphology (the study of abnormal form)
• Evaluation of child (adult, fetus) with unusual
facial characteristics +/- other abnormal
findings in an effort to reach a genetic
(syndrome) diagnosis
Indications for a Genetics Consultation
• Multiple major anomalies
(Remember: mental retardation and growth failure are major
anomalies)
• One major anomaly with multiple minor anomalies
• Multiple minor anomalies
(The “FLK”-funny looking kid)
• Isolated condition with known/suspected genetic basis
• Family history
Why is it important to make a diagnosis?
• Cure? …. No
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•
•
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•
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Prognosis
Management
Recurrence risk counseling
Access support groups
Treatment
‘Why’
How to identify a genetic syndrome
• Look for other problems in patient and family
members
– Major and minor anomalies
– Both similar and seemingly unrelated
Geneticists’ tools
• Personal and family history, and dysmorphologic
physical exam
– Focusing on minor anomalies
M
I
N
O
R
A
N
O
M
A
L
I
E
S
From: ‘The child with multiple
birth defects’, 2nd ED; MM Cohen Jr
“The best clues are the rarest… (T)hese
are not the most obvious anomalies nor
even the ones that have the greatest
significance for the patient’s health. “
John Aase, M.D.
References
• Smith’s Recognizable Patterns of Human
Malformation, 5th edition. KL Jones ed, WB
Saunders, 1997.
• Syndromes of the Head and Neck, Gorlin, Cohen,
eds Oxford Univ Press, 2002
• OMIM (www3.ncbi.nlm.nih.gov/)
• GenReviews & GeneTests (www.geneclinics.org)
Birth defects
• 1-3% of all newborns
• Leading cause of neonatal morbidity and
mortality
– 20% infant deaths
– 10% NICU admissions, 25-35% deaths
• Pediatric Admissions
– 50% have genetic component to illness
– 25-30% have major birth defect
Types of birth defects
•
•
•
•
Deformation
Disruption
Dysplasia
Malformation
Deformation
• Developmental process is
normal
• Mechanical force alters
structure
• External
– low amniotic fluid,
breech presentation
• Internal
– neuromuscular
abnormality
development
structure
Disruption
Interruption of normal development
– usually vascular
– example: amniotic
band sequence,
maternal cocaine use
(?)
development
structure
Amniotic band sequence
• Defects do not follow
anatomic lines
• Asymmetry
From: ‘The child with multiple
birth defects’, 2nd ED; MM Cohen Jr
Dysplasia
• Anomaly of specific type of tissue
– Skeletal dysplasia
• Osteogenesis Imperfecta, Achondroplasia,
Cleidocranial dysplasia
– Connective tissue disorder
• Marfan syndrome, Ehler Danlos syndrome
Malformation
•Developmental process is abnormal
• Possible causes
– mutant gene(s)
– teratogen
– stochastic
development
structure
Causes CLP
• Mutant gene(s)
– IRF6, MSX1, PVL22, FGFR1
• Teratogen
– smoking, alcohol, folate deficiency
• Stochastic
Patterns of birth defects
• Syndrome: A recognizable pattern of
anomalies that are pathogenetically
related.
• Sequence
• Association
Marfan syndrome
•
•
•
•
Prevalence: 1/5000-20,000
Complete penetrance
Inter > intrafamilial variability
Pleiotropic
– long bone overgrowth, joint laxity, eye, &
cardiac
• Diagnosis is clinical, based on
established diagnostic criteria
– requires 2 criteria, plus some
involvement of third
– Genetic testing expensive, not very
sensitive, and not clinically useful in
most cases
Diagnostic criteria
Requires 2 criteria plus some involvement of third
1. Cardiovascular: dilated aortic root w/ AI; cystic medial
necrosis with dissection
2. Skeletal (need at least 4)
–
–
–
–
–
severe pectus carinatum/excavatum
decreased upper/lower seg or increased arm span/ height >1.05
thumb & wrist sign; scoliosis
per planus (flat feet)
protrusio acetabulae (inward protrusion of hip joint by X-ray)
Diagnostic criteria, cont.
Requires 2 criteria plus some involvement of third
3. Ocular: dislocated lens
4. Family history: independent diagnosis in 1st degree
relative
• Other: dural ectasia, recurrent/incisional hernia, stretch marks,
spontaneous pneumothorax, apical blebs, myopia, MVP w/ MR, joint
laxity; mild-mod pectus, scoliosis, high arched palate, dental crowding,
typical facies (dolichocephaly, malar flatening, deep set eyes,
retrognathia, downslanting palpebral fissures)
Marfan syndrome: genetics
• Marfan syndrome due to mutations in Fibrillin 1
gene on chromosome 15q21.1
– Large gene, mutations spread out
– Most mutations are loss of function & null, some
dominant negative
– Testing identifies ~90%
• Location of mutation does not predict phenotype
– correlation of mutation & phenotype very limited
– severe/neonatal Marfan syndrome does cluster
Genetic testing for Marfan syndrome
• Clinical utility of genetic testing
– Positive test confirms diagnosis
– Negative test -> other genes (TGFBR1/2, ACTA2, MYH11), disorders
• Differential diagnosis
– Homocystinuria
• similar body habitus, lens dislocation (down vs. up)
• differences: stiff joints, malar rash, mental retardation
– Congenital contractural arachnodactyly (Beals syndrome)
– ‘Partial’ Marfan Syndrome
• Label is not important - manage what you see
Osteogenesis Imperfecta
• AD (most) skeletal dysplasia
• Easy fracturing + other connective tissue findings
• 7+ overlapping subtypes
– Type 1: Normal stature, little/no deformity; blue sclerae; 50% HL, DI rare
– Type 2: Perinatal lethal; minimal skeletal ossification, beaded ribs, platyspondyly
– Type 3: Progressive deforming; short stature; sclerae blue, lighten with age; DI, HL
common
– Type 4: Variable/mild deformity & short stature; normal sclerae, DI common,
some with HL
• OI incidence (all types): 1/20,000
• Most due to mutations in type I collagen
– Collagen I: 2x COL1A1, 1x COL1A2
Osteogenesis Imperfecta
Wormian bones
Blue sclerae
Femur fracture
Intra-uterine fracture
Patterns of birth defects

Syndrome

Sequence: A series of abnormalities
derived from a single pathogenetic event.

Association
Pierre Robin sequence
• Micrognathia, [Ushaped] cleft palate,
glossoptosis
• 50% syndromic
– Stickler (50%),
– del22q11 (25%)
– Treacher Collins, Rib
gap...
Micrognathia ---> cleft palate ---> glossoptosis
Stickler Syndrome
• Described in 1965 in 5 generation
kindred with AD transmission
• Major clinical manifestations:
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–
–
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Myopia, retinal changes
Early/progressive arthritis , mild SED
Sensorineural hearing loss
Cleft palate/Pierre Robin sequence
• Marshall, Wagner syndromes
Stickler syndrome genes
• AD: COL2A1, COL11A1, COL11A2
– Type II collagen: COL2A1 x 3
• Expressed in joints, inner ear, eye
– Type XI collagen: 1 x COL2A1, 1 x COL11A1, 1 x
COL11A2
• Same expression pattern as type 2 collagen: except in
eye (COL11A2 replaced by COL5A1)
• AR: COL9A1, COL9A2
Patterns of birth defects

Syndrome

Sequence

Association: A constellation of findings
that occur more commonly together than
would be expected by chance alone.
Associations
CHARGE
Coloboma
Heart defect
Atresia choani
Retarded growth and
development
Genital anomalies
Ear anomalies/ deafness
VA(C)TER(L)
Vertebral defects
Anus, imperforate
Cardiac defects
T-E fistula
Renal
Limb
(Hydrocephalus)
Associations
CHARGE
Coloboma
Heart defect
Atresia choani
Retarded growth and
development
Genital anomalies
Ear anomalies/ deafness
VA(C)TER(L)
Vertebral defects
Anus, imperforate
Cardiac defects
T-E fistula
Renal
Limb
(Hydrocephalus)
CHARGE syndrome
• Using comparitive genome hybridization (CGH),
deletions on 8q12 was identified in a CHARGE patient
• Genes sequenced in minimally deleted region
• 10/17 CHARGE patients had mutations in new gene
CHD7
– No phenotypic difference between deleted and nondeleted patients
Etiology of syndromes
• Chromosomal
– Cytogenetic
– FISH
– Array CGH
• Multifactorial
– Genes & environment
• Environmental
– Teratogens, chance
• Multiple genes
– digenic
• Single gene
–
–
–
–
Autosomal dominant
Autosomal recessive
X-linked
Non-traditional
• mitochondrial
• imprinting/UPD
• triplet repeat
Common Chromosomal Anomalies
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•
•
•
•
Trisomy 21
Trisomy 18
Trisomy 13
XXY
45X and variants
Down Syndrome
Down Syndrome
• “They have considerable power of imitation, even bordering
on being mimics. They are humorous, and a lively sense of
the ridiculous often colour their mimicry. This faculty of
imitation may be cultivated to a very great extent, and a
practical direction given to the results obtained. They are
usually able to speak; the speech is thick and indistinct, but
may be improved very greatly by a well-directed scheme of
tongue gymnastics. The coordinating faculty is abnormal,
but not so defective that it cannot be greatly strengthened.
By systematic training, considerable manipulative power
may be obtained. “
Down Syndrome
• Down syndrome
– Most common malformation pattern ~1 in 800
– Due to extra chromosome 21 material
• ‘critical’ region 21q22.3 5 Mb
• between D21S58 and D21S42.
– Non-disjunction trisomy
94%
• 85% due to maternal non-disjunction in Meiosis I
– Trisomy with some mosaicism:
– Translocation (D/G or G/G)
• Quad Screen result:
2.4%
3.3%
Down Syndrome
• Diagnosis in an infant:
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Flat facial profile
Poor Moro Reflex
Hypotonia
Hyperflexibility of joints
Excess skin on back of neck
Slanted palpebral fissures
Dysplasia of Pelvis
Anomalous auricles
Dysplasia midphalanx 5th finger
Single Palmar creases
90%
85%
80%
80%
80%
80%
70%
60%
60%
45%
Down Syndrome
Single Palmar Crease
– (NOT simian crease)
Sandal Gap
Down Syndrome
Age
Life Expectancy in Years
100
90
80
70
60
50
40
30
20
10
0
1920
Average Population
Cystic Fibrosis
Down Syndrome
1930
1940
1950
1960
1970
Year
1980
1990
2000
2010
Down Syndrome
• Problems as they age
– Obesity
– Loss of hearing
– Increasing incidence of hypothyroidism
– Celiac Disease
– Diminished function
– Mental illness – up to 30%
• Depression, obsessive-compulsive disorder
• Mislabeled as Alzheimer disease
Trisomy 18
Trisomy 18
• Incidence:
3/1000
– More males than females
• Shortened life expectancy
– About half die in the first month of life
– 90% die by the first year of life
• Characteristic findings:
– Small for gestational age (beware sono EDC)
– Short Sternum
– “Trisomy 18 clenched hand”
Trisomy 18 Continued …
• Multiple organ system involvement
– Cardiovascular (VSD, ASD, PDA)
– Neuro: Weak, polyhydramnios, hypertonic
– GI: TracheoEsophageal fistula OK to repair (?)
• Mosaicism and partial Trisomy 18
– Milder phenotype, longer survival
• Cause of death
– Reported as central apnea (?monitor at home)
Trisomy 13
Trisomy 13
Trisomy 13
• Incidence about 1/5000 births
• Lifespan limited
– Median survival was 7days
– About 10% live past 1 year
• Characteristics:
– Holoprosencephaly
– Hypotelorism sometimes cyclopia
• Retinal dysplasia and colobomata
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–
–
–
Cardiac defects in 80%
Polydactyly
Scalp defects
Other multiple system involvement.
Trisomy 13
• Mosaicism with less severe phenotype
• Partial Trisomy 13
– Proximal 13pter – q14: nonspecific with longer
lifespan
– Distal 13q14 – qter: resembles classic phenotype.
Klinefelter syndrome 47, XXY
47, XXY
• Klinefelter syndrome
• Incidence about 1/500 males
– More now found earlier in life – some in neonatal
period
• Characteristics
– Taller than average and expected from parental
heights
– Start puberty but do not complete
– Small testes and perhaps small penis
– Gynecomastia – more than the usual male teen
• obesity
47, XXY Continued…
• Taurodontism (enlarged pulp, thin surface)
• Psychosocial difficulties
– Many complete college
• Testosterone supplementation
– Timing
– Consideration of psychosocial issues
• Breast cancer
– 1 in 5000 men which is 20X general population
risk
Turner syndrome
45, X Turner syndrome
• NOT 45, XO – there is no “O” chromosome
• Second most common aneuploidy found in
conceptions (what is the most common?)
• Prenatal detection by sonogram
– Lymphedema
• Incidence about 1 in 2500 liveborn females
• Characteristics: short stature, webbed neck
Turner syndrome continued…
• Characteristics continued
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–
–
–
–
–
–
–
–
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Long thin hyperconvex deeply imbedded nails
Bicuspid Aortic valve and coarctation of the aorta
Short neck with low hair line or obvious nuchal swelling
Puffy hands and feet
Broad thorax with widely spaced nipples
Some learning difficulties
Amenorrhea primary and secondary – gonadal dysgenesis
Abnormal kidney structure (horseshoe kidney)
Hypothyroidism
Growth hormone therapy
Microdeletion syndromes
•
•
•
•
•
•
•
•
Velocardiofacial syndrome (del22q11.22)
Williams (7q11)
Smith Magenis (17p11)
Prader-Willi/Angelman (15q11-13)
WAGR (11p13)
Rubinbstein Taybi (16p13)
Miller Dieker (17p13.3)
Neurofibromatosis I
Fluorescence in situ hybridization (FISH)
Chromosome preparation on slide
Denature DNA
DNA probe labeled by incorporating
nucleotides with attached fluorescent
dye, and denatured
Hybridize, wash, and visualize
using a fluorescent microscope
OR
OR
●
Centromeric
probe
Locus specific
probe
Chromosome
paint
Enhanced resolution -> increased ability to detect missing or
extra chromosomal material
Velocardiofacial syndrome (VCFS)
• One of a spectrum of syndromes caused by a
deletion of chromosome 22q11.22
– DiGeorge syndrome
– Isolated conotruncal congenital heart defects
– Isolated neonatal hypocalcemia
• Overall incidence: 1/2-4000
• Very variable: >180 anomalies described
involving every organ system
VCFS: Physical Manifestations
• No minimal diagnostic criteria, obligatory or
exclusionary findings
• Main clinic manifestations
– Characteristic facial appearance
– Congenital cardiovascular disease
– Speech, cognitive delays
– Psychological and behavioral problems
• Nothing excludes diagnosis
Genetics of del22q11.22
• Deletion 22q11.22 identified
– ~88% de novo
• Common deletion ~3MB, some smaller 1.52MB; no phenotypic correlation
– Flanked by LCR segments
• TBX1: main gene in DGCR
– Mouse tbx1 null elicits 22q11 phenotype
Recurrent microdeletions are due to flanking low copy
number repeats
Mis-aligned crossing over
Normal crossing over
Comparative genome hybridization (CGH)
The main limitation of CGH is the
resolution, which is limited to that of
the metaphase chromosome, i.e. ~5-10
Mb for most clinical applications
Array comparative genome hybridization
Fluorescence ratio
(red/green)
Test DNA
Control DNA
DNA labeling
0.5
(loss)
1.0
1.5
(gain)
Data analysis
Wash and scan
Hybridization
32K BAC tiling path array CGH Chip
32K BAC array - Whole genome
32K BAC array CGH – Whole genome
Pseudo genetic inheritance (phenocopies)
Phenotype
Trisomy 18
Familial DiGeorge
Familial MR/dysmorphia
Familial obesity
Cause
Valproic acid embryopathy
Retinoids
Alcoholism, mat. PKU
Eating too much
Multiple affected family members with colon or breast cancer,
Alzheimers, coronary artery disease, etc. at older age
Multifactorial
• Interaction between genetic and epigenetic
(environment, stochastic) factors.
• General rules:
– more severe, more “genetic” influence
– less frequently affected sex, more “genetic”
• Ex: pyloric stenosis
Holoprosencephaly: a model for multifactorial inheritance
An explanation for the variable expression
in HPE
• Many single gene mutations cause HPE: SHH, SIX3,
ZIC2, TGIF
• But mutation carriers do not ALWAYS have ‘HPE’,
only microforms
• Explanations
– Digenic inheritance: mutation in SHH and TGIF
– Epigenetic modifiers: low cholesterol in mothers of
HPE/SHH