1. Genetics in Medicine Nathaniel H. Robin, MD Department of Genetics
University Alabama at Birmingham

2. 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

3. Dysmorphology vs. Genomic Medicine

4. 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: )
Examples
- Inherited cancer (eg, BRCA1 and 2)
Asthma
Pharmacogenetics
- Warfarin, etc.

5. Family history MI “female” cancer MI 68yr 45 yr 88 yr 87 yrs
28yr 35 yr yr yr yr wks
SIDS
Breast cancer
5 yr 3 yr mo

6. ‘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

7. 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

8. Why is it important to make a diagnosis?
Cure? …. No
Prognosis
Management
Recurrence risk counseling
Access support groups
Treatment
‘Why’

9. 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

10. M I N O R A L E S From: ‘The child with multiple
birth defects’, 2nd ED; MM Cohen Jr

11. “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.

12. 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 (

13. 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

14. Types of birth defects
Deformation
Disruption
Dysplasia
Malformation

15. Deformation Developmental process is normal
Mechanical force alters structure
External
low amniotic fluid, breech presentation
Internal
neuromuscular abnormality
development
structure

16. Disruption Interruption of normal development usually vascular
example: amniotic band sequence, maternal cocaine use (?)
development
structure
Like a deformation, development proceeds normally, but is interrupted by an event.

17. Amniotic band sequence
Defects do not follow anatomic lines
Asymmetry
From: ‘The child with multiple
birth defects’, 2nd ED; MM Cohen Jr

18. Dysplasia Anomaly of specific type of tissue Skeletal dysplasia
Osteogenesis Imperfecta, Achondroplasia, Cleidocranial dysplasia
Connective tissue disorder
Marfan syndrome, Ehler Danlos syndrome

19. Malformation Developmental process is abnormal Possible causes
mutant gene(s)
teratogen
stochastic
development
structure

20. Causes CLP Mutant gene(s) Teratogen Stochastic
IRF6, MSX1, PVL22, FGFR1
Teratogen
smoking, alcohol, folate deficiency
Stochastic

21. Patterns of birth defects
Syndrome: A recognizable pattern of anomalies that are pathogenetically related.
Sequence
Association

22. 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

23. Diagnostic criteria Requires 2 criteria plus some involvement of third
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)

24. Diagnostic criteria, cont
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)

25. 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

26. 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

27. 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

28. Osteogenesis Imperfecta
Wormian bones
Blue sclerae
Femur fracture
Intra-uterine fracture

29. Patterns of birth defects
Syndrome
Sequence: A series of abnormalities derived from a single pathogenetic event.
Association

30. Pierre Robin sequence
Micrognathia, [U-shaped] cleft palate, glossoptosis
50% syndromic
Stickler (50%),
del22q11 (25%)
Treacher Collins, Rib gap...
Micrognathia ---> cleft palate ---> glossoptosis

31. Stickler Syndrome Major clinical manifestations:
Described in 1965 in 5 generation kindred with AD transmission
Major clinical manifestations:
Myopia, retinal changes
Early/progressive arthritis , mild SED
Sensorineural hearing loss
Cleft palate/Pierre Robin sequence
Marshall, Wagner syndromes

32. 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

33. Patterns of birth defects
Syndrome
Sequence
Association: A constellation of findings that occur more commonly together than would be expected by chance alone.

34. 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)

35. 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)

36. 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 non-deleted patients

37. Etiology of syndromes Single gene Chromosomal Multifactorial
Autosomal dominant
Autosomal recessive
X-linked
Non-traditional
mitochondrial
imprinting/UPD
triplet repeat
Chromosomal
Cytogenetic
FISH
Array CGH
Multifactorial
Genes & environment
Environmental
Teratogens, chance
Multiple genes
digenic

38. Common Chromosomal Anomalies
Trisomy 21
Trisomy 18
Trisomy 13
XXY
45X and variants

39. Down Syndrome

40. 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. “

41. Down Syndrome Down syndrome Quad Screen result:
Most common malformation pattern ~1 in 800
Due to extra chromosome 21 material
‘critical’ region 21q Mb
between D21S58 and D21S42.
Non-disjunction trisomy %
85% due to maternal non-disjunction in Meiosis I
Trisomy with some mosaicism: 2.4%
Translocation (D/G or G/G) 3.3%
Quad Screen result:

42. Down Syndrome Diagnosis in an infant: Flat facial profile 90%
Poor Moro Reflex 85%
Hypotonia %
Hyperflexibility of joints 80%
Excess skin on back of neck 80%
Slanted palpebral fissures 80%
Dysplasia of Pelvis 70%
Anomalous auricles 60%
Dysplasia midphalanx 5th finger 60%
Single Palmar creases 45%

44. Down Syndrome
Single Palmar Crease
(NOT simian crease)
Sandal Gap

45. Down Syndrome

46. 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

47. Trisomy 18

48. Trisomy 18 Incidence: 3/1000 Shortened life expectancy
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”

49. 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)

50. Trisomy 13

51. Trisomy 13

52. 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
Cardiac defects in 80%
Polydactyly
Scalp defects
Other multiple system involvement.

53. Trisomy 13 Mosaicism with less severe phenotype Partial Trisomy 13
Proximal 13pter – q14: nonspecific with longer lifespan
Distal 13q14 – qter: resembles classic phenotype.

54. Klinefelter syndrome 47, XXY

55. 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

56. 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

57. Turner syndrome

58. 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

59. Turner syndrome continued…
Characteristics continued
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

60. 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

61. Fluorescence in situ hybridization (FISH)
Chromosome preparation on slide
Denature DNA
Hybridize, wash, and visualize
using a fluorescent microscope
Chromosome
paint OR
DNA probe labeled by incorporating
nucleotides with attached fluorescent
dye, and denatured
Centromeric
probe ●
Locus specific
Enhanced resolution -> increased ability to detect missing or extra chromosomal material

62. 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

63. 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

64. Genetics of del22q11.22 Deletion 22q11.22 identified
~88% de novo
Common deletion ~3MB, some smaller 1.5-2MB; no phenotypic correlation
Flanked by LCR segments
TBX1: main gene in DGCR
Mouse tbx1 null elicits 22q11 phenotype

65. Recurrent microdeletions are due to flanking low copy number repeats
Mis-aligned crossing over
Normal crossing over

66. 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

67. Array comparative genome hybridization
1.0
0.5
(loss)
1.5
(gain)
Fluorescence ratio
(red/green)
Test DNA
Control DNA
DNA labeling
Data analysis
Hybridization
Wash and scan

68. 32K BAC tiling path array CGH Chip

69. 32K BAC array - Whole genome

70. 32K BAC array CGH – Whole genome

71. Pseudo genetic inheritance (phenocopies)
Phenotype Cause Trisomy 18 Valproic acid embryopathy Familial DiGeorge Retinoids Familial MR/dysmorphia Alcoholism, mat. PKU Familial obesity Eating too much Multiple affected family members with colon or breast cancer, Alzheimers, coronary artery disease, etc. at older age

72. 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

73. Holoprosencephaly: a model for multifactorial inheritance

74. 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