Genetics in Medicine

Genetics in Medicine

Nathaniel H. Robin, MD

Department of GeneticsUniversity 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

5 yr 3 yr 10 mo

28yr 35 yr 28 yr 29 yr 40 yr 2 wks

Breast cancer SIDS

68yr 45 yr 88 yr 87 yrs“female” cancer

MI

MI

‘Traditional’ geneticsDysmorphology (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

• 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

Indications for a Genetics Consultation

Why is it important to make a diagnosis?

• Cure? …. No

• 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

From: ‘The child with multiple birth defects’, 2nd ED; MM Cohen Jr

MINOR

ANOMALIES

“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

abnormalitydevelopment

structure

Disruption

– usually vascular– example: amniotic

band sequence, maternal cocaine use (?)

developmentstructure

Interruption of normal development

From: ‘The child with multiple birth defects’, 2nd ED; MM Cohen Jr

Amniotic band sequence

• Defects do not follow anatomic lines

• Asymmetry

Dysplasia• Anomaly of specific type of tissue

– Skeletal dysplasia • Osteogenesis Imperfecta, Achondroplasia,

Cleidocranial dysplasia

– Connective tissue disorder • Marfan syndrome, Ehler Danlos syndrome

Malformation

• Possible causes– mutant gene(s)– teratogen– stochastic

• Developmental process is abnormal

developmentstructure

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

Blue sclerae

Wormian bones

Intra-uterine fractureFemur fracture

Patterns of birth defects

Syndrome Sequence: A series of abnormalities

derived from a single pathogenetic event. Association

Pierre Robin sequence

• Micrognathia, [U-shaped] 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:– 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

CHARGEColobomaHeart defectAtresia choaniRetarded growth and

developmentGenital anomaliesEar anomalies/ deafness

VA(C)TER(L)Vertebral defectsAnus, imperforateCardiac defectsT-E fistulaRenalLimb(Hydrocephalus)

Associations

CHARGEColobomaHeart defectAtresia choaniRetarded growth and

developmentGenital anomaliesEar anomalies/ deafness

VA(C)TER(L)Vertebral defectsAnus, imperforateCardiac defectsT-E fistulaRenalLimb(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 non-

deleted 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

• 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: 2.4%– Translocation (D/G or G/G) 3.3%

• Quad Screen result:

Down Syndrome

• Diagnosis in an infant:– Flat facial profile 90%– Poor Moro Reflex 85%– Hypotonia 80%– 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%

Down SyndromeSingle Palmar Crease

– (NOT simian crease)

Sandal Gap

Down Syndrome

Life Expectancy in Years

0102030405060708090

100

1920 1930 1940 1950 1960 1970 1980 1990 2000 2010

Year

Age Average Population

Cystic Fibrosis

Down Syndrome

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– 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– 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)

Enhanced resolution -> increased ability to detect missing or extra chromosomal material

Chromosome preparation on slide

Denature DNA

Hybridize, wash, and visualizeusing a fluorescent microscope

Chromosomepaint

OR

DNA probe labeled by incorporatingnucleotides with attached fluorescent

dye, and denatured

Centromericprobe

●Locus specific

probe

OR

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 1.5-2MB; 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

Normal crossing over

Mis-aligned 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

Test DNA Control DNA

Hybridization

DNA labeling

Wash and scan

Data analysis

1.00.5(loss)

1.5(gain)

Fluorescence ratio(red/green)

Array comparative genome hybridization

32K BAC tiling path array CGH Chip

32K BAC array - Whole genome

32K BAC array CGH – Whole genome

Pseudo genetic inheritance (phenocopies)

Phenotype CauseTrisomy 18 Valproic acid embryopathyFamilial DiGeorge RetinoidsFamilial MR/dysmorphia Alcoholism, mat. PKUFamilial obesity 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