1

Genomic Technologies

&

Syndrome Recognition

By Samantha Leib, MD, FAAP

Pediatrician

Department of Genetics and Genomic Medicine

Saint Peter’s University Hospital

Objectives

• Understand the benefits and limitations of

commercially-available genetic testing

• Recognize presenting features of common

genetic syndromes

• Improve comfort level managing and

monitoring patients with genetic conditions

in the primary care setting

Understanding the Basics

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Genomic Technologies

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Reasons to Diagnose

• Comprehensive information regarding the diagnosis or probable diagnosis

• Medical management

• Anticipatory guidance and surveillance

• Risk and recurrence assessments for the patient and other family members

Prenatal Screening

Non-invasive Prenatal Testing (NIPT)

• The use of NIPT to screen for the presence of fetal

aneuploidy became feasible with the development of

massive parallel sequencing (MPS) and counting of

cfDNA fragments.

• Most current tests for this purpose use whole

genome MPS in order to quantitatively compare the

amount of, for example, chromosome 21 DNA

molecules in a maternal sample with that of an

euploid reference sample.

• Other tests use targeted sequencing, mapping only

the chromosome regions of interest, or use a

qualitative SNP-based approach.

What is NIPT?

• Non-invasive prenatal testing

• Cell-free fetal DNA (cffDNA)

• Fetal DNA that circulates

freely in the mother’s

bloodstream (2-6% of total)

• Originates from apoptosis

of trophoblasts that make

up the placenta due to

maternal immune system

interaction

• cffDNA is significantly smaller

than maternal DNA and can

be distinguished by size

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How does it actually work?

• Maternal blood sample

obtained

• PCR to replicate DNA to

analyze

• Massively parallel

sequencing (next-

generation sequencing)

• Amount of fetal DNA

compared with

reference DNA with

expected amount

Common Screens

MaterniT21 Plus:

Trisomy 21

Trisomy 18

Trisomy 13

Sex chromosome aneuploidy

22q deletion syndrome (DiGeorge)

5p (Cri-du-chat syndrome)

15q (Prader-Willi/Angelman

syndromes)

1p36 deletion syndrome

4p (Wolf-Hirschhorn syndrome)

8q (Langer-Giedion syndrome)

11q (Jacobsen syndrome)

Trisomy 16

Trisomy 22

Harmony Screens for:

Trisomy 21

Trisomy 18

Trisomy 13

Sex chromosome aneuploidy

Screening Limitations

• These screening tools do not provide a definitive

genetics risk in all individuals.

• Cell-free fetal DNA does not replace the accuracy

and precision of prenatal diagnosis with CVS or

amniocentesis.

• A patient with a positive test result should be

referred for genetic counseling and offered invasive

prenatal testing for confirmatory diagnosis.

• A negative test result does not ensure an

unaffected pregnancy.

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Average Cost

1. Karyotype: $600

2. Microarray: $750 - $2,500

3. NIPT: $100 - $400

4. Gene panels: $1,000 - $3,000

5. Whole exome: $2,500 - $5,000

Syndrome Recognition

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Williams SyndromeFacts:

• Affects an estimated 1 in 7,500 to 10,000 people

• Occurs equally in both males and females

• Autosomal dominant condition

• Majority are de novo deletions

• Caused by a deletion from a specific region on chromosome 7

Distinctive Facies:

Clinical Features

• Broad forehead, bitemporal

narrowing, periorbital fullness

• A stellate/lacy iris pattern, strabismus,

short nose with a broad nasal tip,

malar flattening

• Long philtrum, wide mouth with full

lips, malocclusion, micrognathia, and

large ear lobes (seen at all ages)

• Young children have epicanthal folds,

full cheeks, and widely spaced teeth

• Adults have long face and neck, resulting in a gaunt appearance

Clinical Features

Unique Personality:

• Overfriendliness

• Empathy

• Generalized anxiety

• Specific phobias

• ADHD

Intellect/Cognitive Profile:

• Developmental delays

• Strengths in verbal short-term memory and

language (affinity towards music)

• Weakness in visuospatial construction

• Most have some degree of intellectual disability

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Clinical Features

Cardiovascular disease:

• Any artery may be narrowed (elastin arteriopathy)

• Most commonly supravalvar aortic stenosis (75%)

• Peripheral pulmonic stenosis common in infancy

(PPS)

Connective Tissue Abnormalities:

• Joint limitation or laxity

• Hernias

• Soft/lax skin

• Rectal prolapse

Clinical Features

Growth Abnormalities:

• FTT in infancy

• Short stature

Endocrine Abnormalities:

• Hypercalcemia

• Hypothyroidism

• Early puberty

• DM

Yearly SurveillanceInterval/Age Test/Measurement

InfancySerum calcium determination every

4-6 months until age 2 years

Annual

•Medical evaluation

•Vision screening to monitor for

refractive errors and strabismus

•Hearing evaluation

•Monitoring of blood pressure in both arms

•Measurement of calcium/creatinine

ratio in a random spot urine and

urinalysis

•Cardiology evaluation at least yearly for the first 5 years, every 2-3

years thereafter

Every 2 years •Serum concentration of calcium

Every 3 years •Thyroid function and TSH level

Every 10 years•Renal and bladder ultrasound

examination

In adults

•Oral glucose tolerance test (OGTT)

starting at age 30 years to evaluate

for diabetes mellitus 1

•Evaluation for mitral valve prolapse,

aortic insufficiency, and arterial stenoses

•Evaluation for cataracts

(from Gene Reviews)

Williams Syndrome

Video link

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Klinefelter Syndrome

Facts:

• Affects 1 in 500 to 1,000 newborn males

• Diagnosis is confirmed by chromosomal

analysis

• Paternal meiosis I errors account for 50%-

60% of 47,XXY males with the remainder

due to maternal meiosis I or II errors or to a

postzygotic error

• It’s the most common cause of

hypogonadism and infertility in men

Clinical FeaturesGrowth:

• Long limbs

• Decreased upper-to-lower segment ratio

• Increased arm span

• Mean height at 75%

Hypogonadism with Hypogenitalism:

• Childhood-cryptorchidism, hypospadias,

small penis/testes

• Adolescence/adulthood-testes remain small;

virilization is incomplete with gynecomastia

occurring in 1/3 of adolescents

• Facial hair is sparse

• Testosterone levels decrease in late

adolescence and early adulthood (< ½ of

normal)

• Infertility

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Clinical Features

Performance:

• IQ between 85-90; verbal IQ is usually higher than

performance IQ

• Problems with reading and spelling

• Immature behavior, introverted personality, poor

judgment, difficulty forming peer relationships

• 20-50% will have a fine-to-moderate intention tremor

Clinical FeaturesOccasional Complications:

• Elbow dysplasia

• Taurodontism

• Diabetes

• Autoimmune diseases

• Varicose veins & hypostatic anterior leg ulcerations

• Chronic bronchitis/emphysema/asthma

• Mediastinal germ cell tumors

• Breast cancer (risk is significantly increased over the

general male population, approaching the risk in

normal women)

Management

Development

• Any evidence of delayed milestones deserve prompt referral to early intervention

and a developmental specialist• Any evidence of learning problems should be pursued with a comprehensive

educational evaluation

• Evidence of behavioral/emotional problems should prompt referral to a

behavioral/psychological specialist

Endocrine

• Obtain baseline testosterone, FSH, and LH levels ~11-13 yo• Treatment with testosterone replacement therapy beginning at age 11-12 years

(if testosterone is decreased or gonadotropins increased for maturational age);

this will permit more typical adolescent development and prevent many features

of adult Klinefelter syndrome that are secondary to testosterone insufficiency

• Monitor testosterone levels into adulthood

Neoplasia

• There’s an increased risk for extragonadal, usually mediastinal germ cell tumors;

age of susceptibility is early adolescence to age 30• Increased risk of breast cancer (approaching that of women); 20-fold increase

over the normal male population; monthly self-examination and annual clinical

breast examinations are recommended; the value of periodic mammography has

not been established

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Angelman SyndromeFacts:

• Angelman syndrome affects an estimated

1 in 12,000 to 20,000 people

• The gene involved is UBE3A on

chromosome 15

• Mechanism could be a deletion,

uniparental disomy, or an imprinting defect

• 50% familial, 50% de novo

• Seen in all races

Clinical Features• Happy demeanor that includes

frequent laughing, smiling and

excitability

• Newborns: typically have a

normal phenotype;

developmental delays seen

around 6-12 months

• Speech impairment, with minimal

to no use of words; receptive

language and nonverbal

communication skills better than

expressive language skills

Clinical Features

• Movement or balance disorder, usually ataxia of gait

and/or tremulous movement of limbs; average child

with AS walks between 2.5 -6 yo; jerky, robot-like,

stiff gait with uplifted, flexed, and pronated forearms

• Hypermotoric behaviors

• Absolute or relative microcephaly by age 2

• Seizures, usually starting before age 3

Other Findings• Flat occiput

• Protruding tongue

• Tongue thrusting;

suck/swallow disorders

• Feeding problems and/or

hypotonia during infancy

• Wide mouth and widely

spaced teeth

• Frequent drooling

• Strabismus

• Hypopigmented skin, light

hair and eye color

(compared to family); seen

only in those with deletion

• Hyperactive lower-extremity

deep-tendon reflexes

• Obesity

• Uplifted, flexed arm position

especially during ambulation

• Wide-based gait with

pronated or valgus-

positioned ankles

• Increased sensitivity to heat

• Attraction to/fascination with

water; fascination with crinkly

items

• Abnormal food-related

behaviors

• Hyperactivity

• Scoliosis

• Constipation

• Abnormal sleep-wake cycles

and diminished need for

sleep

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Management

Initial Evaluation

• Evaluation for GER in infants and young children; dietary eval to

assure optimal nutritional status• Baseline MRI and EEG

• Management of seizures

• Musculoskeletal exam for scoliosis and gait impairment;

orthopedic referral as needed

• Ophthalmology exam for strabismus, evidence of ocular albinism, and visual acuity

• Developmental evaluation focused on:

1. Nonverbal language ability and related educational and

teaching strategies (ST)

2. Physical therapy to enable optimal ambulation

Yearly Surveillance

• Annual exam; check for scoliosis

• Assure proper nutrition and monitor for the development of obesity• Treatment for manifestations: like constipation, behavioral

problems, orthopedic problems, sleep disturbances

Angelman Syndrome

Video link

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Turner SyndromeFacts:

• Defined as loss or abnormality of the second

X chromosome in at least one cell line in a

phenotypic female; mosaicism occurs (~ 50%)

• Occurs in about 1 in 2,500 newborn girls

worldwide

• ~99% of 45, X pregnancies spontaneously

abort

• Diagnosis by karyotype

• Short stature and gonadal dysgenesis are the

cardinal features

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Clinical Features

Birth and Neonatal Period:

• Growth: often borderline small for gestational age

• Lymphadema

• Cardiac abnormalities: e.g. coarctation of aorta,

aortic stenosis, bicuspid aortic valve

Clinical Features

Infancy:

• Growth: length usually close to and parallel to the 3rd

percentile

• Feeding difficulties

• Poor sleeping pattern

Clinical Features

Preschool:

• Short stature: height velocity usually low/normal

• High activity levels

• Behavioral difficulties with exaggerated fearfulness

• Recurrent middle ear infections; otitis media with

effusion; variable conductive hearing loss;

sensorineural deafness in a minority

Clinical Features

School:

• Growth: height gradually falls away from 3rd percentile

• Middle ear disease

• Obesity

• Specific learning difficulties (math, visuospatial tasks)

• Social vulnerability

• Foot problems (toenail involution, cellulitis)

• Renal anomalies

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Clinical FeaturesAdolescence:

• Growth: impaired pubertal growth spurt even with estrogen

induction

• Ovarian failure: absent/incomplete puberty

• Hypertension

• Increased prevalence of immune disorders (celiac, thyroiditis, IBD)

• Learning disabilities

• Social vulnerability

• Foot problems

Young Adulthood: (same as above plus)

• Long term estrogen replacement

• Fertility problems

• Osteoporosis

• Sensorineural deafness

• Aortic dilatation/dissection

• Hypertension

Management

Birth to Newborns

• Examine hips for dysplasia

• Review newborn hearing screen• Cardiology consultation

• Renal US

• Discuss the possibilities of feeding problems (due to impaired oral

motor function

• Genetics/Endocrine consultations

Infancy

• Assess weight gain

• Measure BP, check pulses; compare leg and arm systolic BP (coarct)

• Perform ophthalmologic evaluation

• Check ears; evaluate child’s hearing at 6 mos and 12 mos of age

• Monitor developmental milestones

1 to 5 years

• Monitor growth (the age GH is initiated varies, but can be

started as early as 2 to 3 years of age if height below the 5th

percentile or decreasing growth velocity)----Use Turner

Syndrome-specific growth curves

• Check BP/pulses

• Evaluate hearing, and check for OM, serous otitis every visit

• Evaluate renal status as indicated• Test thyroid function every 1 to 2 years; in absence of clinical signs,

can start around 4 yo

• Assess for developmental delays and learning difficulties

Health Supervision

Management

5 to 13 years

• Monitor growth; in addition to GH, the endocrinologist may add

oxandrolone • Check BP and pulses

• Evaluate hearing, check for OM, serous otitis every visit

• Evaluate dentition for malocclusion

• Continue TFT’s at 1-2 year intervals

• Check for scoliosis (lordosis, kyphosis) yearly• Monitor for school problems

• Counsel regarding optimizing bone density (Vit D/Ca)

13 to 21 years

• Examine for pigmented nevi

• Check BP and pulses• Evaluate hearing, check for OM, serous otitis

• Lipid profile

• Check for scoliosis, kyphosis, lordosis

• Refer to cardiologist for complete evaluation

• TFT’s every 1-2 years• Evaluate the adolescent for the development of secondary sex

characteristics. Measure LH and FSH to assess gonadal function.

Initiate Estrogen therapy when ready.

• Referral to Pediatric Endocrinology for hormone replacement

• Evaluate for lymphadema• Monitor school function and behavior

• Discuss social adaptation; tend to be socially immature

• Present information of reproductive options to bearing children

(adoption, medically assisted reproduction)

• If patient has sufficient ovarian function to ovulate, refer for genetic counseling; at risk for having a fetus with chromosome

abnormalities and having miscarriages

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Fragile X Syndrome

Facts:

• It is the most commonly inherited form of mental

retardation

• Occurs in approximately 1 in 4,000 males and 1 in

8,000 (heterozygous) females

• Due to an abnormality in the FMR-1 gene; FMR-1

harbors an unstable CGG trinucleotide repeat

• Full mutations, which cause Fragile X are the

consequence of expansion of the repeats in a CGG

number that exceeds 200

Clinical FeaturesPhysical

• Prominent forehead

• Long, narrow face

• Prominent jaw

• Large, protuberant ears

• Palate frequently arched

• Dental crowding and malocclusion

• Strabismus, refractive errors, nystagmus,

ptosis

• Macro-orchidism (>80% of adolescent and

adult males)

• Connective tissue dysplasia; soft velvet-like

skin, joint hypermobility, scoliosis

• Mitral valve prolapse

• Seizures

• Tall initially, then growth slows in adolescence;

and 25% of adult men have a height ≤ 5%

Clinical FeaturesCognitive/Developmental Profile

• Moderate to severe MR

• Average IQ is 40 in a completely methylated full mutation

• In females with a full mutation, cognitive profile similar to males, but more variability (esp. IQ scores)

• Language delay; may not speak until 2-3 yo

• Abnormal speech (tachylalia and tacyphemia)

• Fine and gross motor delays

Behavior Profile

• ADHD (impulsivity/distractibility)

• Anxiety

• OCD-like behaviors

• Emotional lability

• Features of autism (hand-flapping, biting, perseverative speech, poor eye contact, sensory

defensiveness, lack of interest in social interaction)

• Autism is present in 30% of people with a full mutation; Fragile X is found in 2-6% of people with

autism

Psychiatric Profile

• Oppositional defiant disorder

• OCD

• Mood lability (aggressive and self-injurious behaviors)

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Management

Health supervision

Birth to 1 year

• Monitor for feeding difficulties; assess for GER

• Examine for orthopedic abnormalities (hip dysplasia, clubfoot)

• Monitor head-growth velocity

• Monitor growth and development; look for hypotonia

• Refer for services like early intervention as needed

1 to 5 years

• Eye exam

• Monitor for orthopedic problems related to connective tissue dysplasia

• Check for inguinal hernias

• Assess the child’s history for seizures or staring

episodes; EEG if indicated

• Monitor for OM’s; yearly audiology exams• Communication skills as well as other developmental

milestones should be monitored closely; affected

children require services for speech, motor and

cognitive development

• Monitor behavior, emotional, and psychological status; follow for signs of autism

• OSA

• Cardiac exam

Management

5 to 12 years

• Monitor for macro-orchidism and measure testicular volume

with an orchidometer; check for hernias (occurs in 15%)• Girls should be followed for precocious puberty

• Monitor developmental progress; make certain cognitive,

speech and language, and motor needs are addressed

• Monitor for ADHD; address problems with behavior

modification and/or in combination with medication management

• Monitor for obsessive-compulsive behaviors, anxiety,

aggression, depression

• Make sure support services at school are in place

• Enuresis is common• Monitor for scoliosis

13 to 21 years (same

as above plus)

• Assess for seizures, esp. atypical seizures

• Monitor for cardiac murmur or click• Pursue behavioral/psychological intervention if indicated

• Discuss the availability and need for vocational training and

group home placement if appropriate

• Facilitate transition to adult medical care

Be Available…

• Offer support; offer resources (online/organizations)

• Discuss how to tell family members and friends

about the condition

• Review recurrence risk for subsequent pregnancies;

discuss options like prenatal and preimplantation

genetic diagnosis

• Refer for formal genetic counseling to address these

issues

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Suggested Resources

• Genetics Home Reference

https://ghr.nlm.nih.gov/

• Gene Reviews

https://www.ncbi.nlm.nih.gov/books/NBK1116/

• Clinical practice guidelines from the American

Academy of Pediatrics

Thank You!