genomic technologies objectives - njaap
TRANSCRIPT
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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!