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Genomic Technologies Objectives & • Understand the benefits and limitations of Syndrome Recognition commercially-available genetic testing • Recognize presenting features of common genetic syndromes By Samantha Leib, MD, FAAP Pediatrician • Improve comfort level managing and Department of Genetics and Genomic Medicine monitoring patients with genetic conditions Saint Peter’s University Hospital in the primary care setting Understanding the Basics 1 Genomic Technologies 2 3 Reasons to Diagnose • Comprehensive information regarding the diagnosis or probable diagnosis • Medical management Prenatal Screening • Anticipatory guidance and surveillance • Risk and recurrence assessments for the patient and other family members Non-invasive Prenatal Testing (NIPT) What is NIPT? • The use of NIPT to screen for the presence of fetal • Non-invasive prenatal testing aneuploidy became feasible with the development of massive parallel sequencing (MPS) and counting of • Cell-free fetal DNA (cffDNA) cfDNA fragments. • Fetal DNA that circulates freely in the mother’s • Most current tests for this purpose use whole bloodstream (2-6% of total) genome MPS in order to quantitatively compare the • Originates from apoptosis amount of, for example, chromosome 21 DNA of trophoblasts that make up the placenta due to molecules in a maternal sample with that of an maternal immune system euploid reference sample. interaction • Other tests use targeted sequencing, mapping only • cffDNA is significantly smaller the chromosome regions of interest, or use a than maternal DNA and can qualitative SNP-based approach. be distinguished by size 4 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 Screening Limitations MaterniT21 Plus: Harmony Screens for: • These screening tools do not provide a definitive Trisomy 21 Trisomy 21 genetics risk in all individuals. Trisomy 18 Trisomy 18 Trisomy 13 Trisomy 13 • Cell-free fetal DNA does not replace the accuracy Sex chromosome aneuploidy Sex chromosome aneuploidy and precision of prenatal diagnosis with CVS or 22q deletion syndrome (DiGeorge) amniocentesis. 5p (Cri-du-chat syndrome) 15q (Prader-Willi/Angelman • A patient with a positive test result should be syndromes) 1p36 deletion syndrome referred for genetic counseling and offered invasive 4p (Wolf-Hirschhorn syndrome) prenatal testing for confirmatory diagnosis. 8q (Langer-Giedion syndrome) 11q (Jacobsen syndrome) • A negative test result does not ensure an Trisomy 16 unaffected pregnancy. Trisomy 22 5 Average Cost 1. Karyotype: $600 2. Microarray: $750 - $2,500 Syndrome Recognition 3. NIPT: $100 - $400 4. Gene panels: $1,000 - $3,000 5. Whole exome: $2,500 - $5,000 6 Williams Syndrome Facts: • 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 Clinical Features Clinical Features Distinctive Facies: Unique Personality: • Broad forehead, bitemporal • Overfriendliness narrowing, periorbital fullness • Empathy • A stellate/lacy iris pattern, strabismus, • Generalized anxiety short nose with a broad nasal tip, • Specific phobias malar flattening • ADHD • Long philtrum, wide mouth with full lips, malocclusion, micrognathia, and Intellect/Cognitive Profile: large ear lobes (seen at all ages) • Developmental delays • Strengths in verbal short-term memory and • Young children have epicanthal folds, full cheeks, and widely spaced teeth language (affinity towards music) • Weakness in visuospatial construction • Adults have long face and neck, • Most have some degree of intellectual disability resulting in a gaunt appearance 7 Clinical Features Clinical Features Cardiovascular disease: Growth Abnormalities: • Any artery may be narrowed (elastin arteriopathy) • FTT in infancy • Most commonly supravalvar aortic stenosis (75%) • Short stature • Peripheral pulmonic stenosis common in infancy (PPS) Endocrine Abnormalities: • Hypercalcemia Connective Tissue Abnormalities: • Hypothyroidism • Joint limitation or laxity • Early puberty • Hernias • DM • Soft/lax skin • Rectal prolapse Yearly Surveillance Interval/Age Test/Measurement Williams Syndrome Serum calcium determination every Infancy 4-6 months until age 2 years •Medical evaluation Video link •Vision screening to monitor for refractive errors and strabismus •Hearing evaluation •Monitoring of blood pressure in both arms Annual •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 •Renal and bladder ultrasound Every 10 years examination •Oral glucose tolerance test (OGTT) starting at age 30 years to evaluate for diabetes mellitus 1 •Evaluation for mitral valve prolapse, In adults aortic insufficiency, and arterial stenoses •Evaluation for cataracts (from Gene Reviews) 8 Clinical Features Klinefelter Syndrome Growth: • Long limbs Facts: • Decreased upper-to-lower segment ratio • Affects 1 in 500 to 1,000 newborn males • Increased arm span • Mean height at 75% • Diagnosis is confirmed by chromosomal analysis Hypogonadism with Hypogenitalism: • Childhood-cryptorchidism, hypospadias, • Paternal meiosis I errors account for 50%- small penis/testes 60% of 47,XXY males with the remainder • Adolescence/adulthood-testes remain small; due to maternal meiosis I or II errors or to a virilization is incomplete with gynecomastia occurring in 1/3 of adolescents postzygotic error • Facial hair is sparse • It’s the most common cause of • Testosterone levels decrease in late hypogonadism and infertility in men adolescence and early adulthood (< ½ of normal) • Infertility 9 Clinical Features Clinical Features Occasional Complications: Performance: • Elbow dysplasia • IQ between 85-90; verbal IQ is usually higher than performance IQ • Taurodontism • Problems with reading and spelling • Diabetes • Autoimmune diseases • Immature behavior, introverted personality, poor judgment, difficulty forming peer relationships • Varicose veins & hypostatic anterior leg ulcerations • 20-50% will have a fine-to-moderate intention tremor • 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 • 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 Development educational evaluation • Evidence of behavioral/emotional problems should prompt referral to a behavioral/psychological specialist • Obtain baseline testosterone, FSH, and LH levels ~11-13 yo • Treatment with testosterone replacement therapy beginning at age 11-12 years Endocrine (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 • 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 Neoplasia over the normal male population; monthly self-examination and annual clinical breast examinations are recommended; the value of periodic mammography has not been established 10 Clinical Features Angelman Syndrome • Happy demeanor that includes Facts: frequent laughing, smiling and excitability • Angelman syndrome affects an estimated 1 in 12,000 to 20,000 people • Newborns: typically have a • The gene involved is UBE3A on normal phenotype; chromosome 15 developmental delays seen • Mechanism could be a deletion, around 6-12 months uniparental disomy, or an imprinting defect • Speech impairment, with minimal • 50% familial, 50% de novo to no use of words; receptive • Seen in all races language and nonverbal communication skills better than expressive language skills Clinical Features Other Findings • Flat occiput • Uplifted, flexed arm position • Protruding tongue especially during ambulation • Movement or balance disorder, usually ataxia of gait • Tongue thrusting; • Wide-based gait with and/or tremulous movement of limbs; average child suck/swallow disorders pronated or valgus- positioned ankles • Feeding problems and/or with AS walks between 2.5 -6 yo; jerky, robot-like, • Increased sensitivity to heat hypotonia during infancy stiff gait with uplifted, flexed, and pronated forearms • Attraction to/fascination with • Wide mouth and widely water; fascination with crinkly • Hypermotoric behaviors spaced teeth items • Frequent drooling • Abnormal food-related behaviors • Absolute or relative microcephaly by age 2 • Strabismus • Hypopigmented skin, light • Hyperactivity hair and eye color • Scoliosis • Seizures, usually starting before age 3 (compared to family); seen • Constipation only in those with deletion • Abnormal sleep-wake cycles and diminished need for • Hyperactive lower-extremity sleep deep-tendon reflexes • Obesity 11 Management Angelman Syndrome • Evaluation for GER in infants and young children;
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