4/4/14. Terms and definitions. Clinical Genetics is increasingly relevant for the adult population

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2 Medical Genetics is the field of medicine that deals with genetically influenced biologic variation relevant to human health and disease. Clinical Genetics is increasingly relevant for the adult population Angelina Jolie BRCA 1/2 genetic testing Jay Monaghan Colon cancer Hank Gathers Hypertrophic cardiomyopathy Terms and definitions Gene: unit of inheritance Alleles: alternate versions of a gene Dominant: mutation in 1 copy is sufficient to cause condition. New dominant: mutation started in proband, not inherited. Recessive: mutation in both copies required to cause condition. X-linked: disease gene on the X-chromosome, implies maternal inheritance, and differential effects on males and females. Mitochondrial: DNA encoded by mitochondria are derived from egg Consanguinity: with blood marriage between relatives. Incomplete penetrance: having a gene mutation but not expressing the condition. 2

3 4/4/14 The Road to Being a Geneticist 3-8+ years of training after MD or MD PhD Medical School Internship and Residency (1 to 3 years) Gene5cs Residency & Fellowship (2 to 5 years) Board Cer5fica5on and recer5fica5on. Peter How is Clinical Genetics different from other medical specialties? Not defined by organ system (eye, heart, kidney. (The organ of interest is the genome). Not defined by age. (Genetic conditions occur at every age). Genetic testing can predict future disease, and has immediate implications for family members. Genetics is relevant to neurodevelopmental disorders! Half of genes are expressed in the brain. Global developmental delay: In children < age 5 y, -2 SD in 2 or more domains: motor, language, social, cognitive, ADLs. Intellectual disability: disorder of cognition and adaptive function with onset prior to age 18. Diagnosis made more reliably after age 5y. Prevalence: 2.5% of population. 3

4 Autistic spectrum disorder Core Features include abnormalities of: Social interaction Language and imaginative play Limited range of interests and activities Who is affected by autism? Prevalence of 1:88 children (CDC) Affects all races and ethnic groups Symptoms before 18 months 4:1 ratio of boys:girls with autism Autism is a spectrum disorder from mild to severe, and improvement in some over time. Possible Red flags for Autism Does not: babble by 12 months point/wave by 12 months respond to his/her name smile in response to smile know how to play with toys Pretend or play makebelieve after age 2 Has poor eye contact Not interested in other children Seems to be in his/her own world Violent tantrums Lines up objects Overly attached to objects 4

5 American Academy of Pediatrics Policy Statement (2006) Increasing Increasing Developmental developmental Concern concern 9 month 18 month 24/30 month Administer Screening Tool Normal Schedule Return visit Positive Normal Adapted from Pediatrics v 118: No Refer for Developmental and Medical eval And Early Intervention Positive DSM ADOS ADI Developmental disorder Diagnosed? Special Needs Child Clinical genetic approach to child with ID or autism History and Examination Birth history Teratogens Growth Medical history Developmental history ID or Autism as part of syndrome (5%-10%) ID/ASD alone in an otherwise normal appearing child (90%-95%) Teratogens: Alcohol, CMV, Valproate, Rubella Chromosomal: 47,XYY dup 15q11 dup 17p11 del 22q11.2, del 22q13 Syndromes: Metabolic disorders: Chromosomal Classification of cause Timing: Prenatal, perinatal, postnatal, undetermined. Genetic Acquired Chromosomal XLID CNVs Metabolic Recessive Imprinting Mitochondrial 5

6 Medical Genetics combines very old and advanced methods Figure removed ID or autism as part of a recognizable genetic syndrome Fragile X syndrome Rett syndrome Angelman syndrome Tuberous sclerosis CHARGE Smith-Magenis syndrome Prader-Willi syndrome Sotos syndrome PTEN associated hamartoma syndrome LOW FREQUENCY, HIGH IMPACT 40 yr woman Head circumference 53.25cm(3-10%) Hx of developemtal delay: Intellectual disability Non-verbal Hx of possible epilepsy vs tremulousness Flattening of the back of the head Dysmorphic facial features Uplifted arms Hx of falling forward, but lately falling backward ( like a tree ) Thin Patient photo removed 6

7 Medication at the time of the 1 st visit Keppra (antiepileptic) Clonazepam (Treats seizures, panic disorder, and anxiety) Levothyroxine (Treats hypothyroidism) Loratadine (antihistamine) Miralax Vitamins and Calcium Medication at the time of the 1 st visit Keppra (antiepileptic) Clonazepam (Treats seizures, panic disorder, and anxiety) Levothyroxine (Treats hypothyroidism) Loratadine (antihistamine) Miralax Vitamins and Calcium Tests requested Whole genome chromosomal microarray PWS/AS methylation studies 7

8 Angelman Syndrome Photos removed. Gene Review J Med Genet 2003;40:87-95 Angelman Syndrome Disease characteristics severe developmental delay or intellectual disability, severe speech impairment, gait ataxia and/or tremulousness of the limbs, and a unique behavior with an inappropriate happy demeanor that includes frequent laughing, smiling, and excitability. Microcephaly and seizures are also common. Developmental delays are first noted at around age six months; and it can take several years before the correct clinical diagnosis is obvious. Gene Review J Med Genet 2003;40:87-95 Lab results Whole genome chromosomal microarray arr 15q11.2q13.1(22,770,421-28,981,826)x1 Interpretation: Type I deletion of either Prader-willi or Angelman Syndrome. 8

9 Angelman Syndrome Gene1c Mechanism h7p:// Angelman Syndrome Mechanism Frequency(%) Deletion in AS/PWS region(5-7 Mb) ~68 UPD ~7 Imprinting center deletion (6-200kb) ~3 UBE3A mutation ~11 UBE3A deletion Rare Gene Review Angelman Syndrome UBE3A 9

10 Patient photo removed Array Comparative Genomic Hybridization (acgh) Oligo array Probes are ~25-50bp in length Cover the entire genome Determines copy number Patient DNA and control DNA are differentially labeled then mixed together and hybridized to the chip NimbleGen platform Includes oligo probes Analyzed with Genoglyphix software by Signature Genomics Set at a minimum of 5 oligos to call an abnormality acgh Data Plots 10

11 acgh Result Smith-Magenis Syndrome (SMS) Neurobehavioral disorder > 75% of individuals: Infantile hypotonia Hyporefulxia Sleep disturbances (prolongs napping as infants, difficulty sleeping as adolescents) Generalized lethargy and complacency Distinctive facial features (become more recognizable in adolescence) Developmental Delay Cognitive impairment Behavioral abnormalities 50% - 75% of individuals Hearing loss Short stature Scoliosis Mild ventriculomegaly of brain Hyperaccusis Tracheobronchial problems Hypercholesterolemia/hypertriglyceridemia Smith-Magenis Syndrome (SMS) Typically de novo, with estimated prevalence of 1:15,000-25,000 live births. Microdeletion of 17p11.2 Common deletion is 3.7MB (cause of the majority of cases) ~10% caused by mutations in the RAI1 gene Molecular evidence shows that most SMS features are due to RAI1 haploinsufficiency. RAI1 (retinoic acid induced 1) probably encodes a transcription factor that acts in several biological pathways that are dysregulated in SMS 11

12 Medical Genetics AND Genomics: a rapidly changing field Genetic Research Broadly applicable Gene Discovery Animal models Not used to make clinical decisions Novel diagnostic methods New treatments Clinical Genetics Individual patients and families Validated genetic testing Part of medical record Genetic counseling FDA approved treatments Clinical Genetics THEN Pediatric One gene, one disease Gene as destiny Genetic testing: few, slow, expensive NOW Children, Adults, Families One gene, several diseases One disease, several genes Gene as a risk factor, acting in a context Genetic testing: many, 12

13 UW Medical Genetics Clinic Patient volume Slide courtesy RLB And DLO PCP Organ specific specialist Genetics Uterine cancer 45 d. 39 Uterine cancer or Mutation + Mutation neg 13

14 Fragile X syndrome mod to severe intellectual disability long face large ears hyperactivity autistic behavior macroorchidism Fragile X Premutation Carriers premature ovarian failure FXTAS (fragile X associated tremor and ataxia syndrome) in men after age 50 normal 60 FXTAS POF POF NOT AFFECTED NOT A CARRIER FRAGILE X SYNDROME??? Intellectually disabled Parkinson disease Mutation carrier Classification of Genetic Test Results (Deleterious, disease- POSITIVE causing) Probably deleterious Variant of uncertain significance Probably benign NEGATIVE (No mutation identified) 14

15 Genetic Testing is not just a blood test Complex interpretation. Complicated forms! Written informed consent documents required by lab and by law. Implications for family members. Prediction of future disease. Genetic testing is more like surgery or an invasive procedure than a blood test. When to refer to Genetics: Red flags for genetic conditions Family GENES (from Family history: multiple affected members G group of congenital anomalies >2 E extreme presentation of common condition (early onset, bilateral dz N neurodevelopmental delay in kids or young adult onset neurodegenerative E exceptional pathology: acoustic neuroma, paraganglioma, S surprising lab values. Glucose 20, chol>400 Autistic spectrum disorder Core Features include abnormalities of: Social interaction Language and imaginative play Limited range of interests and activities 15

16 Evidence for a Genetic Etiology of Autism 60%-96% concordance in MZ twins* 0%-24% concordance in DZ twins* Sibling recurrence risk >> population risk (1 in 5) Heritability of 90% *California Twin study 2011 concordance Male MZ twins: 0.58 (strict) 0.77 (broad) Male DZ twins: 0.21 (strict) 0.31 (broad) Moderate genetic heritability and substantial shared twin environmental component Autism has a strong genetic component Height Complex trait Tail-less Manx Cat Single gene Mendelian trait 16

17 Patient photo removed 7 year old boy referred for macrocephaly, delay and autism Born to G10P9Sab1 mother. Polyhydramnios and smoking. BW 10 lb 2 oz. Sibs were 7 lb 4 oz to 9 lb 9 oz. Very large head size. Cruised initially at 15 mo, then did not walk until 3 y. Globally delayed. Now: 15 words, not toilet trained. Autism spectrum disorder. Does not like to be touched! Takes 3 people to cut his nails. Prior workup MRI: low lying cerebellar tonsils. Unusual appearance to vein of Galen Prev genetic eval at Floating Hosp: karyotype and Fragile X normal. Bone age very advanced: SD. Neuro ordered Sotos syndrome testing. Results normal. 17

18 Ht >97 th centile (50 th centile for 9 yo) Wt > 97 th centile (50 th centile for 13 yo) Head circ: 61.5 cm (>>>97 th centile) Inverted nipples, pectus excavatum, hyperextensible joints. Impression: Testing ordered: PTEN: c.1027delg in exon 9 p.v343x Diagnosis: PTEN (dual specificity phosphatase) related syndrome Genetic Counseling: de novo vs. AD. Test parents. PTEN: one gene, many syndromes Cowden syndrome: macrocephaly, tumors of thyroid, breast, endometrium, tricholemmomas Bannayan Riley Ruvulcalba: macrocephaly, delay, pigmented glans, lipomas, intestinal polyposis Proteus syndrome: hamartomatous overgrowth, asymmetry, macrodactyly Macrocephaly/autism 18

19 Not obviously genetic De novo genetic imbalance Genomic Imbalance deletions, duplications Microscopic Visible by karyotype Submicroscopic More common Requires FISH or molecular assay Nat Rev Genet 7: Slide courtesy of David Miller MD PhD, Children s Hosp Boston Chromosome Microarray Patient Reference Patient Reference Hybridize DNA to genomic clone Cy3/Cy5 ratio >1 Duplication Cy3/Cy5 ratio <1 Deletion Cy3/Cy5 ratio <1 Duplication Cy3/Cy5 ratio >1 Deletion Slide courtesy of David Miller MD, Ph.D. 19

20 Girl with a new diagnosis 2 y 7 month old with failure to thrive, and delay 31 yo mother, BW 5 lb 7 oz at 42 wks. Breathing issues, temperature issues, feeding. Observed X 1 week. DC to home. Wt fell off curve Saw Endocrine: w/u negative. Saw GI: constipation.?milk protein intolerance, change to Nutramigen. 11 yo healthy sister. Irish/English X Dominican Speech delay: hearing normal. Ht: 8 th centile Wt.<5 th. Head circ (3-10 th ) Prior Testing: Fragile X, karyotype, MecP2 for Rett syndrome normal. Patient photo removed 20

21 acgh There was a 3.5 megabase duplication at chromosome 17p11.2. VUS 497 Kb dup. at chromosome 7q kb deletion Xq21.33 DIAPH2 gene associated with POF disrupted by translocation. Which are incidental and which are meaningful? Potocki-Lupski syndrome (PLS) 3.5 MB duplication of 17p11.2 Clinical features: Poor feeding, GER, FTT, hypotonia, autism, devel delay, sleep apnea, cardiac anomalies. A 24-year-old with Asperger Normal delivery, birth wt. APGARS 8,9. Walked at 13 months but did not talk until 3 years. Asperger Dx at Children s Hosp Oakland. Stanford Binet at 8 y. VIQ 96, non-verbal reasoning 77, composite 87. Other dx: anxiety, ADD 46,XX and FraX normal at UWMC. Enrolled CHDD autism research study at 14. Saw neurologist recently for gait change and hand posturing. 21

22 MRI brain normal. EEG normal (awake) Studying at CC to become paralegal. Fam Hx: 26 yo brother has unspecific nondegenerative neurologic disorder FraX normal. 21 yo brother grad school. Father has several sibs with social awkardness one to the point of affecting ability to hold jobs. His son is unusual. OFC 58 cm. Poor eye contact, very quiet. Fund of knowledge, language, memory intact. Tendency to posture with right hand while walking, able to relax it on request. Array CGH (2009) 5 MB duplication at 15q11.2q13.1 FISH confirms, indicated tandem interstitial dup Diagnosis: 15q11 duplication syndrome Variable phenotype from delay to intellectual impairment, to autism spectrum disorder to epilepsy. Hand flapping and motor incoordination reported in young children. Cause of 1% to 2% of autism spectrum disorder. Imprinted region: increased susceptibility if inherited from mother. *Clinical implications: 1) her children are at 50% risk to inherit it from her. 2) parents could be tested. 3) brothers should see genetics What about implications for research study? 22

23 Consanguinity increases birth defects due to autosomal recessive causes Homozygosity by descent Identifying Autism Loci and Genes by Tracing Recent Shared Ancestry Chris A. Walsh Lab. Science 2008 Key findings: Large inherited deletions including protocadherin 10 and deleted in autism 1. Homozygosity mapping in complex trait. Convergence on genes whose expression is altered by neural activity. 16p11.2 Deletions in ~1% of autism patients 5/593 AGRE patients 5/512 CHB patients with autism, MR, DD 3/299 Icelandic autism 13/ p11.2 Deletions in controls 0/1420 AGRE parents 3/2184 NIMH samples 0/434 CHB controls 2/18,834 controls not screened for psychiatric dz. 5/22,872 p value 1.1 X X X 10-4 *Does not always cause autism * 23

24 Clinical Genetic Testing for Patients with Autism Spectrum Disorders Y.Shen et al. Boston Autism Consortium Clinical Genetics/DNA diagnostics Collaboration Pediatrics 2010 Guidelines recommend karyotype and Fragile X but not chromosome microarray 933 autism spectrum patients tested. 755 male:178 female. Age 15 months to 22 years Results Results: Fragile X in 2/852 (0.23%) Karyotype abnormal in 20/852 (2.4%) CMA. Variants in 204/848 (24.1%) 59/848 (7.0%) clinically significant Recommend: acgh or CMA as first line genetic test in the evaluation of ASD. American J. Hum Genetics May

25 Genetics in Medicine Nov 2010 Recommendations (1) acgh testing is recommended as a first-line test for postnatal evaluation of: A Multiple anomalies B. DD/ID C. ASD (2) Further determination of the use of acgh for evaluation of growth retardation, speech delay and other indications is recommended by prospective studies etc. (3) Appropriate follow-up for chromosome imbalance identified by CMA is recommended including cytogenetic/fish studies, parental evaluation and clinical genetic evaluation and counseling. Summary: Genetic Causes of Autism Spectrum Disorder Epigenetic Maleness Epilepsy Modifier genes Environment 25

26 4/4/14 Autism: Referral to Clinical Genetics Dysmorphic features Nondysmorphic but multiple medical problems Genetic evaluation > 5 years ago Family history Parental request (is it genetic, what is the chance of next child being affected?) Prior to enrollment in research studies Tel: FAX: Acknowledgments UW Genetic Medicine Clinic 2014 Thank you! Any questions? 26