Genetics and Metabolism for Primary Care Providers. Farrah Rajabi, MD Division of Genetics and Genomics Boston Children s Hospital May 3, 2018

Transcription

1 Genetics and Metabolism for Primary Care Providers Farrah Rajabi, MD Division of Genetics and Genomics Boston Children s Hospital May 3, 2018

2 Financial Disclosures Nothing to disclose 2

3 Topics Reviewed Pediatric and Adult Genetic Cases Review and updates on Genetic Testing Reviews and updates on Newborn Screening Risks and Benefits of Genetic Testing When to Refer Resource Summary 3

4 CASE: 1 day old infant You are on call for the newborn nursery of a community hospital. You receive a page that there is a newborn with dysmorphic features and a heart defect. On exam, the baby is small for gestational age with a small jaw, clenched hands, and prominent heels. You suspect a trisomy disorder. 4

5 Karyotype Emery's Elements of Medical Genetics, CHAPTER 3, Photomicrograph of an individual s chromosomes Obtained from culture of nucleated dividing cells Most commonly circulating lymphocytes from blood Normal male: 46,XY Normal female: 46,XX 5

6 First FISH Fluorescence in situ hybridization Targeted DNA probe fluorescently labeled to identify suspected chromosomal abnormalities Used to identify Common Trisomy disorder rapidly Chromosomes 13,18,21,X,Y Known Submicroscopic deletions Marker chromosomes Rapid results J Med Genet Sep; 31(9):

7 Trisomy Disorders Trisomy 21 Trisomy 18 Trisomy 13 Incidence 15 in 10,000 births 3 in 10,000 births 2 in 10,000 births Neonatal Exam Hypotonia, Small ears, upslanting palpebral fissures, flat facial profile, brachycephaly Small for dates, short sternum, congenital heart anomalies, abnormalities of hands and feet Facial clefts, polydactyly, midline brain defects, holoprosencephaly Down Syndrome (Trisomy 21), The Online Metabolic and Molecular Bases of Inherited Disease Emery's Elements of Medical Genetics, CHAPTER 18, Emery's Elements of Medical Genetics, CHAPTER 18,

8 RESOURCE: AAP Health Supervision Guideline 8

9 Could we have learned the diagnosis Amniocentesis weeks gestational age Chorionic villous sampling 11 weeks gestational age Free fetal DNA After 10 weeks gestational age earlier? JAMA. 2015;314(2):198. doi: /jama

10 CASE: 3 day old with tetralogy of fallot You are still on call for the newborn nursery. An infant failed screening for critical congenital heart disease, and the echocardiogram looks concerning for Tetralogy of Fallot. You are also called by the state lab because the newborn screening has an abnormal screen for t-cell receptor excision circle assay. You arrange transfer to the NICU. What genetic testing can you initiate? 10

11 22q11 deletion syndrome Inheritance: Autosomal dominant Incidence: 1 in 4000 Genotype: Deletion of 22q11 Phenotype: Characteristic facial features Congenital Heart Disease 74% Palate abnormalities 69% Learning difficulties 70% Immune deficiency 77% Hypocalcemia 50% Lancet Oct 20;370(9596):

12 Chromosomal Microarray Taiwan J Obstet Gynecol Jun;53(2): Hybridization of patient and reference DNA Detects any type of gain or loss First line test for severe developmental delay, learning difficulties, or congenital abnormalities 12

13 Uses for chromosomal microarray Developmental delay/intellectual disability Multiple congenital anomalies Autism spectrum disorder Epilepsy, seizures Heart defects Family history of chromosome abnormality Deletions or duplications Unbalanced translocations 13

14 RESOURCE: GeneReviews Genereviews.org Free access Regularly updated Clinical features Management Surveillance Complications Agents to Avoid 14

15 CASE: 4 day old infant You are a community primary care provider seeing an infant for the first well-baby check up. They were scheduled to see you in 2 weeks, but they are concerned their baby is not feeding well. The infant is not dysmorphic with a normal heart and lung exam. On neurologic exam, the infant is floppy and hypotonic with very poor feeding. 15

16 Broad differential for hypotonia Paediatr Child Health Sep; 10(7):

17 Prader-Willi Syndrome Infancy Severe hypotonia, feeding difficulties Childhood Excessive eating, obesity Motor and language delays Short stature Difficult behavior Incidence 1 in 15,000 births Pediatrics in Review. Sept 2009 Vol 30;9 17

18 Genetic Testing for Prader Willi Syndrome Chromosomal Microarray 65-75% caused by interstitial 5- to 6-Mb 15q11.2- q13 deletion <1% unbalanced chromosome rearrangment Methylation (Epigenetic) Testing 20-30% cases caused by maternal uniparental disomy 0.5-2% imprinting defect or deletion of imprinting center 18

19 CASE: 3 year old twin well child check The parents of your 3 year old fraternal male and female twin patients complain that their children never makes eye contact, they are not interested in playing with other children, and they have delayed speech. You are concerned about an autism spectrum disorder. 19

20 Genetic causes of autism Genetic diagnosis identified in 30-40% cases 8-21% chromosome copy number variants Test with chromosomal microarray 16p11.2 deletion most common 6-8% Fragile X syndrome Caused by unstable repeat expansion of CGG in the FMR1 gene Test with southern blot analysis 5-10% Other single gene disorders 20

21 CASE: 10 year old male with birthmarks A 10 year old male is referred to you because the school nurse noticed multiple dark birthmarks. In your office, you notice several café-au-lait macules and freckling. He also has a large head size, and learning problems in school. You are concerned about neurofibromatosis type 1 and refer the child for genetics and ophthalmology evaluation 21

22 Neurofibromatosis Type 1 Inheritance: Autosomal dominant 50% inherited 50% new spontaneous mutations Incidence: 1 in 3,500 Gene: NF1 Diagnostic criteria: 6 of more café au lait macules Axillary or inguinal freckling 2 or more neurofibromas Optic nerve tumor 2 or more lisch nodules Tibial pseudoarthrosis Positive family history in 1 st degree relative 22

23 Single gene vs. Multi-gene panel testing Use a single gene test when you know a gene that runs in the family Use a multiple gene panel when you want to test for multiple overlapping conditions Next Generation Sequencing Parallel sequencing of millions of pieces of DNA Tests multiple genes simultaneously Less expensive than testing genes individually 23

24 RASopathies Annu Rev Genomics Hum Genet. 2013;14:

25 CASE: 13 year old male with tall stature A 13 year old male presents to clinic because his family is very worried about his risk for a genetic cardiac condition. Earlier this month his 17 year old sister collapsed suddenly while playing soccer and could not be resuscitated and died. Her autopsy demonstrated an aortic aneurysm. You review his history and find his height is >99 %ile, and he has myopia and pectus excavatum. 25

26 Marfan Syndrome Inheritance: Autosomal dominant Incidence: 1 in 5,000 Gene: FBN1 Phenotype: Myopia, ectopia lentis, dilation of the aortic root, mitral valve prolapse, pneumothorax, pectus deformity Systemic score based on revised Ghent Criteria 26

27 Other Connective Tissue Disorder Loeys-Dietz Syndrome Familial thoracic aortic aneurysm disease Bicuspid aortic valve and aneurysm syndrome Ehlers-Danlos syndrome Shprintzen-Goldberg syndrome Cutis Laxa syndrome Arterial tortuosity syndrome Stickler Syndrome 27

28 CASE: 17 year old with multiple birth defects and intellectual disability One of your partners in your medical practice retires and you inherit one of his patients, a 17 year old female with a complex history of multiple congenital anomalies, developmental delay, and autism. She s had multiple nondiagnostic tests including a chromosomal microarray, fragile X testing, and an autism gene panel. You strongly suspect a genetic etiology to her symptoms. 28

29 Whole Exome Sequencing Massively-parallel sequencing of ~80% of exons Uses More comprehensive genomic testing in otherwise negative workup Cost benefit over multiple panels Results Variants in coding portions of the genes Incidental findings unrelated to phenotype 29

30 Whole Genome Sequencing Massively parallel sequencing of the entire genome Uses Mainly available on research basis for patient with otherwise negative workup with strong suspicion for a genetic condition Results More uniform coverage of exonic, intronic, and splice site mutations. Incidental findings unrelated to phenotype 30

31 CASE: A gift from the grandson Your 65 year old patient with a history of anxiety makes an urgent clinic appointment. Her grandson bought her a genetic ancestry kit as a gift, and she just got the results with lots of health information. She is very worried about her health risks since the test reports she has an increased risk of Alzheimer s disease, she is a carrier of cystic fibrosis, and she is 5% Neanderthal! 31

32 Direct to Consumer Testing 32

33 CASE: A woman worried about risk A 30 year old woman presents to your clinic. Her mother and 2 of her maternal aunts had breast cancer before the age of 40 years old. Her ancestry is Ashkenazi Jewish. She did testing through a direct to consumer company that demonstrated she tested negative for BRCA1 and BRCA2 changes. Did she have appropriate genetic testing? 33

34 BRCA1 and BRCA2 23andMe Tests for 3 specific mutations Most prevalent in Ashkenazi Jewish ancestry American College of Genetics and Genomics Consumers are best served when testing is done with ready access to unconflicted experts able to both order the most appropriate tests for that individual and then interpret those tests whether the test result is positive or negative. 34

35 Top 5 Genetic Tests in Adults Hereditary Breast and Ovarian Cancer Lynch Syndrome Thrombophilia Factor V Leiden, Prothrombin, Protein C, Protein S Familial Hypercholesterolemia Hemochromatosis 35

36 Hereditary Breast and Ovarian Cancer Inheritance: Autosomal dominant Incidence: 1/800 1/1000 Genes: BRCA1, BRCA2 Phenotype: Increased risk of cancer Female and male breast cancer (46-87%) Ovarian cancer ( %) Lesser extent: prostate cancer, pancreatic cancer, melanoma 36

37 Lynch Syndrome Inheritance: Autosomal dominant Incidence: 1 in 2000 Genes: MLH1, MSH2, MSH6, PMS2, EPCAM Phenotype: Increased risk of cancer Colorectal cancer (52-82%) Endometrial cancer (25-60%) Gastric cancer (6-13%) Ovarian cancer (4-12%) 37

38 Thrombophilia Increased risk of venous thromboembolism (VTE) Factor V Leiden FV gene common variant c.1691g>a 3-8% population Prothrombin F2 common variant c.*97g>a (20210G>A) 1-6% Caucasian populations, 2% overall Protein C and Protein S Combined incidence <1% population 38

39 MTHFR Encodes methylenetetrahydrofolate reductase Two commonly recognized polymorphic variants c.665c>t (C677T; thermolabile variant ) 10-20% population homozygous for variant c.1286a>c Mild hyperhomocysteinemia in setting of suboptimal folate stores Does NOT confer an increased risk for VTE 39

40 Familial Hypercholesterolemia Incidence: 1/200 1/250 Genes: APOB, LDLR, PCSK9 Phenotype: Coronary artery disease (CAD) Heterozygous Untreated men 50% risk for fatal or non-fatal coronary event by age 50 years Untreated women 30% risk by age 60 years Homozygous Severe CAD by their mid-20s 40

41 Hemochromatosis Inheritance: Autosomal recessive Incidence: 1/200 1/400 Gene: HFE Phenotype: Iron overload and clinical symptoms with endorgan damage Biochemical evidence of iron overload with no symptoms No clinical manifestations or iron overload 41

42 Risks and Benefits of Genetic Testing Risks Anxiety Costs False negative results Variants of uncertain significance Insurance issues Benefits Minimize risks with anticipatory management Peace of mind if negative Understanding risk of recurrence in family New treatments 42

43 A BRIEF REVIEW OF NEWBORN SCREENING 43

44 Newborn Screening Started in the early 1960s Uses dried blood spot to rapidly and economically screening newborns Goals Pre-symptomatic treatment Prevention consequences of serious childhood disease 44

45 CASE: 5 day old with abnormal newborn screen A family new to your practice is coming for a routine newborn visit next week. You are contacted by the state lab because the baby s phenylalanine level on newborn screening was 710 umol/l (normal <152) at 30 hours of age. You see the family in clinic and the infant is well appearing. They just moved to the area from Brazil. Their older son has severe autism. 45

46 RESOURSE: ACT Sheets 46

47 RESOURSE: ACT Algorithm 47

48 Phenylketonuria Inheritance: Autosomal Recessive Incidence: 1 in 16,000 live births in U.S. Enzyme deficiency: Phenylalanine hydroxylase Gene: PAH NBS Abnormality: Elevated Phenylalanine Phenotype: If untreated, severe intellectual disability, autistic behavior, pseudoleukodystrophy, seizures, skin lesions 48

49 Phenylketonuria 49

50 Expanded Newborn Screening Combination of screening Tandem mass spectrometry, radioimmunoassay, liquid chromatography, DNA PCR testing, hearing, pulse oximetry Recommended Uniform Screening Panel 34 core disorders 26 secondary disorders Detection of a core disorder 1/4000 live births Hearing loss Primary congenital hypothyroidism Cystic fibrosis Sickle cell disease Medium-chain acyl-coa dehydrogenase deficiency 50

51 RESOURSE: Baby s first test 51

52 CASE: 5 year old with a fatty acid oxidation disorder A 5 year old male you followed since infancy with a known diagnosis of medium chain acyl- CoA dehydrogenase deficiency presents to your clinic with fever. He vomits twice in your waiting room. You check a blood sugar, give oral dextrose solution, and arrange transportation to the nearest emergency department. 52

53 Medium Chain Acyl-CoA Dehydrogenase Deficiency Inheritance: Autosomal Recessive Incidence: 1 in 17,000 Gene: ACADM NBS Abnormality: Elevated C6, C8, C10, C10:1 Phenotype: Undiagnosed: prolonged fasting leads to hypoketotic hypoglycemia, vomiting, lethargy, seizures, coma, death Diagnosed: excellent prognosis with frequent feedings and avoidance of prolonged fasting 53

54 RESOURCE: New England Consortium 54

55 CASE: 4 day old with lethargy You get called from the newborn screening program that one of the infants from your practice has screened positive for Maple Syrup Urine Disease. You page the metabolism team on call and immediately contact the family. The family reports that it s been difficult to wake the infant for feeding this afternoon. 55

56 Maple Syrup Urine Disease Inheritance: Autosomal Recessive Incidence: 1 in 185,000 Enzyme deficiency: Branched Chain Keto-acid dehydrogenase Genes: BCKDHA, BCKDHB, DBT NBS Abnormality: Elevated Leucine Phenotype: If untreated, lethargy, apnea, stereotype movements bicycling, coma, central respiratory failure 56

57 Newest expansions to newborn screening Disorder Added to RUSP Newborn Screen Phenotype Severe Combined Immunodeficiency 2010 T-cell receptor excision circles Genetic immunodeficiencies; incidental findings Pompe Disease 2015 Enzyme activity Hypertrophic cardiomyopathy, muscular weakness. X-linked Adrenoleukodystrophy Mucopolysaccharidosis Type C20-C26 Childhood form with severe neurologic decline and adrenal insufficiency 2016 Enzyme activity Coarsening facial features, progressive skeletal dysplasia, ID, cardiorespiratory failure 57

58 When to suspect metabolic disease and refer Overwhelming illness in the neonatal period Acute acidosis, anion gap Hypoglycemia Coagulopathy Deep coma Seizures, especially myoclonic Unusual odor of urine Pancytopenia Family history of early death in sibling or SIDS 58

59 Resources ACMG ACT Sheets Baby s first test Genetics Home Reference Gene Reviews Farrah.Rajabi@childrens.harvard.edu 59

60 References Bull MJ. Health supervision for children with Down syndrome. Pediatrics Aug;128(2): Cell-free DNA screening for fetal aneuploidy. Committee Opinion No.640. American College of Obstetricians and Gynecologists. Obstet Gynecol 2015;126:e31-7. McDonald-McGinn et al. 22q11.2 deletion syndrome. GeneReviews. Seattle; Driscoll et al. Prader-Willi Syndrome. GeneReviews. Seattle; Miller et al. Consensus Statement: chromosomal microarray in a first-tier clinical diagnostic test for individuals with developmeal disabilities or congenital anomalies. Am J Hum Genet 2010 May 14;86(5): Schaefer et al. Clinical genetics evaluation in identifying the etiology of autism spectrum disorders:2013 guideline revisions. Genet Med 2013 May;15(5): Friedman JM. Neurofibromatosis 1. GeneReviews. Seattle; Dietz H. Marfan Syndrome. GeneReviews. Seattle; ACMG Responds to FDA s approval for Direct-to-Consumer Testing for Three BRCA Gene Mutations. March 7, 2018https:// html Petrucelli N et al. BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer. GeneReviews. Seattle; Kohlmann W, Gruber SB. Lynch Syndrome. GeneReviews. Seattle; Kujovich, JL. Factor V Leiden Thrombophilia. GeneReviews. Seattle; Kujovich, JL. Prothrombin-Related Thrombophilia. GeneReviews. Seattle; Hickey, SE. ACMG Practic Guideline: lack of evidence for MTHFR polymorphism testing. Genet Med. January 3, Youngblom E, et al. Familial Hypercholesterolemia. GeneReviews. Seattle; Seckington R and Powell L. HFE-Associated Hereditary Hemochromatosis. GeneReviews. Seattle; Guthrie R, Susi A. A spimple phenylalanine method for detecting phenylketonuria in large populations of newborn infant. Pediatrics. 1963;32: Landau YE, Licter-Konecki U, Levy HL. Genomics in newborn screening. J Pediatr. 2014;164:14-9. Watson MS, Mann MY, Lloyd-puryear MA, Rinaldo P. Newborn screening: toward a uniform screening panel and system. Genet Med. 2006;8 Suppl 1(5):1S-252S. Recommended Uniform Screening Panel Available at: Accessed March 18, Matern D and Rinaldo P. Medium-Chain Acyl-Coenzyme A Dehydrogenase Deficiency. GeneReviews. Seattle; Staruss KA, et al. Maple Syrup Urine Disease. GeneReviews. Seattle;