THE NEXT GENERATION: Microarray and Beyond

1. Come gather 'round peopleWherever you roamAnd admit that the watersAround you have grownAnd accept it that soonYou'll be drenched to the bone.If your time to youIs worth savin'Then you better start swimmin'Or you'll sink like a stoneFor the times they are a-changin'.

2. THE NEXT GENERATION:Microarray and Beyond

4. Chromosomal Microarray (CMA) Karyotype Resolution: >7-10 Million Base Pairs (7-10 Mb) Resolution: < 0.5 Million Base Pairs (< 500 kb)

5. MicrodeletionSyndromes Non-Syndromic Micro Del /Dups Postnatal Studies 15-20% yield by CMA in children with unexplained developmental delay/ID, and congenital anomalies compared to ~3% with karyotype ID: Intellectual Disability Velo Cardio Facial Syndrome

6. Structural Anomalies Array Adds Significant Clinically Relevant Information in Cases With Normal Karyotype

8. Amniocentesis: Karyotype: 46,XY Array: 1.39 Mb gainin 7q11.23 7q11.23 microduplication syndrome Van der Aa, et al. Fourteen new cases contribute to the characterization of the 7q11.23 microduplication syndrome. European Journal of Medical Genetics 2009

9. Left Foot Right Foot

10. Differential Diagnosis • Aase Syndrome • Diamond-blackfan Syndrome • DOOR Syndrome • Duane-radial Syndrome (DR Syndrome) • Fanconi Anemia (Pancytopenia-dysmelia Syndrome) • Fetal Hydantoin Syndrome (DilantinEmbryopathy) • Goodman Syndrome • Holt-Oram Syndrome • Hypomelanosis Of Ito • IVIC Syndrome • Juberg-hayward Syndrome • Lacrimo-auriculo-dento-digital Syndrome (LADD Syndrome) (Levy-hollister Syndrome) • Mesomelic Dysplasia (Werner Type) • Nager Syndrome • Normal Variant : Isolated Anomaly • Poland Syndrome (Pectoral Muscle Aplasia-syndactyly) • Thalidomide Embryopathy • Townes-brocks Syndrome • Trichorhinophalangeal Dysplasia Type (Langer Gidieon Syndrome) • Trisomy 13 • Trisomy 22 • VATER Association

11. Sequencing Mutation

12. Triphalangeal thumb with Polysyndactyly Sequencing Analysis • Mutation in SHH gene • Mutations in the Sonic hedgehog limb enhancer, the zone of polarizing activity regulatory sequence (ZRS, located within the gene LMBR1), commonly called the ZRS), cause limb malformations

16. BH 2012 SC You’re pregnant and You must know the sex Deep sequencing Ma, It’s all the rage !

17. Clinically Relevant Information Seen by CMA and Reported to Patients in Cases with Normal Karyotype By Indications for Testing

18. Recurrent CNVs That Have The Potential To Cause Neurocognitive Impairment Occurred in approximately 1 in 125(0.8%) cases sampled for AMA or positive screening

19. Conclusion • Based on the increased detection of clinically relevant  abnormalities in both structurally normal and abnormal pregnancies, chromosomal microarray analysis (CMA) should be transitioned to become the first tier test for invasive prenatal cytogenetic diagnosis.

20. Findings of Unknown Significance Variable Expressivity

21. Variants of Uncertain Clinical Significance • 1. Other Cases • - known del/dup or Mendelian disorders • OMIM, DECIPHER (Sanger) • - known benign CNV • DGV (Toronto), dbVar (NCBI) • - comparison with other cases • PubMed, DECIPHER • 2. Large Databases • ISCAConsortium • 3. Genomic/Gene Content • - correlates with size/location • UCSC, Ensembl (Sanger)

22. Counseling Issues Variants Of Uncertain Clinical Significance As CMA Transitions Into Practice Counseling By Professionals With Knowledge And Expertise In CMA Will Be Required

24. Frequency of Findings of Uncertain Significance in Amniocentesis Karyotype CVS: Confined Placental Mosaicism 1-2%

25. Berg, Genetics In Medicine, June 2011 Berg: Genetics in Medicine 2011

26. Incomplete penetrance/ Variable Expressivity CVS: del16p13.12p13.11 ? CVS: 2.0 Mb del16p13.12p13.11 CVS: del16p13.12p13.11 Described with Autism Spectrum Disorder (ASD)/Developmental Delay, and seizures

27. Full Scale IQ difference of 28 or 2 SD Mean 80 SD 15 Mean 108 SD 12

28. Counseling Issues Incomplete Penetrance/ Variable Expressivity Long term prospective study of individuals identified with pathogenic CNVs and variants of uncertain clinical significance

29. Non Invasive Prenatal Diagnosis of Common Trisomies(13,18,21) ( 1:500 Pregnancies) Vs Invasive Diagnosis with Array Analysis (>1:100) All Patients Should be Counseled about the Relative Advantages and Disadvantages of Each Approach

30. PRETEST COUNSELING Issues To Discuss • Additional information about the health/development • of the child • Findings of uncertain significance • Unanticipated information about the health of a parent • Pre-symptomatic recognition of adult on-set condition • Determination of non-paternity • Should be discussed with the patient prior to testing and an understanding of the patients interest in this information should be explored and documented • Who will/can do this?

31. Noninvasive Prenatal Diagnosis of a Fetal MicrodeletionSyndromeDavid Peters, Ph.D.TianjiaoChu, Ph.D.SvetlanaA. Yatsenko, M.D.NancyHendrix, M.D.W.Allen Hogge,M.D. UrvashiSurti, Ph.D. Kimberly Bunce, Ph.D.MaryDunkel, M.S.PatriciaShawB.S.AleksandarRajkovic, M.D.Magee–Womens Research Institute

32. GENOMICS Noninvasive Whole-Genome Sequencing of a Human Fetus Jacob O. Kitzman,1 * Matthew W. Snyder,1 Mario Ventura,1,2 Alexandra P. Lewis,1 Ruolan Qiu,1LaVone E. Simmons,3 Hilary S. Gammill,3,4 Craig E. Rubens,5,6 Donna A. Santillan,7Jeffrey C. Murray,8 Holly K. Tabor,5,9 Michael J. Bamshad,1,5 Evan E. Eichler,1,10 Jay Shendure1 *

33. Concerns of Increasingly Complex Non-Invasive Fetal Testing • Uncertain Reassurance • More Uncertain Findings • Scope Creep • Counseling • Ethics of What to Test For