Medical genetics Dr. Lina Basel Schneider Children’s Medical Center of Israel

1. What is the problem 2. Why did it happen 3. What will it mean for our baby 4. Will it happen again Benefits of genetic evaluation

Reproductive counseling: carrier testing, prenatal diagnosis Presymptomatic screening for associated complications Referral to support groups Benefits of genetic evaluation

How do you make a syndrome diagnosis? History Examination Investigations

Family history  Any relative with mental retardation or known malformations  Neonatal deaths, stillbirths or childhood deaths  Familial disorders or physical features  Consanguinity in parents  Ethnic background  Prior genetic testing or screening

History Family history – pedigree: what is the mode of inheritance? - AR, AD, XL, Y-linked, mitochondrial, trinucleotide repeat expansion

History Maternal health, vitamin supplements and drug use hydantoin

History Maternal health, vitamin supplements and drug use valproic acid

History Maternal health, vitamin supplements and drug use alcohol

History Pregnancy investigations: NT US Biochemical screening Amniocentesis Fetal MRI

Physical examination Height plot on appropriate growth chart

Physical examination Proportions U/L segment Arm span Hand length

Posture and tone: trisomy 18 PWS Physical examination

Facial expression: Angelman syndrome Physical examination

Movements and behavior: Rett syndrome Physical examination

Characteristic personality: Williams syndrome Physical examination

Karyotype, FISH, low- resolution CGH Molecular tests (sequencing, specific mutation testing) CHG arrays, SNP arrays, MLPA

Chromosomal tests

Subtelomeric regions Chromosomal structure

Cytogenetic tests - karyotype

Indications:  Mental retardation  Dysmorphic features  Major anomaly  Recurrent spontaneous abortions  Family history of multiple affected individuals with MR/malformations 5-10 Mb resolution ( cytogenetic bands)

ECARUCA

Cytogenetic tests – high resolution karyotype Indications: High suspicion of chromosomal anomaly

Microdeletions and microduplications Wolf-Hirshhorn Williams DiGeorge/VCFS Miller-Dieker lissencephaly Rubinstein-Taybi Smith-Magenis

Fluorescence in situ hybridization (FISH) Need to suspect a specific diagnosis! Cytogenetic tests – FISH (Fluorescent in situ hybridization)

Cytogenetic tests – FISH

Indications: Detects specific microdeletions/microduplications Quick test for detection of abnormal chromosome number (pregnancy)

Di George/VCFS Aortic arch abnormalities Hypocalcemia Cleft palate Immunodeficiency Developmental delay Psychiatric disorders

Williams syndrome Characteristic facies Supravalvular AS Hypercalcemia Microcephaly Kidney abnormalities Musculoskeletal problems Developmental delay

Prader Willi/Angelman syndrome

Cytogenetic tests – subtelomeric FISH

Indications: Mental retardation/dysmorphic features/congenital anomalies Familial cases (especially if variable clinical features Detects deletions/duplications of the subtelomeric regions

Cytogenetic tests – subtelomeric FISH

SKY – spectral karyotyping Indications: Unidentified chromosomal marker Multiple chromosomal translocations

Molecular cytogenetic techniques Array CGH SNP array

Array CGH Genomic rearrangements detectable by array CGH: % in patients with syndromic MR Depends on the stringency of the clinical criteria Molecular cytogenetic techniques

 Targeted array  1 Mb resolution (aCGH with 3,000-3,500 BAC clones)  kb resolution (aCGH with 32,447 BACs/oligos)  Exon aCGH (all ~250,000 exons in human genome) Array CGH – resolution Various levels of resolution: the higher the resolution, the higher the detection rate

Indications: Mental retardation/dysmorphic features/congenital anomalies Detection of microdeletions, microduplications No need for specific diagnosis Array CGH

Copy number variants (CNVs) How much copy number variations (CNVs) exist? What is the contribution of copy number variation to genetic disease? What role has copy number variation played in recent human evolution?

SNP array CCCCAGCCTCCTTGCCAACGCCCCCTTTCCCTCTCCCCCTCCCGCTCGGCGCTGACCCCCCA TCCCCACCCCCGTGGGAACACTGGGAGCCTGCACTCCACAGACCCTCTCCTTGCCTCTTCC CTCACCTCAGCCTCCGCTCCCCGCCCTCTTCCCGGCCCAGGGCGCCGGCCCACCCTTCCCTC CGCCGCCCCCCGGCCGCGGGGAGGACATGGCCGCGCACAGGCCGGTGGAATGGGTCCAGG CCGTGGTCAGCCGCTTCGACGAGCAGCTTCCAATAAAAACAGGACAGCAGAACACACAT ACCAAAGTCAGTACTGAGCACAACAAGGAATGTCTAATCAATATTTCCAAATACAAGT TTTCTTTGGTTATAAGCGGCCTCACTACTATTTTAAAGAATGTTAACAATATGAGAAT ATTTGGAGAAGCTGCTGAAAAAAATTTATATCTCTCTCAGTTGATTATATTGGATAC ACTGGAAAAATGTCTTGCTGGGCAACCAAAGGACACAATGAGATTAGATGAAACGAT GCTGGTCAAACAGTTGCTGCCAGAAATCTGCCATTTTCTTCACACCTGTCGTGAAGGAA ACCAGCATGCAGCTGAACTTCGGAATTCTGCCTCTGGGGTTTTATTTTCTCTCAGCTGC AACAACTTCAATGCAGTCTTTAGTCGCATTTCTACCAGGTTACAGGAATTAACTGTTT GTTCAGAAGACAATGTTGATGTTCATGATATAGAATTGTTACAGTATATCAATGTGG ATTGTGCAAAATTAAAACGACTCCTGAAGGAAACAGCATTTAAATTTAAAGCCCTAA AGAAGGTTGCGCAGTTAGCAGTTATAAATAGCCTGGAAAAGGCATTTTGGAACTGGGT AGAAAATTATCCAGATGAATTTACAAAACTGTACCAGATCCCACAGACTGATATGGCT GAATGTGCAGAAAAGCTATTTGACTTGGTGGATGGTTTTGCTGAAAGCACCAAACGTA AAGCAGCAGTTTGGCCACTACAAATCATTCTCCTTATCTTGTGTCCAGAAATAATCCA GGATATATCCAAAGACGTGGTTGATGAAAACAACATGAATAAGAAGTTATTTCTGGA CAGTCTACGAAAAGCTCTTGCTGGCCATGGAGGAAGTAGGCAGCTGACAGAAAGTGCT GCAATTGCCTGTGTCAAACTGTGTAAAGCAAGTACTTACATCAATTGGGAAGATAACT CTGTCATTTTCCTACTTGTTCAGTCCATGGTGGTTGATCTTAAGAACCTGCTTTTTAAT CCAAGTAAGCCATTCTCAAGAGGCAGTCAGCCTGCAGATGTGGATCTAATGATTGACT GCCTTGTTTCTTGCTTTCGTATAAGCCCTCACAACAACCAACACTTTAAGATCTGCCTG GCTCAGAATTCACCTTCTACATTTCACTATGTGCTGGTAAATTCACTCCATCGAATCAT CACCAATTCCGCATTGGATTGGTGGCCTAAGATTGATGCTGTGTATTGTCACTCGGTTG AACTTCGAAATATGTTTGGTGAAACACTTCATAAAGCAGTGCAAGGTTGTGGAGCACA CCCAGCAATACGAATGGCACCGAGTCTTACATTTAAAGAAAAAGTAACAAGCCTTAAA TTTAAAGAAAAACCTACAGACCTGGAGACAAGAAGCTATAAGTATCTTCTCTTGTCCA TGGTGAAACTAATTCATGCAGATCCAAAGCTCTTGCTTTGTAATCCAAGAAAACAGGG GCCCGAAACCCAAGGCAGTACAGCAGAATTAATTACAGGGCTCGTCCAACTGGTCCCTC AGTCACACATGCCAGAGATTGCTCAGGAAGCAATGGAGGCTCTGCTGGTTCTTCATCAG TTAGATAGCATTGATTTGTGGAATCCTGATGCTCCTGTAGAAACATTTTGGGAGATTA GCTCACAAATGCTTTTTTACATCTGCAAGAAATTAACTAGTCATCAAATGCTTAGTAG CACAGAAATTCTCAAGTGGTTGCGGGAAATATTGATCTGCAGGAATAAATTTCTTCTT AAAAATAAGCAGGCAGATAGAAGTTCCTGTCACTTTC CCCCAGCCTCCTTGCCAACGCCCCCTTTCCCTCTCCCCCTCCCGCTCGGCGCTGACCCCCCA TCCCCACCCCCGTGGGAACACTGGGAGCCTGCACTCCACAGACCCTCTCCTTGCCTCTTCC CTCACCTCAGCCTCCGCTCCCCGCCCTCTTCCCGGCCCAGGGCGCCGGCCCACCCTTCCCTC CGCCGCCCCCCGGCCGCGGGGAGGACATGGCCGCGCACAGGCCGGTGGAATGGGTCCAGG CCGTGGTCAGCCGCTTCGACGAGCAGCTTCCAATAAAAACAGGACAGCAGAACACACAT ACCAAAGTCAGTACTGAGCACAACAAGGAATGTCTAATCAATATTTCCAAATACAAGT TTTCTTTGGTTATAAGCGGCCTCACTACTATTTTAAAGAATGTTAACTATATGAGAAT ATTTGGAGAAGCTGCTGAAAAAAATTTATATCTCTCTCAGTTGATTATATTGGATAC ACTGGAAAAATGTCTTGCTGGGCAACCAAAGGACACAATGAGATTAGATGAAACGAT GCTGGTCAAACAGTTGCTGCCAGAAATCTGCCATTTTCTTCACACCTGTCGTGAAGGAA ACCAGCATGCAGCTGAACTTCGGAATTCTGCCTCTGGGGTTTTATTTTCTCTCAGCTGC AACAACTTCAATGCAGTCTTTAGTCGCATTTCTACCAGGTTACAGGAATTAACTGTTT GTTCAGAAGACAATGTTGATGTTCATGATATAGAATTGTTACAGTATATCAATGTGG ATTGTGCAAAATTAAAACGACTCCTGAAGGAAACAGCATTTAAATTTAAAGCCCTAA AGAAGGTTGCGCAGTTAGCAGTTATAAATAGCCTGGAAAAGGCATTTTGGAACTGGGT AGAAAATTATCCAGATGAATTTACAAAACTGTACCAGATCCCACAGACTGATATGGCT GAATGTGCAGAAAAGCTATTTGACTTGGTGGATGGTTTTGCTGAAAGCACCAAACGTA AAGCAGCAGTTTGGCCACTACAAATCATTCTCCTTATCTTGTGTCCAGAAATAATCCA GGATATATCCAAAGACGTGGTTGATGAAAACAACATGAATAAGAAGTTATTTCTGGA CAGTCTACGAAAAGCTCTTGCTGGCCATGGAGGAAGTAGGCAGCTGACAGAAAGTGCT GCAATTGCCTGTGTCAAACTGTGTAAAGCAAGTACTTACATCAATTGGGAAGATAACT CTGTCATTTTCCTACTTGTTCAGTCCATGGTGGTTGATCTTAAGAACCTGCTTTTTAAT CCAAGTAAGCCATTCTCAAGAGGCAGTCAGCCTGCAGATGTGGATCTAATGATTGACT GCCTTGTTTCTTGCTTTCGTATAAGCCCTCACAACAACCAACACTTTAAGATCTGCCTG GCTCAGAATTCACCTTCTACATTTCACTATGTGCTGGTAAATTCACTCCATCGAATCAT CACCAATTCCGCATTGGATTGGTGGCCTAAGATTGATGCTGTGTATTGTCACTCGGTTG AACTTCGAAATATGTTTGGTGAAACACTTCATAAAGCAGTGCAAGGTTGTGGAGCACA CCCAGCAATACGAATGGCACCGAGTCTTACATTTAAAGAAAAAGTAACAAGCCTTAAA TTTAAAGAAAAACCTACAGACCTGGAGACAAGAAGCTATAAGTATCTTCTCTTGTCCA TGGTGAAACTAATTCATGCAGCTCCAAAGCTCTTGCTTTGTAATCCAAGAAAACAGGG GCCCGAAACCCAAGGCAGTACAGCAGAATTAATTACAGGGCTCGTCCAACTGGTCCCTC AGTCACACATGCCAGAGATTGCTCAGGAAGCAATGGAGGCTCTGCTGGTTCTTCATCAG TTAGATAGCATTGATTTGTGGAATCCTGATGCTCCTGTAGAAACATTTTGGGAGATTA GCTCACAAATGCTTTTTTACATCTGCAAGAAATTAACTAGTCATCAAATGCTTAGTAG CACAGAAATTCTCAAGTGGTTGCGGGAAATATTGATCTGCAGGAATAAATTTCTTCTT AAAAATAAGCAGGCAGATAGAAGTTCCTGTCACTTTC

SNP array Density – 10K, 50/100K, 500K

DNA tests

Direct mutation analysis –DNA sequencing –Specific mutation analysis –Deletion analysis Linkage analysis – utilization of traceable gene markers next to the gene of interest

Testing for the specific mutation

Sequencing

Deletion testing – MLPA (Multiplex Ligation- dependent Probe Amplification )

Southern blotting

Linkage analysis Looks for pattern of DNA markers near gene of interest that segregate with disease Requires DNA analysis of multiple family members 1, 2 3, 4 1, 3 1, 4 2, 3 2,

0/100 %50/50 % X inactivation

Genetic testing in the fetus Non-disclosing prenatal testing The parent is at 50% risk and is not showing symptoms. In this case, to find that the fetus carries the gene for Huntington's disease automatically reveals that the parent is a gene-carrier as well

Ill grandparent parent fetus Non-disclosing prenatal testing

Sequencing of all the genes– laborious… How do we diagnose children with heterogeneic conditions? hearing loss HMSN mental retardation hereditary ataxia spastic paraplegia

MR: etiology

Resequencing microarray Recently, a resequencing microarray has been developed for XLMR genes On this chip 17 XLMR genes are represented, including frequently mutated genes such as ARX, JARID1C and PQBP1 Together they account for approximately 40% of all mutations in MR genes on the X chromosome

Genetic testing Identification of molecular defect in the affected individual Research lab - no costs - might take a long time - need to confirm the test in the clinical lab Clinical lab - usually quick/reliable - expensive

Attitude of different populations towards prenatal testing Non religious Jews : prenatal testing by CVS or amniocentesis (pregnancy interruption possible up to birth, even at 40 weeks of pregnancy); preimplantation genetic diagnosis Orthodox Jews : preimplantation genetic diagnosis (pregnancy interruption possible up to 40 days only – no prenatal testing possible) Muslim Arabs : prenatal testing by CVS or amniocentesis; (pregnancy interruption possible up to 120 days of pregnancy); preimplantation genetic diagnosis

If mutation in the affected individual found – molecular testing of the fetus by CVS or amniocenthesis Or: Preimplantation genetic diagnosis (PGD) If gene unknown for X- linked diseases – fetal sexing Prenatal testing