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

Subtelomeric regions

Chromosomal structure

Cytogenetic tests - karyotype

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 (300-600 cytogenetic bands)

ECARUCA

Cytogenetic tests – high resolution karyotype

Indications: High suspicion of chromosomal anomaly

Microdeletions and microduplications

Wolf-Hirshhorn

Williams DiGeorge/VCFS

Miller-Dieker lissencephalyRubinstein-Taybi

Smith-Magenis

Fluorescence in situ hybridization (FISH)

Need to suspect a specific diagnosis!

Cytogenetic tests – FISH (Fluorescent in situ

hybridization)

Cytogenetic tests – FISH

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 syndromePrader Willi/Angelman syndrome

Cytogenetic tests – subtelomeric FISH

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: 10-15% 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)

10-100 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

CCCCAGCCTCCTTGCCAACGCCCCCTTTCCCTCTCCCCCTCCCGCTCGGCGCTGACCCCCCATCCCCACCCCCGTGGGAACACTGGGAGCCTGCACTCCACAGACCCTCTCCTTGCCTCTTCCCTCACCTCAGCCTCCGCTCCCCGCCCTCTTCCCGGCCCAGGGCGCCGGCCCACCCTTCCCTCCGCCGCCCCCCGGCCGCGGGGAGGACATGGCCGCGCACAGGCCGGTGGAATGGGTCCAGGCCGTGGTCAGCCGCTTCGACGAGCAGCTTCCAATAAAAACAGGACAGCAGAACACACATACCAAAGTCAGTACTGAGCACAACAAGGAATGTCTAATCAATATTTCCAAATACAAGTTTTCTTTGGTTATAAGCGGCCTCACTACTATTTTAAAGAATGTTAACAATATGAGAATATTTGGAGAAGCTGCTGAAAAAAATTTATATCTCTCTCAGTTGATTATATTGGATACACTGGAAAAATGTCTTGCTGGGCAACCAAAGGACACAATGAGATTAGATGAAACGATGCTGGTCAAACAGTTGCTGCCAGAAATCTGCCATTTTCTTCACACCTGTCGTGAAGGAAACCAGCATGCAGCTGAACTTCGGAATTCTGCCTCTGGGGTTTTATTTTCTCTCAGCTGCAACAACTTCAATGCAGTCTTTAGTCGCATTTCTACCAGGTTACAGGAATTAACTGTTTGTTCAGAAGACAATGTTGATGTTCATGATATAGAATTGTTACAGTATATCAATGTGGATTGTGCAAAATTAAAACGACTCCTGAAGGAAACAGCATTTAAATTTAAAGCCCTAAAGAAGGTTGCGCAGTTAGCAGTTATAAATAGCCTGGAAAAGGCATTTTGGAACTGGGTAGAAAATTATCCAGATGAATTTACAAAACTGTACCAGATCCCACAGACTGATATGGCTGAATGTGCAGAAAAGCTATTTGACTTGGTGGATGGTTTTGCTGAAAGCACCAAACGTAAAGCAGCAGTTTGGCCACTACAAATCATTCTCCTTATCTTGTGTCCAGAAATAATCCAGGATATATCCAAAGACGTGGTTGATGAAAACAACATGAATAAGAAGTTATTTCTGGACAGTCTACGAAAAGCTCTTGCTGGCCATGGAGGAAGTAGGCAGCTGACAGAAAGTGCTGCAATTGCCTGTGTCAAACTGTGTAAAGCAAGTACTTACATCAATTGGGAAGATAACTCTGTCATTTTCCTACTTGTTCAGTCCATGGTGGTTGATCTTAAGAACCTGCTTTTTAATCCAAGTAAGCCATTCTCAAGAGGCAGTCAGCCTGCAGATGTGGATCTAATGATTGACTGCCTTGTTTCTTGCTTTCGTATAAGCCCTCACAACAACCAACACTTTAAGATCTGCCTGGCTCAGAATTCACCTTCTACATTTCACTATGTGCTGGTAAATTCACTCCATCGAATCATCACCAATTCCGCATTGGATTGGTGGCCTAAGATTGATGCTGTGTATTGTCACTCGGTTGAACTTCGAAATATGTTTGGTGAAACACTTCATAAAGCAGTGCAAGGTTGTGGAGCACACCCAGCAATACGAATGGCACCGAGTCTTACATTTAAAGAAAAAGTAACAAGCCTTAAATTTAAAGAAAAACCTACAGACCTGGAGACAAGAAGCTATAAGTATCTTCTCTTGTCCATGGTGAAACTAATTCATGCAGATCCAAAGCTCTTGCTTTGTAATCCAAGAAAACAGGGGCCCGAAACCCAAGGCAGTACAGCAGAATTAATTACAGGGCTCGTCCAACTGGTCCCTCAGTCACACATGCCAGAGATTGCTCAGGAAGCAATGGAGGCTCTGCTGGTTCTTCATCAGTTAGATAGCATTGATTTGTGGAATCCTGATGCTCCTGTAGAAACATTTTGGGAGATTAGCTCACAAATGCTTTTTTACATCTGCAAGAAATTAACTAGTCATCAAATGCTTAGTAGCACAGAAATTCTCAAGTGGTTGCGGGAAATATTGATCTGCAGGAATAAATTTCTTCTTAAAAATAAGCAGGCAGATAGAAGTTCCTGTCACTTTC

CCCCAGCCTCCTTGCCAACGCCCCCTTTCCCTCTCCCCCTCCCGCTCGGCGCTGACCCCCCATCCCCACCCCCGTGGGAACACTGGGAGCCTGCACTCCACAGACCCTCTCCTTGCCTCTTCCCTCACCTCAGCCTCCGCTCCCCGCCCTCTTCCCGGCCCAGGGCGCCGGCCCACCCTTCCCTCCGCCGCCCCCCGGCCGCGGGGAGGACATGGCCGCGCACAGGCCGGTGGAATGGGTCCAGGCCGTGGTCAGCCGCTTCGACGAGCAGCTTCCAATAAAAACAGGACAGCAGAACACACATACCAAAGTCAGTACTGAGCACAACAAGGAATGTCTAATCAATATTTCCAAATACAAGTTTTCTTTGGTTATAAGCGGCCTCACTACTATTTTAAAGAATGTTAACTATATGAGAATATTTGGAGAAGCTGCTGAAAAAAATTTATATCTCTCTCAGTTGATTATATTGGATACACTGGAAAAATGTCTTGCTGGGCAACCAAAGGACACAATGAGATTAGATGAAACGATGCTGGTCAAACAGTTGCTGCCAGAAATCTGCCATTTTCTTCACACCTGTCGTGAAGGAAACCAGCATGCAGCTGAACTTCGGAATTCTGCCTCTGGGGTTTTATTTTCTCTCAGCTGCAACAACTTCAATGCAGTCTTTAGTCGCATTTCTACCAGGTTACAGGAATTAACTGTTTGTTCAGAAGACAATGTTGATGTTCATGATATAGAATTGTTACAGTATATCAATGTGGATTGTGCAAAATTAAAACGACTCCTGAAGGAAACAGCATTTAAATTTAAAGCCCTAAAGAAGGTTGCGCAGTTAGCAGTTATAAATAGCCTGGAAAAGGCATTTTGGAACTGGGTAGAAAATTATCCAGATGAATTTACAAAACTGTACCAGATCCCACAGACTGATATGGCTGAATGTGCAGAAAAGCTATTTGACTTGGTGGATGGTTTTGCTGAAAGCACCAAACGTAAAGCAGCAGTTTGGCCACTACAAATCATTCTCCTTATCTTGTGTCCAGAAATAATCCAGGATATATCCAAAGACGTGGTTGATGAAAACAACATGAATAAGAAGTTATTTCTGGACAGTCTACGAAAAGCTCTTGCTGGCCATGGAGGAAGTAGGCAGCTGACAGAAAGTGCTGCAATTGCCTGTGTCAAACTGTGTAAAGCAAGTACTTACATCAATTGGGAAGATAACTCTGTCATTTTCCTACTTGTTCAGTCCATGGTGGTTGATCTTAAGAACCTGCTTTTTAATCCAAGTAAGCCATTCTCAAGAGGCAGTCAGCCTGCAGATGTGGATCTAATGATTGACTGCCTTGTTTCTTGCTTTCGTATAAGCCCTCACAACAACCAACACTTTAAGATCTGCCTGGCTCAGAATTCACCTTCTACATTTCACTATGTGCTGGTAAATTCACTCCATCGAATCATCACCAATTCCGCATTGGATTGGTGGCCTAAGATTGATGCTGTGTATTGTCACTCGGTTGAACTTCGAAATATGTTTGGTGAAACACTTCATAAAGCAGTGCAAGGTTGTGGAGCACACCCAGCAATACGAATGGCACCGAGTCTTACATTTAAAGAAAAAGTAACAAGCCTTAAATTTAAAGAAAAACCTACAGACCTGGAGACAAGAAGCTATAAGTATCTTCTCTTGTCCATGGTGAAACTAATTCATGCAGCTCCAAAGCTCTTGCTTTGTAATCCAAGAAAACAGGGGCCCGAAACCCAAGGCAGTACAGCAGAATTAATTACAGGGCTCGTCCAACTGGTCCCTCAGTCACACATGCCAGAGATTGCTCAGGAAGCAATGGAGGCTCTGCTGGTTCTTCATCAGTTAGATAGCATTGATTTGTGGAATCCTGATGCTCCTGTAGAAACATTTTGGGAGATTAGCTCACAAATGCTTTTTTACATCTGCAAGAAATTAACTAGTCATCAAATGCTTAGTAGCACAGAAATTCTCAAGTGGTTGCGGGAAATATTGATCTGCAGGAATAAATTTCTTCTTAAAAATAAGCAGGCAGATAGAAGTTCCTGTCACTTTC

SNP array

Density – 10K, 50/100K, 500K

DNA tests

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, 21, 2 3, 43, 4

1, 31, 3 1, 41, 4 2, 32, 3 2, 42, 4

11223344

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

hereditaryataxia

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