"Familial" versus "sporadic" Intellectual Disability: Contribution of DNA Copy Number Variations

Tehran University of Medical Sciences
Department of Medical Genetics
Presented for PhD Degree
2/15/2012 1Rafati M

Presented by:
Maryam Rafati
Supervised by:
SR Ghaffari MSc MD PhD
Tehran University of Medical Sciences
Department of Medical Genetics
2/15/2012 2Rafati M

 Determining the genetic causes of “Familial MR”
2/15/2012 4Rafati M

 Is there any differences between “Sporadic” and
“Familial” MR regarding their underlying genetic
causes?
 Should a different diagnostic approach be adopted for
“Familial” rather than “Sporadic” MR?
2/15/2012 5Rafati M

 Introduction
 Materials and method
 Results
 Discussion
2/15/2012 6Rafati M

 Mental retardation
 Cerebral palsy
 Abnormal motor actions and postural mechanisms
 Non-progressive abnormalities of the developing brain
 limited, stereotypic, and uncoordinated voluntary movements
 Autism
 A behaviorally defined syndrome characterized by
▪ Atypical social interaction
▪ Disordered verbal and nonverbal communication
▪ Restricted areas of interest
▪ Limited imaginative play
▪ A need for sameness
2/15/2012 8Rafati M

 Mental retardation is a serious and lifelong disability that
places heavy demands on society and the health system
2/15/2012 9Rafati M

“ mental retardation is not something you have, like blue
eyes or a bad heart, nor is it something you are, like
short or thin. It is not a medical disorder or a mental
disorder… mental retardation reflects the “ fit “ between
the capabilities of individuals and the structure and
expectations of their environment. “
2/15/2012 10Rafati M

MR is accepted as having three components:
1) Significantly abnormal intellectual performance,
generally determined by a test of intelligence
2) Onset during development before the age of 18
3) Impairment of the ability to adapt to the environment
2/15/2012 11Rafati M

 Reserved for children five years of age or younger
2/15/2012 12Rafati M

 Global developmental delay (DD) describes
significant delay in two or more of the following
areas:
 Cognition
 Speech/language
 Gross/fine motor skills
 Social/personal skills
 Daily living
2/15/2012 13Rafati M

 Prevalence: 1% - 3%
 Mild MR occurring 7-10 times more frequently than
moderate or severe MR.
 Mild MR: 29.8/1000
 Mod-severe MR: 3.8/1000
 In Iranian population: 1.8 – 2.7%
2/15/2012 14Rafati M

 Estimating the recurrence risk in future pregnancies
 Prenatal diagnosis
 Minimizing the number of diagnostic procedures
 Short-term and long-term prognosis
 Treatment options
2/15/2012 15Rafati M

 Variable depending on the etiology
 From very low ( the same as normal population) to
50% and even in rare situations to 75 -100%
 Irrespective of etiology, empiric risk: 8.4%
2/15/2012 16Rafati M

2/15/2012 17
Study Brothers Sisters All Sibs
Male index case
Herbst and Baird
(1982)
1 in 12 1 in 33 1 in 18
Bundey et al.
(1985)
1 in 10 1 in 20 1 in 13
Female index case
Herbst and Baird
(1982)
1 in 22 1 in 17 1 in 19
Rafati M

 Severity:
2/15/2012 18
• (IQ : 50-70)Mild
• (IQ : 35-50)Moderate
• (IQ : 20-35)Severe
• (IQ < 20)Profound
Rafati M

 Pedigree analysis:
2/15/2012 19
Sporadic
Familial
Rafati M

Genetic
Non-genetic
2/15/2012 20
Prenatal and
perinatal events
Infections
Environmental
factors
Rafati M

2/15/2012 22
33%
3%
9%
1%
54%
Chromosomal abnormalities
Fragile-X syndrome
X-linked MR
Inborn errors of metabolism
De novo dominant mutations
Rafati M

2/15/2012 23
8%
24%
3%
9%
1%
55%
Microscopic aberrations
Submicroscopic aberrations
Fragile-X syndrome
X-linked MR
Inborn errors of metabolism
De novo dominant mutations
Rafati M

Subtelomeric Rearrangements
• 0.5-15%
• Unselected patients: 5%
Common Microdeletion and Microduplication
(CMMSs) Syndromes
• 5.8-9.5%
Genomic Copy Number Variations (CNVs)
• 10-17%
2/15/2012 24Rafati M

 Guidelines based on the assessment of
1. Chromosomal abnormalities
▪ Microscopic
▪ Submicroscopic
2. Fragile-X syndrome
2/15/2012 25Rafati M

 2005 (Van Karnebeek et al.)
 For all the patients:
1. Family history, neurologic and dysmorphologic exam
2. Karyotype
3. Assessment of Fragile-X syndrome
 For highly selected patients:
1. Investigation of Subtelomeric aberrations (FISH)
2. Investigation of common microdeletion and
microduplication syndromes (CMMSs)
2/15/2012 26Rafati M

 Many studies during 2005-2010
1. Karyotype
2. Assessment of Fragile-X syndrome
3. Assessment of DNA copy number differences
(Array-CGH, MLPA, …)
2/15/2012 27Rafati M

 2009 (Hochstenbach et al.), retrospective
investigation of 36325 patients karyotype
 2010 (Miller et al.), analysis of array testing on
21698 patients
 Conclusion:
chromosomal microarray is a first-tier clinical
diagnostic test
2/15/2012 28Rafati M

 Karyotype
 Assessment of fragile-X syndrome
 FISH
 MLPA
 Array-based techniques
 Array-CGH
 SNP Array
 Exome sequencing
 Next-generation sequencing
2/15/2012 29Rafati M

 The first technique for studying chromosomal
abnormalities
 Advantages:
 Genomic
 Detection of balanced abnormalities
 Disadvantages:
 Low resolution (3-5 Mb)
 Labor intensive
2/15/2012 30Rafati M

 The first molecular
cytogenetic
technique
 Advantages:
 Higher resolution
 Disadvantages:
 Limited tergets
2/15/2012 31Rafati M

 Advantages:
 Investigation of 40-50 genomic regions in a single reaction
 Quantitative results (carrier detection)
 Detection of duplications
 High-throughput
 Universal primers
 Relatively inexpensive
 Disadvantages:
 Inability to detect
▪ Balanced abnormalities
▪ Low-level mosaicism
▪ Novel DNA copy number differences
 Limited genomic targets
2/15/2012 33Rafati M

 BAC-array CGH
 Oligonucleotide
array-CGH
2/15/2012 34Rafati M

 Advantages:
 Very high resolution
(>1000000 probes)
 Detection of LOH
2/15/2012 35Rafati M

 Promising technique in
detecting novel genetic
changes (CNVs, single
gene disorders)
 Technique of choice in
near future
2/15/2012 36Rafati M

2/15/2012 38
Sporadic
Patients
Clinical
screening
Laboratory
investigations
Familial
patients
Clinical screening
Questionnaire
Scoring
Laboratory
investigations of
selected families
Rafati M

 Inclusion criteria:
 Developmental delay (DD)
or
 Mental retardation (MR)
or
 Multiple congenital anomalies (MCA)
 Exclusion criteria:
 Known inborn errors of metabolism
 Documented non-genetic causes of DD/MR
▪ Neonatal uncontrolled icter
▪ Perinatal events
2/15/2012 39Rafati M

 Inclusion criteria:
 The presence of at least two individuals in the first
degree relatives affected with DD/MR/MCA
 Exclusion criteria:
 Families with known genetic causes
2/15/2012 40
UNIQUE SAMPLE
SET
Rafati M

 Place:
 Imam Khomeini Hospital
 Duration:
 1386 (Aban) -1390 (Mehr)
2/15/2012 41Rafati M

Completing the questionnaire
2/15/2012 43Rafati M

 Drawing pedigree based on the questionnaires data
 Data entry to the Progeny
2/15/2012 44Rafati M

Number of affected individuals in siblings
(example: 4 affected persons 1+2+3+4=10)
Affected parents: each of them 2 scores
Prenatal onset (sonographic positive
findings)
Multiple organ involvements: each one 1
Non-consanguinity of parents: 1
2/15/2012 46Rafati M

2/15/2012 48
Drawing pedigree
Past medical history
Prenatal
Perinatal
postnatal
Recording past medical history
in detail
Rafati M

2/15/2012 49
Pedigree drawn real time
Rafati M

Informed consent signed
before sampling by patients
and their guardians
2/15/2012 51Rafati M

 Measurement of height
and head circumference
 Neurologic exam
 Dysmorphologic exam
2/15/2012 52Rafati M

2/15/2012 53
 Example: accessory
nipples in 3 affected
individuals in a family
Rafati M

 Heparinized Blood
 EDTA Blood
2/15/2012 54Rafati M

2/15/2012 63
Karyotype
Assessment of Fragile-X
syndrome
Assessment of subtelomeric
rearrangements (MLPA)
Assessment of CMMSs
(MLPA)
Scoring
Array-CGH
SNPArrayRafati M

 G-Banding:
 Lymphocyte culture
 Harvest
 Slide preparation
 Giemsa staining
2/15/2012 64Rafati M

 PCR screening:
 Determining CGG repeat expansion of FMR1 gene
 Triplet-primed PCR:
 Determining pre-mutations and full mutations
2/15/2012 65Rafati M

 Step 1:
 Detection of common chromosomal aneuploidies
 Step 2:
 Assessment of deletions and duplications of F8 gene in
severe hamophilia A patients
2/15/2012 66Rafati M

 Techniques:
 MLPA
▪ Using two alternative probe mixes
▪ Family study to rule out polymorphisms
 FISH (in case of positive findings)
2/15/2012 67Rafati M

 Technique:
 MLPA
 Using 1 screening and 2 confirmatory probe mixes
2/15/2012 68Rafati M

Cri du Chat syndrome MECP2 / Xq28
duplication
1p36 deletion syndrome
DiGeorge syndrome 22q Rubinstein-Taybi
syndrome
2p16 microdeletion
DiGeorge region 2 Smith-Magenis syndrome 3q29 microdeletion
Langer-Giedion syndrome Sotos syndrome 5q35.3 9q22.3 microdeletion
Miller-Dieker syndrome WAGR syndrome 15q24 deletion syndrome
NF1 microdeletion
syndrome
Williams syndrome 17q21 microdeletion
Prader-Willi / Angelman Wolf-Hirschhorn 4p16.3 22q13 / Phelan-Mcdermid
2/15/2012 69Rafati M

Number of affected individuals 1+2+3+…
Non-consanguinity +3
Recurrent abortion +2
Pedigree analysis (Dominant) +3
Multiple congenital anomalies +3
Severity of MR
Moderate +2
Severe +3
Affected parents (each of them) +2
Dysmorphism +2
 Negative scores
2/15/2012 71
Number of normal siblings -1-2-3…
Consanguinity -3
Pedigree analysis (Recessive) -3
Pedigree analysis (X-linked) -3
•Positive scores
Rafati M

2/15/2012 72
array-CGH
Rafati M

 Array-CGH
 Agilent 44K
 EmArray Cyto6000
 SNP Array
 Illumina humanOmni 1-Quad
 1134514 markers
 Resolution: 6 kbp
2/15/2012 73Rafati M

Number of families Number of patients
Sporadic patients 279 279
Familial patients
• First step 551 1260
• Second step (questionnaire) 355 647
Total 830 1539
2/15/2012 75Rafati M

Number of families Number of patients
Sporadic 55 55
Familial 116 371
Total 171 426
2/15/2012 76Rafati M

Diagnosis Number of patients Diagnostic method
 Chromosomal abnormalities
 Numerical 23 karyotype
 Structural 9 karyotype
• Mosaicism 4 karyotype
 Syndromes
 DiGeorge Syndrome 2 FISH
 Miller-Dieker Syndrome 1 Clinical and paraclinical findings
 Rubinstein-Taybi Syndrome 1 Clinical and paraclinical findings
 Kabuki Syndrome 1 Clinical and paraclinical findings
 Hallermann-Streiff Syndrome 1 Clinical and paraclinical findings
 Laurence-Moon-Bardet-Biedl
Syndrome
1 Clinical and paraclinical findings
2/15/2012 78Rafati M

 Single gene disorders
 Phenylketonuria (PKU) 3 Measurement of Phenylalanine level
 Methylmalonic Acidemia (MMA) 1 MS/MS
Aminoacids HPLC
 Maple Syrup Urine Disease
(MSUD)
2
 GM2 Gangliosidosis (Tay-Sachs
Disease)
2 Enzyme activity assessment of
Hexosaminidase A
 GM2 Gangliosidosis (Sandhoff
Disease)
1 assessment of Hexosaminidase A and B
Enzyme activity
 Niemenn-Pick Disease 1
 Mucopolysaccharidosis type I
(MPS1)
1
 Krabbe Disease 1 Whole gene sequencing
 Non-ketotic Hyperglycinemia
(Glycin Encephalopathy)
1 Whole gene sequencing
 Metachromatic Leukodystrophy 1 assessment of arylsulfatase Enzyme
activity
 Saposine-B Deficiency 1 Whole gene sequencing
 Total 582/15/2012 79Rafati M

2 3
4
5
6
8
12
49.40%
30.20%
10.60%
4.70%
1.70%
0.40%
0%
36.30% 36.30%
17.50%
5%
2%
2%
0.98%
Screening phase Laboratory phase
2/15/2012 81Rafati M

 STEP 1:
 Prenatal diagnosis of chromosomal aneuploidies
 As a stand-alone test:
2/15/2012 83
74 amniotic
fluid samples
5 Trisomy 21
1 XXY
Rafati M

 STEP 2:
2/15/2012 84
347 Previously
Investigated Severe
Hemophilia A Patients
10 Patients
No PCR amplification in
some exons
Confirmation of deletions
Determining the deletion
extension
Carrier detection
1 patient with no
mutation detected
Duplication
of exon 24
Rafati M

 Optimization
2/15/2012 85Rafati M

Genetic test Abnormal finding Number (%)
Karyotype Trisomy 21 4 (7.2%)
Partial deletion of 9p
telomeric region
1 (1.8%)
Fragile-X syndrome CGG repeat expansion 1 (1.8%)
Subtelomeric
rearrangements
Duplication of 2p telomeric
region
1 (1.8%)
CMMSs Williams syndrome 1 (1.8%)
Cat Eye syndrome 1 (1.8%)
Cytogenetically visible
chromosomal abnormalities
5 (9%)
Cryptic chromosomal
abnormalities
3 (5.4%)
Fragile-X syndrome 1 (1.8%)
Total 9 (16.3%)/55
2/15/2012 86Rafati M

Summary of clinical findings:
 Global Developmental delay
 Mental retardation
 Facial dysmorphic features
▪ Micrognathia
▪ Midface hypoplasia
▪ Wide mouth
▪ Prominent upper and lower lips
▪ Short philtrum
▪ Full nose tip
▪ Periorbital fullness
 Non-facial dysmorphic features
▪ Additional skin creases of the fingers
 Personality
▪ Outgoing overfriendly personality
 Investigations with normal results
 Karyotype
 Visual status
▪ Hearing status 2/15/2012 87Rafati M

Summary of clinical findings:
 Developmental delay
 Hypotonia
 Facial dysmorphic features
▪ Dolichocephaly
▪ Cleft palate
▪ Low-set ears
▪ External ears deformity
 Failure to thrive (FTT)
 Congenital Heart Disease (CHD)
 Large ASD with left to right shunt
 Bilateral inguinal hernia
2/15/2012 90Rafati M

Patient results
Investigated genes using 4
MLPA probemixes
GenesGenomic regions
GainP070IL17RA
Cat eye syndrome
region
-SLC25A18
GainP036BID
-MICAL3
-USP18
-LCR22-A
GainP064CLTCL1
commonly
-deleted
DiGeorge
region
DiGeorge
region
-HIRA
GainP064CDC45
GainP245 / P064CLDN5
GainP245GP1BB
-TBX1
-TXNRD2
-DGCR8
GainP064ARVCF
LCR22-B
-ZNF74
GainP064KLHL22
-MED15
LCR22-C
NormalP245 / P064SNAP29
Not Investigated
-LZTR1
-LCR22-D
-HIC2
-PPIL2
-TOP3B
LCR22-E
-RTDR1
-GNAZ
-RTDR1
-RAB36
LCR22-F
2/15/2012 92Rafati M

 All normal
 Inversion of chromosome 2 (normal variation)
2/15/2012 94Rafati M

Description Number (%)
Diagnosed families 8 (6.9%)
Diagnosed patients 23
Males 21 (91.3%)
Females 2 (8.7%)
2/15/2012 95Rafati M

 Control (unaffected)
 Control (affected)
 Contrlo (unaffected)
 MR-63 (No Band)
 MR-35 (No Band)
 Control (unaffected)
 Control negative (No DNA)
 Size marker (100-1000bp)
2/15/2012 96
1 2 3 4 5 6 7 8 1 2 3 4 5 6
•Control (affected)
•MR-69-MO (Mother)
•MR-69-S2M (Normal male)
•MR-69-P2M (Affected male)
•Size marker (100-1000bp)
•Control negative (No DNA)
Rafati M

2/15/2012 98
Family ID
MLPA
probemix
ResultsType of aberrations
MR-92
P036
P070
Partial monosomy of 13qter and partial trisomy
of 9pter
Clinically significant pathogenic
changes
MR-51
P036
P070
Xpter and Xqter Gain
MR-130
P036
P070
1pter Gain
Aberrations with unknown
clinical significance
MR-130
P036
P070
12qter Gain
MR-1P0703pter loss
Genomic variants
MR-1P0704qter Gain
MR-61P0704qter Gain
MR-105P0704qter Gain
MR-109P03621q11.2 Gain
MR-116P0704qter loss (homozygous)Rafati M

 Non-consanguineous healthy parents
 History of one abortion at 12 weeks of gestation
 Two infantile deaths due to Multiple Congenital
Anomalies (MCA)
 One affected child with developmental delay/mental
retardation (DD/MR)
2/15/2012 101Rafati M

 Second pregnancy:
 Cleft lip/cleft palate
 Intestinal atresia
 Death at 2 months of age
 Failure to thrive (FTT)
2/15/2012 102Rafati M

 Third pregnancy: (A 12-year old girl )
 At birth:
 Wt: 2850 gr
 HC: 33 cm
 Microcephaly
 Poor sucking (feeding difficulties)
 Facial Dysmorphism:
2/15/2012 103Rafati M

▪ Hypertelorism
▪ Ptosis
▪ Epicanthal fold
▪ Low-set ears
▪ Broad nasal bridge
▪ Long forehead
▪ Broad distance
between 1st and 2nd
toes
2/15/2012 104Rafati M

 Developmental delay/mental retardation
 Intractable seizure (onset: 3.5 y)
 Behavioral disorder
 Autistic features
2/15/2012 105Rafati M

 Karyotype: 46,XX
2/15/2012 106Rafati M

 Fourth pregnancy:
 Prenatal:
▪ IUGR
▪ Choanal atresia
▪ Polyhydramnios
▪ Intestinal obstruction
 Prenatal diagnosis (Cordocentesis):
 karyotype: normal
 Postnatal:
 Club foot
 Duodenal atresia
 Death at 3 months of age
2/15/2012 107Rafati M

 Technique: MLPA
 Result:
• Deletion of 13q
telomeric region
• Duplication of 9p
telomeric region
2/15/2012 108Rafati M

 Confirmatory test: FISH
 Result:
• Partial monosomy of
13qter
• Partial trisomy of 9pter
2/15/2012 109
9pter
13qter
Rafati M

 Technique: Metaphase
FISH
 Mother: normal
 Father: balanced
translocation of 13q and 9p
telomeric regions
2/15/2012 110
9pter
13qter
Chr 9
Chr 13
Rafati M

 A familiy with hereditary Williams syndrome
 Others: no deletion or duplication detected
2/15/2012 111Rafati M

 Clinical findings:
▪ Developmental delay (most prominently in
walking)
▪ Mental retardation
▪ Growth retardation
 Dysmorphic features:
▪ Microcephaly
▪ Micrognathia
▪ Midface hypoplasia
▪ Wide mouth
▪ Prominent lower lip
▪ Long philtrum
▪ Strabismus
 Personality: outgiong overfriendly
personality
 Echocardigraphy
 Pulmonary stenosis 2/15/2012 113Rafati M

 Summary of clinical and paraclinical findings
 At age of 37-year:
 Ht: 165.5 cm (<5th centile)
 HC: 53.5 cm (<5th centile)
 Dysmorphic features:
 Micrognathia
 Strabismus
 Periorbital fullness
 Long philtrum
 No hypertension (blood pressure: 125/80 mmHg)
 Echocardiography:
 Mild aortic stenosis
 Tricuspid valva regurgitation
 Mitral valave regurgitation
 Mitral valve prolapse
2/15/2012 114Rafati M

Reference
Number of Reported
Families (Cases)
Method of WBS
Ascertainment
Molecular
Confirmation
Technique
Morris et al. (1993) 3 (6) Clinical manifestations Quantitative southern
analysis (Ewart et al
(1993) confirmed the
deletion in two of the
families]
Sadler et al. (1993) 1 (2) Clinical manifestations -
Ounap et al. (1999) 1 (2) Clinical manifestations FISH1 (just the son was
investigated, the mother
was not available)
Pankau et al. (2001) 2 (4) Clinical manifestations FISH (both of the
patients)
Metcalfe et al. (2005) 1 (2) Clinical manifestations FISH (both of the
patients)
The present study 1(2) Screening for cryptic
chromosomal
abnormalities
MLPA2 ((both of the
patients))
2/15/2012 117Rafati M

 Clinically significant findings:
 Related to familial MR: 0
 Unrelated to familial MR: 1
▪ Charcot-Marie-Tooth
 Benign copy number changes: 3 families
2/15/2012 119Rafati M

2/15/2012 122
case a CGH ISCN nomenclature # probes
Size
loss(bp) Size gaine (bp) Clinical target
MR-82 arr chg 6P25.3 (204528-284802)X1 6 80274 Benign CNC
arr chg 8P23.1 (7040596-8117330)X1 6 1076762 Benign CNC
arr chg 10q26.3 (135104029-135227522)X3 6 123,494
<500Kb, CYP2E1 gene, SYCE1
gene
arr chg 16p11.2-11.1 (34339543-34584850)X3 5 245,308Benign CNC
arr chg 17p12 (14052497-
15382791)X3 38 1,330,295
CNC with
significance
pathogenic effect,
COX10,
HS3ST3B1, PMP22
Genes
Rafati M

 Summary of results
 Comparison of “Familial” MR with “Sporadic” MR
 Comparison of the current study with the previous
investigations of “Familial” MR
 Diagnostic algorithms
 Suggestions
2/15/2012 127Rafati M

0.00%
2.00%
4.00%
6.00%
8.00%
10.00%
12.00%
14.00%
16.00%
Sporadic MR
(current study)
Sporadic MR
(previous studies)
2/15/2012 128Rafati M

0%
2%
4%
6%
8%
Familial MR (current
study)
2/15/2012 129Rafati M

371 Patients from 116 Families
2/15/2012 130Rafati M

 Sporadic MR: 9.5%
 Present study: 0% (371
patients from 116
families)
0.00%
2.00%
4.00%
6.00%
8.00%
10.00%
Sporadic
MR
Familial
MR
Cytogenetically visible
abnormalities
2/15/2012 131Rafati M

 Sporadic MR: 2-5%
(mean: 3%)
 Present study: 7% (371
patients from 116
families)
0%
1%
2%
3%
4%
5%
6%
7%
Sporadic MR Familial MR
Fragile-X syndrome
2/15/2012 132Rafati M

 Sporadic MR: 0.5-9%
(mean: 5%)
 Present study: 0.9%
(248 patients from 108
families)
0%
1%
2%
3%
4%
5%
Subtelomeric
Rearrangements
2/15/2012 133Rafati M

 Reports in support of the importance of “positive
family history” (most of the studies)
 Reports with conflicting data
2/15/2012 134Rafati M

 Positive family history is the main single predicting factor of
subtelomeric rearrangements
2/15/2012 136Rafati M

 Our results could be compared with the prevalence of
hereditary subtelomeric aberrations (0-2%)
 The present study finding:
Severity of MR, dysmorphism and multiple congenital
anomalies are more important than positive family
history by alone
2/15/2012 138Rafati M

 Sporadic MR: 5.8-9%
 Present study: 0.9% (245
patients from 107 families)
 More coverage of common
syndromes in this study (18
CMMSs)
0%
1%
2%
3%
4%
5%
CMMSs
2/15/2012 140Rafati M

 Mechanisms:
 De novo: misalignment during recombination due to LCRs
 Hereditary:
▪ Balanced translocation in the parents
▪ Autosomal dominant transmissions
2/15/2012 141Rafati M

 Sporadic MR: 10-17%
 The findings were not
explanatory for
“familial” mental
retardation
0%
2%
4%
6%
8%
10%
12%
14%
16%
18%
Genomic CNVs
2/15/2012 143Rafati M

0
5
10
15
Familial MR
Sporadic MR
2/15/2012 145Rafati M

0.00%
5.00%
10.00%
15.00%
20.00%
25.00%
30.00%
35.00%
40.00%
Chromosomal
Abnormalities
Fragile-X syndrome
2/15/2012 146Rafati M

 2011, Jehee et al.
Karyotype + MLPA investigations of subtelomeric
rearrangements and CMMSs = detection of 76.5%
of all chromosomal abnormalities detected by whole
genomic array screening
2/15/2012 147Rafati M

2/15/2012 148
No
pathogenic
CNV is
expected in
the remained
families
More coverage
on CMMSs
Karyotype
MLPA, subtelomeric
aberrations
MLPA, CMMSs
75.6%
No pathogenic
change in array-
CGH study of
highly selected
patients
Rafati M

 2009-2011, Hamdan et al.
 Investigation of 197 synaptic genes (glutamate receptor, …)
in 95 patients: 11 new mutations found
 2011, Nature, Vissere et al.
 Exome sequencing of 10 patients with sporadic MR: 6
pathogenic mutations found (60%)
 More than all of the previous investigations
New paradigm of de novo dominant mutations in MR
2/15/2012 150Rafati M

0.00%
20.00%
40.00%
60.00%
80.00%
100.00%
Sporadic MR
Familial MR
Chromosomal
Abnormalities
Fragile-X syndrome
Single gene disorders
2/15/2012 151Rafati M

 Few published studies
 Studies on Iranian population
 Autosomal recessive MR (2011, Najmabadi et al.)
 X-linked MR
 A. R. Pouya et al. Fragile X syndrome screening of families with consanguineous
and non-consanguineous parents in the Iranian population. European Journal of
Medical Genetics (2009), doi:10.1016/j.ejmg.2009.03.014
 Najmabadi H et al. Homozygosity mapping in consanguineous families reveals
extreme heterogeneity of non-syndromic autosomal recessive mental retardation
and identifies 8 novel gene loci. Hum Genet. 2007 Mar;121(1):43-8. Epub 2006
Nov 21
 Kahrizi K et al. An autosomal recessive syndrome of severe mental retardation,
cataract, coloboma and kyphosis maps to the pericentromeric region of
chromosome 4. Eur J Hum Genet. 2009 Jan;17(1):125-8. Epub 2008 Sep 10.2/15/2012 153Rafati M

55%
15%6%
24%
First Cousin
Second Cousin
76%
24%
Parents Relationship
Consanguineous
Non-consanguineous
2/15/2012 154Rafati M

78%
5%
17%
Pedigree analysisAutosomal Recessive Established X-linked
Putative X-linked
2/15/2012 155Rafati M

40%
60%
Selected families
Consanguineous
Non-consanguineous
39%
49%
6% 2% 4%
Screening phase
Non-consanguinous
First Cousin
First Cousin, Once removed
Second Cousin
Far related
2/15/2012 156Rafati M

66%
24%
10%
Chromosomal or Autosomal Dominant
Autosomal Recessive
X-linked
2/15/2012 157Rafati M

0%
20%
40%
60%
80%
Autosomal
Recessive X-Linked
Autosomal
Dominant
The present study
Najmabadi et al.
2/15/2012 158Rafati M

2/15/2012 161
Karyotype
Numerical or Structural Chromosomal
Abnormality Normal
Assessment of Fragile-
X syndrome
Fragile-X
syndrome No CGG repeat expansion
Availability of array-based techniques + cost
Aavailable
array-CGH or
SNP array
Pathogenic
Copy Number
Variation
No
pathogenic
change
Exome Sequencing (de novo
dominant mutations)
New Suggestion
Rafati M

2/15/2012 162
Karyotype
Numerical or Structural Chromosomal
Abnormality Normal
Assessment of Fragile-
X syndrome
Fragile-X
syndrome No CGG repeat expansion
Availability of array-based techniques + cost
Aavailable
array-CGH or
SNP array
Pathogenic
Copy Number
Variation
No
pathogenic
change
Exome Sequencing (de novo
dominant mutations)
Not
Available
MLPA (Subtelomeric
Rearrangements + CMMSs)
Subtelomeric
Aberration
CMMSs
No
pathogenic
change
Rafati M

2/15/2012 164
Pedigree
Analysis
Autosomal
Recessive
Assessment
of Known
single gene
disorders
Mutation
Detected
No Mutation
Detected
Exome
Sequencing
Next-
generation
Sequencing
X-linked
Assessment
of Fragile-X
Syndrome
Fragile-X
Syndrom
e
No CGG
repeat
Expansion
Assessment of
Known XLMR
Mutation
Detected
No Mutation
Detected
Exome
Sequencing
Next-
generation
Sequencing
Autosomal
Dominant
Dysmorphism
Multiple Congenital Anomalies
Recurrent Abortion/Infertility
Yes
Karyotyp
e
Numerical or
Structural
Abnormalities
Normal
Availability of
array-based
techniques +
cost
Aavailable
array-CGH or
SNP array
Pathogenic
Copy Number
Variation
No pathogenic
change
Exome Sequencing
(de novo dominant
mutations)
Not Available
MLPA
(Subtelomeric
Rearrangeme
nts + CMMSs)
Subtelomeric
Aberration
CMMSs
No pathogenic
change
Rafati M

2/15/2012 165
Pedigree
Analysis
Autosomal
Recessive
Assessment
of Known
single gene
disorders
Mutation
Detected
No Mutation
Detected
Exome
Sequencing
Next-
generation
Sequencing
X-linked
Assessment
of Fragile-X
Syndrome
Fragile-X
Syndrom
e
No CGG
repeat
Expansion
Assessment of
Known XLMR
Mutation
Detected
No Mutation
Detected
Exome
Sequencing
Next-
generation
Sequencing
Autosomal
Dominant
Dysmorphism
Multiple Congenital Anomalies
Recurrent Abortion/Infertility
Yes
Karyotyp
e
Numerical or
Structural
Abnormalities
Normal
Availability of
array-based
techniques +
cost
Aavailable
array-CGH or
SNP array
Pathogenic
Copy Number
Variation
No pathogenic
change
Exome Sequencing
(de novo dominant
mutations)
Not Available
MLPA
(Subtelomeric
Rearrangeme
nts + CMMSs)
Subtelomeric
Aberration
CMMSs
No pathogenic
change
No
Exome
Sequencing
Next-generation
sequencing
Unknow
n
Assessment
of Fragile-X
syndrome
Fragile-X
syndrom
e
No CGG
repeat
expansion
New Suggestion
Rafati M

 Comprehensive Genetic Center, Imam Khomeini
Hospital
 Department of Medical Genetics, TUMS
 Hope Generation Foundation
 Tehran Welfare Organization
 Gene clinic
2/15/2012 167Rafati M

"Familial" versus "sporadic" Intellectual Disability: Contribution of DNA Copy Number Variations

Recommended

Recommended

More Related Content

Similar to "Familial" versus "sporadic" Intellectual Disability: Contribution of DNA Copy Number Variations

Similar to "Familial" versus "sporadic" Intellectual Disability: Contribution of DNA Copy Number Variations (20)

More from Maryam Rafati

More from Maryam Rafati (6)

Recently uploaded

Recently uploaded (20)

"Familial" versus "sporadic" Intellectual Disability: Contribution of DNA Copy Number Variations