# Chromosomal Aberrations in Pediatric Patients with Developmental Delay/Intellectual Disability: A Single-Center Clinical Investigation

Authors: Ting Hu; Zhu Zhang; Jiamin Wang; Qinqin Li; Hongmei Zhu; Yi Lai; He Wang; Shanling Liu
Journal: BioMed Research International
 (2019)

---

## Abstract

Introduction. Chromosomal microarray analysis (CMA) has currently been considered as the first-tier genetic test for patients with developmental delay/intellectual disability (DD/ID) in many countries. In this study, we performed an extensive assessment of the value of CMA for the diagnosis of children with ID/DD in China. Methods. A total of 633 patients diagnosed with DD/ID in West China Second University Hospital, Sichuan University, were recruited from January 2014 to March 2019. The patients were classified into 4 subgroups: isolated DD/ID, DD/ID with multiple congenital anomalies (MCA), isolated autism spectrum disorders (ASDs), and DD/ID with epilepsy. CMA was performed on Affymetrix 750K platform. Results. Among the 633 patients, 127 cases were identified as having pathogenic copy number variations (pCNVs) with an overall positive rate of 20.06%. Of the 127 cases with abnormal results, 76 cases had 35 types of microdeletion/microduplication syndromes (59.84%) including 5 cases caused by uniparental disomy (UPD), and 18 cases had unbalanced rearrangements (14.17%) including 10 cases inherited from parental balanced translocations or pericentric inversions. The diagnostic yields of pCNVs for the subgroups of isolated DD/ID, DD/ID with MCA, isolated ASD, and DD/ID with epilepsy were 18.07% (60/332), 34.90% (52/149), 3.70% (3/81), and 16.90% (12/71), respectively. The diagnostic yield of pCNVs in DD/ID patients with MCA was significantly higher than that of the other three subgroups, and the diagnostic yield of pCNVs in isolated ASD patients was significantly lower than that of the other three subgroups (p<0.05). Conclusion. Microdeletion/microduplication syndromes and unbalanced rearrangements are probably the main genetic etiological factors for DD/ID. DD/ID patients with MCA have a higher rate of chromosomal aberrations. Parents of DD/ID children with submicroscopic unbalance rearrangements are more likely to have chromosome balanced translocations or pericentric inversions, which might have been missed by karyotyping. CMA can significantly improve the diagnostic rate for patients with DD/ID, which is of great value for medical management and clinical guidance for genetic counseling.


---

## Body

## 1. Introduction

Developmental delay/intellectual disability (DD/ID) affects approximately 3% of the general population [1]. In China, 11,820,000 people were diagnosed with DD/ID, of whom 954,000 were younger than 6 years of age [2]. Taking care of a patient with DD/ID exerts a substantial financial and emotional burden on his/her family and society. Approximately more than half of DD/ID cases resulted from genetic etiologies, including chromosomal abnormalities, microduplication or microdeletion syndromes, and monogenic disorders [3]. Other etiologies include teratogenic exposures, perinatal asphyxia, infections, etc. [4].Submicroscopic chromosomal aberrations (copy number variants, CNVs) play a significant role in the pathogenesis of DD/ID, and the diagnostic yield of chromosomal microarray analysis- (CMA-) detected CNVs associated with these disorders ranges from 12% to 29% [5–8]. Currently, the clinical utility of CMA has been recognized by several professional societies and has been recommended as the first-tier genetic test for patients with unexplained DD/ID, autism spectrum disorders (ASDs), and/or multiple congenital anomalies (MCAs) [9–12]. In this study, we investigated 633 Chinese children with unexplained DD/ID combined with other conditions by the Affymetrix® CytoScan™ 750K Array over a period of 5 years and extensively assessed the value of CMA for the diagnosis of children with DD/ID.


## 2. Methods

### 2.1. Patients

A total of 633 Chinese patients with varying degrees of DD/ID (359 males; 274 females), with ages from 3 months to 17 years, were recruited from the Department of Neurological Rehabilitation at West China Second University Hospital, Sichuan University, from January 2014 to March 2019. All patients were classified into 4 subgroups: isolated DD/ID (n = 332), DD/ID with MCA (n = 149), isolated ASD (n = 81), and DD/ID with epilepsy (n = 71).The detailed evaluations of the patients included prenatal/birth history, family history, pedigree, physical examinations, and imageological examination. The inclusive criteria were as follows: DD/ID diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) with IQ/DQ < 70 assessed by the Gesell Development Scale, the Wechsler Preschool and Primary Scale Intelligence, or the Wechsler Intelligence Scale for Children. The exclusion criteria were as follows: (1) history of hypoxia, toxication, central nervous system infection, and cranial trauma; (2) evidence of recognizable inherited metabolic disorder; (3) typical clinical manifestation of Rett syndrome for female patients; (4) mutations in the FMR1 gene for male patients; and (5) fetus or newborns with multiple malformations.The peripheral blood samples of the patients were analyzed by CMA. Informed consent was obtained from their mentally healthy parents before detection. In addition, the peripheral blood samples of their parents underwent CMA to determine whether the CNVs of the patients were inherited orde novo to determine the clinical significance. The research was approved by the Medical Ethics Committee of West China Second University Hospital, Sichuan University.


### 2.2. Chromosomal Microarray Analysis

Whole genomic DNA was extracted from peripheral blood cells of each patient and his or her parents using QIAamp DNA Blood Mini Kit (Qiagen, Valencia, CA, USA) and subjected to CMA-single nucleotide polymorphism (SNP) array analysis by using the Affymetrix® CytoScan™ 750K Array (Affymetrix, Santa Clara, CA, USA). The procedure was described in our previous publication [13].When the fragment size of absence of heterozygosity (AOH) was larger than one-third of the chromosome, analysis software UPD tool_0.2 was used to separate the AOH into uniparental disomy (UPD) or consanguinity by comparison with the parental results.The detected CNVs were systematically evaluated for clinical significance. The procedure was also described in our previous publication [13].


### 2.3. Chromosomal Karyotyping

When a gain and a loss of more than 5 Mb were simultaneously detected at one end of two different chromosomes or at the both ends of a single chromosome in one sample, peripheral blood samples of the normal parents were karyotyped to confirm whether the parents had chromosomal balanced translocations or inversions.


### 2.4. Statistical Analysis

Statistical analysis was performed by using SPSS software, version 24. The frequency of pCNVs was compared among subgroups of isolated DD/ID, DD/ID with MCA, DD/ID with ASD, and DD/ID with ASD by using the chi-square test. A value ofp<0.05 was considered to indicate statistical significance.


## 2.1. Patients

A total of 633 Chinese patients with varying degrees of DD/ID (359 males; 274 females), with ages from 3 months to 17 years, were recruited from the Department of Neurological Rehabilitation at West China Second University Hospital, Sichuan University, from January 2014 to March 2019. All patients were classified into 4 subgroups: isolated DD/ID (n = 332), DD/ID with MCA (n = 149), isolated ASD (n = 81), and DD/ID with epilepsy (n = 71).The detailed evaluations of the patients included prenatal/birth history, family history, pedigree, physical examinations, and imageological examination. The inclusive criteria were as follows: DD/ID diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) with IQ/DQ < 70 assessed by the Gesell Development Scale, the Wechsler Preschool and Primary Scale Intelligence, or the Wechsler Intelligence Scale for Children. The exclusion criteria were as follows: (1) history of hypoxia, toxication, central nervous system infection, and cranial trauma; (2) evidence of recognizable inherited metabolic disorder; (3) typical clinical manifestation of Rett syndrome for female patients; (4) mutations in the FMR1 gene for male patients; and (5) fetus or newborns with multiple malformations.The peripheral blood samples of the patients were analyzed by CMA. Informed consent was obtained from their mentally healthy parents before detection. In addition, the peripheral blood samples of their parents underwent CMA to determine whether the CNVs of the patients were inherited orde novo to determine the clinical significance. The research was approved by the Medical Ethics Committee of West China Second University Hospital, Sichuan University.


## 2.2. Chromosomal Microarray Analysis

Whole genomic DNA was extracted from peripheral blood cells of each patient and his or her parents using QIAamp DNA Blood Mini Kit (Qiagen, Valencia, CA, USA) and subjected to CMA-single nucleotide polymorphism (SNP) array analysis by using the Affymetrix® CytoScan™ 750K Array (Affymetrix, Santa Clara, CA, USA). The procedure was described in our previous publication [13].When the fragment size of absence of heterozygosity (AOH) was larger than one-third of the chromosome, analysis software UPD tool_0.2 was used to separate the AOH into uniparental disomy (UPD) or consanguinity by comparison with the parental results.The detected CNVs were systematically evaluated for clinical significance. The procedure was also described in our previous publication [13].


## 2.3. Chromosomal Karyotyping

When a gain and a loss of more than 5 Mb were simultaneously detected at one end of two different chromosomes or at the both ends of a single chromosome in one sample, peripheral blood samples of the normal parents were karyotyped to confirm whether the parents had chromosomal balanced translocations or inversions.


## 2.4. Statistical Analysis

Statistical analysis was performed by using SPSS software, version 24. The frequency of pCNVs was compared among subgroups of isolated DD/ID, DD/ID with MCA, DD/ID with ASD, and DD/ID with ASD by using the chi-square test. A value ofp<0.05 was considered to indicate statistical significance.


## 3. Results

### 3.1. Diagnostic Yields of pCNVs

We detected 149 pCNVs (including 5 UPDs) in 127 cases (65 males; 62 females), accounting for 20.06% of the series (Table1). These pCNVs, including 100 deletions and 44 duplications, were highly variable in size, ranging from 223 kb to 102,400 kb (Table 2).Table 1
Summary of CMA results in 633 patients.
Category
Microarray results (%)
Total
Pathogenic CNVs
VUS
Normal
Isolated DD/ID
60 (18.07)
5 (1.51)
267 (80.42)
332
DD/ID with MCA
52 (34.90)
0 (0.00)
97 (65.10)
149
DD/ID with ASD
3 (3.70)
0 (0.00)
78 (96.30)
81
DD/ID with epilepsy
12 (16.90)
2 (2.82)
57 (80.28)
71
Total
127 (20.06)
7 (1.11)
499 (78.83)
633
DD: developmental delay; ID: intellectual disability; MCA: multiple congenital anomaly; ASD: autism spectrum disorder.Table 2
Characteristics of pCNVs detected by CMA among the 127 patients.
No.
Clinical feature
Age
Gender
CMA results
Sizes of CNVs (kb)
Copy number
Syndromes
OMIM gene
Inherited orde novo
1
ID
17 y
F
arr[GRCh37] 12p12.1(21369190_25634175)x1
3995
Loss
Lamb-Shaffer syndrome
SOX5
de novo
2
DD
3 y
F
arr[GRCh37] 4p16.3p16.1(68345_8066350)x1
7998
Loss
Wolf–Hirschhorn syndrome
de novo
3
ID
5 y
M
arr[GRCh37] 7q11.23(72723370_74136633)x1
1413
Loss
Williams-Beuren syndrome
ELN
de novo
4
DD
4 y
M
arr[GRCh37] Xq28(153118233_153878720)x2
760
Gain
Xq28 (MECP2) duplication
MECP2
Inherited from normal mother
5
ID
5 y
M
arr[GRCh37] 15q11.2q26.3(22817870_102397317)hmz
79,579
LOH (paternal UPD15)
Angelman syndrome
UBE3A
de novo
6
DD
4 y
M
arr[GRCh37] 7q11.23(72718123_74136633)x1
1419
Loss
Williams-Beuren syndrome
ELN
de novo
7
DD
19 m
M
arr[GRCh37] 15q11.2q13.1(23632677_28704050)x1
5071
Loss
Angelman syndrome
UBE3A
de novo
8
ID
16 y
F
arr[GRCh37] 7q11.23(72718123_74141494)x1
1423
Loss
Williams-Beuren syndrome
ELN
de novo
9
DD
16 m
M
arr[GRCh37] 11p11.2(44506359_47897669)x1
3391
Loss
Potocki–Shaffer syndrome
MYBPC3
de novo
10
ID
6 y
M
arr[GRCh37] 15q11.2q13.1(23290787_28526905)x1
5147
Loss
Angelman syndrome
UBE3A
de novo
11
ID
7 y
M
arr[GRCh37] Xq28(153030708_155233098)x2
2202
Gain
Xq28 (MECP2) duplication
MECP2
Inherited from normal mother
12
ID
16 y
F
arr[GRCh37] 15q11.2q26.3(22817870_102397317)hmz
79,579
LOH (paternal UPD15)
Angelman syndrome
UBE3A
de novo
13
ID
6 y
M
arr[GRCh37] 7q11.23 (72611954_75147402)x1
1745
Loss
Williams-Beuren syndrome
ELN
de novo
14
ID
5 y
M
arr[GRCh37] 16p13.3(85880_2045435)x1
1960
Loss
ATR-16 syndrome
de novo
15
DD
17 m
F
arr[GRCh37] 7q11.23(72692112_74184702)x1
1496
Loss
Williams-Beuren syndrome
ELN
de novo
16
ID
16 y
F
arr[GRCh37] 22q13.33(50974299_51197766)x1
223
Loss
22q13 deletion syndrome (Phelan–Mcdermid syndrome)
SHANK3
de novo
17
ID
9 y
F
arr[GRCh37] 17p11.2 (16761814_20304118)x3
3542
Gain
Potocki–Lupski syndrome (17p11.2 duplication syndrome)
de novo
18
DD
9 m
F
arr[GRCh37] 7q11.23(72723370_74136633)x1
1413
Loss
Williams-Beuren syndrome
ELN
de novo
19
ID
6 y
F
arr[GRCh37] 22q13.31q13.33(48234841_51197766)x1
2963
Loss
22q13 deletion syndrome (Phelan–Mcdermid syndrome)
SHANK3
de novo
20
DD
13 m
F
arr[GRCh37] 22q11.21(18919477_21436003)x3
2516
Gain
22q11 duplication syndrome
de novo
21
ID
9 y
M
arr[GRCh37] 7q11.23(72723370_74136633)x1
1413
Loss
Williams-Beuren syndrome
ELN
de novo
22
ID
12 y
M
arr[GRCh37] 16p13.11(14892975_16538596)x3
1646
Gain
16p13.11 recurrent microduplication (neurocognitive disorder susceptibility locus)
Inherited from normal mother
23
ID
5 y
F
arr[GRCh37] 15q11.2q13.1(22770421_28560664)x3
5790
Gain
15q11-q13 duplication syndrome
Inherited from normal mother
24
ID
17 y
F
arr[GRCh37] 15q11.2q13.1(22770421_28526905)x3
5756
Gain
15q11-q13 duplication syndrome
Inherited from normal mother
25
DD
13 m
F
arr[GRCh37] 5q23.3q31.2(129203365_139475046)x3
10,272
Gain
de novo
26
ID
16 y
F
arr[GRCh37] 8p23.3p23.1(158048_9781509)x1
9623
Loss
8p23.1 deletion syndrome
CSMD1
de novo
27
ID
9 y
F
arr[GRCh37] 7q36.1q36.3(151376795_159119707)x1
7743
Loss
SHH; KMT2C; DPP6; MNX1
de novo
28
DD
3 y
M
arr[GRCh37] 1q43q44(239750391_249224684)x1
9474
Loss
1q43-q44 deletion syndrome
CHRM3; AKT3; HNRNPU
de novo
29
ID
12 y
M
arr[GRCh37] 3q23q25.1(141486765_151354816)x1
9868
Loss
ZIC1; ZIC4
de novo
30
DD
4 y
F
arr[GRCh37] 18p11.32p11.21(136227_12342194)x1
12,206
Loss
TGIF1
de novo
31
ID
16 y
F
arr[GRCh37] 11q24.2q25(124419306_134937416)x1
10,518
Loss
de novo
32
ID
17 y
F
arr[GRCh37] 3q27.3q29(187068732_194767726)x1
7699
Loss
TP63; FGF12
de novo
33
DD
8 m
M
arr[GRCh37] 10q26.13q26.3(123584147_135426386)x1
11,842
Loss
EBF3
de novo
34
DD
3 y
M
arr[GRCh37] 11q14.1(77492774_85312824)x1
7820
Loss
DLG2
de novo
35
DD
4 y
M
arr[GRCh37]Mosaic 15q14q24.1(35050247_75972909)x1.63
40,923
Loss (Mosaic)
15q24 recurrent microdeletion syndrome
de novo
36
DD
4 y
M
arr[GRCh37] 1q42.13q44(228801122_249181598)x3
20,380
Gain
de novo
37
ID
6 y
M
arr[GRCh37] 1q42.13q44(229917977_249224684)x3
19,307
Gain
de novo
38
DD
3 y
F
arr[GRCh37] 12p13.33q12(173786_40931729)x3
40,758
Gain
Partial chromosome 12trisomy
de novo
39
ID
8 y
M
arr[GRCh37] Xp21.3p11.23(27954516_48270449)x1
20,316
Loss
Xp11.23 region (includes MAOA and MAOB)
de novo
40
ID
10 y
F
arr[GRCh37] 18q21.32q23(58617060_78013728)x1
19,847
Loss
de novo
41
ID
16 y
F
arr[GRCh37] 11q14.2q22.3(87455736_109777755)x1
22,322
Loss
de novo
42
DD
4 y
F
arr[GRCh37] 4p16.3p15.31(290685_18118492)x3
17,828
Gain
4p16.3 terminal (Wolf–Hirschhorn syndrome) region
de novo
arr[GRCh37] 4q34.1q35.2(176152080_190957460)x1
14,805
Loss
43
DD
3 y
M
arr[GRCh37] 8p23.3p23.1(158048_10915395)x3
10,757
Gain
8p23.1 duplication syndrome
SOX7
de novo
arr[GRCh37] 9p24.3p24.1(208454_6308953)x1
6100
Loss
DMRT1
44
ID
8 y
M
arr[GRCh37] 4p16.3p16.1(68345_9514461)x3
9446
Gain
4p16.3 terminal (Wolf–Hirschhorn syndrome) region
Paternal balancedtranslocation 46,XY,t(4; 8) (p16q23)
arr[GRCh37] 8p23.3p23.1(158048_7044046)x1
6886
Loss
CSMD1
45
ID
17 y
F
arr[GRCh37] 9p24.3p24.1(208454_8748943)x3
8540
Gain
de novo
arr[GRCh37] 18q22.1q23(65906752_78013728)x1
12,107
Loss
46
ID
3 y
M
arr[GRCh37] 6q27(169727875_170914297)x3
1186
Gain
de novo
arr[GRCh37] 13q33.3q34(107636085_115107733)x1
7472
Loss
CHAMP1; BSVD2
47
ID
17 y
M
arr[GRCh37] 11q25(131001110_134937416)x1
3936
Loss
Maternal balancedtranslocation 46,XX,t(11; 18) (q25; q21.2)
arr[GRCh37] 18q21.2q23(50912872_78013728)x3
27,101
Gain
48
ID
16 y
F
arr[GRCh37] 9p24.3p21.1(208454_30555044)x3
30,347
Gain
Paternal balancedtranslocation 46,XY,t(9; 18) (p21; p11.3)
arr[GRCh37] 18p11.32p11.31(136227_5485196)x1
5349
Loss
TGIF1
49
ID
7 y
M
arr[GRCh37] 3p26.3p26.1(61891_5189701)x1
5128
Loss
CNTN4; CNTN6; ITPR1
de novo
arr[GRCh37] 7q33q36.3(134287922_159119707)x3
24,832
Gain
SHH
50
DD
3 y
F
arr[GRCh37] 6q25.3q27(159131590_170914297)x3
11,783
Gain
Maternal balancedtranslocation 46,XX,t(6; 10) (q25.3; p15.3)
arr[GRCh37] 10p15.3(100047_1947393)x1
1847
Loss
ZMYND11
51
ID
16 y
F
arr[GRCh37] 9p24.3p13.3(208454_33702198)x3
33,494
Gain
de novo
arr[GRCh37] 19p13.3(260911_1247822)x1
987
Loss
52
DD
3 y
M
arr[GRCh37] 12q12(44719567_46210900)x1
1491
Loss
ARID2
de novo
53
ID
7 y
F
arr[GRCh37] Xq27.3q28(145269560_149282242)x1
4013
Loss
FMR1; AFF2; IDS
de novo
54
DD
4 y
M
arr[GRCh37] 2q22.3(144457537_145255844)x1
798
Loss
ZEB2
de novo
55
ID
16 y
M
arr[GRCh37] Xq28(154476199_155233098)x1
759
Loss
RAB39B
Inherited from normal mother
56
ID
10 y
M
arr[GRCh37] 8p11.22(38344498_39172014)x3
8575
Gain
de novo
57
ID
10 y
M
arr[GRCh37] 1p36.33p36.32(1156338_2468052)x1
1302
Loss
GNB1; GABRD
de novo
58
ID
14 y
F
arr[GRCh37] 9q34.11(131231815_132005416)x1
774
Loss
SPTAN1
de novo
59
ID
17 y
F
arr[GRCh37] 6q27(169471201_170914297)x1
1443
Loss
ERMARD; TBP
de novo
60
ID
12 y
F
arr[GRCh37] 1p36.33p36.32(849466_2516031)x1
1667
Loss
GNB1; GABRD
de novo
61
DD + MCA (short status)
3 y
M
arr[GRCh37] Xp11.22(53359258_53647606)x2
288
Gain
Xp11.22-linked intellectual disability
HUWE1
Inherited from normal mother
62
DD + MCA (microtia, cleft palate, ventricular septal defect)
8 m
F
arr[GRCh37] 4p16.3(68345_3488721)x1
3420
Loss
Wolf–Hirschhorn syndrome
de novo
63
DD + MCA (facial dysmorphism, supravalvular aortic stenosis (SVAS) and supravalvular pulmonary stenosis)
11 m
M
arr[GRCh37] 7q11.23(72718123_74136633)x1
1419
Loss
Williams-Beuren syndrome
ELN
de novo
64
ID + MCA (facial dysmorphism, short status)
6 y
M
arr[GRCh37] 17p11.2(16657318_20287758)x1
3630
Loss
Smith–Magenis syndrome
RAI1; FLCN
de novo
65
DD + MCA (facial dysmorphism, short status)
9 m
M
arr[GRCh37] 7q11.23(72697461_74136633)x1
1439
Loss
Williams-Beuren syndrome
ELN
de novo
66
ID + MCA (facial dysmorphism, short status)
16 y
F
arr[GRCh37] 17p11.2(16736261_20417235)x1
3681
Loss
Smith–Magenis syndrome
RAI1; FLCN
de novo
67
ID + MCA (facial dysmorphism, cleft palate, short status)
6 y
F
arr[GRCh37] 7q11.23(72713282_74154209)x1
1441
Loss
Williams-Beuren syndrome
ELN
de novo
68
DD + MCA (facial dysmorphism, muscular hypotonia)
2 y
F
arr[GRCh37] 7p22.3p11.1(50943_58019983)hmz
57,969
LOH (maternal UPD7)
Silver–Russell syndrome
de novo
69
ID + MCA (ventricular septal defect)
5 y
F
arr[GRCh37] 15q11.2q13.1(22770421_28704050)x1
5934
Loss
Prader–Willi syndrome
UBE3A
de novo
70
DD + MCA (facial dysmorphism, short status)
16 m
M
arr[GRCh37] 7q11.23(72697239_74136633)x1
1439
Loss
Williams-Beuren syndrome
ELN
de novo
71
DD + MCA (facial dysmorphism, hypoplasia of the corpus callosum, ventricular septal defect, short status)
9 m
M
arr[GRCh37] 17p13.3(525_2780094)x1
2780
Loss
Miller–Dieker syndrome
PAFAH1B1
de novo
72
DD + MCA (facial dysmorphism, supravalvular aortic stenosis (SVAS), ventricular septal defect)
9 m
M
arr[GRCh37] 7q11.23(72713282_74136633)x1
1423
Loss
Williams-Beuren syndrome
ELN
de novo
73
DD + MCA (muscular hypotonia, dysphagia, cryptorchidism)
3 m
M
arr[GRCh37] 15q11.2q13.1(23290787_28540345)x1
5250
Loss
Prader–Willi syndrome
UBE3A
de novo
74
DD + MCA (triangular shaped face, short status, body asymmetry)
13 m
F
arr[GRCh37] 7p22.3p11.1(50943_58019983)hmz
57,969
LOH (maternal UPD7)
Silver–Russell syndrome
de novo
75
DD + MCA (facial dysmorphism, cafe-au-lait spots, atrial septal defect)
18 m
M
arr[GRCh37] 17q11.2(29025996_30369402)x1
1343
Loss
NF1-microdeletion syndrome
NF1
de novo
76
ID + MCA (facial dysmorphism, short status)
13 y
F
arr[GRCh37] 5p15.33p15.31(113576_9756329)x1
9643
Loss
Cri du chat syndrome (5p deletion)
de novo
77
ID + MCA (facial dysmorphism, brachydactyly)
9 y
F
arr[GRCh37] 2q37.3(239755969_242782258)x1
3026
Loss
2q37 monosomy
HDAC4
de novo
78
DD + MCA (hypertelorism, overgrowth)
5 m
F
arr[GRCh37] 15q24.3q26.3(78160033_102429040)x3
24,269
Gain
15q26 overgrowth syndrome
Paternal balancedtranslocation 46,XY,t(3; 15) (p26; q24)
arr[GRCh37] 3p26.3(61891_1542088)x1
1480
Loss
CNTN6
79
DD + MCA (facial dysmorphism, esophageal atresia, external auditory canal atresia)
7 m
M
arr[GRCh37] 22q13.31q13.33(48283717_51197766)x1
2914
Loss
22q13 deletion syndrome (Phelan–Mcdermid syndrome)
SHANK3
de novo
arr[GRCh37] 9q34.2q34.3(136244652_141018648)x3
4774
Gain
EHMT1
80
ID + MCA (atrial septal defect, cleft palate, hearing impairment)
5 y
M
arr[GRCh37] 22q11.1q11.21(16888899_20716903)x3
3828
Gain
Cat eye syndrome
Maternal balanced translocation 46,XX,t(11; 22) (q23.3; q11.2)
arr[GRCh37] 11q23.3q25(116683754_134937416)x3
18,254
Gain
81
DD + MCA (polysyndactyly)
7 m
M
arr[GRCh37] 16p11.2(29351825_30176508)x1
825
Loss
16p11.2 recurrent microdeletion
de novo
82
DD + MCA (triangular shaped face, short status, muscular hypotonia)
14 m
F
arr[GRCh37] 7p22.3p11.1(50943_58019983)hmz
57,969
LOH (maternal UPD7)
Silver–Russell syndrome
de novo
83
ID + MCA (atrial septal defect, ventricular septal defect)
9 y
M
arr[GRCh37] 22q11.21(18648855_21800471)x1
3152
Loss
22q11 deletion syndrome (velocardiofacial/DiGeorge syndrome)
TBX1
de novo
84
DD + MCA (short status)
3 y
M
arr[GRCh37] 15q11.2q13.1(23290787_28928730)x1
5638
Loss
Angelman syndrome
UBE3A
de novo
85
ID + MCA (congenital heart disease, polysyndactyly)
16 y
F
arr[GRCh37] 22q11.21(18648855_21800471)x1
3152
Loss
22q11 deletion syndrome (velocardiofacial/DiGeorge syndrome)
TBX1
de novo
86
DD + MCA (facial dysmorphism)
13 m
M
arr[GRCh37] 16p13.11(14913788_16282869)x3
1369
Gain
16p13.11 recurrent microduplication (neurocognitive disorder susceptibility locus)
Inherited from normal mother
87
DD + MCA (muscular hypotonia, ventricular septal defect, cryptorchidism)
3 m
M
arr[GRCh37] 15q11.2q13.1(23290787_28540345)x1
5250
Loss
Prader–Willi syndrome
UBE3A
de novo
88
DD + MCA (cleft palate)
3 y
M
arr[GRCh37] 16p11.2(29428531_30176508)x1
748
Loss
16p11.2 recurrent microdeletion
de novo
89
ID + MCA (facial dysmorphism, cleft palate, polysyndactyly, short status)
11 y
M
arr[GRCh37] 17q21.31q21.32(43170339_44988790)x1
1818
Loss
17q21.31 recurrent microdeletion syndrome (Koolen–de Vries syndrome)
KANSL1
de novo
90
ID + MCA (short status)
9 y
F
arr[GRCh37] 22q11.21(18648855_21800471)x1
3169
Loss
22q11 deletion syndrome (velocardiofacial/DiGeorge syndrome)
TBX1
de novo
91
DD + MCA (cleft palate)
3 y
F
arr[GRCh37] 16p13.11(15481747_16390970)x3
909
Gain
16p13.11 recurrent microduplication (neurocognitive disorder susceptibility locus)
de novo
92
ID + MCA (cleft palate)
13 y
F
arr[GRCh37] 15q11.2q13.1(23281885_28526905)x3
5245
Gain
15q11-q13 duplication syndrome
Inherited from normal mother
arr[GRCh37] 16p11.2(29428531_30176508)x1
748
Loss
16p11.2 recurrent microdeletion
Inherited from normal father
93
DD + MCA (facial dysmorphism, catlike cry, ventricular septal defect, short status)
3 m
F
arr[GRCh37] 5p15.33p13.3(113576_32114177)x1
32,001
Loss
Cri du chat syndrome (5p deletion)
TRIO; CTNND2
de novo
94
DD + MCA (short status)
11 m
F
arr[GRCh37] Xp22.33p22.31(168551_8030262)x1
7862
Loss
Leri–Weill dyschondrosteosis (LWD): SHOX deletion
SHOX; ARSE
de novo
95
ID + MCA (cleft palate)
6 y
F
arr[GRCh37] 7q11.23(72692112_74154209)x1
1462
Loss
Williams-Beuren syndrome
ELN
de novo
96
ID + MCA(micrognathia)
16 y
F
arr[GRCh37] 8p23.3p23.1(158048_10029980)x1
9872
Loss
8p23.1 deletion syndrome
CSMD1
de novo
97
ID + MCA (atrial septal defect, microtia, polysyndactyly)
7 y
M
arr[GRCh37] 5q34q35.3(162638031_180329359)x3
17,691
Gain
5q35 recurrent (Sotos syndrome) region (includes NSD1)
FBXW11
Maternal balancedtranslocation 46,XX,t(5; 12) (q34; p13.32)
arr[GRCh37] 12p13.33p13.32(173786_4264694)x1
4091
Loss
12p13.33 microdeletion syndrome
98
DD + MCA (cryptorchidism, short status)
19 m
M
arr[GRCh37] 4q34.1q35.2(174352834_190957460)x3
16605
Gain
de novo
arr[GRCh37] Xp22.33p22.31(168551_6455151)x0
6287
Loss
Leri–Weill dyschondrosteosis (LWD): SHOX deletion
SHOX; ARSE
99
DD + MCA (gallbladder agenesis)
3 y
F
arr[GRCh37] 8p23.3p23.1(158048_7044046)x1
6686
Loss
CSMD1
de novo
arr[GRCh37] 8p23.1p12(11936000_33616243)x3
21,860
Gain
100
ID + MCA (atrial septal defect, hypermyotonia)
6 y
M
arr[GRCh37] 2p23.1p22.1(32046639_38823958)x1
6777
Loss
SPAST
de novo
101
DD + MCA (hypoplasia of the corpus callosum)
3 m
F
arr[GRCh37] 13q33.2q34(106348324_115107733)x1
8759
Loss
CHAMP1; BSVD2
de novo
102
ID + MCA (micrognathia, polysyndactyly)
14 y
F
arr[GRCh37] 18p11.32q11.2(136227_20989843)x3
20,854
Gain
Maternal balancedtranslocation 46,XX,t(18; 21) (q11.2; q21)
arr[GRCh37] 21q11.2q21.1(15016486_20371429)x1
5355
Loss
103
DD + MCA (hypermyotonia, blepharophimosis)
3 m
M
arr[GRCh37] 3q22.1q23(132876177_139772196)x1
6896
Loss
FOXL2
de novo
104
DD + MCA (facial dysmorphism)
8 m
F
arr[GRCh37] 10p15.3p12.2(100047_23162330)x3
23,062
Gain
Paternal inversion 46,XY,inv(10) (p12q26)
arr[GRCh37] 10q26.3(134248768_135426386)x1
1178
Loss
105
DD + MCA (ventricular septal defect, aortic stenosis)
21 m
M
arr[GRCh37] 7p21.1p11.2(16641066_56373573)x3
39,733
Gain
de novo
arr[GRCh37] 4q13.1q13.2(65818383_68116457)x1
2298
Loss
106
DD + MCA (facial dysmorphism, cryptorchidism)
3 y
M
arr[GRCh37] 3q13.33q25.1(121200603_151876470)x3
30,676
Gain
de novo
107
ID + MCA (facial dysmorphism)
3 y
M
arr[GRCh37] 14q12(28897081_31268243)x1
2371
Loss
Rett syndrome
FOXG1
de novo
108
DD + MCA (atrial septal defect)
14 m
F
arr[GRCh37] 20p13(61661_2150330)x1
2089
Loss
CSNK2A1; PDYN
de novo
109
DD + MCA (facial dysmorphism, overgrowth, body asymmetry)
2 y
F
arr[GRCh37] Xq21.31q27.3(86577241_145860589)x3
59,283
Gain
Pelizaeus–Merzbacher disease (carrier)
PLP1
de novo
110
DD + MCA (cryptorchidism, hypospadias)
3 m
M
arr[GRCh37] 5p14.3p12(19454082_45506818)x3
26,053
Gain
de novo
111
DD + MCA (facial dysmorphism, bilateral single transverse palmar creases)
3 m
F
arr[GRCh37] 9p24.3q13(208454_68216577)x3
10,188
Gain
Chromosome 9p trisomy
de novo
112
ID + MCA (facial dysmorphism, webbed neck, low-set ears)
5 y
F
arr[GRCh37] Xp22.33p11.22(168551_52706689)x1
52,538
Loss
de novo
arr[GRCh37] Xp11.22q28(52833230_155233098)x3
102,400
Gain
113
ID + ASD
13 y
F
arr[GRCh37] 17p11.2(16657318_20463423)x1
3806
Loss
Smith–Magenis syndrome
RAI1; FLCN
de novo
114
DD + ASD
3 y
M
arr[GRCh37] 17p11.2 (16745600_20417235)x3
3672
Gain
Potocki–Lupski syndrome (17p11.2 duplication syndrome)
de novo
115
ID + ASD
10 y
M
arr[GRCh37] 2q37.2q37.3(235790877_242782258)x1
6991
Loss
2q37 monosomy
HDAC4
Paternal inversion 46,XY,inv(2) (p24q37.2)
arr[GRCh37] 2p25.3p24.3(12770_12658812)x3
12,646
Gain
116
ID + epilepsy (ichthyosis)
12 y
M
arr[GRCh37] Xp22.31(6455151_8141076)x0
1686
Loss
Steroid sulphatase deficiency (STS)
STS
Inherited from normal mother
117
ID + epilepsy
8 y
M
arr[GRCh37] 15q11.2q13.1(22770421_28704050)x1
5934
Loss
Angelman syndrome
UBE3A
de novo
118
DD + epilepsy
3 y
F
arr[GRCh37] 16p13.12p13.11(14777379_16533107)x1
1756
Loss
16p13.11 recurrent microdeletion (neurocognitive disorder susceptibility locus)
de novo
119
ID + epilepsy
6 y
M
arr[GRCh37] 15q11.2q13.1(23620191_28526905)x1
4907
Loss
Angelman syndrome
UBE3A
de novo
120
DD + epilepsy
3 y
F
arr[GRCh37] 16p11.2(28557432_30176508)x1
1619
Loss
16p11.2 microduplication syndrome
SH2B1
de novo
121
DD + epilepsy
11 m
F
arr[GRCh37] 20q13.33(61485437_62790113)x1
1305
Loss
CHRNA4; KCNQ2
de novo
122
ID + epilepsy
5 y
F
arr[GRCh37] 13q33.3q34(108237906_115107733)x1
6870
Loss
CHAMP1; BSVD2
de novo
123
DD + epilepsy
4 y
F
arr[GRCh37] Xq23q24(111170674_117964845)x1
6794
Loss
de novo
124
ID + epilepsy
8 y
M
arr[GRCh37] Xp22.13p21.3(17125886_28993521)x2
11,868
Gain
de novo
125
ID + epilepsy
6 y
M
arr[GRCh37] 2p24.3p24.2(15850097_16790467)x1
940
Loss
MYCN
de novo
126
ID + epilepsy
3 y
M
arr[GRCh37] 2q24.3(164444391_168745074)x1
4301
Loss
SCN1A; SCN2A; SCN9A
de novo
127
ID + epilepsy
6 y
M
arr[GRCh37] 1p36.33(849466_2226509)x1
1377
Loss
GNB1; GABRD
de novo
LOH: loss of heterozygosity; UPD: uniparental disomy.Fifty-two pCNVs (34.90%, 52/149) were detected in patients with MCA. In the subgroup of MCA, several clinical manifestations were found, including facial dysmorphic features, growth disorders, micro/macrocephaly, cleft palate, ear deformity, abnormal hands or feet, abnormal heart morphology, and abnormal genital system. In addition, 60 pCNVs (18.07%, 60/332) were detected in patients with isolated DD/ID, 3 pCNVs (3.70%, 3/81) were detected in patients with isolated ASD, and 12 pCNVs (16.90%, 12/71) were detected in patients with epilepsy. The proportion of pCNVs detected in patients with MCA was significantly higher than that in patients with isolated DD/ID (p≤0.001 (34.90% vs. 18.07%)) or patients with isolated ASD (p≤0.001 (34.90% vs. 3.70%)) or patients with epilepsy (p=0.004 (34.90% vs. 16.90%)). The proportion of pCNVs in patients with isolated ASD was significantly lower than that in patients with isolated DD/ID (p≤0.001 (3.70% vs. 18.07%)) or patients with ASD (p=0.007 (3.70% vs. 16.90%)).


### 3.2. Microdeletion/Microduplication Syndromes

Of the 127 cases with abnormal results, 76 cases had 35 types of microdeletion/microduplication syndromes (59.84%), including Williams-Beuren syndrome, Angelman syndrome, Prader–Willi syndrome, 22q11 deletion syndrome (velocardiofacial/DiGeorge syndrome), and Wolf–Hirschhorn syndrome. Twenty-nine microdeletion/microduplication syndromes were detected in patients with isolated DD/ID (8.73%, 29/332), 40 in patients with MCA (26.85%, 40/149), 3 in patients with isolated ASD (3.70%, 3/81), and 5 in patients with epilepsy (7.04%, 5/71) (Table3).Table 3
Microdeletion/microduplication syndromes in the 76 patients.
Syndromes
Isolated DD/ID
DD/ID with MCA
DD/ID with ASD
DD/ID with epilepsy
Total
Williams-Beuren syndrome
7
6
0
0
13
Angelman syndrome
4
1
0
2
7
Silver–Russell syndrome
0
3
0
0
3
15q11-q13 duplication syndrome
2
1
0
0
3
16p11.2 recurrent microdeletion
0
3
0
0
3
16p13.11 recurrent microduplication (neurocognitive disorder susceptibility locus)
1
2
0
0
3
22q11 deletion syndrome (velocardiofacial/DiGeorge syndrome)
0
3
0
0
3
8p23.1 deletion syndrome
2
1
0
0
3
Prader–Willi syndrome
0
3
0
0
3
Smith–Magenis syndrome
0
2
1
0
3
22q13 deletion syndrome (Phelan–Mcdermid syndrome)
2
1
0
0
3
2q37 monosomy
0
1
1
0
2
Cri du chat syndrome (5p deletion)
0
2
0
0
2
Leri–Weill dyschondrosteosis (LWD): SHOX deletion
0
2
0
0
2
Potocki–Lupski syndrome (17p11.2 duplication syndrome)
1
0
1
0
2
Wolf–Hirschhorn syndrome
1
1
0
0
2
Xq28 (MECP2) duplication
2
0
0
0
2
Cat eye syndrome
0
1
0
0
1
12p13.33 microdeletion syndrome
0
1
0
0
1
15q24 recurrent microdeletion syndrome
1
0
0
0
1
15q26 overgrowth syndrome
0
1
0
0
1
16p11.2 microduplication syndrome
0
0
0
1
1
16p13.11 recurrent microdeletion (neurocognitive disorder susceptibility locus)
0
0
0
1
1
17q21.31 recurrent microdeletion syndrome (Koolen–de Vries syndrome)
0
1
0
0
1
1q43-q44 deletion syndrome
1
0
0
0
1
22q11 duplication syndrome
1
0
0
0
1
ATR-16 syndrome
1
0
0
0
1
Lamb-Shaffer syndrome
1
0
0
0
1
Miller–Dieker syndrome
0
1
0
0
1
NF1-microdeletion syndrome
1
0
0
0
1
Pelizaeus–Merzbacher disease (carrier)
0
1
0
0
1
Potocki–Shaffer syndrome
1
0
0
0
1
Rett syndrome
0
1
0
0
1
Steroid sulphatase deficiency (STS)
0
0
0
1
1
Xp11.22-linked intellectual disability
0
1
0
0
1
Total
29
40
3
5
77Most of the microdeletion/microduplication syndromes werede novo (63/77), including 2 patients with AS caused by paternal UPD15 and 3 patients with Russell–Silver syndrome (RSS) caused by maternal UPD7. However, some patients inherited neurocognitive disorder susceptibility loci, including 16p11.2 recurrent microdeletion (1/3) and 16p13.11 recurrent microduplication/microdeletion (2/4) from their normal parents. Two male patients had maternally inherited Xq28 (MECP2) duplication, and 1 male patient had maternally inherited Xp11.22-linked intellectual disability. All 3 cases with 15q11-q13 duplication syndrome were inherited from their normal mothers, in which one also suffered from 16p11.2 recurrent microdeletion inherited from her normal father (Figure 1(a)).Figure 1
Characterization of pCNVs in the patients with DD/ID. (a) The inheritance of the 77 microdeletion/microduplication syndromes. (b) The inheritance of the 18 submicroscopic unbalance rearrangements.
(a)
(b)


### 3.3. Submicroscopic Unbalance Rearrangements

Of the 127 cases with abnormal results, 18 cases were detected with submicroscopic unbalance rearrangements (14.17%), including 10 cases inherited from parental balanced translocations or pericentric inversions (Figure1(b)). Fifteen cases had subtelomeric aberrations at the end of two different chromosomes, of which 8 cases were inherited from normal parents with balanced translocations confirmed by karyotyping. Three cases had subtelomeric aberrations at both ends of the same chromosome, of which 2 cases were inherited from normal parents with pericentric inversions confirmed by karyotyping.


## 3.1. Diagnostic Yields of pCNVs

We detected 149 pCNVs (including 5 UPDs) in 127 cases (65 males; 62 females), accounting for 20.06% of the series (Table1). These pCNVs, including 100 deletions and 44 duplications, were highly variable in size, ranging from 223 kb to 102,400 kb (Table 2).Table 1
Summary of CMA results in 633 patients.
Category
Microarray results (%)
Total
Pathogenic CNVs
VUS
Normal
Isolated DD/ID
60 (18.07)
5 (1.51)
267 (80.42)
332
DD/ID with MCA
52 (34.90)
0 (0.00)
97 (65.10)
149
DD/ID with ASD
3 (3.70)
0 (0.00)
78 (96.30)
81
DD/ID with epilepsy
12 (16.90)
2 (2.82)
57 (80.28)
71
Total
127 (20.06)
7 (1.11)
499 (78.83)
633
DD: developmental delay; ID: intellectual disability; MCA: multiple congenital anomaly; ASD: autism spectrum disorder.Table 2
Characteristics of pCNVs detected by CMA among the 127 patients.
No.
Clinical feature
Age
Gender
CMA results
Sizes of CNVs (kb)
Copy number
Syndromes
OMIM gene
Inherited orde novo
1
ID
17 y
F
arr[GRCh37] 12p12.1(21369190_25634175)x1
3995
Loss
Lamb-Shaffer syndrome
SOX5
de novo
2
DD
3 y
F
arr[GRCh37] 4p16.3p16.1(68345_8066350)x1
7998
Loss
Wolf–Hirschhorn syndrome
de novo
3
ID
5 y
M
arr[GRCh37] 7q11.23(72723370_74136633)x1
1413
Loss
Williams-Beuren syndrome
ELN
de novo
4
DD
4 y
M
arr[GRCh37] Xq28(153118233_153878720)x2
760
Gain
Xq28 (MECP2) duplication
MECP2
Inherited from normal mother
5
ID
5 y
M
arr[GRCh37] 15q11.2q26.3(22817870_102397317)hmz
79,579
LOH (paternal UPD15)
Angelman syndrome
UBE3A
de novo
6
DD
4 y
M
arr[GRCh37] 7q11.23(72718123_74136633)x1
1419
Loss
Williams-Beuren syndrome
ELN
de novo
7
DD
19 m
M
arr[GRCh37] 15q11.2q13.1(23632677_28704050)x1
5071
Loss
Angelman syndrome
UBE3A
de novo
8
ID
16 y
F
arr[GRCh37] 7q11.23(72718123_74141494)x1
1423
Loss
Williams-Beuren syndrome
ELN
de novo
9
DD
16 m
M
arr[GRCh37] 11p11.2(44506359_47897669)x1
3391
Loss
Potocki–Shaffer syndrome
MYBPC3
de novo
10
ID
6 y
M
arr[GRCh37] 15q11.2q13.1(23290787_28526905)x1
5147
Loss
Angelman syndrome
UBE3A
de novo
11
ID
7 y
M
arr[GRCh37] Xq28(153030708_155233098)x2
2202
Gain
Xq28 (MECP2) duplication
MECP2
Inherited from normal mother
12
ID
16 y
F
arr[GRCh37] 15q11.2q26.3(22817870_102397317)hmz
79,579
LOH (paternal UPD15)
Angelman syndrome
UBE3A
de novo
13
ID
6 y
M
arr[GRCh37] 7q11.23 (72611954_75147402)x1
1745
Loss
Williams-Beuren syndrome
ELN
de novo
14
ID
5 y
M
arr[GRCh37] 16p13.3(85880_2045435)x1
1960
Loss
ATR-16 syndrome
de novo
15
DD
17 m
F
arr[GRCh37] 7q11.23(72692112_74184702)x1
1496
Loss
Williams-Beuren syndrome
ELN
de novo
16
ID
16 y
F
arr[GRCh37] 22q13.33(50974299_51197766)x1
223
Loss
22q13 deletion syndrome (Phelan–Mcdermid syndrome)
SHANK3
de novo
17
ID
9 y
F
arr[GRCh37] 17p11.2 (16761814_20304118)x3
3542
Gain
Potocki–Lupski syndrome (17p11.2 duplication syndrome)
de novo
18
DD
9 m
F
arr[GRCh37] 7q11.23(72723370_74136633)x1
1413
Loss
Williams-Beuren syndrome
ELN
de novo
19
ID
6 y
F
arr[GRCh37] 22q13.31q13.33(48234841_51197766)x1
2963
Loss
22q13 deletion syndrome (Phelan–Mcdermid syndrome)
SHANK3
de novo
20
DD
13 m
F
arr[GRCh37] 22q11.21(18919477_21436003)x3
2516
Gain
22q11 duplication syndrome
de novo
21
ID
9 y
M
arr[GRCh37] 7q11.23(72723370_74136633)x1
1413
Loss
Williams-Beuren syndrome
ELN
de novo
22
ID
12 y
M
arr[GRCh37] 16p13.11(14892975_16538596)x3
1646
Gain
16p13.11 recurrent microduplication (neurocognitive disorder susceptibility locus)
Inherited from normal mother
23
ID
5 y
F
arr[GRCh37] 15q11.2q13.1(22770421_28560664)x3
5790
Gain
15q11-q13 duplication syndrome
Inherited from normal mother
24
ID
17 y
F
arr[GRCh37] 15q11.2q13.1(22770421_28526905)x3
5756
Gain
15q11-q13 duplication syndrome
Inherited from normal mother
25
DD
13 m
F
arr[GRCh37] 5q23.3q31.2(129203365_139475046)x3
10,272
Gain
de novo
26
ID
16 y
F
arr[GRCh37] 8p23.3p23.1(158048_9781509)x1
9623
Loss
8p23.1 deletion syndrome
CSMD1
de novo
27
ID
9 y
F
arr[GRCh37] 7q36.1q36.3(151376795_159119707)x1
7743
Loss
SHH; KMT2C; DPP6; MNX1
de novo
28
DD
3 y
M
arr[GRCh37] 1q43q44(239750391_249224684)x1
9474
Loss
1q43-q44 deletion syndrome
CHRM3; AKT3; HNRNPU
de novo
29
ID
12 y
M
arr[GRCh37] 3q23q25.1(141486765_151354816)x1
9868
Loss
ZIC1; ZIC4
de novo
30
DD
4 y
F
arr[GRCh37] 18p11.32p11.21(136227_12342194)x1
12,206
Loss
TGIF1
de novo
31
ID
16 y
F
arr[GRCh37] 11q24.2q25(124419306_134937416)x1
10,518
Loss
de novo
32
ID
17 y
F
arr[GRCh37] 3q27.3q29(187068732_194767726)x1
7699
Loss
TP63; FGF12
de novo
33
DD
8 m
M
arr[GRCh37] 10q26.13q26.3(123584147_135426386)x1
11,842
Loss
EBF3
de novo
34
DD
3 y
M
arr[GRCh37] 11q14.1(77492774_85312824)x1
7820
Loss
DLG2
de novo
35
DD
4 y
M
arr[GRCh37]Mosaic 15q14q24.1(35050247_75972909)x1.63
40,923
Loss (Mosaic)
15q24 recurrent microdeletion syndrome
de novo
36
DD
4 y
M
arr[GRCh37] 1q42.13q44(228801122_249181598)x3
20,380
Gain
de novo
37
ID
6 y
M
arr[GRCh37] 1q42.13q44(229917977_249224684)x3
19,307
Gain
de novo
38
DD
3 y
F
arr[GRCh37] 12p13.33q12(173786_40931729)x3
40,758
Gain
Partial chromosome 12trisomy
de novo
39
ID
8 y
M
arr[GRCh37] Xp21.3p11.23(27954516_48270449)x1
20,316
Loss
Xp11.23 region (includes MAOA and MAOB)
de novo
40
ID
10 y
F
arr[GRCh37] 18q21.32q23(58617060_78013728)x1
19,847
Loss
de novo
41
ID
16 y
F
arr[GRCh37] 11q14.2q22.3(87455736_109777755)x1
22,322
Loss
de novo
42
DD
4 y
F
arr[GRCh37] 4p16.3p15.31(290685_18118492)x3
17,828
Gain
4p16.3 terminal (Wolf–Hirschhorn syndrome) region
de novo
arr[GRCh37] 4q34.1q35.2(176152080_190957460)x1
14,805
Loss
43
DD
3 y
M
arr[GRCh37] 8p23.3p23.1(158048_10915395)x3
10,757
Gain
8p23.1 duplication syndrome
SOX7
de novo
arr[GRCh37] 9p24.3p24.1(208454_6308953)x1
6100
Loss
DMRT1
44
ID
8 y
M
arr[GRCh37] 4p16.3p16.1(68345_9514461)x3
9446
Gain
4p16.3 terminal (Wolf–Hirschhorn syndrome) region
Paternal balancedtranslocation 46,XY,t(4; 8) (p16q23)
arr[GRCh37] 8p23.3p23.1(158048_7044046)x1
6886
Loss
CSMD1
45
ID
17 y
F
arr[GRCh37] 9p24.3p24.1(208454_8748943)x3
8540
Gain
de novo
arr[GRCh37] 18q22.1q23(65906752_78013728)x1
12,107
Loss
46
ID
3 y
M
arr[GRCh37] 6q27(169727875_170914297)x3
1186
Gain
de novo
arr[GRCh37] 13q33.3q34(107636085_115107733)x1
7472
Loss
CHAMP1; BSVD2
47
ID
17 y
M
arr[GRCh37] 11q25(131001110_134937416)x1
3936
Loss
Maternal balancedtranslocation 46,XX,t(11; 18) (q25; q21.2)
arr[GRCh37] 18q21.2q23(50912872_78013728)x3
27,101
Gain
48
ID
16 y
F
arr[GRCh37] 9p24.3p21.1(208454_30555044)x3
30,347
Gain
Paternal balancedtranslocation 46,XY,t(9; 18) (p21; p11.3)
arr[GRCh37] 18p11.32p11.31(136227_5485196)x1
5349
Loss
TGIF1
49
ID
7 y
M
arr[GRCh37] 3p26.3p26.1(61891_5189701)x1
5128
Loss
CNTN4; CNTN6; ITPR1
de novo
arr[GRCh37] 7q33q36.3(134287922_159119707)x3
24,832
Gain
SHH
50
DD
3 y
F
arr[GRCh37] 6q25.3q27(159131590_170914297)x3
11,783
Gain
Maternal balancedtranslocation 46,XX,t(6; 10) (q25.3; p15.3)
arr[GRCh37] 10p15.3(100047_1947393)x1
1847
Loss
ZMYND11
51
ID
16 y
F
arr[GRCh37] 9p24.3p13.3(208454_33702198)x3
33,494
Gain
de novo
arr[GRCh37] 19p13.3(260911_1247822)x1
987
Loss
52
DD
3 y
M
arr[GRCh37] 12q12(44719567_46210900)x1
1491
Loss
ARID2
de novo
53
ID
7 y
F
arr[GRCh37] Xq27.3q28(145269560_149282242)x1
4013
Loss
FMR1; AFF2; IDS
de novo
54
DD
4 y
M
arr[GRCh37] 2q22.3(144457537_145255844)x1
798
Loss
ZEB2
de novo
55
ID
16 y
M
arr[GRCh37] Xq28(154476199_155233098)x1
759
Loss
RAB39B
Inherited from normal mother
56
ID
10 y
M
arr[GRCh37] 8p11.22(38344498_39172014)x3
8575
Gain
de novo
57
ID
10 y
M
arr[GRCh37] 1p36.33p36.32(1156338_2468052)x1
1302
Loss
GNB1; GABRD
de novo
58
ID
14 y
F
arr[GRCh37] 9q34.11(131231815_132005416)x1
774
Loss
SPTAN1
de novo
59
ID
17 y
F
arr[GRCh37] 6q27(169471201_170914297)x1
1443
Loss
ERMARD; TBP
de novo
60
ID
12 y
F
arr[GRCh37] 1p36.33p36.32(849466_2516031)x1
1667
Loss
GNB1; GABRD
de novo
61
DD + MCA (short status)
3 y
M
arr[GRCh37] Xp11.22(53359258_53647606)x2
288
Gain
Xp11.22-linked intellectual disability
HUWE1
Inherited from normal mother
62
DD + MCA (microtia, cleft palate, ventricular septal defect)
8 m
F
arr[GRCh37] 4p16.3(68345_3488721)x1
3420
Loss
Wolf–Hirschhorn syndrome
de novo
63
DD + MCA (facial dysmorphism, supravalvular aortic stenosis (SVAS) and supravalvular pulmonary stenosis)
11 m
M
arr[GRCh37] 7q11.23(72718123_74136633)x1
1419
Loss
Williams-Beuren syndrome
ELN
de novo
64
ID + MCA (facial dysmorphism, short status)
6 y
M
arr[GRCh37] 17p11.2(16657318_20287758)x1
3630
Loss
Smith–Magenis syndrome
RAI1; FLCN
de novo
65
DD + MCA (facial dysmorphism, short status)
9 m
M
arr[GRCh37] 7q11.23(72697461_74136633)x1
1439
Loss
Williams-Beuren syndrome
ELN
de novo
66
ID + MCA (facial dysmorphism, short status)
16 y
F
arr[GRCh37] 17p11.2(16736261_20417235)x1
3681
Loss
Smith–Magenis syndrome
RAI1; FLCN
de novo
67
ID + MCA (facial dysmorphism, cleft palate, short status)
6 y
F
arr[GRCh37] 7q11.23(72713282_74154209)x1
1441
Loss
Williams-Beuren syndrome
ELN
de novo
68
DD + MCA (facial dysmorphism, muscular hypotonia)
2 y
F
arr[GRCh37] 7p22.3p11.1(50943_58019983)hmz
57,969
LOH (maternal UPD7)
Silver–Russell syndrome
de novo
69
ID + MCA (ventricular septal defect)
5 y
F
arr[GRCh37] 15q11.2q13.1(22770421_28704050)x1
5934
Loss
Prader–Willi syndrome
UBE3A
de novo
70
DD + MCA (facial dysmorphism, short status)
16 m
M
arr[GRCh37] 7q11.23(72697239_74136633)x1
1439
Loss
Williams-Beuren syndrome
ELN
de novo
71
DD + MCA (facial dysmorphism, hypoplasia of the corpus callosum, ventricular septal defect, short status)
9 m
M
arr[GRCh37] 17p13.3(525_2780094)x1
2780
Loss
Miller–Dieker syndrome
PAFAH1B1
de novo
72
DD + MCA (facial dysmorphism, supravalvular aortic stenosis (SVAS), ventricular septal defect)
9 m
M
arr[GRCh37] 7q11.23(72713282_74136633)x1
1423
Loss
Williams-Beuren syndrome
ELN
de novo
73
DD + MCA (muscular hypotonia, dysphagia, cryptorchidism)
3 m
M
arr[GRCh37] 15q11.2q13.1(23290787_28540345)x1
5250
Loss
Prader–Willi syndrome
UBE3A
de novo
74
DD + MCA (triangular shaped face, short status, body asymmetry)
13 m
F
arr[GRCh37] 7p22.3p11.1(50943_58019983)hmz
57,969
LOH (maternal UPD7)
Silver–Russell syndrome
de novo
75
DD + MCA (facial dysmorphism, cafe-au-lait spots, atrial septal defect)
18 m
M
arr[GRCh37] 17q11.2(29025996_30369402)x1
1343
Loss
NF1-microdeletion syndrome
NF1
de novo
76
ID + MCA (facial dysmorphism, short status)
13 y
F
arr[GRCh37] 5p15.33p15.31(113576_9756329)x1
9643
Loss
Cri du chat syndrome (5p deletion)
de novo
77
ID + MCA (facial dysmorphism, brachydactyly)
9 y
F
arr[GRCh37] 2q37.3(239755969_242782258)x1
3026
Loss
2q37 monosomy
HDAC4
de novo
78
DD + MCA (hypertelorism, overgrowth)
5 m
F
arr[GRCh37] 15q24.3q26.3(78160033_102429040)x3
24,269
Gain
15q26 overgrowth syndrome
Paternal balancedtranslocation 46,XY,t(3; 15) (p26; q24)
arr[GRCh37] 3p26.3(61891_1542088)x1
1480
Loss
CNTN6
79
DD + MCA (facial dysmorphism, esophageal atresia, external auditory canal atresia)
7 m
M
arr[GRCh37] 22q13.31q13.33(48283717_51197766)x1
2914
Loss
22q13 deletion syndrome (Phelan–Mcdermid syndrome)
SHANK3
de novo
arr[GRCh37] 9q34.2q34.3(136244652_141018648)x3
4774
Gain
EHMT1
80
ID + MCA (atrial septal defect, cleft palate, hearing impairment)
5 y
M
arr[GRCh37] 22q11.1q11.21(16888899_20716903)x3
3828
Gain
Cat eye syndrome
Maternal balanced translocation 46,XX,t(11; 22) (q23.3; q11.2)
arr[GRCh37] 11q23.3q25(116683754_134937416)x3
18,254
Gain
81
DD + MCA (polysyndactyly)
7 m
M
arr[GRCh37] 16p11.2(29351825_30176508)x1
825
Loss
16p11.2 recurrent microdeletion
de novo
82
DD + MCA (triangular shaped face, short status, muscular hypotonia)
14 m
F
arr[GRCh37] 7p22.3p11.1(50943_58019983)hmz
57,969
LOH (maternal UPD7)
Silver–Russell syndrome
de novo
83
ID + MCA (atrial septal defect, ventricular septal defect)
9 y
M
arr[GRCh37] 22q11.21(18648855_21800471)x1
3152
Loss
22q11 deletion syndrome (velocardiofacial/DiGeorge syndrome)
TBX1
de novo
84
DD + MCA (short status)
3 y
M
arr[GRCh37] 15q11.2q13.1(23290787_28928730)x1
5638
Loss
Angelman syndrome
UBE3A
de novo
85
ID + MCA (congenital heart disease, polysyndactyly)
16 y
F
arr[GRCh37] 22q11.21(18648855_21800471)x1
3152
Loss
22q11 deletion syndrome (velocardiofacial/DiGeorge syndrome)
TBX1
de novo
86
DD + MCA (facial dysmorphism)
13 m
M
arr[GRCh37] 16p13.11(14913788_16282869)x3
1369
Gain
16p13.11 recurrent microduplication (neurocognitive disorder susceptibility locus)
Inherited from normal mother
87
DD + MCA (muscular hypotonia, ventricular septal defect, cryptorchidism)
3 m
M
arr[GRCh37] 15q11.2q13.1(23290787_28540345)x1
5250
Loss
Prader–Willi syndrome
UBE3A
de novo
88
DD + MCA (cleft palate)
3 y
M
arr[GRCh37] 16p11.2(29428531_30176508)x1
748
Loss
16p11.2 recurrent microdeletion
de novo
89
ID + MCA (facial dysmorphism, cleft palate, polysyndactyly, short status)
11 y
M
arr[GRCh37] 17q21.31q21.32(43170339_44988790)x1
1818
Loss
17q21.31 recurrent microdeletion syndrome (Koolen–de Vries syndrome)
KANSL1
de novo
90
ID + MCA (short status)
9 y
F
arr[GRCh37] 22q11.21(18648855_21800471)x1
3169
Loss
22q11 deletion syndrome (velocardiofacial/DiGeorge syndrome)
TBX1
de novo
91
DD + MCA (cleft palate)
3 y
F
arr[GRCh37] 16p13.11(15481747_16390970)x3
909
Gain
16p13.11 recurrent microduplication (neurocognitive disorder susceptibility locus)
de novo
92
ID + MCA (cleft palate)
13 y
F
arr[GRCh37] 15q11.2q13.1(23281885_28526905)x3
5245
Gain
15q11-q13 duplication syndrome
Inherited from normal mother
arr[GRCh37] 16p11.2(29428531_30176508)x1
748
Loss
16p11.2 recurrent microdeletion
Inherited from normal father
93
DD + MCA (facial dysmorphism, catlike cry, ventricular septal defect, short status)
3 m
F
arr[GRCh37] 5p15.33p13.3(113576_32114177)x1
32,001
Loss
Cri du chat syndrome (5p deletion)
TRIO; CTNND2
de novo
94
DD + MCA (short status)
11 m
F
arr[GRCh37] Xp22.33p22.31(168551_8030262)x1
7862
Loss
Leri–Weill dyschondrosteosis (LWD): SHOX deletion
SHOX; ARSE
de novo
95
ID + MCA (cleft palate)
6 y
F
arr[GRCh37] 7q11.23(72692112_74154209)x1
1462
Loss
Williams-Beuren syndrome
ELN
de novo
96
ID + MCA(micrognathia)
16 y
F
arr[GRCh37] 8p23.3p23.1(158048_10029980)x1
9872
Loss
8p23.1 deletion syndrome
CSMD1
de novo
97
ID + MCA (atrial septal defect, microtia, polysyndactyly)
7 y
M
arr[GRCh37] 5q34q35.3(162638031_180329359)x3
17,691
Gain
5q35 recurrent (Sotos syndrome) region (includes NSD1)
FBXW11
Maternal balancedtranslocation 46,XX,t(5; 12) (q34; p13.32)
arr[GRCh37] 12p13.33p13.32(173786_4264694)x1
4091
Loss
12p13.33 microdeletion syndrome
98
DD + MCA (cryptorchidism, short status)
19 m
M
arr[GRCh37] 4q34.1q35.2(174352834_190957460)x3
16605
Gain
de novo
arr[GRCh37] Xp22.33p22.31(168551_6455151)x0
6287
Loss
Leri–Weill dyschondrosteosis (LWD): SHOX deletion
SHOX; ARSE
99
DD + MCA (gallbladder agenesis)
3 y
F
arr[GRCh37] 8p23.3p23.1(158048_7044046)x1
6686
Loss
CSMD1
de novo
arr[GRCh37] 8p23.1p12(11936000_33616243)x3
21,860
Gain
100
ID + MCA (atrial septal defect, hypermyotonia)
6 y
M
arr[GRCh37] 2p23.1p22.1(32046639_38823958)x1
6777
Loss
SPAST
de novo
101
DD + MCA (hypoplasia of the corpus callosum)
3 m
F
arr[GRCh37] 13q33.2q34(106348324_115107733)x1
8759
Loss
CHAMP1; BSVD2
de novo
102
ID + MCA (micrognathia, polysyndactyly)
14 y
F
arr[GRCh37] 18p11.32q11.2(136227_20989843)x3
20,854
Gain
Maternal balancedtranslocation 46,XX,t(18; 21) (q11.2; q21)
arr[GRCh37] 21q11.2q21.1(15016486_20371429)x1
5355
Loss
103
DD + MCA (hypermyotonia, blepharophimosis)
3 m
M
arr[GRCh37] 3q22.1q23(132876177_139772196)x1
6896
Loss
FOXL2
de novo
104
DD + MCA (facial dysmorphism)
8 m
F
arr[GRCh37] 10p15.3p12.2(100047_23162330)x3
23,062
Gain
Paternal inversion 46,XY,inv(10) (p12q26)
arr[GRCh37] 10q26.3(134248768_135426386)x1
1178
Loss
105
DD + MCA (ventricular septal defect, aortic stenosis)
21 m
M
arr[GRCh37] 7p21.1p11.2(16641066_56373573)x3
39,733
Gain
de novo
arr[GRCh37] 4q13.1q13.2(65818383_68116457)x1
2298
Loss
106
DD + MCA (facial dysmorphism, cryptorchidism)
3 y
M
arr[GRCh37] 3q13.33q25.1(121200603_151876470)x3
30,676
Gain
de novo
107
ID + MCA (facial dysmorphism)
3 y
M
arr[GRCh37] 14q12(28897081_31268243)x1
2371
Loss
Rett syndrome
FOXG1
de novo
108
DD + MCA (atrial septal defect)
14 m
F
arr[GRCh37] 20p13(61661_2150330)x1
2089
Loss
CSNK2A1; PDYN
de novo
109
DD + MCA (facial dysmorphism, overgrowth, body asymmetry)
2 y
F
arr[GRCh37] Xq21.31q27.3(86577241_145860589)x3
59,283
Gain
Pelizaeus–Merzbacher disease (carrier)
PLP1
de novo
110
DD + MCA (cryptorchidism, hypospadias)
3 m
M
arr[GRCh37] 5p14.3p12(19454082_45506818)x3
26,053
Gain
de novo
111
DD + MCA (facial dysmorphism, bilateral single transverse palmar creases)
3 m
F
arr[GRCh37] 9p24.3q13(208454_68216577)x3
10,188
Gain
Chromosome 9p trisomy
de novo
112
ID + MCA (facial dysmorphism, webbed neck, low-set ears)
5 y
F
arr[GRCh37] Xp22.33p11.22(168551_52706689)x1
52,538
Loss
de novo
arr[GRCh37] Xp11.22q28(52833230_155233098)x3
102,400
Gain
113
ID + ASD
13 y
F
arr[GRCh37] 17p11.2(16657318_20463423)x1
3806
Loss
Smith–Magenis syndrome
RAI1; FLCN
de novo
114
DD + ASD
3 y
M
arr[GRCh37] 17p11.2 (16745600_20417235)x3
3672
Gain
Potocki–Lupski syndrome (17p11.2 duplication syndrome)
de novo
115
ID + ASD
10 y
M
arr[GRCh37] 2q37.2q37.3(235790877_242782258)x1
6991
Loss
2q37 monosomy
HDAC4
Paternal inversion 46,XY,inv(2) (p24q37.2)
arr[GRCh37] 2p25.3p24.3(12770_12658812)x3
12,646
Gain
116
ID + epilepsy (ichthyosis)
12 y
M
arr[GRCh37] Xp22.31(6455151_8141076)x0
1686
Loss
Steroid sulphatase deficiency (STS)
STS
Inherited from normal mother
117
ID + epilepsy
8 y
M
arr[GRCh37] 15q11.2q13.1(22770421_28704050)x1
5934
Loss
Angelman syndrome
UBE3A
de novo
118
DD + epilepsy
3 y
F
arr[GRCh37] 16p13.12p13.11(14777379_16533107)x1
1756
Loss
16p13.11 recurrent microdeletion (neurocognitive disorder susceptibility locus)
de novo
119
ID + epilepsy
6 y
M
arr[GRCh37] 15q11.2q13.1(23620191_28526905)x1
4907
Loss
Angelman syndrome
UBE3A
de novo
120
DD + epilepsy
3 y
F
arr[GRCh37] 16p11.2(28557432_30176508)x1
1619
Loss
16p11.2 microduplication syndrome
SH2B1
de novo
121
DD + epilepsy
11 m
F
arr[GRCh37] 20q13.33(61485437_62790113)x1
1305
Loss
CHRNA4; KCNQ2
de novo
122
ID + epilepsy
5 y
F
arr[GRCh37] 13q33.3q34(108237906_115107733)x1
6870
Loss
CHAMP1; BSVD2
de novo
123
DD + epilepsy
4 y
F
arr[GRCh37] Xq23q24(111170674_117964845)x1
6794
Loss
de novo
124
ID + epilepsy
8 y
M
arr[GRCh37] Xp22.13p21.3(17125886_28993521)x2
11,868
Gain
de novo
125
ID + epilepsy
6 y
M
arr[GRCh37] 2p24.3p24.2(15850097_16790467)x1
940
Loss
MYCN
de novo
126
ID + epilepsy
3 y
M
arr[GRCh37] 2q24.3(164444391_168745074)x1
4301
Loss
SCN1A; SCN2A; SCN9A
de novo
127
ID + epilepsy
6 y
M
arr[GRCh37] 1p36.33(849466_2226509)x1
1377
Loss
GNB1; GABRD
de novo
LOH: loss of heterozygosity; UPD: uniparental disomy.Fifty-two pCNVs (34.90%, 52/149) were detected in patients with MCA. In the subgroup of MCA, several clinical manifestations were found, including facial dysmorphic features, growth disorders, micro/macrocephaly, cleft palate, ear deformity, abnormal hands or feet, abnormal heart morphology, and abnormal genital system. In addition, 60 pCNVs (18.07%, 60/332) were detected in patients with isolated DD/ID, 3 pCNVs (3.70%, 3/81) were detected in patients with isolated ASD, and 12 pCNVs (16.90%, 12/71) were detected in patients with epilepsy. The proportion of pCNVs detected in patients with MCA was significantly higher than that in patients with isolated DD/ID (p≤0.001 (34.90% vs. 18.07%)) or patients with isolated ASD (p≤0.001 (34.90% vs. 3.70%)) or patients with epilepsy (p=0.004 (34.90% vs. 16.90%)). The proportion of pCNVs in patients with isolated ASD was significantly lower than that in patients with isolated DD/ID (p≤0.001 (3.70% vs. 18.07%)) or patients with ASD (p=0.007 (3.70% vs. 16.90%)).


## 3.2. Microdeletion/Microduplication Syndromes

Of the 127 cases with abnormal results, 76 cases had 35 types of microdeletion/microduplication syndromes (59.84%), including Williams-Beuren syndrome, Angelman syndrome, Prader–Willi syndrome, 22q11 deletion syndrome (velocardiofacial/DiGeorge syndrome), and Wolf–Hirschhorn syndrome. Twenty-nine microdeletion/microduplication syndromes were detected in patients with isolated DD/ID (8.73%, 29/332), 40 in patients with MCA (26.85%, 40/149), 3 in patients with isolated ASD (3.70%, 3/81), and 5 in patients with epilepsy (7.04%, 5/71) (Table3).Table 3
Microdeletion/microduplication syndromes in the 76 patients.
Syndromes
Isolated DD/ID
DD/ID with MCA
DD/ID with ASD
DD/ID with epilepsy
Total
Williams-Beuren syndrome
7
6
0
0
13
Angelman syndrome
4
1
0
2
7
Silver–Russell syndrome
0
3
0
0
3
15q11-q13 duplication syndrome
2
1
0
0
3
16p11.2 recurrent microdeletion
0
3
0
0
3
16p13.11 recurrent microduplication (neurocognitive disorder susceptibility locus)
1
2
0
0
3
22q11 deletion syndrome (velocardiofacial/DiGeorge syndrome)
0
3
0
0
3
8p23.1 deletion syndrome
2
1
0
0
3
Prader–Willi syndrome
0
3
0
0
3
Smith–Magenis syndrome
0
2
1
0
3
22q13 deletion syndrome (Phelan–Mcdermid syndrome)
2
1
0
0
3
2q37 monosomy
0
1
1
0
2
Cri du chat syndrome (5p deletion)
0
2
0
0
2
Leri–Weill dyschondrosteosis (LWD): SHOX deletion
0
2
0
0
2
Potocki–Lupski syndrome (17p11.2 duplication syndrome)
1
0
1
0
2
Wolf–Hirschhorn syndrome
1
1
0
0
2
Xq28 (MECP2) duplication
2
0
0
0
2
Cat eye syndrome
0
1
0
0
1
12p13.33 microdeletion syndrome
0
1
0
0
1
15q24 recurrent microdeletion syndrome
1
0
0
0
1
15q26 overgrowth syndrome
0
1
0
0
1
16p11.2 microduplication syndrome
0
0
0
1
1
16p13.11 recurrent microdeletion (neurocognitive disorder susceptibility locus)
0
0
0
1
1
17q21.31 recurrent microdeletion syndrome (Koolen–de Vries syndrome)
0
1
0
0
1
1q43-q44 deletion syndrome
1
0
0
0
1
22q11 duplication syndrome
1
0
0
0
1
ATR-16 syndrome
1
0
0
0
1
Lamb-Shaffer syndrome
1
0
0
0
1
Miller–Dieker syndrome
0
1
0
0
1
NF1-microdeletion syndrome
1
0
0
0
1
Pelizaeus–Merzbacher disease (carrier)
0
1
0
0
1
Potocki–Shaffer syndrome
1
0
0
0
1
Rett syndrome
0
1
0
0
1
Steroid sulphatase deficiency (STS)
0
0
0
1
1
Xp11.22-linked intellectual disability
0
1
0
0
1
Total
29
40
3
5
77Most of the microdeletion/microduplication syndromes werede novo (63/77), including 2 patients with AS caused by paternal UPD15 and 3 patients with Russell–Silver syndrome (RSS) caused by maternal UPD7. However, some patients inherited neurocognitive disorder susceptibility loci, including 16p11.2 recurrent microdeletion (1/3) and 16p13.11 recurrent microduplication/microdeletion (2/4) from their normal parents. Two male patients had maternally inherited Xq28 (MECP2) duplication, and 1 male patient had maternally inherited Xp11.22-linked intellectual disability. All 3 cases with 15q11-q13 duplication syndrome were inherited from their normal mothers, in which one also suffered from 16p11.2 recurrent microdeletion inherited from her normal father (Figure 1(a)).Figure 1
Characterization of pCNVs in the patients with DD/ID. (a) The inheritance of the 77 microdeletion/microduplication syndromes. (b) The inheritance of the 18 submicroscopic unbalance rearrangements.
(a)
(b)


## 3.3. Submicroscopic Unbalance Rearrangements

Of the 127 cases with abnormal results, 18 cases were detected with submicroscopic unbalance rearrangements (14.17%), including 10 cases inherited from parental balanced translocations or pericentric inversions (Figure1(b)). Fifteen cases had subtelomeric aberrations at the end of two different chromosomes, of which 8 cases were inherited from normal parents with balanced translocations confirmed by karyotyping. Three cases had subtelomeric aberrations at both ends of the same chromosome, of which 2 cases were inherited from normal parents with pericentric inversions confirmed by karyotyping.


## 4. Discussion

The establishment of genetic etiological diagnoses for DD/ID children is usually challenging due to the high frequency of relatively nonspecific symptoms shared by numerous potential syndromes. We identified pCNVs in 20.06% of cases, which was comparable to other reported series [8, 14–17]. Interestingly, our study revealed some new findings with certain clinical significance.


### 4.1. More Deletions than Duplications in pCNVs

In our study, the proportion of deletions was extremely higher than duplications in pCNVs. This finding is consistent with the notion of Ruderfer et al. [18] that many duplications present in the human genome are benign, and most phenotypically normal individuals possess a higher number of duplications than deletions. The dosage-sensitive genes have the ability to cause phenotypes [9]. In our study, 32 genes were confirmed with “sufficient evidence for haploinsufficiency” in the pathogenic deletions, while only 2 genes were confirmed with “sufficient evidence for triplosensitivity” in the pathogenic duplications (https://www.clinicalgenome.org/), which influenced the phenotypes of these patients. Thus, deletions contributed more pathogenic interpretations than duplications.


### 4.2. Diagnostic Yields Associated with the Phenotypes

The diagnostic yield of pCNVs (including microdeletion/microduplication syndromes) in the MCA subgroup was significantly higher than that in the other 3 subgroups, which implied that severe and complex phenotypes, such as dysmorphology or congenital anomalies, tend to have a higher likelihood of identifying a genetic etiology [4]. Case 92 is a 13-year-old female who has mild ID, specifically a learning disability with a cleft palate. CMA revealed a 5242-kb duplication in the 15q11.2q13.1 (15q11-q13 duplication syndrome) inherited from her normal mother and a 748-kb deletion in 16p11.2 (16p11.2 recurrent microdeletion) inherited from her normal father. Evidence suggests that maternally derived 15q11.2q13.1 duplications are more frequently associated with abnormal phenotypes [19]. Weiss et al. [20] reported that the phenotype of 16p11.2 recurrent microdeletion is characterized by DD, ID, and/or ASD. It is rare that one patient suffers from two different microdeletion/microduplication syndromes. We hypothesized that both the duplication and deletion contributed to the phenotype of the patient. The probability of her parents having another baby with one of the pCNVs or for both is extremely as high as 75%. Wolfe et al. [21] identified that 16p11.2 deletions and 15q11.2q13.1 duplications had incomplete penetrance with high frequencies in neurodevelopmental disorders; however, they sometimes can be observed in healthy controls. So, the phenotype of the baby with pCNV(s) could not be confirmed before birth.In the isolated DD/ID subgroup and DD/ID with epilepsy subgroup, the diagnostic yields of pCNVs were significantly lower than those of the MCA subgroup but significantly higher than those of the isolated ASD subgroup. The more phenotypes the patients had, such as epilepsy, the higher the likelihood of finding a genetic etiology [9]. However, the diagnostic yields of pCNVs between these two subgroups were not statistically significant. Next-generation sequencing (NGS) also contributes to the identification of epilepsy caused by monogenic mutations [22], which might be omitted by CMA.The diagnostic yield of pCNVs was significantly lower in the patients with isolated ASD than in the other 3 subgroups, which was consistent with the results of Ho et al. [16]. We assumed that some other genetic etiologies, such as single-gene disorders, may contribute to the pathogenesis of ASD, which requires further investigation. We detected 3 microdeletion/microduplication syndromes in this subgroup, including Smith–Magenis syndrome, Potocki–Lupski syndrome, and 2q37 monosomy, which were reported in the previous studies [23, 24].Thus, we believe that the correct genetic diagnosis confirmed by CMA is imperative to medical management and prognostic evaluation of patients with DD/ID.


### 4.3. Assessment of Recurrence Risks

In our study, microdeletion/microduplication syndromes were detected in 76 patients. As most of the syndromes arede novo (63/77), the recurrence risk of these sporadic syndromes is extremely low. However, the parents of the DD/ID patients with maternally derived 15q11-q13 duplication (Cases 23, 24, and 92) or some parentally derived recurrent CNVs such as 16p11.2 microdeletion (Case 92) or 16p13.11 microduplication/microdeletion (Cases 22 and 86) have a recurrence risk of 50%. In addition, the parents of male patients with maternally derived X-chromosomal aberrations including Xp22.31 deletion, Xq28 duplication, or Xp11.22 duplication have a recurrence risk of 25%. Hence, the CMA results of these parents are more vital to evaluate the recurrence risk in reproduction.In the 127 cases with pCNVs, 18 cases (14.17%) were identified with submicroscopic subtelomeric aberrations, including 7 patients suffering from microdeletion/microduplication syndromes, which was consistent with the results of Cheng et al. [25]. In the 18 cases, 8 families were confirmed with parental balanced translocations and 2 families were confirmed with pericentric inversions by karyotyping. These families have an extremely high risk of having another child with submicroscopic subtelomeric aberrations induced DD/ID (10/18). Conventional cytogenetics can only recognize chromosomal rearrangements with a limited resolution of 5∼10 Mb [9]. There were still 8 cases diagnosed as de novo submicroscopic subtelomeric aberrations by comparing with the karyotypes of their parents. These parents should be further tested whether they have balanced translocations or pericentric inversions by locus specific FISH probes according to the results of CMA. Fortunately, all the 18 families may possibly have a healthy child if effective genetic counseling was given based on reasonable techniques of prenatal or preimplantational diagnosis.


### 4.4. Limitations of CMA

Parental study is usually indispensable because it not only helps with the interpretation of the clinical significance of CNVs but also contributes to genetic counseling and the evaluation of recurrence risk of genetic abnormalities [26]. However, even though the results of normal parents were compared with their children, there was still 1.11% VUS in our study. In general, the rate of VUS will decrease as more CMA results are obtained from the normal parents. The establishment of a normal individual CMA database might be helpful to address this issue.CMA has been confirmed as a vital technology to offer extremely higher diagnostic yield compared with chromosomal karyotype analysis in DD/ID. However, the genetic etiology of approximately 80% of patients remains unknown. Development of NGS offers another option for the genetic diagnosis of DD/ID. Currently, with an increased number of pathogenic mutations of genes associated with DD/ID detected by NGS, the diagnostic yield could be further improved by 20∼30% [27, 28]. A combination of CMA and NGS could be a comprehensive strategy, but the cost-effectiveness should be considered.


## 4.1. More Deletions than Duplications in pCNVs

In our study, the proportion of deletions was extremely higher than duplications in pCNVs. This finding is consistent with the notion of Ruderfer et al. [18] that many duplications present in the human genome are benign, and most phenotypically normal individuals possess a higher number of duplications than deletions. The dosage-sensitive genes have the ability to cause phenotypes [9]. In our study, 32 genes were confirmed with “sufficient evidence for haploinsufficiency” in the pathogenic deletions, while only 2 genes were confirmed with “sufficient evidence for triplosensitivity” in the pathogenic duplications (https://www.clinicalgenome.org/), which influenced the phenotypes of these patients. Thus, deletions contributed more pathogenic interpretations than duplications.


## 4.2. Diagnostic Yields Associated with the Phenotypes

The diagnostic yield of pCNVs (including microdeletion/microduplication syndromes) in the MCA subgroup was significantly higher than that in the other 3 subgroups, which implied that severe and complex phenotypes, such as dysmorphology or congenital anomalies, tend to have a higher likelihood of identifying a genetic etiology [4]. Case 92 is a 13-year-old female who has mild ID, specifically a learning disability with a cleft palate. CMA revealed a 5242-kb duplication in the 15q11.2q13.1 (15q11-q13 duplication syndrome) inherited from her normal mother and a 748-kb deletion in 16p11.2 (16p11.2 recurrent microdeletion) inherited from her normal father. Evidence suggests that maternally derived 15q11.2q13.1 duplications are more frequently associated with abnormal phenotypes [19]. Weiss et al. [20] reported that the phenotype of 16p11.2 recurrent microdeletion is characterized by DD, ID, and/or ASD. It is rare that one patient suffers from two different microdeletion/microduplication syndromes. We hypothesized that both the duplication and deletion contributed to the phenotype of the patient. The probability of her parents having another baby with one of the pCNVs or for both is extremely as high as 75%. Wolfe et al. [21] identified that 16p11.2 deletions and 15q11.2q13.1 duplications had incomplete penetrance with high frequencies in neurodevelopmental disorders; however, they sometimes can be observed in healthy controls. So, the phenotype of the baby with pCNV(s) could not be confirmed before birth.In the isolated DD/ID subgroup and DD/ID with epilepsy subgroup, the diagnostic yields of pCNVs were significantly lower than those of the MCA subgroup but significantly higher than those of the isolated ASD subgroup. The more phenotypes the patients had, such as epilepsy, the higher the likelihood of finding a genetic etiology [9]. However, the diagnostic yields of pCNVs between these two subgroups were not statistically significant. Next-generation sequencing (NGS) also contributes to the identification of epilepsy caused by monogenic mutations [22], which might be omitted by CMA.The diagnostic yield of pCNVs was significantly lower in the patients with isolated ASD than in the other 3 subgroups, which was consistent with the results of Ho et al. [16]. We assumed that some other genetic etiologies, such as single-gene disorders, may contribute to the pathogenesis of ASD, which requires further investigation. We detected 3 microdeletion/microduplication syndromes in this subgroup, including Smith–Magenis syndrome, Potocki–Lupski syndrome, and 2q37 monosomy, which were reported in the previous studies [23, 24].Thus, we believe that the correct genetic diagnosis confirmed by CMA is imperative to medical management and prognostic evaluation of patients with DD/ID.


## 4.3. Assessment of Recurrence Risks

In our study, microdeletion/microduplication syndromes were detected in 76 patients. As most of the syndromes arede novo (63/77), the recurrence risk of these sporadic syndromes is extremely low. However, the parents of the DD/ID patients with maternally derived 15q11-q13 duplication (Cases 23, 24, and 92) or some parentally derived recurrent CNVs such as 16p11.2 microdeletion (Case 92) or 16p13.11 microduplication/microdeletion (Cases 22 and 86) have a recurrence risk of 50%. In addition, the parents of male patients with maternally derived X-chromosomal aberrations including Xp22.31 deletion, Xq28 duplication, or Xp11.22 duplication have a recurrence risk of 25%. Hence, the CMA results of these parents are more vital to evaluate the recurrence risk in reproduction.In the 127 cases with pCNVs, 18 cases (14.17%) were identified with submicroscopic subtelomeric aberrations, including 7 patients suffering from microdeletion/microduplication syndromes, which was consistent with the results of Cheng et al. [25]. In the 18 cases, 8 families were confirmed with parental balanced translocations and 2 families were confirmed with pericentric inversions by karyotyping. These families have an extremely high risk of having another child with submicroscopic subtelomeric aberrations induced DD/ID (10/18). Conventional cytogenetics can only recognize chromosomal rearrangements with a limited resolution of 5∼10 Mb [9]. There were still 8 cases diagnosed as de novo submicroscopic subtelomeric aberrations by comparing with the karyotypes of their parents. These parents should be further tested whether they have balanced translocations or pericentric inversions by locus specific FISH probes according to the results of CMA. Fortunately, all the 18 families may possibly have a healthy child if effective genetic counseling was given based on reasonable techniques of prenatal or preimplantational diagnosis.


## 4.4. Limitations of CMA

Parental study is usually indispensable because it not only helps with the interpretation of the clinical significance of CNVs but also contributes to genetic counseling and the evaluation of recurrence risk of genetic abnormalities [26]. However, even though the results of normal parents were compared with their children, there was still 1.11% VUS in our study. In general, the rate of VUS will decrease as more CMA results are obtained from the normal parents. The establishment of a normal individual CMA database might be helpful to address this issue.CMA has been confirmed as a vital technology to offer extremely higher diagnostic yield compared with chromosomal karyotype analysis in DD/ID. However, the genetic etiology of approximately 80% of patients remains unknown. Development of NGS offers another option for the genetic diagnosis of DD/ID. Currently, with an increased number of pathogenic mutations of genes associated with DD/ID detected by NGS, the diagnostic yield could be further improved by 20∼30% [27, 28]. A combination of CMA and NGS could be a comprehensive strategy, but the cost-effectiveness should be considered.



---

*Source: 9352581-2019-11-06.xml*