Received: 31 July 2018 Revised: 17 October 2018 Accepted: 17 October 2018

DOI: 10.1111/ahg.12294

ORIGINAL ARTICLE

Diagnostic approach with genetic tests for global developmental

delay and/or intellectual disability: Single tertiary
center experience

Ji Yoon Han1 Woori Jang2 Joonhong Park2 Myungshin Kim2 Yonggoo Kim2
In Goo Lee1

1 Department of Pediatrics, College of

Medicine, The Catholic University of Korea,
Seoul, Republic of Korea
2 Department of Laboratory Medicine, Col-
lege of Medicine, The Catholic University of
Korea, Seoul, Republic of Korea
Correspondence
Joonhong Park, Department of Laboratory
Medicine, Daejeon St. Mary's Hospital, Col-
lege of Medicine, The Catholic University of
Korea, 64 Daeheung-ro, Jung-gu, Daejeon
34943, Republic of Korea.
Email: miziro@catholic.ac.kr
Myungshin Kim, Department of Laboratory
Medicine, Seoul St. Mary's Hospital, College
of Medicine, The Catholic University of Korea,
222 Banpo-daero, Seocho-gu, Seoul 06591,
Republic of Korea.
Email: microkim@catholic.ac.kr
Abstract
The child with global developmental delay (GDD)/intellectual disability (ID) is
deserving of the appropriate evaluation available for improving the health and well-
being of patients and their families. To better elucidate the diagnostic approach of
genetic tests for patients with GDD and/or ID, we evaluated the results in a cohort of
75 patients with clinical features of GDD and/or ID who were referred for diagnos-
tic workup. A total of 75 children were investigated for GDD or ID in the pediatric
neurology department. Ten patients (13%, 10/75) with a clinically recognizable syn-
drome were diagnosed by single-gene analysis. Next, chromosomal microarray was
performed as a first-tier test, and 25 patients (33%, 25/75) showed structural abnor-
malities. Then, two fragile X syndrome (3%, 2/75) were confirmed by FMR1 gene
fragment analysis. Thirty-eight remaining patients received a gene panel by next-
generation sequencing. Eight patients were found to have an underlying genetic eti-
ology: CHD8, ZDHHC9, MBD5, CACNA1H, SMARCB1, FOXP1, NSD1, and PAX6.
As a result, 45 patients (60%, 45/75) had been diagnosed by genetic tests. Among 30
undiagnosed patients, brain structural abnormalities related to GDD/ID were observed
in eight patients (11%, 8/75). However, in 22 patients (29%, 22/75), the causes of
GDD/ID remained uncertain. A genetic diagnostic approach of GDD/ID by sequen-
tial molecular analysis can help in the planning of treatment, assigning the risk of
occurrence in siblings, and providing emotional relief for the family.

KEYWORDS
chromosomal microarray, diagnostic approach, global developmental delay, intellectual disability, next-
generation sequencing

1 I N T RO D U C T I O N childhood or adolescent performance in standardized cogni-

Global developmental delay (GDD) is defined as signifi-
cant delay in development in two or more of the follow-
ing domains: gross or fine motor, speech/language, cogni-
tive, social/personal, and activities of daily living. GDD is
thought to be a predictor of future diagnosis of intellectual
disability (ID) (Moeschler, 2008b). ID is characterized by
tive tests of at least two SDs below average (Helsmoortel
et al., 2015). The American Association on Intellectual and
Developmental Disability uses measures of three domains
to define ID: intelligence quotient (IQ), adaptive behavior,
and systems of support afforded the individual (Schalock
et al., 2007). Current prevalence of GDD/ID is estimated at
∼3% in the general population (Shevell et al., 2003). The

Ann Hum Genet. 2018;1–9. wileyonlinelibrary.com/journal/ahg © 2018 John Wiley & Sons Ltd/University College London 1
2 HAN ET AL.
full range of etiologies underlying GDD/ID remains largely
unexplained. In the past decade, however, progress has been
made in identifying some neurobiological and genetic under-
pinnings of, and risk factors for, this complex condition (Lyall
et al., 2017). Though clinical genetic testing, including chro-
mosome analysis, is a standard practice for patients with
diagnoses including unexplained GDD/ID, most patients lack
sufficient specific history or features from physical exami-
nation to suggest a specific genetic or environmental cause
(Rauch et al., 2006). As patients with GDD/ID seldom repro-
duce, large pedigrees are rare. This scarcity of data has cre-
ated a bias for de novo genetic causes (Vandeweyer & Kooy,
2013).
Chromosomal microarray (CMA) is increasingly utilized
as a first-tier clinical diagnostic genetic test for individ-
uals with unexplained GDD/ID. It encompasses all types
of array-based genomic copy-number analyses, including
array-based comparative genomic hybridization (CGH) and
single-nucleotide polymorphism (SNP) arrays (Miller et al.,
2010).
On the other hand, next-generation sequencing (NGS)
analysis has enabled genome-wide mutation screening with-
out prior knowledge on the affected gene or gene function.
Whole-exome sequencing (WES), a variant of NGS focus-
ing on the coding regions of the genome, can discover novel
genes involved in ID and redefine the phenotypic spectrum
of currently known disorders (Helsmoortel et al., 2015).
NGS brings opportunities in the diagnosis of patients with
unexplained ID and in researching the mechanisms of these
disorders (Gauthier-Vasserot et al., 2017; Thevenon et al.,
2016).
In this study, to better elucidate the diagnostic approach of
genetic tests for patients with GDD and/or ID, we evaluated
the results in a cohort of 75 patients with clinical features of
GDD and/or ID referred for single gene testing, CMA (as first-
tier tests), and FMR1 gene testing, followed by NGS with gene
panel. And we described our experience in efforts to find the
etiology of GDD/ID at a single tertiary center in Korea.
2 M AT E R I A L S A N D M E T H O D S
2.1 Patients
Based on a medical record review, a total of 75 patients (51
males and 24 females) with GDD and/or ID and their unaf-
fected parents (trios) were enrolled. This series is broadly rep-
resentative of patients with GDD and/or ID referred to the
Department of Pediatrics, Daejeon St. Mary's Hospital, Dae-
jeon, Korea, from January 2016 to March 2017. Clinical man-
ifestations were reviewed following a standardized clinical
record highlighting prenatal history, developmental history,
and neurological and behavioral disorders. DD was defined
as significant developmental delay (>2 standard deviations
below age-matched peers) in two or more of the following
areas: gross and fine motor, speech and language, cognition,
personal and social, or activities of daily living in patients
under the age of 6 years. The Wechsler Intelligence Test or
the Bayley Scales of Infant Development (3rd edition) were
used by a neurological pediatrician in a clinical evaluation to
evaluate the severity of ID. ID is defined as an IQ of 70 or
below, with deficits in at least two behaviors related to adap-
tive functioning originating before age 18 years. ID was subdi-
vided into four groups based on intellectual functioning, using
the following ranges: mild (IQ between 50 to 55 and 70), mod-
erate (IQ between 35 to 40 and 50 to 55), severe (IQ between
20 to 25 and 35 to 40, and profound (IQ less than 20). Severity
of the DD was subdivided according to the overall functional
age based on the results of developmental assessments with
regard to chronological age. Mild DD was defined as a func-
tional age of 66% of the chronological age, moderate DD as
a functional age of 34% to 66% of the chronological age, and
severe DD as a functional age below 33% of chronological
age. This study was approved by the institutional review board
of The Catholic University of Korea, Daejeon Saint Mary's
Hospital (DC17RESI0101). All participants and their parents
provided written informed consent for clinical and molecular
analyses. Patient consent for publication of medical informa-
tion was obtained from the participants’ parents.
2.2 Chromosomal microarray
The use of CMA in place of G-band karyotyping as the first-
tier clinical diagnostic test for individuals with developmental
disabilities or congenital anomalies is strongly supported by
available evidence (Battaglia et al., 2013; Miller et al., 2010).
Thus, array CGH analysis was performed with SurePrint G3
Human CGH Microarray 8 × 60 K kit (Agilent Technologies,
Santa Clara, CA) according to the manufacturer's instruc-
tions. Agilent Feature Extraction software was used to quan-
tify scanned images. Resulting data were imported into Agi-
lent Genomic Workbench 7.0.4.0 software for visualization.
The Aberration Detection Method-2 (ADM-2) algorithm was
used to detect copy number variants (CNVs). Genomic posi-
tions were defined according to human reference genome
hg19/GRCh37.
To assist clinical laboratories in the evaluation of CNVs
and to promote consistency in interpretation and report-
ing of genomic microarray results, the American College
of Medical Genetics standards and guidelines for interpre-
tation and reporting of postnatal constitutional CNVs were
adapted (Miller et al., 2010). To determine the clinically sig-
nificant CNVs, we used DGV, DECIPHER, ClinGen, OMIM,
dbVar databases, and peer-reviewed literature. Pathogenic
variants or variants of possible significance (VPS) were
considered as abnormal. Whenever available, the known
HAN ET AL.
deletion/duplication found via CMA was confirmed by FISH
or MLPA. The term VPS was used when the imbalance was
>200 kb for deletions and >500 kb for duplications involv-
ing multiple genes that had never or rarely been reported in
healthy controls or candidate genes for inherited disease, but
in which the significance of the imbalance could not be deter-
mined based on available knowledge or family studies. When
CNVs were reported as normal variants in healthy controls or
seen in ≥1% of our patient population, they were considered
benign.
2.3 Next-generation sequencing
Library preparation was conducted using a TruSight One
Sequencing Panel (Illumina, San Diego, CA) to enrich a 12-
Mb region spanning 4813 genes with clinical relevance. An
Illumina NextSeq platform (Illumina) was used to perform
massive parallel sequencing. Sequence reads were aligned
to human reference genome hg19 using a Burrow-Wheeler
Aligner 0.7.12. Picard-tools 1.96 were used to remove dupli-
cate reads. Local realignment and base-quality recalibration
were performed using a Genome Analysis Tool Kit 3.5 from
the Broad Institute according to GATK's best practice guide-
lines for germline SNP and indel discovery in whole genome
and exome sequences. Variants were called by GATK Hap-
lotypeCaller and annotated with a Variant Effect Predic-
tor and dbNSFP 2.4, a database developed for functional
prediction and annotation of all potential nonsynonymous,
single-nucleotide variants in the human genome (Liu, Jian, &
Boerwinkle, 2013). Variant prioritization was carried out by
the following criteria: selection of candidate genes based on
patient phenotype, severity of the predicted impact on gene
function, conservation of affected amino acid, and frequency
of the variant in the literature and public sequence databases,
including the 1,000 genomes phase 3 database (http://
phase3browser.1000genomes.org/index.html), Exome Aggre-
gation Consortium (http://exac.broadinstitute.org), ClinVar
(https://www.ncbi.nlm.nih.gov/clinvar/), Human Gene Muta-
tion Database (http://www.hgmd.cf.ac.uk/ac/all.php), and
Exome Variant Server (http://evs.gs.washington.edu/EVS/).
All unknown variants were also searched in 622 Korean pop-
ulations based on the Korean Reference Genome Database
(http://152.99.75.168/KRGDB/). Standards and guidelines
for the interpretation of sequence variants were adopted
according to a joint consensus recommendation (Richards
et al., 2015). We generated a candidate gene list by using the
resultant disease name(s) to query databases describing geno-
type and phenotype associations by OMIM and ClinVar, and
filtered the dbNSFP variant annotation to retain pathogenic
variants from the TruSight One Sequencing 4813 gene panel.
Then, Sanger sequencing was used to confirm candidate vari-
ants and to define a genetic inheritance mode of candidate
variant as familial segregation testing.
3
2.4 Metabolic investigations
Metabolic laboratory studies were included for qualita-
tive urinary organic acids, plasma amino acids, lactate,
venous blood gas, creatine phosphokinase, electrolytes, full
blood counts, liver function tests, thyroid function test,
urine glycosaminoglycans, acylcarnitine profile, homocys-
teine, purine/pyrimidines, and urine creatine metabolites.
2.5 Statistical analysis
SPSS software version 21 (SPSS, Chicago, IL) was used to
perform statistical analyses, and comparisons were conducted
using chi-square and t-test statistics. We considered probabil-
ity values less than 0.05 to be statistically significant.
3 RESULTS
We recruited 75 consecutive pediatric patients with GDD
and/or ID who met the criteria for CMA, and NGS was
offered in parallel with clinical genetic testing. The medical
and genetic diagnostic evaluation algorithmic approach for
our patients with GDD and/or ID is described in Figure 1.
The mean age ± SD was 5.72 ± 5.08 months, and the
male-to-female ratio was 2:1. None of the families reported
consanguinity. About 52% of patients in this study showed
comorbid problems, such as attention deficit hyperactiv-
ity syndrome (ADHD), autism spectrum disorder (ASD),
anomaly, and facial dysmorphism. Some patients had comor-
bidities: epilepsy, 13 patients (17%); ASD, 12 patients (16%);
ADHD, five patients (7%); facial dysmorphism, nine patients
(12%); cardiac anomaly, one patient (1%); and hypospadias,
one patient (1%). Four patients (5%) showed microcephaly
and two patients (3%) showed macrocephaly.
The first step of the evaluation is a comprehensive history
and physical examination. Complete medical histories were
done. These included three-generation family histories as well
as physical, dysmorphic, and neurological examinations. If a
specific syndrome was suspected, we arranged for the proper
diagnostic tests to confirm, including single-gene analysis.
In a total of 75 patients, 10 patients were diagnosed with a
clinically recognizable syndrome (13%, 10/75): two Rett syn-
drome, one myotonic dystrophy, two Duchenne muscular dys-
trophy, one neurofibromatosis type 1, one myoclonic epilepsy
with ragged red fibers, and three Prader–Willi syndrome. Ten
patients were confirmed by single gene testing because the
features of each disorder are related to a certain gene that is
known to cause a disease.
In the 65 remaining patients, G-band karyotyping, CMA,
and FMR1 gene testing were performed. Among these
patients, the regions of known disease-causing variants asso-
ciated with GDD/ID listed on DECIPHER were identified in
4 HAN ET AL.
Children with GDD and/or ID
Recognizable syndromes?
[Negative]
Chromosomal microarray
G banded karyotype
Fragile X gene test
[Negative]
Brain MRI
Hearing tests
Eye examination
Metabolic evaluation
Electroencephalography
Electomyelography
Skeletal survey
[Negative]
Next-generation sequencing
with gene panel
[Unknown aetiology of GDD and/or ID]
N=22
FIGURE 1 Algorithmic approach for children with global developmental delay (GDD)/intellectual disability (ID). MRI, magnetic resonance
imaging
25 patients (Table 1). Then, two fragile X syndrome (3%,
2/75) were confirmed by FMR1 gene fragment analysis.
Thirty-eight undiagnosed patients were evaluated using
brain magnetic resonance imaging (MRI), metabolic eval-
uations, hearing test, eye examination, and (in the case
of patients who exhibited seizures) electroencephalography.
Metabolic testing included plasma amino acids, urine organic
acids, ammonia, lactate/pyruvate, blood gas analysis, homo-
cysteine, acylcarnitine profile, very long chain fatty acids,
oligosaccharides, and acid mucopolysaccharides. More selec-
tive testing was performed based on the patient's specific fea-
tures. Among these patients, eight patients (11%, 8/75) were
found to have brain structural abnormalities, such as dys-
genesis of corpus callosum, schizencephaly, band heteropia,
and polymicrogyria. No one was diagnosed by metabolic
evaluation. Two patients (3%, 2/75) exhibited sensorineural
hearing loss and five patients (7%, 5/75) exhibited abnormal
electroencephalography.
Among 30 undiagnosed patients and eight brain structural
abnormalities who received a gene panel by NGS, only eight
patients without brain structural abnormalities were found to
have underlying genetic etiology: CHD8, ZDHHC9, MBD5,
CACNA1H, SMARCB1, FOXP1, NSD1, and PAX6. These can-
didate variants were filtered as pathogenic variants associ-
ated with GDD/ID based on OMIM and ClinVar databases
(Table 2).
Despite multidimensional diagnostic workups, 22 patients
(29%, 22/75) did not reveal the etiology of GDD and/or ID.
Specific genetic testing
[pathologic for the suspected conditions
variant identified]
N=10
Genetic counseling
Appropriate medical surveillance
[pathologic Parental studies
variant identified]
N=27
[Brain structural
abnormalities ]
N=8
[pathologic
variant identified]
N=8
Among undiagnosed patients, seven patients (32%, 7/22) had
comorbidities, and 13 patients (59%, 13/22) were found to
have nonsyndromic (NS) GDD/ID. These are statically sig-
nificant compared to diagnosed GDD/ID (P = 0.045, 0.038,
respectively). There was no difference in the male/female
ratio, mean age, and percentage of severe GDD/ID between
two groups (P = 0.764, 0.683, 0.837, respectively) (Table 3).
4 DIS CUS S IO N
In etiologic suspicion subsequent to taking a history and
performing a physical examination, the approach to eval-
uating a patient with GDD/ID included a G-banded kary-
otyping, fragile X molecular genetic testing, aCGH, and
neuroimaging, based on the evidence to date (Moeschler,
2008a). Clinical testing for most Mendelian disorders should
be based on sequencing and/or platforms such as custom
arrays with high resolution for small intragenic deletions.
However, most genomic copy-number alterations associated
with GDD/ID are sporadic. CMA is intended to detect large
deletions or duplications that include part, or all, of the tar-
geted gene, but it is not intended to replace complete gene
sequencing or high-resolution array (Miller et al., 2010).
CMA offers a much higher diagnostic yield (15%–20%) for
genetic testing of individuals with unexplained DD/ID, ASD,
or middle cerebral artery stroke than a G-banded karyotype
(∼3%, excluding Down syndrome and other recognizable
HAN ET AL. 5

TABLE 1 Summary of copy number changes detected by array-based comparative genomic hybridization (CGH), short clinical description,
and parental analysis
Age Clinical
Case Sex (year) phenotypes Array CGH results Size (Mb) Inheritance Remarks
1 M 18 Severe ID, short 46, XY,arr[hg19]14q32.11 17.2 De novo Dysgenesis of
stature, right q32.33(90,017,463_ corpus
hemiplegia 107,240,869)x3 callosum
2 F 12 Moderate ID 47,XX,+mar,arr[hg19] 12.6/5.7 De novo
2q11.1q12.3(95,529,039_
108,083,956)x3,18p11.32_
p11.31(142,096_5,853,
122)x1
3 M 5 GDD 46,XY, arr[hg19]20p13 0.8 De novo
(439,387_1,227,535)x3
4 M 5 GDD 46,XY, arr[hg19]7q11.23 1.4 De novo
(72,726,578_74,139,390)x3
5 M 5 GDD, ASD 46,XY,arr[hg19]2p25.3p25. 7.3 ND
1(42,444_7,304,259)x3
6 F 3 GDD 46,XX,arr[hg19]1q43q44 1.2 De novo Dysgenesis of
(243,653,438_244,844,522)x1 corpus
callosum
7 M 6 Mild ID, epilepsy 46,XY,arr[hg19]2q37.3 2.6 De novo
(240,469,961_243,041,364)x1
8 M 2 GDD 46,XY,arr[hg19]22q13.33 1.6 De novo Dysgenesis of
(49,595,767_51,178,264)x1 corpus
callosum
9 M 3 GDD 46,XY,arr[hg19]5q35.2q35 2.1 ND Microcephaly
.3(175,310,835_177,422,
760)x3
10 F 5 GDD, facial 46,XX,arr[hg19]10q11.22q 22.4 De novo
dysmorphism, 22.1(49,741,476_72,138,939)x1
cardiac anomaly
11 M 5 GDD 46,XY,arr[hg19]7q11.23 1.5 De novo Williams
(72,701,098_74,154,209)x1 syndrome
12 M 5 GDD 46,XY,arr[hg19]15q11. 8.4 De novo
1q13.1(20,102,541-
28,525,460)x3
13 F 5 GDD, ASD 46,XX,arr[hg19]Xp22.31 1.6 De novo Microcephaly
(6,552,712_8,164,803)x3
14 M 9 Severe ID, epilepsy 46,XY,arr[hg19]5q31.2 0.9 De novo Demyelinating
(137,260,366_138,206,885)x3 change of
white matter
15 M 7 Moderate ID 46,XY,inv(9)(p12q13), De novo Smith–Magenis
del(17)(p11.2p11.2) syndrome
16 M 18 Severe ID, epilepsy 46,XY,arr[hg19]12p13.33p 27.5/0.9 De novo Polymicrogyria
11.23(230,421_27,768,
451)x3,18p11.32(142,096_
1,038,964)x1
17 F 16 Severe ID, ASD, 46,XX,arr[hg19] 4.7 ND
amenorrhea, Xp11.4p.11.3(41,306,936_
cleft palate 45,980,483)x1
(Continues)
6 HAN ET AL.

TABLE 1 (Continued)
Age Clinical
Case Sex (year) phenotypes Array CGH results Size (Mb) Inheritance Remarks
18 F 16 Severe ID, short 46,XX,arr[hg19]14q32.11 17.2 De novo Right MCA
stature, chronic q32.33(90,043,558_107, infarction
anemia, atopic 258,824)x3
dermatitis
19 M 1 GDD, café-au-lait 47,XY,mar[8]/46,XY[42] 9.8/1.4 De novo/ Prematurity
spot arr[hg19]2q11.1q12.1 Maternal
(95,529,039_105,358,887)
x3,7q11.23(72,726,578_74,
139,390)x3 mat
20 M 2 GDD 46,XY,arr[hg19]5q13.3 0.6 De novo
(73,470,360_74,032,634)x1
21 F 12 Moderate ID, 46,XX,arr[hg19]12p 3.2 Maternal
epilepsy 13.33p13.32(230,421_3,
394,129)x1
22 M 1 GDD, epilepsy 46,XY,inv(5)(q34q35.2) Paternal Father-
epilepsy
23 F 2 GDD, epilepsy 46,XX,arr[hg19]16p 2.6 De novo Microcephaly
13.11p12.3(15,492,317_18,
112,776)x3
24 F 5 GDD, cleft palate 46,XX,arr[hg19]6q14.3q15 1.9 De novo
(86,185,546_88,051,322)x1
25 F 18 Severe ID 46,XX,arr[hg19]8q23 0.7/3.2 De novo
(113,498,500-114,173,066)
x1,12p13.33p13.32(230,421-
3,394,129)x1
M, male; F, female; GDD, global developmental delay; ID, intellectual disability; ASD, autism spectrum disorder; ND, not determined; MCA, middle cerebral artery.

chromosomal syndromes). This is primarily because it has
a higher sensitivity for submicroscopic deletions and dupli-
cations (Miller et al., 2010; Shin et al., 2015). In our study,
CMA yielded a diagnosis of GDD/ID in about 33% (25/75)
of the time. However, the diagnostic yield of CMA is likely
lower in patients with mild ID without additional findings.
Many CNVs have been reported to have variable or incom-
plete penetrance, thus caution must be taken when counsel-
ing families. Public databases available, such as the Database
of Genomic Variants (http://dgv.tcag.ca/dgv/app/home) and
DECIPHER (https://decipher.sanger.ac.uk/) catalogue chro-
mosomal imbalances and list the associated phenotypes with
appropriate references (Srour & Shevell, 2014).
Children with GDD/ID are commonly screened using
CMA to identify submicroscopic aberrations on a genome-
wide level. In addition, targeted analysis may be needed
in response to clinical suspicion of a specific syndrome.
Physicians often supplement CMA with repeated testing by
sequence analysis of known specific genes or gene panels.
Advancements in DNA sequencing technology have improved
not only the development of multigene panels but, more
recently, have allowed genome-wide analyses to move from
the research to the clinical field. NGS has allowed a variable
set of known disease genes to be analyzed simultaneously and
at lower cost than if each gene were sequenced separately. In
particular, WES has been identified as an effective tool for
diagnosis of de novo gene mutations that represent an impor-
tant cause of GDD/ID (de Ligt et al., 2012). Gene panels can
be utilized in any sequencing technology and pipeline, but the
capture kit used, sequencing design, bioinformatic pipeline,
and selected gene panel are crucial to the results. It is pos-
sible that the great reduction in sequencing expense may be
the most outstanding benefit of WES for smaller gene panels.
With a diagnostic yield of 25%, targeted sequencing appears
relevant as a first intention test for the diagnosis of ID. Clin-
ical interpretation of novel uncertain variants also remains
challenging but should gradually come to be understood with
regard to the specific contribution of the many genes impli-
cated as well as locus-specific disease databases in GDD/ID
(Redin et al., 2014). Analyzing gene panels isolated with tar-
geted capture represents an alternative and is considerably
more cost-effective, but it will only lead to a diagnosis if
the disease-causing gene is included in the gene panel. The
21% (8/38) diagnostic rate that we observed will probably
increase in future case series. Improvement in bioinformat-
ics tools, updates in the genetic databases and literature, and
patients’ clinical phenotype updates increase the yield of a
reanalysis of ID negative exome cases after data reannotation
HAN ET AL. 7

TABLE 2 Characteristics and candidate mutations in the patients with global developmental delay and/or intellectual disability
Age
Case Sex (year) Phenotypes Base change AA change Gene Related disease Inheritance Remarks
A M 13 Mild ID, ADHD, c.4651C > T p.Arg1551Cys CHD8 Autism, De novo
obesity susceptibility to,
18
B M 2 GDD, hypotonia c.286C > T p.Arg96Trp ZDHHC9 Mental retardation, De novo
X-linked
syndromic,
Raymond type
C F 9 Severe ID, ASD, c.254_255 p.Arg85Asnfs*6 MBD5 Mental retardation, Paternal
epilepsy delGA autosomal
dominant 1
D M 13 Mild ID, c.5675G > A p.Arg1892His CACNA1H Epilepsy, idiopathic De novo Encephalomalacic
epilepsy, generalized, change of right
ventricular susceptibility to, 6 temporal areas
septal defect
E F 12 GDD, hypotonia, c.31G > A p.Gly11Arg SMARCB1 Coffin–Siris De novo
small hands syndrome
and feet
F F 9 Severe ID, ASD c.155C > T p.Ala52Val FOXP1 Mental retardation De novo
with language
impairment and
with or without
autistic features
G M 12 Severe ID, ASD, c.19G > T p.Gly7* PAX6 Gillespie syndrome De novo
aniridia
H M 5 Mild ID, c.1789G > T p.Glu866* NSD1 Sotos syndrome De novo
overgrowth
M, male; F, female; GDD, global developmental delay; ID, intellectual disability; ASD, autism spectrum disorder; ADHD, attention deficit hyperactivity syndrome; AA,
amino acid.

TABLE 3 Comparison with diagnosed global developmental delay (GDD)/intellectual disability (ID) and unexplained global developmental
delay/intellectual disability
Diagnosed GDD/ID (%) Undiagnosed GDD/ID (%) P value
Male:female ratio 36:17 15:7 0.764
Mean age (year) 5.91 ± 3.75 5.30 ± 2.07 0.683
Comorbidities 32 (60%) 7 (32%) 0.045
Nonsyndromic GDD/ID 12 (23%) 13 (59%) 0.038
Severe GDD/ID 11 (21%) 6 (27%) 0.837

(Al-Murshedi, Meftah, & Scott, 2018; Al-Nabhani et al.,
2018). Wright et al. reported overall diagnostic yield to
454/1133 (40%), and another 43 (4%) have a finding of
variants of uncertain significance by reanalysis of existing
data (UK-wide Deciphering Developmental Disorders study)
(Wright et al., 2018). However, challenges such as cost,
time, processing, clinical interpretation, and storage of vast
amounts of data exist, and evidence is required to confirm the
diagnostic utility of NGS (Brett et al., 2014). Various targeted
NGS are important according to clinical individualized phe-
notype, because the actual coverage proposed with the WES/
whole-genome sequencing (WGS) strategies is still frequently
insufficient, which may result in missing mutations (Gilissen
et al., 2014). Interpretation of variants identified by WES and
WGS can be a challenge in a clinical setting, because the time
frame required for characterization and validation of a novel
gene is often too long to be of practical help for GDD/ID
(Ankala et al., 2015).
Our results showed that about 29% (22/75) of patients
were undiagnosed with GDD/ID, despite broad testing for
genetic and metabolic disorders. In the undiagnosed group,
the mean age was younger, and the other clinical features—
such as dysmorphism, anomaly, and psychiatric problems—
were not present to as great an extent as they were in the
8 HAN ET AL.
diagnosed GDD/ID group. The presence of GDD/ID as the
sole clinical feature was difficult to diagnose. Additionally, a
WES or WGS study was needed to find associated mutations.
NS GDD/ID is highly associated with external environmen-
tal factors, such as level of maternal education, maternal age,
paternal age, trauma, nutritional states, and access to educa-
tion/opportunity.
The worth of genetic diagnosis of GDD/ID extends to clin-
ical considerations, management planning, the assignment of
the recurrence risk for siblings, and emotional relief for the
family. Developmental disabilities have a tremendous effect
on children's quality of life and functioning, so they need addi-
tional coordinated services, support, or other assistance dur-
ing their lifetimes. Some patients remain undiagnosed, and
this can have considerable adverse effects for their parents
and families, including failure to identify proper management,
failure to recognize the risk of recurrence in future pregnan-
cies, and failure to provide anticipatory guidance and neuro-
logic prognosis.
Particular attention needs to be directed to potential clues
for a genetic or acquired etiology. The practitioner faces chal-
lenges with respect to the selection of diagnostic tests and
accurate diagnosis because of the multiplicity of individually
rare genetic causes (Srour & Shevell, 2014). To assist in deter-
mining the most proper, cost-effective study strategy, the prac-
titioner should seriously consider consultation with a clinical
geneticist when progressing beyond first-tier approach. In a
small way, our genetic and medical approach to the diagno-
sis of children with GDD/ID can help in creating guidelines
for investigation. The limitations of our study are (1) a small
sample size, and (2) the fact that we did not perform further
genetic workups, such as WES or WGS, that have the poten-
tial to identify nearly all types of genetic variation. Variation
exists in clinic-specific guidelines and provider preferences
regarding when to consider a gene panel study by NGS.
In conclusion, GDD/ID is a common neurologic problem
encountered in pediatric practice. Recent advances in genetic
technologies have provided great new opportunities for identi-
fying genetic defects associated with GDD or ID. In this study,
multiple diagnostic tests including CMA, brain MRI, and gene
panel were performed, and about two thirds of these tests
revealed causes. Despite several technological developments
that have substantially increased our insights into genetic eti-
ology, there is an absence of decisive information in a substan-
tial percentage of GDD or ID patients. Newly evolving diag-
nostic tools for GDD/ID and optimistic guidelines are called
for in the near term.
ACKNOW LEDGMENTS
This research was supported by a grant from the Korean
Healthcare Technology R&D Project, Ministry for Health,
Welfare & Family Affairs, Republic of Korea (HI14C3417),
and a grant from the Korea Health Technology R&D
Project, Ministry of Health and Welfare, Republic of Korea
(A120175).
CO N F L I C T O F I N T E R E ST STAT E M E N T
All authors have declared no conflicts of interest.
AU T H O R CO N T R I B U T I O N S
Conceived and designed the experiments: WJ, JP. Per-
formed all data analyses and interpretations and drafted the
manuscript: JYH, JP. Contributed to critically revising the
manuscript for important intellectual content: MK, YK, IGL.
All authors read and approved the manuscript and are account-
able for all aspects of the study.
O RC I D
Joonhong Park https://orcid.org/0000-0001-7354-4234
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How to cite this article: Han JY, Jang W, Park J,
Kim M, Kim Y and Lee IG. Diagnostic approach with
genetic tests for global developmental delay and/or
intellectual disability: Single tertiary center experi-
ence. Ann Hum Genet. 2018;1–9. https://doi.org/10.
1111/ahg.12294