Extending the phenotype of recurrent rearrangements of 16p11.2: Deletions in mentally retarded patients without autism and in normal individuals
Array CGH (comparative genomic hybridization) screening of large patient cohorts with mental retardation and/or multiple congenital anomalies (MR/MCA) has led to the identification of a number of new microdeletion and microduplication syndromes. Recently, a recurrent copy number variant (CNV) at chromosome 16p11.2 was reported to occur in up to 1% of autistic patients in three large autism studies. In the screening of 4284 patients with MR/MCA with various array platforms, we detected 22 individuals (14 index patients and 8 family members) with deletions in 16p11.2, which are genomically identical to those identified in the autism studies. Though some patients shared a facial resemblance and a tendency to overweight, there was no evidence for a recognizable phenotype. Autism was not the presenting feature in our series. The assembled evidence indicates that recurrent 16p11.2 deletions are associated with variable clinical outcome, most likely arising from haploinsufficiency of one or more genes. The phenotypical spectrum ranges from MR and/or MCA, autism, learning and speech problems, to a normal phenotype.
Extending the phenotype of recurrent rearrangements of 16p11.2: Deletions
in mentally retarded patients without autism and in normal individuals
, A.C.J. Gijsbers
, J.H.M. Schuurs-Hoeijmakers
, A. van Haeringen
D.E. Fransen van de Putte
, B.-M. Anderlid
, J. Lundin
, P. Lapunzina
, L.A. Pe
B. Delle Chiaie
, B. Loeys
, B. Menten
, A. Oostra
, H. Verhelst
, D.J. Amor
, D.L. Bruno
, A.J. van Essen
, B. Sikkema-Raddatz
, K.T. Verbruggen
, M.C.J. Jongmans
, R. Pfundt
, H.M. Reeser
, C.A.L. Ruivenkamp
Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Clinical Genetics, Karolinska Universitetssjukhuset, Stockholm, Sweden
INGEMM – Instituto de Gene
dica y Molecular, Hospital Universitario La Paz, Universidad Auto
noma de Madrid, Madrid, Spain
CIBERER (Centro de Investigacio
dica en Red de Enfermedades Raras), Madrid, Spain
CIBERER (Centro de Investigacio
dica en Red de Enfermedades Raras), Barcelona, Spain
Unitat de Gene
tica, Universitat Pompeu Fabra and Hospital Univeristario Vall d’Hebro
n, Barcelona, Spain
Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium
Department of Pediatric Neurology, Ghent University Hospital, Ghent, Belgium
Victorian Clinical Genetics Service, Murdoch Childrens Research Institute, Royal Children’s Hospital, Victoria, Australia
Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Victoria, Australia
Department of Genetics, University Medical Center Groningen, University of Groningen, The Netherlands
Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, The Netherlands
Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
Department of Pediatric Endocrinology, Juliana Children’s Hospital/HAGA Teaching Hospital, The Hague, The Netherlands
Received 22 January 2009
Accepted 8 March 2009
Available online 21 March 2009
Array CGH (comparative genomic hybridization) screening of large patient cohor ts with mental retar-
dation and/or multiple congenital anomalies (MR/MCA) has led to the identiﬁcation of a number of new
microdeletion and microduplication syndromes. Recently, a recurrent copy number variant (CNV) at
chromosome 16p11.2 was reported to occur in up to 1% of autistic patients in three large autism studies.
In the screening of 4284 patients with MR/MCA with various array platforms, we detected 22 individuals
(14 index patients and 8 family members) with deletions in 16p11.2, which are genomically identical to
those identiﬁed in the autism studies. Though some patients shared a facial resemblance and a tendency
to overweight, there was no evidence for a recognizable phenotype. Autism was not the presenting
feature in our series.
The assembled evidence indicates that recurrent 16p11.2 deletions are associated with variable clinical
outcome, most likely arising from haploinsufﬁciency of one or more genes. The phenotypical spectrum
ranges from MR and/or MCA, autism, learning and speech problems, to a normal phenotype.
Ó 2009 Elsevier Masson SAS. All rights reserved.
Array CGH (comparative genomic hybridization) screening of
large patient cohorts with mental retardation (MR) and/or multiple
congenital anomalies (MCA) has lead to the identiﬁcation of
a number of new microdeletion and microduplication syndromes
(for recent review, see ). An additional and important outcome
of this testing has been the discovery that several recurrent
microdeletion and microduplication syndromes are caused by non-
allelic homologous recombination (NAHR) between paired
segmental duplications. As the short arm of chromosome 16 is rich
in intrachromosomal segmental duplications (also known as low
copy repeats, LCRs), it has previously been suggested that this
region may harbour novel genomic disorders  . Indeed,
a number of recent reports have provided evidence for this. Ballif
et al. identiﬁed a microdeletion syndrome in 16p11.2–p12.2
Corresponding author. Center for Human and Clinical Genetics, Leiden
University Medical Center (LUMC), P.O. Box 9600, 2300 RC Leiden, The Netherlands.
Tel.: þ31 71 5268033; fax: þ31 71 5266749.
E-mail address: firstname.lastname@example.org (E.K. Bijlsma).
Contents lists available at ScienceDirect
European Journal of Medical Genetics
journal homepage: http://www.elsevier.com/locate/ejmg
1769-7212/$ – see front matter Ó 2009 Elsevier Masson SAS. All rights reserved.
European Journal of Medical Genetics 52 (2009) 77–87
involving a 7–8 Mb deletion . Ullman et al. reported reciprocal
16p13.1 deletions and duplications which predispose to MR and/or
autism , while Hannes et al. found that this deletion was
signiﬁcantly associated with MR/MCA, and that the reciprocal
duplication was a common variant in the general population .
Finally, copy number variants (CNVs) in the region of 16p11.2 have
been identiﬁed in up to 1% of autistic individuals [10,13,22], rep-
resenting a substantial susceptibility risk to development of autism.
The phenotypic spectrum of rearrangements in this genomic region
remains to be fully characterized, especially in regard to their
association with autism.
By screening 4284 patients with MR/MCA , we detected 14
patients with deletions in 16p11.2, which are genomically identical
to those identiﬁed in the autism studies [10,13,22]. Of these, six
deletions were de novo and six were inherited from parents with
a milder or normal phenotype; in one index case the inheritance
could not be assessed, in another case segregation analysis is
pending. We also detected an inherited smaller deletion of an
adjacent region on 16p11.2.
Here we present clinical and molecular data on our patients
with a 16p11.2 deletion and compare them with previously
reported cases. As autism was not the pres enting sym ptom in
our series o f patients, our data indicate th at the recurrent
del etion of 16p11.2 gives rise to a broader phenotype than
2.1. Selection of patients tested by various array platforms
We studied 4284 patients with MR/MCA in several genetic
centres. Patients were ascertained by clinical geneticists in Leiden,
The Netherlands (n ¼ 318), and through a collaborative effort with
cytogenetic laboratories of Groningen, The Netherlands (n ¼ 600),
Nijmegen, The Netherlands (n ¼ 1525), Stockholm, Sweden
(n ¼ 560), Melbourne, Australia (n ¼ 325), Madrid, Spain (n ¼ 60),
and Ghent, Belgium (n ¼ 896).
2.2. Array platforms
Each of the genetic centres used one of the following array
platforms to analyse their group of patients.
The Affymetrix GeneChip Human Mapping 262K NspI and 238K
StyI arrays (together 500K) (Affymetrix, California, USA) contain
262,262 and 238,304 25-mer oligonucleotides respectively, with an
average spacing of approximately 12 kb per array. An amount of
250 ng DNA was processed according to the manufacturer’s
instruction (http://www.affymetrix.com). Single nucleotide poly-
morphism (SNP) copy numbers were assessed using the software
program CNAG Version 3.0 .
The Affymetrix Genome-Wide Human SNP Array 6.0 features 1.8
million genetic markers, including more than 906,600 SNPs and
more than 946,0 00 probes for the detection of copy number vari-
ation. DNA was processed according to the manufacturer’s
instruction (http://www.affymetrix.com). SNP copy numbers were
assessed using Genotyping ConsoleÔ version 3.0.2.
The Illumina HumanHap300 BeadCh ip contains 317,000
TagSN Ps with a mean resolution of approximately 9 kb. The Illu-
mina HumanCNV370 BeadChip contains 317,000 TagSNPs and
52,000 non-polymorphic markers to speciﬁcally target nearly
14,000 known CNVs. This array has a mean resolution of
approximate ly 7.7 kb. A total of 750 ng DNA was processed
acc ording to the manufacturer’s instruction (http://www.
NP copy numbers (logRratio) and B allele
frequencies were asses sed using the software programs
BeadStudio Version 3.2 (Illumina, Inc.) and Partek Genomics Suite
Version 6.3 (Partek, Inc.).
The 38K high-resolution CGH array contains 41,760 bacterial
artiﬁcial chromosome (BAC) clones produced by the Swegene DNA
Microarray Resource Centre, Department of Oncology, Lund
University, Sweden (http://swegene.onk.lu.se) as previously
The Agilent Human Genome CGH Microarray Kit 44K contains
42,433 probes and the assay was performed according to the
manufacturer’s instructions with minor modiﬁcations. In brief,
400 ng of genomic DNA was labeled with Cy3 (patient) or Cy5
(control) (BioPrime Array CGH Genomic Labeling System, Invi-
trogen). After precipitation, patient and control samples were
pooled together with Cot-1 DNA, Agilent 10 Blocking Agent and
Agilent 2 Hybridization Buffer. This hybridization mixture was
hybridized on the microarrays for 24 h at 65
C. After washing, the
slides were scanned with an Agilent DNA microarray scanner. The
scan images were processed with Agilent Feature extraction soft-
ware version 9 and further analysed with an in-house developed
and freely available software tool arrayCGHbase (http://medgen.
ugent.be/arraycghbase/) . Proﬁles were also evaluated by
circular binary segmentation (CBS) to detect regions with aberrant
The Agilent Human Genome CGH Microarray Kits 105K and
244K (Santa Clara, CA) contain respectively w99,000 and
w237,000 probes, and the assays were performed following the
protocols provided by the manufacturer. The slides were scanned
on an Agilent microarray scanner. Data analysis was performed
using the Agilent Feature extraction sof tware version 9 and Agilent
CGH analytics version 3.5.14 software.
2.3. Multiplex ligation-dependent probe ampliﬁcation (MLPA)
MLPA experiments were performed as described previously
. MLPA probes were designed within the 16p11.2 region
(located in the genes MVP, SPN, CORO1A (kit1); SEZ6L2, MVP,
FAM57B (kit2); SPN, ALDOA (kit 3)). Ampliﬁcation products were
identiﬁed and quantiﬁed by capillary electrophoresis on an ABI
3130 genetic analyzer (Applied Biosystems, Nieuwerkerk aan de
IJssel, The Netherlands). Fragment analysis was performed with
the GeneMarker Software V1.51 (SoftGenetics, USA). Thresholds
for deletions and duplications were set at 0.75 and 1.25
2.4. Fluorescent in situ hybridisation (FISH)
FISH analysis was carried out by standard procedures as
described previously . BAC clones mapping to the 16p11.2 dele-
tion region were used (RP11-114A14 and RP11-301D18).
2.5. Gene prioritisation and sequencing
The software tool Anni 2.0 (http://www.biosemantics.org/
Anni) was used to search for candidate genes in the 16p11.2
region. For each gene a proﬁle of related concepts is constructed
that summarizes the context in which the gene is mentioned in
the literature. Genes associated with similar topics are identiﬁed
by hierarchical clustering of the corresponding gene concept
proﬁles . The software was used according to the software’s
Direct sequencing of genomic PCR products covering the coding
regions of ALDOA, TBX6 and SPN was performed. Primers were
selected using the Primer3 program (http://frodo.wi.mit.edu/cgi-
bin/primer3/primer3_www.cgi). Sequencing was performed as
described previously .
E.K. Bijlsma et al. / European Journal of Medical Genetics 52 (2009) 77–8778
2.6. Case reports
2.6.1. Patients carrying a w600 kb 16p11.2 deletion
Case 1 is a mildly retarded, 44-year old male with normal height
(1.72 m, þ0.2 SDS) and overweight (BMI 28.7 kg/m
). He does not
have autistic behaviour, but has signiﬁcant speech problems. He has
some mild dysmorphic features: short palpebral ﬁssures, dysplastic
ears, retrognathia, a broad neck with sloping shoulders, and
a unilateral simian crease. Parents were not available for testing,
but were reported to be of normal intelligence.
Case 2 is a mildly retarded 18-year old male (Fig. 1a), born to
a 30-year old mother and a 39-year old father. He was born at term
with a birth weight of 4 kg.
His motor development was normal (started walking at 13
months of age), however speech development was delayed (ﬁrst
words at 2.5 years of age). A formal test for autism in childhood
showed no autism spectrum disorder (ASD).
When ﬁrst assessed at the age of 7 years and 3 months, his
height was 1.36 m (þ2.3 SDS), and his head circumference 54.5 cm
(þ1.3 SDS). At the age of 17 years and 2 months his height was
1.80 m (0.2 SDS), his weight was 130.5 kg (þ4.2 SDS, BMI 40.1 kg/
) and his head circumference 60 cm (þ1.8 SDS). He does not
show autistic behaviour. He has mild dysmorphic features: short
and down-slanted palpebral ﬁssures, mild malar hypoplasia,
anteverted nares, simple external ears, retrognathia, a broad neck,
and sloping shoulders.
An MRI at the age of 8 years showed an arachnoidal cyst with
a diameter of 5 cm, and partial agenesis of the left temporal lobe.
His family history is negative for obesity or mental retardation.
MLPA analysis of the 16p11.2 region (kit 1) showed normal copy
numbers in both parents.
Case 3 is a mildly retarded, 10-year old girl, born to a 38-year old
mother and a 31-year old father (Fig. 1b). She was born at term with
a birth weight of 3300 g. In infancy she was treated for epilepsy. Her
motor milestones were reached late and speech development was
delayed (ﬁrst words at the age of 20 months). A formal test for
autism in childhood showed no ASD.
On examination at the age of 8 years and 2 months her height
was 1.30 m (0.4 SDS), her weight 45 kg (þ3 SDS for height, BMI
) and her head circumference 54.5 cm (þ1.7 SDS). She
did not have autistic features. She speaks with a lisp. Apart from
mild malar hypoplasia, she has no apparent facial dysmorphisms.
She has a unilateral single palmar crease and mild syndactyly of the
2nd and 3rd toes.
A brain MRI was reported normal.
The paternal family history is positive for dyslexia and mild
mental retardation. Only her parents and a paternal uncle could be
examined with MLPA-analysis (kit 1). Other family members were
Her father carried the same microdeletion. He had speech
retardation (ﬁrst words at the age of 4 years) and is dyslectic. He
went to a special school because of these problems. Apart from
bilateral 4/5 syndactyly of his toes, he has no apparent dysmorphic
The deletion was also found in the paternal uncle. In infancy he
was treated for pyloric stenosis. He is reported to have mental
retardation and dyslexia. Dysmorphic features were not recorded.
He lives in a sheltered home.
Case 4 is a 13-year old boy. He is the only child of healthy, non-
consanguineous parents. He was born at term after a normal
pregnancy and delivery. His birth weight was 4.3 kg. In early
childhood, he suffered from obstructive bronchitis. Enuresis was
Fig. 1. Phenotypical characteristics of cases with a 16p11.2 deletion. a. Case 2 (overview aged 16 years (left), face aged 7 years (top) and 17 years), b. case 3, c. case 6, d. case 10, e. case
11, f. case 12, g. father of case 12, h. case 13, i. case 14 (at the age of 9 months (left) and 4 years). Some of the cases share facial characteristics (long nose in cases 6, 12, and father of
case 12) (c, f, g); narrow palpebral ﬁssures in cases 6 and 14 (c, i); periorbital fulness in cases 2, 3, and 11 (a, b, e); ptosis in cases 13 and 14 (h, i). Overall however, patients show no
common facial features.
E.K. Bijlsma et al. / European Journal of Medical Genetics 52 (2009) 77–87 79
present till the age of 10 years. His motor and speech development
were slightly delayed; he started to speak single words at 2 years of
age. He was diagnosed with attention deﬁcit disorder (ADD) with
motor immaturity and muscular hypotonia. His cognitive level was
in the low normal range. On examination he was rather tall (þ2
SDS), and overweight (þ3 SDS). He had no apparent dysmorphic
FISH analysis for the 16p11.2 region showed normal copy
numbers in both parents.
Case 5 is a 3-year old boy, the second in a sibship of three. His
parents are ﬁrst cousins. Pregnancy, delivery and neonatal period
were reported as normal. His growth parameters are within normal
limits (0 SDS for height and weight, 0.8 SDS for head circumfer-
ence). His development (motor function, speech and cognitive
function) was severely delayed. He walked independently at the
age of 24 months. He has a disturbed sleeping pattern, with difﬁ-
culties falling asleep as well as waking up in the middle of the night.
At the age of 18 months he scored positive in the CHecklist for
Autism in Toddlers (CHAT)-screening. Evaluation at the age of 20
months showed lack of eye contact, stereotypic behaviour and no
speech. He had no dysmorphic features. Since the age of 18 months,
he has had frequent periods with diarrhea.
Psychological evaluation (Grifﬁth and Merril Palmer R) revealed
a cognitive level corresponding to the 4–10 months of age interval
at a chronological age of 20 months, in addition to autistic symp-
toms. A brain MRI at 17 months of age was normal.
His family history is positive for speech retardation.
MLPA analysis of the 16p11.2 region (kit 2) in his parents and
brother showed a normal copy number in his mother, and a dele-
tion in his father and brother.
As a child, his father had delayed speech development. At
present he is working full time as a sailor. He has no apparent
His 5-year old brother was born at term with good Apgar scores.
At birth, his weight was 3055 g, his length 49 cm. His motor
development was unremarkable (crawling at 8–9 months, walking
independently at 19 months). He had a severe speech delay; at the
age of 2 years he only spoke a few single words. Psychological
evaluation at the age of 4 years and 6 months revealed a speech
disorder. His cognitive function is in the low normal range. His
growth parameters are at the median for weight and height. He has
no apparent dysmorphic features.
Case 6 is a 7-year old mentally retarded girl (IQ 65), without
autistic behaviour (Fig. 1c). On examination, her height was 122 cm
(0.7 SDS), her weight 25 kg (0 SDS), and her head circumference
52.5 cm (þ0.8 SDS). She has a nasal speech.
She has several dysmorphic features: low frontal hairline,
hypertelorism, bilateral epicanthic folds, short palpebral ﬁssures,
mild ptosis, a broad nasal bridge, a broad based nose with upturned
nares, a long philtrum, a tented mouth with thin upper lip, a high
and narrow palate, a pointed chin, low set ears, a broad neck,
widely spaced nipples, short ﬁngers, broad and proximally
implanted thumbs, and mild clinodactyly of both ﬁfth ﬁngers.
Testing of the 16p11.2 region in the parents, using the 44K
Agilent Human Genome CGH Microarray Kit detected the same
deletion in the mother. She is a normal functioning female, with an
IQ within normal limits, without speech problems or major health
problems. The further family history is negative for mental retar-
dation or autism.
Case 7 is a 1 year and 8 month old boy, born after an uneventful
pregnancy with a birth weight of 2770 g, a birth length of 46 cm
and a head circumference of 34 cm. His neonatal period was
uncomplicated. His neuromotor development was slow, with
sitting independently at 13 months of age. At the age of 18 months
he was able to crawl, roll over, and pull himself up to an upright
position, but he could not yet stand unsupported. He could speak
two words. Formal developmental testing revealed a develop-
mental level of 12 months at the age of 17 months. He had no major
health problems. At the age of 18 months his height was 72 cm (4
SDS), his weight 8.2 kg (1.5 SDS for height), and his head
circumference 47.5 cm (0.7 SDS). Physical examination revealed
mild facial dysmorphism with sparse blond hair, anteverted nares,
low-set ears, a broad mouth and a narrow nasal bridge. He has mild
hypospadias with bilateral descended testis. He has small hands.
Neurological examination showed symmetrical reﬂexes, axial
hypotonia, and joint hyperlaxity.
His family history is positive for developmental delay: his
mother, father and brother are all developmentally delayed. The
probands brother had normal anthropometric parameters at birth,
but suffered from asphyxia and has convulsions and developmental
delay. He has not been tested for the deletion.
Analysis of the 16p11.2 region in the parents, using the 44K
Agilent Human Genome CGH Microarray Kit detected the same
mother. She has short stature (height 1.50 m, 3.2
SDS). She attended a school for children with learning disabilities
and works in a sheltered workshop. There is no further family
history of developmental delay, other family members were not
available for testing.
Case 8 is an 11-year old, mildly mentally retarded girl. She was
born as the third child of healthy, non-consanguineous parents.
Pregnancy and delivery were uneventful. At the age of 2 years
speech retardation was evident. At the age of 2.5 years, she used
about 20 words and at the age of 3 years she spoke 2-word sen-
tences. At the age of 3 years, she suffered from complex partial
epilepsy, which was successfully treated.
Psychological testing revealed mild mental retardation (total IQ
(TIQ) 62) and a severe expressive language disorder. Apart from
some hand stereotypes, she had no behavioural problems or
autistic features. On examination, she had a normal height (146 cm,
0 SDS) and weight (42.8 kg, þ0.7 SDS). Apart from mild truncal
obesitas no abnormalities were noted, especially no dysmorphic
features. A brain MRI showed no abnormalities.
Despite intensive therapy, she did not achieve scholarly skills
such as reading, writing and calculating. At the age of 11 years she
still has poor expressive verbal skills.
Her family history is positive for mental retardation. Her oldest
sister is equally affected with mild mental retardation (TIQ 66),
expressive language disorder and epilepsy. Their father had
Analysis of t he 16p11.2 region in the parents, using the 44K
Agilent Human Genome CGH Microarray Kit detected the same
deletion in the mother, who is of normal intelligence and
without major health problems. Array analysis in the sister is
Case 9 is a 34-year old mentally retarded male, reported as
case 7 in a previously described series . He was born at term
after normal pregnancy and delivery. He was reported to be small
for gestational age (2.8 kg). His developmental milestones were
reached late. In childhood he had intensive speech therapy
because of speech delay. On examination at the age of 34 years,
he had slow speech and was overweight. Apart from mild malar
hypoplasia, he had no apparent dysmorphisms. He had no autistic
Formal neuropsychological assessment indicated moderate
mental retardation, with major difﬁculties with working memory,
attention and self-monitoring. He does not live independently, but
has been able to do simple (cleaning) jobs.
FISH analysis in his parents conﬁrmed a de novo deletion.
Case 10 is an 8-year old girl with signiﬁcant intellectual
disability, born to a 30-year old mother and a 31-year old father. She
E.K. Bijlsma et al. / European Journal of Medical Genetics 52 (2009) 77–8780
has no speech, but she is socially interactive. She is able to walk and
has a happy disposition. She is not toilet trained and has major
sleeping problems. Apart from pyloric stenosis at the age of 5
weeks, she had no major health problems, especially no seizures.
On examination she had normal height (128 cm, 0.5 SDS),
weight (24 kg, 0.7 SDS), and head circumference (53 cm, þ1 SDS).
She has subtle dysmorphic features (Fig. 1d): a relatively ﬂat nose
and maxilla, prominent infra-orbital skin creases, small ears, an
unusual hairline which extends over the lateral forehead, small
hands with abnormal palmar creases and small feet.
Her family history is negative for mental retardation.
FISH analysis in the parents is ongoing.
Case 11 is a 4.5-year old boy, born to a 33-year old father and
a 28-year old mother. He was born at term in poor condition, but
quickly recovered from hypotonia and cyanosis using an oxygen
mask (Apgar scores 5 and 9 at 1 and 5 min, respectively).
At birth, his weight was 3 kg, his length 49 cm, and his head
circumference 35 cm. In infancy and childhood he had failure to
thrive. He has no autistic features. He loves water and music. He has
normal hearing and vision.
His gross and ﬁne motor development were delayed; he walked
independently at the age of 2.5 years. At the age of 3 years and 8
months he had no comprehensible language, but only varied
utterances mimicking sentences. Language comprehension was
clearly present. At the age of 4 years and 4 months he was able to
speak a few single words, with poor articulation.
IQ-testing at the age of 3 years and 8 months showed scores
in the slightly retarded range (non-verbal IQ (teste d with SON-R
2½–7) 74, language comprehension quotient (Reynell): 73, and
expressive language quotients word s/sentences (Schlichting):
Physical examination at the age of 4 years showed a skinny boy
with a height of 101.5 cm (0.5 SDS), a weight of 15 kg (0.9 SDS
for height), and a head circumference of 51.5 cm (þ0.1 SDS). He had
mild facial dysmorphism: retrognathia, small teeth, and posteriorly
rotated ears with a slightly larger ear on the left (Fig. 1e). Neuro-
logical examination showed clumsy walking, but was otherwise
unremarkable. There was no indication of a speciﬁc motor deﬁcit
A brain MRI was reported normal.
The maternal family history is positive for mental retardation:
two maternal uncles are mentally retarded.
Analysis of the 16p11.2 region using the 105K Agilent Human
Genome CGH Microarray Kit showed normal copy numbers in both
Case 12 is a 3.5-year old girl, born as the third child of a 32-year
old mother and the second child of a 31-year old father (Fig. 1f). She
presented prenatally with intrauterine growth retardation. In
pregnancy, her mother had thrombosis and hypertension. Delivery
was induced at 37 weeks of gestation. Birth weight was 2.5 kg (1.3
SDS), and head circumference 31.5 cm (2 SDS). In the ﬁrst year,
she had muscular hypertonia. Her development is within normal
limits and she has no autistic features.
Physical examination at the age of 11 months showed a length of
77.5 cm (þ1.5 SDS), a weight of 8.4 kg (0.9 SDS), and a head
circumference of 45.5 cm (0 SDS). She had minor facial dys-
morphisms: slightly deep-set eyes, a thin upper lip, a smooth
philtrum, long and slender ﬁngers, and camptodactyly of both ﬁfth
At the age of 2 years and 9 months she was diagnosed with
a Wilms’ tumor with liver metastases. At the age of 3 years and 4
months she was fully recovered after standard treatment.
The family history is positive for mental retardation. Her older
brother is mentally retarded, with an estimated IQ of 60. He also
had muscular hypertonia in infancy. He was not tested for the
deletion. Her maternal half-sib is mentally retarded and has
attention deﬁcit hyperactivity disorder (ADHD).
The Wilms’ tumor, combined with the family history and
hypertonia in the neonatal period, were reason to perform array
Analysis of the 16p11.2 region in her parents, using the 105K
Agilent Human Genome CGH Microarray Kit, detected the same
deletion in the father. He is of normal intelligence and has no
apparent dysmorphic features (
In childhood, he had
problems nor speech problems. He had two
episodes of meningitis, at the ages of 9 months and 31 years,
respectively. During the latter episode he developed seizures due to
post-viral cerebral damage. He has a full time job.
He is the only child of healthy parents. Further family studies
have not been performed.
Case 13 is a 4 years and 10 months old boy (Fig. 1h). He is the
second child of a 31-year old mother and a 33-year old father. He
was born at term after a normal pregnancy, with a birth weight of
2790 g. At the age of 7 weeks he was diagnosed with short segment
(w5 cm) Hirschsprung’s disease, for which he underwent surgery.
At the age of 2 years and 6 months he started to have seizures, for
which he was successfully treated. He suffers from frequent infec-
tions, particularly otitis media and upper respiratory tract
His psychomotor development was delayed: he walked inde-
pendently at the age of 21 months and spoke his ﬁrst words at the
age of 3 years and 9 months. At the age of 4 years and 6 months his
IQ score was 83. A formal test for autism showed no ASD.
On examination he had normal height (112 cm, 0 SDS) and
weight (21 kg, þ1 SDS). He has a mild ptosis, a unilateral simean
crease, and a pectus excavatum. He has a high forehead, but this is
also observed in his unaffected brother and father.
Analysis of the 16p11.2 region using the 500K Affymetrix Gen-
eChip Human Mapping array, showed normal copy numbers in
Case 14 is a 4-year old girl with psychomotor and growth
retardation. She is microcephalic with facial dysmorphisms: ble-
pharophimosis, ptosis, epicanthus inversus, telecanthus, a ﬂattened
and broad nose with biﬁd tip, and large ears (Fig. 1i). She also has
scoliosis and clinodactyly of her ﬁngers. Autistic features are not
MLPA analysis of the 16p11.2 region (kit 3) showed normal copy
numbers in both parents.
2.6.2. Patients carrying atypical 16p11.2 deletions
Case 15 is a 5-year old mentally retarded boy. He was born at
term after an uncomplicated pregnancy. Birth weight and length
were 3750 g and 53 cm, respectively. Both his motor and speech
development were delayed; he started to walk at the age of 2 years,
and at times speech is barely comprehensible. Because of behav-
ioural problems he is on Risperdal. He has a normal sleeping
On examination at the age of 5 years and 3 months he was
hypotonic and had dysmorphic features: a long narrow face,
a prominent forehead, downslanted and narrow palpebral ﬁssures,
an open mouth with down turned corners, and ﬂeshy earlobes
A brain MRI was reported normal.
Analysis of the 16p11.2 region in the parents, using the 44K
Agilent Human Genome CGH Microarray Kit detected the same
deletion in the father. As a child, his father had learning difﬁculties.
He works as a truck driver. He has the same facial appearance as his
son (Fig. 2b).
Further family members were not accessible. The family history
is negative for learning problems.
E.K. Bijlsma et al. / European Journal of Medical Genetics 52 (2009) 77–87 81
3.1. Recurrent microdeletion of 16p11.2
Array analysis was performed on 4284 patients with MR/MCA.
We detected 14 cases (0.3%) with a microdeletion of approximately
60 0 kb in the same area of 16p11.2, from genomic location 29.5 to
30.1 Mb (Ensembl release 52, December 2008) (Fig. 3). In case 14
a de novo deletion of 16p11.2 was found in a mosaic state (Fig. 4).
Table 1 summarizes all detected 16p11.2 deletions in the index
cases (n ¼ 14). Of these, six occurred de novo, six were inherited
(three paternal and three maternal), one could not be assessed, and
one is still under study.
Table 2 provides a summary of the phenotypic characteristics
of the 14 index cases with a 16p11.2 deletion. Twelve out of 14
had d evelopmental del ay, ranging from motor retardation to
severe mental retardation. Ten were recorded to have speech
problems. Autism was formally diagnosed in one index patient
(case 5). In nine index cases dysmorphic features were noted.
Five index cases had overweight or obesity. Major congenital
malformations were not a f requent symptoms, however pyloric
sten osis was repor ted twic e ( uncle of case 3, case 10), but this
co-occurrence is most likely coincidental. The intracerebral cyst
in case 2 is regarded a chance ﬁnding, as this anomaly is not
known to be associated with (spe ech) retardation. Among the
index ca ses, one patient had a malignancy (case 12, Wilms’
In the six familial cases, three of the transmitting parents (two
males, one female) had developmental problems of a varying
degree (parents of cases 3, 5, and 7). Other family members
carrying the deletion were also reported to have developmental
problems (uncle and sib of cases 3 and 5, respectively). Three
apparently normal transmitting parents were identiﬁed (in cases 6,
8, and 12).
In the common 600 kb recurrent microdeletion more than 25
genes are located. To determine whether the remaining intact
16p11.2 region harbored recessive mutations, which might be
contributing to the phenotype in these individuals, we sought to
identify gene candidates for sequence analysis. After analysing this
region with the Anni tool, the genes ALDOA, TBX6 and SPN seemed
good candidates to test for a mutation on the remaining allele.
However, sequencing of genomic PCR products covering the coding
regions of ALDOA, TBX6 and SPN in four of the deletion patients
(cases 1–3, and the paternal uncle of case 3) showed no mutations.
3.2. Atypical deletion of 16p11.2
In addition to the common recurrent microdeletion of 16p11.2
observed in 22 individuals (14 patients and 8 family members), an
atypical rearrangement was detected in two related patients. In
case 15, a 205 kb deletion in 16p11.2 was detected (28.74–
28.95 Mb) (Fig. 5). The same deletion was detected in his father. The
205 kb deletion in 16p11.2 is ﬂanking the common deleted region.
Fig. 2. Facial characteristics of cases with an atypical 16p11.2 deletion. a. Case 15, b. father of case 15. Note long narrow face, prominent forehead, downslanted and narrow palpebral
ﬁssures, and down turned corners of the mouth in both.
E.K. Bijlsma et al. / European Journal of Medical Genetics 52 (2009) 77–8782
We describe 22 individuals (14 index patients and 8 family
members) carrying a common deletion in 16p11.2 (from genomic
location 29.5 Mb to 30.1 Mb), one of them in mosaic form. In addi-
tion, two related patients showed a smaller deletion of an adjoining
region, presumably representing a rearrangement of adjacent LCRs.
Previous reports have shown that the same (w600 kb) 16p11.2
deletion recurrently occurs in patients diagnosed with autism
[10,13,22]. Weiss et al. reported a recurrent microdeletion on
chromosome 16p11.2 in ﬁve of 751 families with one or more cases
with ASD, in three of 299 ASD patients, in ﬁve of 512 children
referred for MR and/or autism, and in two of 18,834 Icelandic
controls who had not been screened for psychiatric or language
disorders . The reciprocal duplication was found in 11 patients
and in ﬁve controls. In another study, the same deletion was
detected in four of 712 autistic patients and none of 837 controls
. This study identiﬁed the reciprocal duplication in one autism
case and two controls. Similarly, Marshall et al. detected two de
novo 16p11.2 deletions in 427 families with autism . In this
series, the reciprocal duplication was also found twice. The authors
stated that deletions and duplications of 16p11.2 carry substantial
susceptibility to autism, and that the deletions appear to account
for approximately 1% of cases. In contrast, in our series autism was
not a frequent symptom, only one of the cases had formally been
diagnosed with autism. Although the other patients were not
extensively assessed for autistic features, their behaviour and social
interaction were not suggestive of autism.
Fig. 3. Examples of array results showing a 16p11.2 deletion using various array platforms. (a) LogRratio proﬁle of a 500K Affymetrix array, showing a minimal deletion of w525 kb
in case 13, (b) LogRratio proﬁle of a 317K Illumina array, showing a minimal deletion of w522 kb in case 1, (c) LogRratio proﬁle of a 244K Agilent array, showing a minimal deletion
of w 505 kb in case 5, (d) LogRratio proﬁle of a 44K Agilent array, showing a minimal deletion of w526 kb in case 6, (e) LogRratio proﬁle of a 38K BAC array, showing a minimal
deletion of w612 kb in case 4.
E.K. Bijlsma et al. / European Journal of Medical Genetics 52 (2009) 77–87 83
Additional, single reports of individuals with 16p11.2 micro-
deletions have been documented, mainly without autism. Rosen-
berg et al. reported a deletion in a patient with mild mental
retardation, severe speech delay, and facial dysmorphism .A
w600 kb 16p11.2 microdeletion was reported in a pair of mono-
zygotic twins with mild mental retardation, mild dysmorphism,
a seizure disorder: and aortic valve disease. Autistic features were
not reported . A similar de novo deletion was identiﬁed in
a female with Asperger syndrome, without further details
regarding her phenotype .
Comparison of the phenotypes is hampered by limited clinical
data in previous reported series (Table 2). Dysmorphic features
were not reported in the deletion cases in the series of Kumar et al.
. As further phenotypical data are not provided, these patients
were not included in Table 2. Regarding behaviour, there was
a trend towards aggression and overactivity in patients carrying the
deletion . This was not observed in our series.
Phenotypic data are available on two autism patients ,ﬁve
children referred for MR and/or autism (including a pair of mono-
zygous twins), and three autism patients in the series of Weiss et al.
. Seven out of ten cases had developmental delay, and speech
development was delayed in each case, when it was recorded
(n ¼ 9). Only one patient was reported with facial dysmorphisms,
which were not further speciﬁed . In our series, dysmorphic
features were reported in nine of 14 index cases. Some patients
have facial features in common (Fig. 1), however no speciﬁc pattern
of dysmorphic features could be distinguished.
Five of our 14 index cases were overweight, as were four out of
ten autism cases [13,22]. However, patients with a weight on the
other side of the spectrum are also reported (case 12, ). Three of
our index cases and four previously reported patients (including
monozygous twins) had seizures [7,22].
In summary, though some of our patients show a facial resem-
blance and 16p11.2 deletion patients share a tendency to over-
weight and obesity, there is no evidence in our group of index cases
to suggest a recognizable phenotype.
In the previous autism studies almost all microdeletions were de
novo [10,13,22]. Among a total of 20 cases (including monozygous
twins), 18 were de novo and only one familial case was reported: an
index patient with autism inherited the deletion from his father
with ADHD . In contrast, we identiﬁed six familial cases among
14 index patients. In half of familial cases, the transmitting parent
(and other family members that carried the deletion) had devel-
opmental problems, which were frequently speech related. Inter-
estingly, in a study of Icelandic subjects with a psychiatric or
language disorder, the 16p11.2 deletion was found in a higher
frequency than in the control population, 0.1% vs. 0.01%. For
instance in patients with dyslexia, 1 in about 750 carried the
16p11.2 deletion, suggesting an association between the deletion
and this speciﬁc phenotype .
Fig. 4. Mosaic 16p11.2 deletion. LogRratio proﬁle (upper panel) showing a slight decrease in copy number and B-allele frequency plot (lower panel) showing ABB and AAB
genotypes (317K Illumina array).
Index cases with 16p11.2 deletion.
Case ID (DECIPHER code) Platform Starting probe Ending probe Start position End position Status of inheritance
1 (LEI00248634) 317K Illumina rs8054172 rs7202714 29563365 30085308 n/a
2 (LEI00248635) 317K Illumina rs8054172 rs7202714 29563365 30085308 de novo
3 (LEI00248636) 370K Illumina rs28455095 rs7202714 29531748 30085308 Paternal
4 38K BAC array RP11-753J6 RP11-787F23 29536903 30149118 de novo
5 244K Agilent A_16_P03134009 A_14_P129228 29500284 30240082 Paternal
6 (GHE00002722) 44K Agilent A_14_P200817 A_14_P124319 29581455 30106054 Maternal
7 (GHE00248753) 44K Agilent A_14_P200817 A_14_P124319 29581455 30106054 Maternal
8 (GHE00248754) 44K Agilent A_14_P200817 A_14_P124319 29581455 30106054 Maternal
9 262K NspI Affymetrix SNP_A-2236020 SNP_A-2272043 29580704 30085308 de novo
10 Affymetrix SNP 6.0 SNP_A-8559376 CN_728581 29488122 30134457 Pending
11 105K Agilent A_16_P20442189 A_14_P124319 29563984 30106253 de novo
12 105K Agilent A_16_P20442189 A_14_P124319 29563984 30106253 Paternal
13 500K Affymetrix SNP_A-2117335 SNP_A-2272043 29559989 30085308 de novo
317K Illumina rs8054172 rs7202714 29563365 30085308 de novo
15 (atypical) 44K Agilent A_14_P134515 A_14_P106155 28744951 28949560 Paternal
n/a, DNA of parents not available.
Deletion found in mosaic state.
E.K. Bijlsma et al. / European Journal of Medical Genetics 52 (2009) 77–8784
In two families, the transmitting fathers were less affected than
their children (cases 3 and 5). In one family with maternal trans-
mission, the mother was mentally retarded and probably as
affected as her child (case 7). As the region of chromosome 16 is not
known to be imprinted, it is unlikely that imprinting explains this
Noticeably, in case 5 and his family clinical expression seems to
include both ends of the phenotypic spectrum: case 5 is severely
mentally retarded and the only patient in our series with autism;
his father and brother are of normal intelligence but do have speech
problems. It is possible that the consanguinity in this family plays
a role in this variability. As his parents are ﬁrst cousins, an addi-
tional effect of an autosomal recessive trait may be present.
Homozygosity for this hypothetical trait in case 5, but not in his
brother and father, would then explain the difference in expression
in this family. Segregation studies however, point to considerable
intrafamilial variability in expression in our non-consanguineous
families as well.
Unexpectedly, the mosaic 16p11.2 deletion was identiﬁed in
a patient with a severe phenotype (case 14), not observed in any
other known carrier. Without knowledge about the full spectrum of
the 16p11.2 deletion phenotype, it is difﬁcult to presume a causal
Phenotypic features of index cases with a 16p11.2 deletion.
Index cases Gender Developmental delay Speech retardation Autism Dysmorphism Overweight Seizures
Case 1 m þþþþ
Case 2 m þþþþ
Case 3 f þþþþ
Case 4 m þþ
Case 5 m þþþ
Case 6 f þ ? þ
Case 7 m þ ? þ
Case 8 f þþþ
Case 9 m þþþ
Case 10 f þþþ
Case 11 m þþþ
Case 12 f þ
Case 13 m þþþþ
f þ ??þ
Marshall et al. 
MM 0088-003 f þþ??
SK 0019-004 m þþþþ?
Weiss et al. 
pt 1 m þþþ
pt 2 m þþþ?
pt 3 m þþþ
Aut 1 f þþþ?
Aut 2 m þþ? þþ
Aut 3 f þ ? þ ??þ
Total (index cases) 15m/9f 19/24 19/20 11/23 10/21 9/21 5/22
Combined carrier family members
(this series; n ¼ 8)
5m/3f 2/8 3/6 0/8 0/6 0/3 0/6
Total (all carriers) 20m/12f 21/32 22/26 11/31 10/27 9/24 5/28
þ, present; , absent; ?, unknown.
Excluding seizures secondary to known causes.
Fig. 5. Atypical 16p11.2 deletion. Array analysis with 44K Agilent array revealing a 205 kb atypical 16p11.2 deletion from 28,74 Mb to 28,95 Mb.
E.K. Bijlsma et al. / European Journal of Medical Genetics 52 (2009) 77–87 85
relationship between the mosaic deletion and the severe pheno-
type in this patient. As this patient seems to have dysmorphic
features suggestive of BPES (Blepharophimosis, Ptosis, Epicanthus
inversus Syndrome), this may well be caused by another genetic
defect (FOXL2 gene mutations were excluded).
Likewise, it is difﬁcult to speculate on the signiﬁcance of the
atypical deletion found in case 15 and his father. There are no
previous reports about patients with this deletion. The deletion
may be causal, since the father has a comparable phenotype and
had learning problems. More evidence is needed however, and
further family studies would have to be performed to gain more
insight in the segregation of the deletion and the phenotype. The
identiﬁcation and characterization of additional deletions like the
two described here are needed.
In a previous paper, the question was raised whether the
16p11.2 microdeletion might be non-pathogenic, or a coincidental
ﬁnding . Given the negative results in their control group, the
authors suggest that chance ﬁnding is unlikely. Further evidence to
support pathogenicity for this microdeletion has come from several
sources: in the autism studies, the deletion was almost always de
novo [10,13,18,22], and the deletion was found in only 2 of almost
18,900 non-characterized Icelandic controls . In our series, six
out of 14 deletion cases were familial, half of the transmitting
parents however had a (mild) phenotype. Hence, it seems plausible
that the 16p11.2 deletion is pathogenic.
Kumar et al. suggested that the 16p11.2 microdeletion is not
associated with MR, and is more likely to cause autism . Our
series proves that the deletion does not necessarily cause autism,
but is associated with other developmental and speech disorders as
well, and may even be found in normal individuals. Finally, the
marked phenotypic variation in our series of deletion cases proves
that the 16p11.2 deletion does not by itself cause ASD, as has been
suggested previously .
The assembled evidence indicates that recurrent 16p11.2 dele-
tions are associated with variable clinical outcome, most likely
arising from haploinsufﬁciency of one or more genes located
between the two paired LCRs. Several well known microdeletion
syndromes, such as the 22q11 microdeletion syndrome, show
a wide range in phenotypic expression with non-obligatory MR,
congenital anomalies, dysmorphisms and psychiatric disorders,
including autism. The reciprocal 22q11 duplication appears to be
even more variable, including more ‘normal’ individuals with mild,
but characteristic facial features [3,5,6].
As an alternative explanation for the variability in phenotype in
new microdeletion cases, it has been hypothesized that the dele-
tion may unmask a mutation in a recessive gene on the homologous
allele, and thus cause a more severe phenotype . However,
sequencing of three selected candidate genes in four patients
described here, failed to detect any sequence alterations. As there
are more than 25 genes in this region, one explanation for the
negative ﬁndings could be the fact that we chose the wrong genes.
However, the cellular functions of TBX6 (a transcription factor) and
ALDOA (a glycolytic enzyme) make them strong candidate genes,
and it may be worthwhile to explore them in more detail. We may
have missed mutations in the promotor regions, the untranslated
regions or introns. Alternatively, we may have selected an inap-
propriate set of patients. Better still would be to screen patients
with a more severe phenotype than their transmitting parent.
Further studies of additional genes and patients are needed.
In summary, a w600 kb deletion in 16p11.2 is described in
autistic patients without apparent dysmorphic features
[10,13,18,22], in mentally retarded patients with minor dysmorphic
features ([7,16], this series), and in individuals with normal intel-
ligence (this series) who may have had isolated developmental
problems such as speech retardation and dyslexia. We therefore
conclude that this deletion at 16p11.2 is associated with a variable
phenotype. With our series of 16p11.2 deletion carriers we have
extended the spectrum of the associated phenotype. The pheno-
type is not restricted to autism, and the deletion does not always
result in autism. The deletions are most likely pathogenic and are
associated with a variable clinical outcome, including a normal
phenotype. However, further studies of more patients and normal
individuals with 16p11.2 deletions (and duplications) are needed to
gain better insight in the potential pathology associated with
rearrangements in this area.
We would like to thank the patients and their families for their
kind collaboration, and Jacqueline Schoumans, Clinical Genetics
lm, for bringing case 9 to our attention.
 B.C. Ballif, S.A. Hornor, E. Jenkins, S. Madan-Khetarpal, U. Surti, K.E. Jackson,
A. Asamoah, P.L. Brock, G.C. Gowans, R.L. Conway, J.M. Graham Jr., L. Medne,
E.H. Zackai, T.H. Shaikh, J. Geoghegan, R.R. Selzer, P.S. Eis, B.A. Bejjani,
L.G. Shaffer, Discovery of a previously unrecognized microdeletion syndrome
of 16p11.2–p12.2, Nat. Genet. 39 (2007) 1071–1073.
 D.L. Bruno, D. Ganesamoorthy, J. Schoumans, A. Bankier, D. Coman, M. Dela-
tycki, M.R. Gardner, M. Hunter, P.A. James, P. Kannu, G. McGillivray, N. Pachter,
H. Peters, C. Rieubland, R. Savarirayan, I.E. Scheffer, L. Shefﬁeld, T. Tan, S.M.
White, A. Yeung, Z. Bowman, C. Ngo, K. Choy, V. Cacheux, L. Wong, D. Amor,
H.R. Slater, Detection of cryptic pathogenic copy number variations and
constitutional loss of heterozygosity using high resolution SNP microarray
analysis in 117 patients referred for cytogenetic analysis and impact on clinical
practice, J. Med. Genet. 46 (2009) 123–131.
 W. Courtens, I. Schramme, A. Laridon, Microduplication 22q11.2: a benign
polymorphism or a syndrome with a very large clinical variability and reduced
penetrance? report of two families, Am. J. Med. Genet. Part A 146A (2008)
 J.G. Dauwerse, T. Kievits, G.C. Beverstock, D. van der Keur, E. Smit,
H.W. Wessels, A. Hagemeijer, P.L. Pearson, G.J. van Ommen, M.H. Breuning,
Rapid detection of chromosome 16 inversion in acute nonlymphocytic
leukemia, subtype M4: regional localization of the breakpoint in 16p, Cyto-
genet. Cell. Genet. 53 (1990) 126–128.
 L. Edelmann, R.K. Pandita, E. Spiteri, B. Funke, R. Goldberg, N. Palanisamy,
R.S.K. Chaganti, E. Magenis, R.J. Shprintzen, B.E. Morrow, A common molecular
basis of rearrangement disorders on chromosome 22q11, Hum. Mol. Genet. 8
 R.E. Ensenauer, A. Adeyinka, H.C. Flynn, V.V. Michels, N.M. Lindor,
D.B. Dawson, E.C. Thorland, C.P. Lorentz, J.L. Goldstein, M.T. McDonald,
W.E. Smith, E. Simon-Fayard, A.A. Alexander, A.S. Kulharya, R.P. Ketterling,
R.D. Clark, S.M. Jalal, Microduplication 22q11, an emerging syndrome: clinical,
cytogentic and molecular analysis of thirteen patients, Am. J. Hum. Genet. 73
 N. Ghebranious, P.F. Giampietro, F.P. Wesbrook, S.H. Rezkalla, A novel micro-
deletion at 16p11.2 harbors candidate genes for aortic valve development,
seizure disorder, and mild mental retardation, Am. J. Med. Genet. Part A 143A
 F.D. Hannes, A.J. Sharp, H.C. Mefford, T. de Ravel, C.A. Ruivenkamp, M.H.
Breuning, J.P. Fryns, K. Devriendt, G. van Buggenhout, A. Vogels, H.H. Stewart,
R.C. Hennekam, G.M. Cooper, R. Regan, S.J. Knight, E.E. Eichler, J.R. Vermeesch,
Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is
a risk factor for MR/MCA while the duplication may be a rare benign variant,
J. Med. Genet., 2008, doi:10.1136/jmg.2007.055202.
 R. Jelier, G. Jenster, L.C. Dorssers, B.J. Wouters, P.J. Hendriksen, B. Mons,
R. Delwel, J.A. Kors, Text-derived concept proﬁles support assessment of DNA
microarray data for acute myeloid leukemia and for androgen receptor stim-
ulation, BMC Bioinform. 18 (20 07) 14.
 R.A. Kumar, S. KaraMohamed, J. Sudi, D.F. Condrad, C. Brune, J.A. Badner,
T.C. Gilliam, N.J. Nowak, E.H. Cook jr., W.B. Dobyns, S.L. Christian, Recurrent
16p11.2 microdeletion in autism, Hum. Mol. Genet. 17 (2008) 628–638.
 S.A. Lesnik Oberstein, M. Kriek, S.J. White, M.E. Kalf, K. Szuhai, J.T. den
Dunnen, M.H. Breuning, R.C. Hennekam, Peters plus syndrome is caused by
mutations in B3GALTL, a putative glycosyltransferase, Am. J. Hum. Genet. 79
 M. Losekoot, C. Haarloo, C. Ruivenkamp, S.J. White, M.H. Breuning, D.J. Peters,
Analysis of missense variants in the PKHD1-gene in patients with autosomal
recessive polycystic kidney disease (ARPKD), Hum. Genet. 118 (2005) 185–206.
 C.R. Marshall, A. Noor, J.B. Vincent, A.C. Lionel, L. Feuk, J. Skaug, M. Shago,
R. Moessner, D. Pinto, Y. Ren, B. Thiruvahindrapduram, A. Fiebig, S. Schreiber,
J. Friedman, C.E. Ketelaars, Y.J. Vos, C. Ficicioglu, S. Kirkpatrick, R. Nicolson,
L. Sloman, A. Summers, C.A. Gibbons, A. Teebi, D. Chitayat, R. Weksberg,
E.K. Bijlsma et al. / European Journal of Medical Genetics 52 (2009) 77–8786
A. Thompson, C. Vardy, V. Crosbie, S. Luscombe, R. Baatjes, L. Zwaigenbaum,
W. Roberts, B. Fernandez, P. Szatmari, S.W. Scherer, Structural variation of
chromosomes in autism spectrum disorder, Am. J. Hum. Genet. 82 (2008)
 B. Menten, F. Pattyn, K. De Preter, P. Robbrecht, E. Michels, K. Buysse,
G. Mortier, A. De Paepe, S. van Vooren, J. Vermeesch, Y. Moreau, B. De Moor,
S. Vermeulen, F. Speleman, J. Vandesompele, arrayCGHbase: an analysis
platform for comparative genomic hybridization microarrays, BMC Bioinform.
6 (2005) 124.
 Y. Nannya, M. Sanada, K. Nakazaki, N. Hosoya, L. Wang, A. Hangaishi,
M. Kurokawa, S. Chiba, D.K. Bailey, G.C. Kennedy, S. Ogawa, A robust algorithm
for copy number detection using high-density oligonucleotide single nucleo-
tide polymorphism genotyping arrays, Cancer Res. 65 (2005) 6071–6079.
 C. Rosenberg, J. Knijnenburg, E. Bakker, A.M. Vianna-Morgante, W. Sloos,
P.A. Otto, M. Kriek, K. Hansson, A.C.V. Krepischi-Santos, H. Fiegler, N.P. Carter,
E.K. Bijlsma, A. van Haeringen, K. Shuhai, H.J. Tanke, Array-CGH detection of
micro rearrangements in mentally retarded individuals: clinical signiﬁcance of
imbalances present both in affected children and normal parents, J. Med.
Genet. 43 (2006) 180–186.
 J. Schoumans, B. Johansson, M. Corcoran, E. Kuchinskaya, I. Golovleva,
r, E. Forestier, J. Staaf, A. Borg, B. Gustafsson, E. Blennow, A. Nordgren,
Characterisation of dic(9;20)(p11-13;q11) in childhood B-cell precursor acute
lymphoblastic leukaemia by tiling resolution array-based comparative
genomic hybridisation reveals clustered breakpoints at 9p13.2 and 20q11.2, Br.
J. Haematol. 135 (2006) 492–499.
 J. Sebat, B. Lakshmi, D. Malhotra, J. Troge, C. Lese-Martin, T. Walsh, B. Yamrom,
S. Yoon, A. Krasnitz, J. Kendall, A. Leotta, D. Pai, R. Zhang, Y.H. Lee, J. Hicks,
S.J. Spence, A.T. Lee, K. Puura, T. Lehtima
ki, D. Ledbetter, P.K. Gregersen,
J. Bregman, J.S. Sutcliffe, V. Jobanputra, W. Chung, D. Warburton, M.C. King,
D. Skuse, D.H. Geschwind, T.C. Gilliam, K. Ye, M. Wigler, Strong association of
de novo copy number mutations with autism, Science 316 (2007) 445–449.
 A.J. Sharp, S. Hansen, R.R. Selzer, Z. Cheng, R. Regan, J.A. Hurst, H. Stewart,
S.M. Price, E. Blair, R.C. Hennekam, C.A. Fitzpatrick, R. Segraves, T.A. Richmond,
C. Guiver, D.G. Albertson, D. Pinkel, P.S. Eis, S. Schwartz, S.J. Knight, E.E. Eichler,
Discovery of previously unidentiﬁed genomic disorders from the duplication
architecture of the human genome, Nat. Genet. 38 (2006) 1038–1042.
 A.M. Slavotinek, Novel microdeletion syndromes detected by chromosome
microarrays, Hum. Genet. 124 (2008) 1–17.
 R. Ullman, G. Turner, M. Kirchhoff, W. Chen, B. Tonge, C. Rosenberg, M. Field,
A.M. Vianna-Morgante, L. Christie, A.C. Krepischi-Santos, L. Banna,
A.V. Brereton, A. Hill, A.M. Bisgaard, I. Muller, C. Hultschig, F. Erdogan,
G. Wieczorek, H.H. Ropers, Array CGH identiﬁes reciprocal 16p13.1 duplica-
tions and deletions that predispose to autism and/or mental retardation, Hum.
Mutat. 28 (2007) 674–682.
 L.A. Weiss, D. Yiping Shen, J.M. Korn, D.E. Arking, D.T. Miller, R. Fossdal,
E. Seamundsen, H. Stefansson, M.A.R. Ferreira, T. Green, O.S. Platt,
D.M. Ruderfer, C.H. Walsh, D. Altshuler, A. Chakravarti, R.E. Tanzi,
K. Stefansson, S.L. Santangelo, J.F. Gusella, P. Sklar, B.L. Wu, M.J. Daly, Associ-
ation between microdeletion and microduplication at 16p11.2 and autism, N.
Engl. J. Med. 358 (2007) 1–9.
 S.J. White, G.R. Vink, M. Kriek, W. Wuyts, J. Schouten, B. Bakker, M.H. Breuning,
J.T. den Dunnen, Two-color multiplex ligation-dependent probe ampliﬁcation:
detecting genomic rearrangements in hereditary multiple exostoses, Hum.
Mutat. 24 (2004) 86–92.
E.K. Bijlsma et al. / European Journal of Medical Genetics 52 (2009) 77–87 87