SUPPLEMENTARY MATERIAL
Clinical Information
Patient 1
Patient 1 is a two-year-old girl with a relevant medical history of developmental delay,
severe hypotonia, and failure to thrive. She was born at 42 weeks to a 26 year old mother
via normal spontaneous vaginal delivery after an uncomplicated pregnancy. Her birth
weight was 3.43 kg. At 4 months of age, she was noted to have a flat occiput,
plagiocephaly, and brachycephaly. At 6 months of age, she was not sitting up, reaching
out, or trying to roll. At 9 months of age, a developmental evaluation revealed her speech
to be at the level of a 3 month-old. Physical and speech therapy were initiated. The
patient had axial hypotonia, appendicular hypertonia, and esotropia. At 11 months, during
her first neurological evaluation, she was able to reach out, sit with partial support, prop
herself up with her hands or on her knees, and make syllable sounds. On her review of
systems, there was no evidence of epilepsy or developmental regression. On physical
examination her weight was 8.87 kg (25th-50th centile), length 72 cm (50th centile), and
her head circumference was 33 cm (10th centile). She had a flat occiput, plagiocephaly,
and prominent sutures. She was hyperteloric and she had a capillary hemangioma on her
back. She exhibited axial hypotonia with a marked head lag and appendicular hypertonia
and her hands were kept in a clenched position. A brain MRI reported no structural
abnormalities. Her initial diagnostic work-up included normal high-resolution karyotype,
CPK, plasma amino acid, urine organic acid, and very long chain fatty acids analyses. At
2 years and 7 months of age, she sat on her own but did not reach to a sitting position or
pull to a stand. She had only a two word vocabulary. Her weight of 12.3 kg and her
height of 85 cm were at the 5th centile. She had microcephaly with a head circumference
of 45.5 cm (below the 5th centile).
Patient 2
Patient 2 is a 3 years and 3 month-old girl with a history of epilepsy and developmental
delay. She initially presented with IS at 3 months of age that prompted treatment with
ACTH. Subsequently, the proband developed myoclonic epilepsy that resolved with the
use of zonisamide at 8 months of age. At 17 months of age, she had startle and tonic
episodes that interrupted her daytime naps; however, her EEG was normal. Her medical
course was complicated by nephrocalcinosis, gastroesophageal reflux, and strabismus
that required surgery. She was affected by developmental delay and continued to make
developmental gains at a slower pace. Her delay prompted the initiation of physical,
occupational, speech, and vision therapies. At 17 months of age, she had a two word
vocabulary, sat alone for 5 minutes, tended to throw herself backward, rolled from her
abdomen to her back but not from her back to her abdomen, and bore weight on her lower
extremities with her trunk supported but did not initiate any stepping movements. When
lying prone, she did not mobilize. She used both hands in a raking manner to obtain
objects. She did not finger feed. She drank from a bottle. At 18 months of age, she sat
independently, had a six word vocabulary, and began to exhibit receptive language. She
made good eye contact and demonstrated intermittent drooling. On physical exam, she
had a head circumference of 44.5 cm, a weight of 9.7 kg and a height of 73.6 cm. She
exhibited hypotonia and demonstrated shoulder slip through when vertically suspended.
Her deep tendon reflexes were brisk. She had speech apraxia and motor dyspraxia. At 3
years and one month of age, due to respiratory distress and low oxygen saturation levels,
she had a chest MRI that revealed two pulmonary arteriovenous malformations (AVMs)
with subsequent embolization. Brain and abdominal MRI did not reveal other AVMs.
Patient 3
A 6-year-old boy was born at 36 weeks gestation with a birthweight of 2.3 kg to a 28year-old G3P0 mother via C-section. The pregnancy was complicated by placental
abruption and decreased fetal heart rate. On physical examination at the age of 6 months,
his height, weight and head circumference were below the 3rd percentile. He had a flat
occiput, an open anterior fontanel, bilateral 5th finger clinodactyly, and bilateral single
transverse palmar creases. At 3-year-of age, he was referred for evaluation of failure to
thrive, developmental delay, and dysmorphic features. At that time, he was noted to have
plagiocephaly, epicanthal folds, cupped ears, flat philtrum, a thin upper lip, and
strabismus. He had a posterior fossa decompression for a Chiari type I malformation,
along with a C-1 laminectomy. Ophthalmological evaluation showed myopic
astigmatism. He had significant developmental delay; he was unable to sit, crawl or walk
and he had a vocabulary of three words. The parents reported intermittent tongue clicking
and hand flapping. At age 6 years, he was diagnosed with localization-related epilepsy.
EEG showed frequent right temporal spikes. Anticonvulsant therapy was started with
levetiracetam, but seizures continue to occur.
Patient 4
Patient 4 is an 8-year-old boy with a history of intractable epilepsy, encephalopathy, and
ASD. He was the product of an uncomplicated full term pregnancy with a birthweight of
3.8 kg. He was born to non-consanguineous parents. At 5 weeks of age, he developed
partial seizures. Seizures were intermittent and initially consisted of left eye twitching
and orolingual movements. CT scan of the head, brain MRI and lumbar puncture with
cerebrospinal fluid analysis were normal. Treatment with anticonvulsants normalized his
EEG. His anticonvulsants were discontinued after 6 months and he continued to be
seizure-free until age 3 years and 9 months. At that time during an evaluation for
developmental delay, an EEG revealed bifrontal temporal spikes and the anticonvulsant
therapy was resumed. Shortly thereafter, he was found to have nocturnal myoclonicatonic epilepsy. Since that time, he has had generalized symptomatic epilepsy refractory
to anticonvulsant therapy. At 4 years and 6 months, he was re-evaluated by Neurology
and his epileptic phenotype was consistent with symptomatic myoclonic epilepsy
and nocturnal myoclonic atonic seizures in clusters. He exhibited global developmental
delay, prominent ataxia, and tremulousness. A repeat brain MRI revealed a Chiari type I
malformation. His cerebrospinal fluid analysis revealed normal neurotransmitters, lactate,
and amino acids. He had normal serum folic acid, urine organic acid analysis, DNA for
fragile X, and FISH analyses for Prader-Willi and Angelman syndromes, carnitine levels
and very long chain fatty acids. His development continued to improve; however, his
motor abilities fluctuated and he had an awkward gait. He only said a couple of words
and had few simple signs. At the time of the evaluation, he was receiving Applied
Behavior
Analysis
(ABA)
for
ASD.
On
neurological
exam,
he
had
decreased appendicular tone and when standing he had truncal ataxia, tremulousness and
an ataxic gait. At 6 years and 7 months of age, a vagal nerve stimulator was placed to
control his epilepsy.
Patient 5
This patient has been previously reported, please see Moretti et al.1 This patient’s
genomic deletion was detected by an exon-targeted array, please see Boone et al.2
Patient 6
Patient 6 is a 5 year and 4 month-old girl with a clinical presentation of global
developmental delay and predominant speech delay. She was born at term with
a birthweight of 2.86 kg to a 22-year-old G1P1A0 mother, whose pregnancy was
complicated by placenta previa and decreased fetal movements. Family history was
unremarkable for consanguinity or birth defects although a maternal great-uncle exhibited
intellectual disability. The parents were concerned about her developmental delay at 3
months since she did not have a social smile. She did not roll over consistently until 6
months of age. At 6 months she could not sit which prompted a referral for early
childhood intervention and the initiation of physical and occupational therapies. She sat
alone at 12 months, crawled on hands and knees at 18 months, took her first steps at 30
months and walked at 3 years. She uttered her first words at 12 months and was able to
combine words at age 3 years. She had mild speech regression which prompted
enrollment in speech therapy. Initial diagnostic evaluation for developmental delay at one
year of age included a brain MRI that revealed a small pituitary gland but otherwise
normal anatomy. She had a normal chromosome analysis, DNA test for fragile
X, acylcarnitine profile, and urine organic acid analyses. A swallowing study done at 3
years and 4 months revealed dysphagia. Upon evaluation at a Neurogenetics Clinic at
age 4 years, she had a weight of 18.2 kg (73rd centile), height of 100 cm (21st centile) and
a head circumference of 51 cm (35th centile). She did not exhibit dysmorphic features,
but exhibited intermittent esotropia bilaterally. The rest of the physical exam was relevant
for inverted nipples, bilateral pes planus, appendicular hypotonia with increased tone in
her ankles, lack of ankle reflexes and circumduction gait. At this time, carbohydrate
deficient transferrin analysis for congenital disorders of glycosylation was requested with
normal results.
Patient 7
The proband is a 3 year and 5 month-old male with a significant history of developmental
delay and dysmorphic features. He was born at term via induced vaginal delivery with a
birthweight of 3.65 kg and a length of 54.65 cm to a G5P4A1 mother. The pregnancy was
complicated by gestational diabetes and decreased fetal movements. The family history
was unremarkable and parents were non-consanguineous. He was noted to have poor
weight gain and extreme irritability at 5 months of age. An initial head CT examination to
address the prolonged irritability revealed a Chiari type I malformation. At 22 months, he
had his first genetic evaluation. Developmentally, he did not crawl but scooted. He
babbled but said no words. He was able to remain in a sitting position. His physical
examination revealed a head circumference of 41.5 cm (25th centile), height of 79.4 cm
(10th centile), and weight of 10.88 kg (10th-25th centile). He was noted to have a
prematurely fused metopic suture, frontal recession, and a glabellar nevus flammeus. He
had a single right parietal hair whorl, coarse and slightly sparse hair, supraorbital ridge
hypoplasia, epicanthal folds, and long-appearing palpebral fissures. Examination of his
back revealed a pilonidal dimple. His extremities revealed broad knees with lateral
dimples, pronounced 5th finger clinodactyly with a single crease on the right 5th finger,
and broad halluces with mild intoeing on his feet. A neurological exam revealed
hypotonia. His initial diagnostic work-up had included normal fragile X DNA studies and
a normal karyotype.
Patient 8
The proband is 15 year and 11 month-old male teenager with a significant history
of dystonia and intellectual disability (ID). He was born at term via C-section for breech
presentation with a birthweight of 3.34 kg to non-consanguineous parents. The family
history is only remarkable for two cousins with developmental delay. He was noted to
have delayed milestones at 3 months of age when he had poor eye contact and he was not
able to hold a rattle or reach for objects in a timely manner. At eleven months of age, he
sat without support. He walked at two years of age. At three years of age, he was able to
say single words. He has been enrolled in speech, occupational and physical therapy
since the age of 6 months. He had surgical lengthening of his Achilles tendons to
decrease his hypertonia at age 5 years. He had orchiopexy at age 6 years for an
undescended testicle. At a neurological evaluation at the age of 14 years and 10 months,
he exhibited the intellectual functioning of an 8 year-old boy. He attended grade 9 in a
special education classroom. At the time of this evaluation, his weight was 58.5 kg (50th75th centile), his height was 151.5 cm (3rd centile), and his head circumference was 56
cm. His physical exam was relevant for coarse facial features, a prominent philtrum, a
thin upper lip, large ears with fleshy pinnae, and a short and broad neck. He exhibited
short, broad fingers and broad feet. Neurologically, he revealed saccades on smooth
pursuit. On neurological examination, he had an unsteady gait with inversion of his feet
while walking. He exhibited dystonic posturing of his upper extremities. He was hesitant
to walk on his toes and heels, had difficulty with tandem gait but did not demonstrate
ataxia. He had an advanced bone age. His initial diagnostic work-up consisted of a
normal karyotype, FISH for all subtelomeres, FISH studies for Prader-Willi, SmithMagenis and Williams syndromes, fragile X DNA analysis, and urine oligosaccharides. A
brain MRI revealed mild dysplasia of the corpus callosum with absence of the rostrum
and small anterior pituitary.
Patient 9
Patient 9 is a 3 year and 2 month-old boy with a relevant history of developmental and
growth delay. He was born at term via spontaneous vaginal delivery with a birth-weight
of 2.81 kg to non-consanguineous parents. His family history did not reveal a history of
birth defects but a maternal great-uncle exhibited ID. At birth, bilateral clubfeet were
noted and the treatment required serial casting, bracing and surgery done at 5 months of
age. He followed a growth curve between the third and the fifth percentiles after birth;
however, his growth velocity decelerated since then with decreased food intake, leading
to failure to thrive. He had an initial evaluation for hypotonia and developmental delay
that prompted a brain MRI revealing delayed myelination at one year of age. At 21
months of age, he was evaluated by the genetics service. He did not walk or crawl but he
was able to scoot. He was able to do ‘pat-a-cake’. He was not able to feed himself and did
not say specific words; however, he was able to babble. At that time, his development
was estimated to be at the level of a 15 month old male infant. He was receiving physical,
occupational, and speech therapy. He had a length of 74 cm below the 5th percentile (50th
percentile for a 10-month-old), a weight of 8.8 kg and a head circumference of 48.5 cm at
the 50th percentile. On physical exam, he had a square skull shape and retrognathia. He
exhibited axial hypotonia with hyperextensibility of knees, elbows, and shoulders and
genu varum. He had a café-au-lait spot on the left side of his abdomen. At the time of the
visit, his bone age was 7 months. Brain MRI revealed symmetric patchy nonspecific T2
signal hyperintensity in the white matter of both cerebral hemispheres and dorsal
brainstem, representing delayed white matter myelination. No obvious arterio-venous
malformation was seen. His initial diagnostic work-up included normal plasma amino
acid analysis, urine organic acid analysis, CPK and thyroid function tests.
Patient 10
Patient 10 is a 6 year and 5 month-old boy born to a 25-year-old G8P1A6 mother via
emergency C-section for antepartum hemorrhage at 32 weeks of gestation weighing 1762
grams, following an uncomplicated pregnancy. He had Apgar scores of 6 and 8 at 1 and 5
minutes, respectively. His head circumference at delivery was 30.5 cm. He had a normal
physical exam in the newborn period. He was intubated and ventilated for a short period
of time and was discharged at age 7 days with no other complications. Family history was
relevant for a healthy older sister, a paternal second cousin with autism, and a maternal
great-aunt with severe language delay who began speaking at 6 years of age.
He was referred for a neurological assessment at age 3.5 years for suspected seizures. At
that time, he had severe global developmental delay with a functional level of 1.5 to 2
years of age and he also had hyperactivity. Clinically, he had what appeared to be an
atonic seizure followed by a clonic element with no focality. There was no postictal
period reported. In addition, he had two brief staring spells. His motor development was
delayed; he sat at 10 months and walked at 18 months. At age 3.5 years his fine motor
skills were delayed. He had no pincer grasp and he was able to transfer from one hand to
the other from the age of 2 years. At age 3 years, he had 10 words and was babbling. He
understood one step commands. He was affectionate and engaged in attention with his
parents. At age 5.5 years, he was not able to ride a tricycle, but was able to ascend and
descend stairs on one foot at a time. He was able to run, but he was not able to hop. He
was ambidextrous. He was unable to feed himself. His hearing and vision have not been
formally tested, but he passed his newborn hearing screening. He had a 20-word
vocabulary. He was not toilet trained. On occasion he would be aggressive towards other
children.
On physical examination at age 6.5 years, he was an overweight and hyperactive
boy. His head circumference was 51.5 cm (25th centile), height was 110.7 cm (10th
centile), and weight was 29.7 kg, (95th - 97th) centile. He had brachycephaly and a normal
hair whorl. He had a prominent mid forehead, deep set and almond shaped eyes with
upslanting palpebral fissures. He had borderline low set ears with fleshy lobules. His
eyebrows were very thick in the medial two thirds and very fine in the outer one third. He
had alternating strabismus. He had a long philtrum and a broad nasal tip. Examination of
the chest revealed inverted nipples bilaterally. Heart and breath sounds were normal.
External genitalia were normal. He had short fingers and very wide feet. The skin had no
hypo or hyperpigmented lesions and no vascular lesions such as telangiectasia.
Neurological examination showed an ability to gaze in all four directions and pupils that
were equally reactive to light. . Fundoscopic exam was normal. Motor examination
revealed normal symmetrical power and hypotonia. Deep tendon reflexes were 2+
throughout and symmetrical and plantars were down-going. His gait was wide-based and
he was clumsy. Previous investigations included plasma amino acid analysis, urine
organic acid analysis, transferrin isoelectric focusing, karyotype, fragile X DNA testing
with normal results. MRI of the head and MR spectroscopy were normal at 3.25 years.
EEG at the time of the initial neurological evaluation was normal with no evidence of
seizure activity.
Supplemental Reference
1. Moretti, P., Sahoo, T., Hyland, K., Bottiglieri, T., Peters, S., del Gaudio, D., Roa, B.,
Curry, S., Zhu, H., Finnell, R.H., et al. (2005). Cerebral folate deficiency with
developmental delay, autism, and response to folinic acid. Neurology 64, 1088–1090.
2. Boone, P.M., Bacino, C.A., Shaw, C.A., Eng, P.A., Hixson, P.M., Pursley, A.N., Kang,
S.-H.L., Yang, Y., Wiszniewska, J., Nowakowska, B.A., et al. (2010). Detection of
clinically relevant exonic copy-number changes by array CGH. Hum. Mutat. 31, 1326–
1342.