Supplementary Case Reports

Supplementary case reports

Deletions

Patient 1

This 22-year-old, mildly retarded woman (Fig. 3A) was born after an uneventful pregnancy in breech position at 39 weeks gestation with a birthweight of 2,560 g (5th centile). Early development was normal and she spoke her first words at 12 months of age and started to walk at 18 months of age. From 6 years of age she attended special school for children with mild cognitive impairment, where she learned to read and write.

At 13 years of age she exhibited a congenital aplasia of her left breast, which required surgical correction. In addition to normal puberty, she showed normal development of her right breast. At 15 years of age her height was 157 cm (10th centile) and her head circumference was 53 cm (15th centile). Her facial dysmorphisms included hypotelorism, upward slanting and narrowing of her palpebral fissures, ptosis, low-set small ears with an angle in the helix rim, a broad nasal base and a flat philtrum. In addition, she had broad thumbs and halluces, similar to that of her father, mild volar finger pads, mild partial cutaneous syndactyly of her 2nd and 3rd toes and soft skin. At 22 years of age her height was 161.5 cm (10th centile) and her head circumference 53 cm (10th centile). BAC array CGH analysis showed a de novo 10q22.3q23.2 deletion of approximately 7.2 Mb, which was cytogenetically visible in retrospect. Fine mapping of the deletion by high-resolution oligonucleotide array CGH showed breakpoints within LCR3 and LCR4, respectively (81.6 - 88.9/89.1 Mb).

Patient 2

This 2½-year-old girl was born at eight months gestation by caesarean section with a birthweight of 2,440 g (< 3rd centile). The mother has epilepsy and was treated with carbamazapine during the pregnancy. Further family history revealed a maternal half- brother with Attention Deficit Hyperactivity Disorder (ADHD). History on the paternal side of the family was not available, but it was reported that the father attended ‘special school’. At one month of age, the proband was found to be tachypneic and evaluation revealed a fenestrated atrial septum defect and a moderately large ventricular septal defect. She underwent surgical correction of the septal defects at seven months, after which she developed feeding problems and recurrent episodes of pneumonia. Motor development was appropriate; she could roll and sit without support at eight months and she was able to walk at 13 months of age. Although she had cooed at 2-3 months, had mono-syllables by six months, her vocabulary at 2 years consisted of only seven words. At that age she still had recurrent pneumonias, which required hospitalization and mechanical ventilation. In addition, she vomited two or three times a day. Allergic and immunologic studies were normal. The pneumonias were most likely caused by aspiration due to gastro-oesophageal reflux. She apparently improved after starting proton pump inhibitor therapy.

At 2½ years of age she was proportionately small for age with a height of 85.1 cm (< 3rd centile), a weight of 9.7 kg (<3rd centile) and a head circumference of 45.5 cm (3rd centile). She had hypertelorism, telecanthus, low set ears, anteverted nares, a flat nasal bridge and a large mouth with downturned corners. No other dysmorphisms were noted.

Array analysis showed a 7.2 Mb deletion in 10q22.3q23.2. Fine mapping of the deletion by high-resolution oligonucleotide array CGH showed breakpoints within LCR3 and LCR4, respectively (81.6 - 88.7/89.1 Mb).

Patient 3

This boy (Fig. 3A) was born with a weight of 3,090 g (10th centile) and a length of 48.3 cm (10th centile). Family history was unremarkable. He started to crawl at 12 months, walk at 22 months and verbalize single words at 24 months of age. At three years and seven months of age he was referred for genetic evaluation because of short stature, developmental delay, hyperactivity, epilepsy and staring episodes. At 44 months of age he scored at 36 months for fine and gross motor development, 28 months for language development, and 40 months for personal social development using the Denver Developmental test. He could talk using short phrases. He weighed 12.7 kg (10th centile), had a height of 97 cm (50th centile) and an OFC of 48.5 cm (10th centile). He had dolichocephaly, low-set prominent ears, hypertelorism, bilateral epicanthal folds, a flat nasal bridge, midface retraction, a high-arched palate, maligned teeth and tall, narrow retroplaced thumbs. MRI of the brain showed a Chiari I malformation with low-lying cerebellar tonsils and crowding of the posterior fossa. EEG was abnormal and suggestive of bifrontal multifocal epileptogenic potential. Cardiac, ophthalmologic, metabolic and endocrine evaluations were normal. Array analysis showed two de novo aberrations: a 722 kb gain in 2q36.3q36.3 and a 10q22.3q23.2 deletion of approximately 7.7 Mb. Fine mapping of the deletion by high-resolution oligonucleotide array CGH showed breakpoints within LCR3 and LCR4, respectively, of which the distal breakpoint was difficult to map (81.4 - 89.1/89.3 Mb).

Patient 4

The proband (Fig. 3A) is a 12 year old Hispanic male born at full term gestation with a weight of 3,200 g (10th centile). The prenatal history was uncomplicated. The family history was significant for a paternal aunt and a paternal cousin with mental retardation. He was referred to the clinical genetics department at 20 months of age for evaluation of speech regression, developmental delay, and aggressive behaviour. During that evaluation it was noted that he did have global developmental delay with his expressive language consisting of only one bi-syllabic word, and his gross motor and fine motor skills lagging behind by four and 12 months, respectively. His height was 89 cm (90th centile), his weight was 13 kg (70th centile) and his OFC was 58 cm (>97th centile). Facial dysmorphisms included hypertelorism, and almond-shaped eyes. Nine café-au-lait spots were noted on the left leg, thigh, abdomen, and back. A systolic murmur was heard over the left sternal border and echocardiogram showed tricuspid regurgitation. MRI of the brain was unremarkable. By 12 years of age, he was in the fifth grade, and he was receiving special education classes. He had developed mild pectus excavatum, kyphosis, scoliosis, and radioulnar synostosis. His height was 169 cm (>97th centile) and his weight was 51.9 kg (90th centile). A repeat echocardiogram revealed mild triscuspid valve regurgitation, and minimal pulmonic valve regurgitation. Peripheral blood karyotyping showed 47,XYY. Detailed testing including FISH analyses with multiple subtelomeric probes and probes for NF-1 and 22q11.2 were normal. Fragile X syndrome testing was negative. In addition, chromosome array analysis showed a de novo deletion in 10q22.3q23.2. Fine mapping of the deletion by high-resolution oligonucleotide array CGH showed breakpoints within the LCRs, at nucleotide position 81.2/81.6 Mb and 88.9/89.1 Mb. Patient 5

This 5-year-old boy was born after 42 weeks of gestation with a weight of 3900 g (50th centile). His parents were non-consanguineous and his mother attended special school in childhood.

After birth, clubfeet were noted and surgically repaired at seven months of age. As a neonate, he had mild feeding problems. Motor development was normal; he could sit unsupported at nine months and walk at 17 months of age. However, speech development was delayed; he used his first words at age two years and at four years and six months the Schlichting test for language production indicated a clear language/speech delay. At five years he could speak three word sentences. At that age, he had a height of 111 cm (30th centile) and an OFC of 53 cm (84th centile). Facial dysmorphisms included hypertelorism (ICD 3.6 cm >98th centile), low-set posteriorly rotated ears, a depressed nasal bridge and a broad base of the nose. In addition, he had tapered fingers, mild volar finger pads, short fifth fingers and a shawl scrotum. In the near future he will attend a special school. Array analysis showed a maternally inherited deletion in 10q22.3q23.2. Fine mapping of the deletion by high-resolution oligonucleotide array CGH showed breakpoints within the LCRs, at nucleotide position 81.1/81.6 Mb and 89.14 Mb.

Patient 6

This girl was born at 38 weeks gestation with a weight of 3,500 g (90th centile), a length of 50 cm (50th centile) and an OFC of 37 cm (90th centile). Early childhood was noted for hypotonia and progressive macrocephaly. Her motor milestones were mildly delayed: she rolled over at about four months of age, sat unassisted at ten months and walked at 23 months. At 24 months, she could say two word statements. At three years and eleven months of age she had a weight of 18.9 kg (85th centile), a height of 102.4 cm (70th centile) and an OFC of 54.5 cm (>>98th centile; 50th centile for a 15-year-old girl). At that time, multiple colonic juvenile polyps developed and by the age of five years, approximately 20 juvenile polyps had been found. Physical examination revealed that she had hypertelorism and a slightly upturned nose. Furthermore, she had a coordination disorder, dyspraxia and sensorimotor integration difficulties. Mental development appeared to be normal. At five years and seven months of age, she was diagnosed with Attention Deficit Hyperactivity Disorder (ADHD). Array analysis revealed that she had a de novo deletion in 10q23.1q23.31, 4.7 Mb in size, including the PTEN gene. Fine mapping of the deletion by high-resolution oligonucleotide array CGH showed a 4 Mb deletion with breakpoints in unique sequences at nucleotide positions 86.2 Mb – 90.9 Mb. In addition, the LCR3 locus showed two shorter regions of copy number loss at 81.1-81.2 Mb and 81.5-81.6 Mb. Multiple CNVs have been reported for the LCR3 area, therefore the observed shorter deletions may represent this variation.

Patient 7

The proband is a 5-year-old male born to non-consanguineous Caucasian parents at full term. The prenatal history was complicated by preterm labor at 32 weeks. Apgar scores were 2 and 3 at one and five minutes, respectively; however, mechanical ventilation was not required. The birthweight was 3,090 g (10th centile) and birth length was 49.5 cm (10th centile). He was noted to have diaphragmatic eventration, undescended testes, an enlarged right heart, a coronary sinus defect, patent foramen ovale and an atrial septal defect. Exploratory laparotomy and a diaphragmatic plication were performed. He underwent surgical correction at 2 ½ years of age to repair the cardiac anomalies. His motor development was mildly delayed and he did not walk until 18 months of age. However, his further motor development was normal and by two years of age his gross motor development was age appropriate. Fine motor development and speech were appropriate for age and at two years he had a vocabulary of 50 words. At two years of age his weight was 12.2 kg (35th centile), height was 80.3 cm (<3rd centile) and OFC was 51 cm (95th centile). He had a prominent forehead, downslanting palpebral fissures, hypertelorism, anteverted nares, small posteriorly rotated ears with malformed helices, a short neck, widely spaced nipples, small hands and feet and one café-au-lait macule. As the constellation of symptoms suggested the possibility of Noonan Syndrome, he had sequential sequencing of PTPN11, K- RAS, SOS1 and RAF1, and no deleterious changes were found. Chromosomal array analysis showed a 0.2 Mb intragenic deletion of the GRID1 gene in 10q23.1. Fine mapping of the deletion by high-resolution oligonucleotide array CGH showed breakpoints outside LCRs, at nucleotide position 87.5 Mb and 87.7 Mb. In addition to the 0.2 Mb deletion, we identified a copy number loss in the region between 84.118 Mb and 84.119 Mb that overlaps with a reported benign CNV.27 Parental studies could not be performed.

Patient 8

The proband is a 5 ½-year-old Hispanic male child born at full term gestation to nonconsanguineous parents. Family history revealed a paternal aunt with schizophrenia, agoraphobia and eating disorders. In addition, the daughter of his paternal uncle had developmental delay and autism. The growth parameters at birth are not available. At 2 ½ years and then again at 5 ½ years of age, he was seen in the Genetics clinic for evaluation of autism, severe mental retardation and absent speech. At three years of age, a brain MRI showed no abnormalities. However, an EEG revealed frontal paroxysmal activity with spikes and delta waves, and irritative activity in the temporal region; during sleep, the paroxystic activity was generalized. Absence and myoclonic seizures were observed. Treatment with Depakine reduced the number of seizures, but the EEG pattern remained abnormal. Formal neuropsychological evaluation at the age of 4.8 years showed moderate to severe mental retardation, severe hyperactivity and autistic features. His non-verbal performance was equivalent to 12-13 months. At 5 ½ years of age he weighed of 24.3 kg (50th centile), his height was 118.5 cm (50th centile) and his OFC was 50.3 cm (10th centile). No dysmorphic features were noted. Array analysis showed a small deletion on 10q23.1 which was inherited from the healthy father. Fine mapping by high-resolution oligonucleotide array CGH identified 30 Kb deletion with breakpoints mapping outside LCRs, at nucleotide position 84.118 Mb and 84.148Mb. In addition, his sister and cousin were tested; both did not have the deletion.

In the past, the patient’s father was seen by a psychiatrist after paranoid symptoms, but he discontinued these sessions. His cognitive abilities are in the normal range and neuropsychological testing did not reveal any executive function deficits. Physical examination was within normal limits. Duplications

Patient 9

The proband is a Caucasian male born to a primigravida mother at term gestation with a birthweight of 4000 g (50th centile). The first two years of life were characterized by recurrent episodes of otitis media. The motor development was age appropriate but there was a marked delay in expressive language. He was noted to have impaired social interaction and was referred to a clinical geneticist at the age of two years and ten months for further evaluation. His weight (13.2 kg; 30th centile), height (94.6 cm; 50th centile) and OFC (49.5 cm; 50th centile) were normal. Physical examination was unremarkable except for deep-set eyes. He continued to have significant difficulties with expressive language and social skills and was diagnosed with pervasive developmental delay. There was no history of seizures, features of motor or sensory deficits or abnormalities in coordination. He was reevaluated at nine years and four months and at this exam dysmorphic features were better appreciated and included a triangular face with a broad forehead, lateral flaring of eyebrows, up-slanting palpebral fissures, slightly deep-set eyes, prominent ears with thickened horizontal superior helices and small earlobes with two dimples, anteverted nares, a smooth philtrum, widely spaced large upper central incisors and a thin upper lip (Fig. 3B). In addition, he had squared and broad distal finger-tips and broad great toes. The laboratory evaluation including peripheral blood karyotyping, fluorescent in-situ hybridization (FISH) for 22q11.2 and subtelomeric regions, as well as testing for fragile X syndrome and congenital disorders of glycosylation were unremarkable. Chromosomal array analysis showed a 10q22.3q23.2 duplication including LCR 3. Fine mapping of the duplication by high-resolution oligonucleotide array CGH showed breakpoints within unique sequences, at nucleotide position 79.4 Mb and 86.6 Mb. Parental studies could not be performed.

Patient 10 and patient 11

Patient 10 and 11 (Fig 3B ) are a brother and sister of whom only minimal clinical information is available. Both siblings had a similar phenotype including mental retardation, strabismus, upslanting palpebral fissures, hypotelorism, a smooth philtrum, anteverted nares, micrognathia, large wide-spaced teeth and a thin built. Chromosomal array analysis showed a 10q22.3q23.2 duplication, which was inherited from their intellectually normal mother. Fine mapping of the duplication by high-resolution oligonucleotide array CGH showed breakpoints within LCRs 3 and 4, at nucleotide position 81.6 Mb and 89.0 Mb.

Patient 12 This 4-years-old girl was the second child of healthy non-consanguineous parents. Family history revealed a mild speech delay in the father, in a father’s aunt and in a proband’s cousin. She was born after an uneventful pregnancy at 39 weeks of gestation by cesarean delivery because of breech presentation. The birthweight was 2750 g (20th centile) the length 52 cm (80th centile) and the OFC 33.5 cm (35th centile). She was referred at four years of age to a pediatric neurologist because of hypotonia, speech delay, difficulties in social skills and behavioral problems. Her weight was 15 kg (25th centile), her height 104 cm (>90th centile) and the OFC 49 cm (25th centile). She showed a long face, broad forehead, deep-set eyes, hypotelorism, epicanthal folds, broad nasal bridge, anteverted nares and a broad mouth with a thin upper lip and prominent lower lip. She had joint hypermobility. Cerebral MRI was normal. Chromosomal array analysis showed a 10q22.3q23.2 duplication and a second deletion at 16p13.11 (14.8 - 16.3). Fine mapping of the de novo duplication by high- resolution oligonucleotide array CGH showed breakpoints within LCRs 3 and 4, at nucleotide position 81.6 Mb and 89.0 Mb.

Patient 13

This girl was born at 27 weeks and three days gestation, after a caesarean section due to abruption of the placenta and perinatal asphyxia. She was one of a dizygotic twin and she weighed 940 g (50 th centile). After birth retinopathy of prematurity and congenital abnormalities of the retina were noted, which led to ablatio retinae causing complete blindness. Her twin brother, who also developed retinopathy of prematurity, acquired normal visual function later in life. At three years and seven months of age she had a height of 97 cm (10th centile) cm and a weight of 11.4 kg (<3rd centile). She had a prominent forehead, deep-set eyes, strabismus, a full lower lip and anteverted nares. She showed normal motor development.

Array analysis showed a duplication comprising part of the NRG3 gene on 10q23.1. The duplication was inherited from her healthy father. Fine mapping of the duplication by high- resolution oligonucleotide array CGH showed breakpoints at nucleotide position 84.5 and 84.8 Mb.

Patient 14

This male child was born at full term gestation to non-consanguineous Hispanic parents. Prenatal ultrasound was abnormal and revealed a two vessel cord, intrauterine growth restriction, and congenital heart anomalies. His growth parameters at birth were all below the 3rd centile; he had a weight of 2,440 g, a length of 42 cm and an OFC of 32.5 cm. He had Tetralogy of Fallot, hypospadias, micropenis, an imperforate anus, fusion of the sacral vertebrae, long and slender ribs and long clavicles. He had a colostomy created in the first week of life. He underwent surgical correction of the Tetralogy of Fallot at six months and a posterior sagittal anorectoplasty at eight months of age. There was no evidence of developmental delay; he smiled and cooed at three months, rolled over at six months, crawled at eight months, and had two words at nine months. At 19 months of age he had no dysmorphic features. His height was 85.5 cm (75th centile) and his weight was 14.9 kg (>97th centile). A peripheral blood chromosomal analysis showed a normal 46,XY karyotype and FISH confirmed the presence of SRY. Chromosomal array analysis showed two paternally inherited aberrations, a 2.2 Mb gain in 6q25.1 and a gain in 10q23.1 including part of the NRG3 gene. Fine mapping of the 10q23.1 duplication by high-resolution oligonucleotide array CGH showed breakpoints at nucleotide position 84.2 and 85.0 Mb.