Supplemental Data 1



Supplemental Figure 1. 15q13.2q13.3 del/dup FISH

Panel A shows metaphase FISH for patient 1 with BP4-BP5 deletion using probes RP11-98L6 (arrow) for the region of interest and RP11-120o11 (arrowheads) as a control probe. Panel B shows metaphase FISH for patient 5 with BP4-BP5 duplication using probe RP11-303I17 (arrows). Double arrows represent a stronger signal on the chromosome bearing the 15q13.2q13.3 duplication. The inset in panel B represents an interphase from the duplication case where three FISH signals were detected (arrows).

Supplemental Figure 2. 15q13.2q13.3 del/dup MLPA

Panel A shows results of MLPA for patient 1 with deletion. Panel B shows patient 5 with duplication. Top panels are overlapping MLPA traces for case (lighter traces) and control (darker traces) samples. Bottom panels are histograms of normalized peak height for probes located within the imbalanced 15q13.2q13.3 region (arrows), probes on chromosome 15 outside the imbalance interval (unlabelled black bars), and control probes located on other chromosomes (C).

Supplemental Methods for MLPA

Independent confirmation of deletion/duplication of the 15q13.2q13.3 region was performed using four pairs of multiplex ligation-dependent probe amplification (MLPA) probes based on unique sequences of four genes within this interval: MTMR15, TRPM1, OTUD7A and CHRNA7. The assay included seven pairs of MLPA control probes, three pairs corresponding to unique sequences of TJP1, CHRFAM7A and RYR3 genes located on chromosome 15 outside the deletion interval, and four pairs corresponding to unique sequences on other chromosomes. All probes were synthetic oligonucleotides. MLPA reagents were commercially available (MRC-Holland, Amsterdam, Netherlands), and reactions were performed according to the manufacturer’s instructions.

Supplemental Clinical information for 15q13.2q13.3 BP4-BP5 microdeletion cases

Patient 1

Patient 1 is an 8 year 11 month old Caucasian male with a diagnosis of PDD-NOS (by DSM-IV criteria) manifested by variable eye contact, limitations in forming and maintaining relationships with peers, difficulty in participating in organized group activities, mildly delayed receptive and expressive language, and stereotypical behaviors (hand-flapping).

Patient 1 completed developmental evaluation at age 2 years 10 months. At that time, testing with the Bayley II Scales of Infant Development revealed significantly delayed performance on the mental scale, with abilities clustering around a 20-22 month level. His play skills were somewhat more delayed, with most activities involving simple exploration of toys and cause and effect manipulation (13-17 month level by Westby Developmental Playscale). Additional assessment with the Receptive-Expressive Emergent Language test (parent report measure) indicated receptive language at the 14-16 month level and expressive language at the 18-20 month level.

In psychological testing at age 4 years 10 months, Patient 1 displayed a complex cognitive profile, characterized by average verbal abilities that were significantly better developed than his borderline nonverbal skills (Differential Ability Scale: Verbal Cluster = 97, 42nd percentile; Nonverbal Cluster = 69, 2nd percentile). He had slight articulation difficulty and some echolalia. Parent report on the Vineland Adaptive Behavior Scales indicated that his communication, motor, and self-help skills clustered around an early 3 year level. Social skills were less robust, clustering around a 2 year 9 month level.

At home, he has some self-stimulatory and oppositional behaviors, as well as problems with anger, aggression, mood regulation, and attentional regulation. However, he performs academically at grade level in a full inclusion classroom and his behavior is well regulated in this setting. He has a history of staring spells and had a single seizure as an infant, but does not have epilepsy. His mother, who has the same deletion, describes herself as having a similar personality as her son and similar learning challenges, but no history of mental retardation or epilepsy.

Physical features include a large head, downslanting palpebral fissures, epicanthal folds, prominent chin and widely spaced teeth, hypopigmented and hyperpigmented macules and café-au-lait macules, and bilateral fifth finger clinodactyly. Neurological exam revealed mild diffuse hypotonia, normal strength, and normal reflexes. His past medical history is unremarkable aside from an isolated seizure as an infant and staring spells as a child. He had a normal waking EEG and has not had brain imaging. No antiepileptic medications have been required.

Patient 2

Patient 2 is a 3 year 10 month old Caucasian female with developmental delay, severely reduced receptive and expressive language (Reynell Developmental Language Scales; Expressive One Word Picture Vocabulary Test), significant articulation defects with unusual resonance, and normal hearing. Stuttering, primarily whole word repetitions, developed around age 3 years.

She scored in the normal range of IQ. Psychological evaluation at the age of 2 years and 9 months involved administration of the WPPSI-III and the Behavior Assessment for Children, Second Edition Parent Rating Scales Preschool (BASC II). On the WPPSI, verbal IQ was 93, performance IQ was 90, full IQ was 91, and general knowledge was 91. On the BASC II, clinically significant parents' ratings were noted in hyperactivity, aggression, externalizing problems, depression, withdrawal, and at risk in all other categories except atypicality. She has variable eye contact, but did not meet criteria for autism spectrum disorder by ADOS performed at age 3 year 10 months with score 3/25.

She has mild dysmorphic features including mild frontal bossing, upslanting palpebral fissures, epicanthal folds, bilateral fifth finger clinodactyly, and a single hypopigmented macule. Neurological exam was significant for diffuse hypotonia and axial and proximal appendicular weakness noted in the first year of life that improved gradually. Strength and deep tendon reflexes were normal. MRI showed right frontal venous anomaly with abnormal T2 hyperintense subcortical white matter signal intensity and thickening of the right frontal cortex consistent with dysplasia. Her affected mother has mild mental retardation (Verbal IQ 71, Performance IQ 65, and Full IQ 67 by WAIS-R), and nonspecific white matter changes on MRI, but no history of seizures.

Patient 3

Patient 3 is a 10 year 9 month Asian male with bipolar disorder, ADHD, generalized anxiety disorder, and a nonverbal learning disability. He has required medication with Depakote, Risperdal, and Cogentin.

He scored in the normal range of IQ. His Wechsler Intelligence Scale for Children-Fourth Edition (WISC-IV) scores were Verbal Comprehension 93 (32nd percentile), Perceptual Reasoning 90 (25th percentile), Working Memory 77 (6th percentile) and Processing Speed 93 (34th percentile), Full Scale IQ is 86 (18th percentile). His receptive language is moderately to severely impaired while his expressive language is moderately impaired. Executive functions were compromised based on the Behavior Rating Inventory of Executive Function Global Executive Composite score of 87 (99th percentile). 

He has particular difficulty with executive functions and has weak social skills. His play skills are particularly immature. He has difficulty reading social cues and interacting with other children. Behavioral problems include impulsivity, aggression, and anxiety. He has significant learning disabilities, attentional problems, and psychiatric symptoms, but not cognitive developmental delay. He has not had an ADOS.

Mild dysmorphic facial features include a slightly long midface, upslanting palpebral fissures, epicanthal folds, broad nasal root, and posteriorly rotated ears. Extremity exam is notable for tapering fingers, fifth finger clinodactyly, hyperextensible elbows, and pes planus. There were no neurocutaneous lesions. Neurological exam revealed only mild diffuse hypotonia with normal strength and deep tendon reflexes.

Patient 4

Patient 4 with a BP4-BP5 deletion is a 20 year old Asian male who has PDD-NOS, ADHD, and mental retardation. When younger he had echolalia and also some self-stimulatory repetitive vocalizations. He had sensory integration issues, including aversion to physical contact with people, and hitting and biting himself. He has a history of poor eye contact and stereotypies including repetitive spinning in place. He performs in the moderately mentally retarded range with an IQ below 50 with higher nonverbal than verbal abilities, and very limited speech. He has aggressive and impulsive behaviors in addition to ADHD.

His dysmorphic facial features include a triangular face, thick eyebrows with synophrys, a short philtrum, a small mouth, and relatively large ears. He had widely spaced nipples, long fingers and toes, and fifth finger clinodactyly. He had a single café-au-lait macule on his chest. Diffuse hypotonia was present during childhood, but resolved in adulthood. Strength and deep tendon reflexes were normal.

Patient 5

Patient 5 with a BP4-BP5 deletion is a 5 year 11 month old Caucasian male with developmental delay and autistic features. Gross and fine motor skills were mildly delayed. Walking commenced at age 18 months and at age 5 he was still having difficulty drawing simple shapes such as a circle. Wechsler Preschool Intelligence Test (WPPSI-III) at age 5y9m: Verbal 72 (3rd %ile) and Perceptual Reasoning 75 (5th %ile). He has better abilities with visual cognitive formation than verbal concept formation/comprehension.

He has difficulty with social interactions. Gilliam Autism Rating Scale (GARS) Teacher Rating was 109 (73%ile) scored because of concerns that his performance was compromised due to his distractibility. Subjectively, he had substantial difficulties in the areas of receptive and expressive communication. He had below average receptive vocabulary on Peabody Picture Vocabulary Test (PPVT). Speech and language evaluation noted inconsistent eye contact with his conversational partner and that his basic concepts, play, and communication skills were developing but inconsistent. He had problems with articulation and word retrieval deficits.

Behavioral assessment with the Conners' Behavior Rating Scales showed significant scores in several domains, including oppositional (89), cognitive problems/inattention (88), hyperactivity (81), anxious/shy (79), social problems (78), Conners' ADHD Index (80), restless/impulsive (77), emotional lability (90+), DSM-IV inattentive (84), DSM-IV hyperactive/impulsive (79), hyperactive/impulsive (72). On the BASC II, clinically significant teachers’ ratings were noted in hyperactivity, withdrawal, depression, atypicality, and behavioral symptoms. He was considered at risk in the areas of aggression and attentional problems.

Physical exam showed mild midface hypoplasia, low nasal bridge, and bilaterally short 5th fingers with no clinodactyly, no neurocutaneous lesions. There was no history of hypotonia and neurological exam revealed normal tone, strength, and deep tendon reflexes. There is no history of seizures. EEG and MRI have not been performed, but will be recommended.

Supplemental Clinical information for 15q13.2q13.3 microduplication cases

Patient 6

Patient 6 is a 20y/o Caucasian male with BP4-BP5 duplication and a diagnosis of autism, moderate mental retardation, and obsessive-compulsive disorder. His receptive language is moderately to severely impaired while expressive language is severely impaired. He is nonverbal, uses only a few signs, and uses keyboard and other communication aid with speech therapy. He has a history of repetitive behaviors (hand flapping; swinging; spinning) and poor eye contact. His social interactions are significantly impaired, and he has difficulty with transitions.

Dysmorphology exam revealed small midface and apparent frontal bossing due to the large cranium with deep set eyes. He is also significant for severe dental crowding and supernumerary teeth. He has a very tall narrow palate; narrow palpebral fissures, and hyperpigmetned macules on the penis which has led to a diagnosis of Bannayan-Riley-Ruvalcaba syndrome. Gene sequencing for PTEN was normal in clinical and research laboratories. At age 2-11/12, axial hypotonia noted, but tone was recorded as normal by age 7y1m (at that time, noted to have tight heel cords). As a teenager, poorly cooperative for a neurological exam, but apparently nonfocal with a normal gait. He has no history of seizures and has not had an EEG other than a sleep study performed at age 7 which did not mention any abnormal EEG. He had a head CT at 6 months due to macrocephaly and an MRI at age 1y that were both read as normal.

Patient 7

Patient 7 is a 2y10m Caucasian female with BP4-BP5 duplication and a diagnosis of developmental delay and cleft lip s/p repair. She has borderline average receptive language and below average expressive language abilities (by REEL-3 parent report performed at 14 months) with an ability score of 79 (8th percentile). Repeated evaluation at age 2y5m showed more age-appropriate ability in receptive and expressive language skills, although articulation and phonological abilities were assessed as below age level. She socialized well in preschool with occasional instances of aggressive behavior. She has some repetitive behaviors such as pulling her hair out and then playing with it in her mouth, and hand flapping.

Dysmorphology exam revealed long head and triangular face; hypertelorism and up slanting eyes; her nose was asymmetric; narrow palpebral fissures, right small toe clinodactyly; hyperextensible joints (c/w EDS). She had no neurocutaneous lesions. Neurological exam was notable for diffuse hypotonia with normal reflexes and no muscle weakness. She has no history of seizures and has not had an EEG. MRI showed a choroid plexus cyst with no obstruction (previously identified on head US). She also had slight accentuation of the usual thinning of the posterior body of the corpus callosum, correlating to the ultrasound findings. There is probable minimal reduction in volume of the parietal white matter

Patient 8

Patient 8 from the AGRE repository is an 8y male (mix of Caucasian and Africa American) with a de novo BP4-BP5 duplication and a diagnosis of autism based on the Autism Diagnostic Inventory-Revised (ADI-R). This child had significant delays in expressive language with a performance level equivalent to 1y4m at chronolofical age 7y7m on the Vineland Adaptive Behavior Scales. This child had one sibling with autism who did not have the BP4-BP5 duplication. No additional phenotypic information was available.

 

Patients 9 and 10

Patient 9 and 10 from the AGRE repository are Caucasian male siblings with a maternally inherited duplication of 502kb (Chr15: 28902339-29404603; hg18; MTMR15, MTMR10, TRPM genes) and a diagnosis of autism based on the Autism Diagnostic Inventory-Revised (ADI-R). The mother who carries the same duplication is apparently unaffected. No additional phenotypic information was available.  

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