A Highly Penetrant Form of Childhood Apraxia of Speech Due to Deletion of 16P11.2

A highly penetrant form of childhood apraxia of speech due to deletion of 16p11.2

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Citation Fedorenko, Evelina et al. “A Highly Penetrant Form of Childhood Apraxia of Speech Due to Deletion of 16p11.2.” European Journal of Human Genetics 24, 2 (July 2015): 302–306 © 2016 Macmillan Publishers Limited

As Published https://doi.org/10.1038/ejhg.2015.149

Publisher Nature Publishing Group

Version Author's final manuscript

Citable link http://hdl.handle.net/1721.1/113018

Detailed Terms http://creativecommons.org/licenses/by-nc-sa/4.0/

A highly penetrant form of childhood apraxia of speech due to deletion of 16p11.2

Authors:

Evelina Fedorenko1^, Angela Morgan2^, Elizabeth Murray2, Annie Cardinaux3, Cristina

Mei2, Helen Tager-Flusberg4, Simon E. Fisher5,6, Nancy Kanwisher3,7

1Massachusetts General Hospital, Department of Psychiatry (Boston, MA); 2Murdoch

Childrens Research Institute (Melbourne, Australia); 3Massachusetts Institute of

Technology, Brain and Cognitive Sciences Department (Cambridge, MA); 4Boston

University, Department of Psychological and Brain Sciences (Boston, MA); 5Max Planck

Institute for Psycholinguistics (Nijmegen, Netherlands); 6Donders Institute for Brain,

Cognition and Behaviour (Nijmegen, Netherlands); 7McGovern Institute for Brain

Research (Cambridge, MA)

^ These authors contributed equally to this manuscript.

Running title: Speech apraxia in children with 16p11.2

Corresponding author:

Professor Evelina Fedorenko

Psychiatry Department

Massachusetts General Hospital

Building 149, East 13th St

Charlestown, MA 02129

Email: [email protected]. Phone: 1-617-417-5044

Summary

Individuals with heterozygous 16p11.2 deletions reportedly suffer from a variety of difficulties with speech and language. Indeed, recent copy number variant screens of children with childhood apraxia of speech (CAS), a specific and rare motor speech disorder, have identified three unrelated individuals with 16p11.2 deletions. However, the nature and prevalence of speech and language disorders in general, and CAS in particular, is unknown for individuals with 16p11.2 deletions. Here we took a genotype- first approach, conducting detailed and systematic characterization of speech abilities in a group of 11 unrelated children ascertained on the basis of 16p11.2 deletions. To obtain the most precise and replicable phenotyping, we included tasks that are highly diagnostic for CAS, and we tested children under age 18, an age group where CAS has been best characterized. Two individuals were largely non-verbal, preventing detailed speech analysis, while the remaining nine met the standard accepted diagnostic criteria for CAS.

These results link 16p11.2 deletions to a highly penetrant form of CAS. Our findings underline the need for further precise characterization of speech and language profiles, in larger groups of affected individuals, which will also enhance our understanding of how genetic pathways contribute to human communication disorders.

Key words: 16p11.2 deletions; Childhood Apraxia of Speech; articulation; language disorders

Main text

Introduction

Deletions of a ~600kb region in human chromosomal band 16p11.2 occur in approximately 1/2000 individuals1,2, and have been associated with a number of neurodevelopmental disorders, including autism3. Individuals with heterozygous 16p11.2 deletions have increased head circumference1,4, high rates of obesity 3,5, and seizures6.

Cognitively, these individuals have a reduced intelligence quotient (IQ), approximately two standard deviations below that of familial non-carriers6. Furthermore, affected individuals have a variety of speech and/or language difficulties6,7. However, the precise nature of these difficulties remains unknown. Here, we focus on the speech domain, testing whether 16p11.2 deletions confer a risk of developing a specific speech disorder:

Childhood Apraxia of Speech (CAS)8.

CAS is a rare motor speech disorder that affects the production, sequencing and timing of sounds, syllables and words8, with a diagnosis distinct from other speech (e.g., stuttering) and language disorders (e.g., specific language impairment). Although CAS has been linked to a number of genes and genomic pathways, including FOXP2 and ELKS/ERC1 9–

11, the confirmed genetic risk factors explain only a small proportion of cases12. Recently, however, three unrelated individuals with 16p11.2 deletions were identified in children diagnosed with CAS and screened for copy number variations13,14, thus implicating

16p11.2 deletions as one of the genetic causes of CAS. However, a crucial question remains: how common is CAS among individuals with 16p11.2 deletions?

No standardized or systematic testing of speech abilities has been reported in a group of individuals with 16p11.2 deletions. Further, in existing studies, the terms “speech” (the perception and production of speech sounds) and “language” (understanding and use of syntax, morphology, semantics and pragmatics) are often used interchangeably. Yet these terms refer to broad multicomponent domains, and deficits within each encompass many distinct disorders. Precise phenotyping, with the use of correct terminology, diagnostic tools and criteria accessible and hence replicable to others, is thus critical to elucidate genotype-phenotype relations in this relatively common deletion syndrome.

Here, we conduct the first systematic differential diagnostic assessment of speech disorders in a cohort of individuals with 16p11.2 deletions. In contrast to prior phenotype-driven studies of CAS13,14, we have taken a genotype-first approach15 and recruited participants with 16p11.2 deletions to conduct speech and neuropsychological assessment.

Materials and methods

Participants. Eleven children (8 males) ages 5;4-18;1 (mean 10;8) with 16p11.2 deletions from the Simons Variation In Individuals Project (Simons VIP) cohort

(http://sfari.org/resources/simons-vip) participated (see SupplTable 1, for SFARIbase

IDs). Participants were recruited from attendees of the 2013 Simons VIP Connect Family

Meeting in Orlando, Florida. The study was advertised to attendees as a “language study”. Inclusion criteria were: presence of a 16p11.2 deletion, an IQ of at least 80,

based on previously performed phenotyping (cognitive testing is challenging for individuals with lower IQ), and age ≤ 18 years. The presentation of CAS is known to change across the lifespan, with little or no information available on core features of the disorder to guide informed diagnosis in mid to late adulthood. Hence we excluded individuals older than 18 years. Thirteen individuals met these criteria, and eleven agreed to be tested. As described previously, all 11 children carry the canonical deletion

(∼600 kb, chr16.hg18:g.29557497_30107356del) at the locus, and do not have any other copy number variant that is known to affect function, or another neurogenetic or neurological diagnosis unrelated to 16p11.2 (e.g., tuberous sclerosis)16. Written consent and assent was provided, in accordance with the requirements of the Internal Review

Board at MIT. A testing battery of approximately one hour was conducted. Families were compensated with Amazon.com gift cards and other prizes.

Speech sampling and analysis. Speech samples for transcription were derived from audio

(Sony Digital ICD-PX312) and video (Sony HDR-CX260V) recordings of conversation with the examiner and/or parent/guardian during and between standardized tests, and also from three cognitive tasks (SRT, CTOPP, and RAN; see below). Conversations were elicited for a total of at least 10 minutes to seek a sample of at least 100 words45.

Samples were transcribed by a speech language pathologist (EM) using broad phonetic transcription with supplemental diacritics to note distortion errors.

Samples were analyzed for speech features associated with articulation disorder, phonological disorder, dysarthria and CAS. A phonetic inventory was determined,

including initial, medial and final consonant and vowel inventories. Percentage phoneme correct scores were calculated based on conversational speech. An overall impression of intelligibility was provided by EM and AM using a perceptual intelligibility rating scale.17 Ability to repeat pronounceable nonsense words was additionally examined using nonword repetition and the SRT (see below). Phonological process analysis was conducted (Table 1). Traditional articulation errors were noted where present (e.g., interdental or lateral /s/ or /z/, distorted /r/). Motor speech features (encompassing symptoms of dysarthria and apraxia) were rated using the ‘Mayo Clinic Motor Speech

Characteristics Rating Scale’18 (Table 1) and further diagnostic criteria for CAS were adapted from Murray et al.19,20 based on the three American Speech and Hearing

Association (ASHA)8 consensus-based criteria (Table 2). Two SLPs (EM, AM) examined the resultant data to make a final diagnosis by consensus.

Neuropsychological tests. Not every participant was able to perform all of the tasks because of general unwillingness to perform particular tasks, fatigue, insufficient time, and because two (male) participants were mostly non-verbal, as confirmed by parent report. Eight participants were tested on the syllable repetition task (SRT)21, the nonword repetition subtest from the Comprehensive Test of Phonological Processing (CTOPP)22, and rapid automatized naming tasks (RAN)23. In the syllable and nonword repetition tasks, participants are presented with spoken syllable sequences or nonwords, respectively, of increasing length and are asked to repeat each one. The SRT21 and nonword repetition tasks are particularly sensitive for detecting errors in children with speech sound disorder, including CAS. Poor performance on the SRT in particular, a tool

that overcomes some of the methodological limitations of standard nonword repetition tasks (see8 for review), has been suggested to have diagnostic accuracy for identifying the signature transcoding deficits seen in CAS46. The RAN task requires participants to name in order, as quickly as possible, sequences of letters, digits, pictures of objects or colored dots. Seven participants were tested on the Peabody Picture Vocabulary Task (PPVT) 24, and four on the Test for Reception of Grammar (TROG)25. In these tasks, participants are shown sets of four pictures accompanied by a word (PPVT) or sentence (TROG) and have to choose the picture that corresponds to the word/sentence. Non-verbal IQ was assessed in ten of the eleven participants with the matrices subtest of the Kaufman Brief

Intelligence Test (KBIT)26. Fine and gross motor skills were evaluated in ten participants with the Bruininks-Oseretsky Test of Motor Proficiency (BOT)27, which requires participants to string beads and copy and draw figures (fine motor skills), as well as catch a ball, walk on a straight line and jump on one leg (gross motor skills). Raw scores, computed for all tasks following the instructions in the manuals, were converted into standardized scores and percentiles. The parents/guardians of nine participants completed the Children’s Communication Checklist (CCC)28.

The phenotyping data have been uploaded to the Simons Foundation Autism Research

Initiative (SFARI) database (available at http://sfari.org/resources/sfari-base).

Results

Speech results and diagnosis (Tables 1-2). The limited verbal output for two participants precluded speech diagnosis. All 9 remaining participants met the three ASHA-based consensus diagnostic criteria for CAS8 (Table 2). All 9 also had additional motor speech deficits that could be associated with either dysarthria or CAS including phoneme imprecision (8/9), hypernasality (7/9), slow speech rate (6/9) and equal stress (9/9), characterized by the Mayo clinic rating scale18. Further, some features more commonly associated with dysarthria than CAS included mildly reduced overall loudness (7/9) and breathy voice (6/9). The majority also demonstrated phonological errors (Table 1), with final consonant deletion, gliding, weak syllable deletion, cluster reduction and cluster simplification most common. Some of these error patterns could reflect motor features of

CAS rather than being purely phonological in nature. Poorer performance with increasing stimulus length was noted on the SRT and nonword repetition tasks (Table 1), a hallmark characteristic of CAS. Participants scored in the 7th percentile (SEM=1.22) on nonword repetition. Conversational speech intelligibility was reduced in all, with most rated as “somewhat intelligible”, with corroborating percent phoneme correct ratings

(range 66-88%, Table 1) falling well below the expected intelligibility range for this age range.29

Neuropsychological results (Table 3, SupplTable2). Here we include the two largely non- verbal participants excluded from the speech analyses. Consistent with prior reports

(e.g., 6), non-verbal IQ (n=10) was about two standard deviations below the general population mean (average standard score=78.8, SEM=5.57; average percentile=18.4,

SEM=4.25). Participants performed poorly on tasks assessing higher levels of language

processing. In particular, on lexical knowledge (PPVT), participants (n=7) scored on average in the 36th percentile (SEM=10.2), and on grammatical comprehension (TROG), participants (n=4) scored on average in the 21st percentile (SEM=15.4). Participants

(n=8) scored relatively higher on the RAN task: in the 57th percentile (SEM=12.7), with a large range. Finally, on the motor-skills assessment, participants (n=10) scored on average in the 22nd percentile (SEM=9.33), again with a large range. The summed CCC scores were in the 11th percentile on average, with the speech subscale revealing the lowest score (6th percentile on average, SEM=3.59).

In terms of inter-task relationships (SupplTable2), parental assessments of children’s speech abilities (CCC speech subscale) predicted nonword repetition scores (r=0.52), as did the overall CCC scores (r=0.46). Interestingly, IQ didn’t show a strong relationship with nonword repetition scores (r=0.34), although it did predict performance on PPVT

(r=0.57) and TROG (r=0.89), consistent with prior reports revealing such correlations in both healthy individuals (e.g., 30,31) and individuals with neuropsychiatric disorders (e.g.,

32). PPVT and TROG were also highly correlated with each other (r=0.94). BOT performance was weakly correlated with nonword repetition scores (r=0.23) and not correlated with IQ (r<0.1).

Discussion

Systematic differential diagnostic assessment of speech disorders in a cohort of children with 16p11.2 deletions revealed a high number of individuals with features of CAS: of

eleven children, two were mostly nonverbal, and the remaining nine met the core consensus based ASHA criteria for CAS8. This finding is striking given that CAS is a specific speech disorder, distinct from – though often co-morbid with – other speech and language disorders, and exhibiting low prevalence in the general population (for example, one study estimates prevalence of ~0.01-0.02%33). Nonetheless, the cognitive profile associated with 16p11.2 deletion is not characterized by a selective deficit in speech production. Our participants were additionally intellectually impaired and had difficulties with lexical and syntactic processing and general motor coordination. The relatively low inter-task correlations, however, suggest that these language and general cognitive deficits are at least somewhat independent from the speech production difficulties.

Our findings are in line with a handful of previous reports of CAS13(2 cases); 14(1 case); dysarthria 34(2/3 cases); 35(1/10 cases); and articulation difficulties 35(2/10 cases); 36(1/15 cases); 37(1/18 cases) in individuals with 16p11.2 deletions (SupplTable 3). However, most studies of individuals with 16p11.2 deletions have used the non-specific term

"speech delay", making it impossible to identify the precise sub-type(s) of speech disorder. Our data go beyond these earlier reports by establishing, with detailed phenotyping, that many individuals with 16p11.2 deletions do not just have generalized speech and language disorders, but features of CAS in particular. Ours is the first genotype-driven study to apply the systematic analyses necessary to distinguish features of CAS from other speech and language disorders in individuals with 16p11.2 deletions.

One limitation in our speech phenotyping was the absence of an oral peripheral exam.

An oral exam can determine the presence of altered tone (spasticity, flaccidity), reduced range and rate of movement of the articulators, or structural deficits (high arched palate, submucous cleft, bifid uvula). These data can assist in more precisely differentiating between dysarthria, apraxia and structural speech deficits.

As in many other clinical reports, our sample may not be fully free of ascertainment bias; genetic anomalies in these children were discovered after they presented cognitive and/or behavioral problems and were evaluated by medical professionals. Yet, any such bias is unlikely to be specific to CAS and is instead a general bias toward neurodevelopmental problems. Although we found that 9/9 of the 16p11.2 individuals we tested met criteria for CAS (two additional participants were non-verbal and thus not tested for CAS), we do not conclude that features of CAS will be found in every individual with a 16p11.2 deletion. Nevertheless, given the rarity of CAS in the general population, and the high proportion of features of CAS cases in our sample, it seems likely that CAS is a reasonably frequent component of the phenotype of the 16p11.2 deletion syndrome.

One important aim for future research will be to test a larger number of individuals with

16p11.2 deletions, to precisely quantify the penetrance of this genomic rearrangement with respect to features of CAS. Another important direction would be to attempt to link

CAS-related deficits to some aspects of brain structure and function. Some recent studies have reported neurological markers associated with the 16p11.2 deletion syndrome (e.g., increased brain volume, including increased gray and white matter, subcortical and

cerebellar volumes38,39, some regional differences39, and aberrant white matter microstructure40). However, the neurobiological mechanisms underlying these effects are not yet well understood41-42. Also, there have been no consistent reports of relationships between speech/language problems in 16p11.2 deletion cases and neuroanatomical abnormalities4,34-37 and no investigations into potential dysfunction of language networks41 or brain regions related to speech articulation42. Finally, it will be of considerable interest to eventually determine which of the 25 or so genes that are contained within the deleted region contribute to the different neurodevelopmental aspects of this major chromosomal rearrangement.

Conflict of interest

The authors declare no conflict of interest.

Acknowledgments and affiliations

We thank the participants and their families for taking part in our study. We are also grateful to the Simons Foundation team (especially Alexandra Bowe, Debra Olchick,

Nicole Takahashi, and Jennifer Tjernagel) for help with recruiting and scheduling participants. We thank Heather Mabie and Larry Shriberg for sharing the audio materials for the SRT. We thank Zuzanna Balewski, Cara Borelli, Jenelle Feather, Jeanne Gallée,

Kyle Mahowald, Caitlin Malloy, and Terri Scott for help in preparing everything for testing and analyzing the data. We thank Kim Leeds for administrative support. This work was supported by a grant to N.K. from the Simons Foundation. E.F. is supported by the R00 award HD-057522 from NICHD. S.E.F. is supported by the Max Planck

Society. H.T.F’s contribution to this research is supported by support from NIDCD (P50

DC 13027). A.M. is supported by the NHMRC (#607315). Preparation of this paper was also supported by the Victorian’s Government’s Operational Infrastructure Support

Program, Australia.

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Table captions

Table 1. Speech (phonetic, phonemic and intelligibility) features for the participants with

16p11.2 deletion.

Table 2. Speech features categorized under the three consensus diagnostic criteria for

CAS diagnosis (ASHA 2007).

Table 3. Neuropsychological test results.

Supplementary table 1. SFARIbase IDs.

Supplementary table 2. Inter-task relationships.

Supplementary table 3. Phenotype for 16p11.2 deletion [and duplication].

19 Supplementary Table 3. SFARIbase IDs.

Participant number* SFARIbase ID

P1 3062.101

P2 3199.101

P3 3092.101

P4 3015.101

P5 3008.101

P6 3023.101

P7 3036.101

P8 3029.101

P9 3014.101

P10 3001.101

P11 3024.101

* as they are numbered in Tables 1-3. Supplementary Table 2. Inter-task relationships.

Correlations (a Spearman rank correlation was used) between pairs of tasks. The color of the box reflects the strength and direction of the correlation (darker blue boxes are ones with higher positive correlations, darker red boxes are ones with higher negative correlations, and lighter boxes have values close to 0). Given the small sample size, only the correlation between the two CCC measures was reliable. Supplementary Table 3. Phenotype for 16p11.2 deletion [and duplication]

Author n Genetic Age Se Ethnicity Speech Oromotor Language Cognition Physical Developmen Other variant (yrs) x features t Al-Kateb 7/10 with 16p11.2 2-17 4F African- Articulation NR Language delay ID (Pt 5) Dysmorphic Delayed (Pt Neonatal et al. 2014 speech or del (n=7) 3 American problems (Pt (Pt 1) (Pt 1,3, 5, 7, 1-3,5,8,9) encephalopathy, language 490 kb M (Pt 3) 1,2) 2 single words 8) Motor generalised cerebral delay 8q11.3 dup Caucasian Dysarthria (Pt at 2yrs (Pt 8) High palate impairment dysfunction (Pt 3); (Pt 2) (Pt 5,7) 2) (Pt 1,2,5,7) (Pt 2) feeding difficulties 77 kb Hmong (Pt Speech delay Scoliosis (Pt Normal (Pt 3); reading 15q14 del 9) (Pt 2,5,7,9) 5, 9) motor impairment (Pt 5); (57.9 Mb No speech milestones ADHD (Pt 2); ADD, of long (laryngeal (Pt 9) seizures (Pt 7); stretches of dysgenesis, congenital hmz (Pt 8) absence of vocal hemivertebrae (Pt 8) cords) (Pt 3) Bachmann 3/6 with 200 kb 3-15 N NR Speech delay NR NR NR NAD Delayed (Pt Autism & social -Gagescu speech delay 16p11.2 R (Pt 2,5,6) 2,5,6) delay (Pt 5) et al. 2010 del (gene Seizures (Pt 6) SH2B1) 3/5 with 200 kb NR N NR Speech delay NR Possible NR Cleft palate Ataxia (n=1) ASD (n=2); ADHD speech delay 16p11.2 R (n=3) expressive (n=2) & conduct disorder dup (gene language delay (n=1); seizures (n=1) SH2B1) (n=1) Ballif et al. 2/5 with 8.7 Mb 13y F NR NR Drooling Speaks few Significant Dysmorphic; NR Pierre Robin 2007 speech or 16p11.2 – 8m words delay cleft lip & Sequence; hearing language p12.2 del Sign language palate; loss; hypotonia; impairment vocab ~500 unsteady infant feeding gait difficulties

7.8 Mb 2y F NR No Speech NR NR Significant Dysmorphic NR Hypotonia; feeding 16p11.2 – 9m delay difficulties p12.2 del Battaglia et 1 8.2 Mb 8 F NR 3y 10mo: no NR Expressive ID Dysmorphic Delayed Hypotonia; poor al. 2009 16p11.2- speech language deficit High-arched concentration; hyper- p12.2 8yrs: poor palate activity; feeding & speech fine motor difficulties Bijlsma et 12/15 with 600 kb 3-44 7 NR Speech delay NR Delayed 1st ID (Pt 1-3, Dysmorphic Delayed (Pt Epilepsy (Pt 3,8,13); al. 2009 speech or 16p11.2 M (Pt 1-5, 8- words (Pt 2-4, 9,10); low (Pt 1-3,5,6,8- ADD (Pt 4); motor language del 4F 11,13); nasal 13); severe average (Pt 1,2,6,10,11,1 11,13) immaturity & delay speech (Pt 6); expressive 4); delayed 3); Motor delay muscular hypotonia lisp (Pt 3); slow language (Pt 5) high/narrow (Pt 4) (Pt 4); autism (Pt 5); speech (Pt 9); disorder (Pt 8); palate (Pt 6) failure to thrive (Pt no speech (Pt Pt 11: IQ: 65 (Pt 11) 10); poor Comprehension 6), 74 (Pt articulation with (RDLS) SS: 73; 11), 83 (Pt no specific Expressive 13), 62 (Pt motor deficit (STLP) SS: 58 8) affecting speech (words), 55 (Pt 11) (sentences) 205 kb 5 M NR Speech delay NR NR ID Dysmorphic Delayed Behavioural atypical problems; hypotonia 16p11.2 del Egger et al. 1 970 kb 33 M NR Paucity of NR Poor pragmatic FSIQ 112 NAD Normal Asperger’s syndrome 2014 16p11.2 speech language BP1-BP4 del Fernandez 3/3 16p11.2 5-18 2 NR Non-verbal (Pt NR OWLS Oral Delayed (Pt Dysmorphic Motor delay ASD (Pt 1); autism et al. 2010 (Pt 1 & 2 del M 3) Expression AE: 1,3); PIQ: 78 (Pt 1,3) (Pt 1,3) (Pt 2,3); spastic described in Pt 1: 1F 6;7 (Pt 1, CA (Pt 1) cerebral palsy (Pt 3) Marshall et mosaic del 12;4), 6;4 (Pt 2 Leiter SS: 87 al. 2008) CA 7;4) (Pt 1), 93 (Pt OWLS 2) Listening Comprehension AE: 6;1 (Pt 1, CA 12;4), 7;2 (Pt 2 CA 7;4) 3/3 16p11.2 26m- 1 NR NR NR OWLS AE (Pt Delayed (Pt Dysmorphic Delayed (Pt ASD (Pt 5); autism, (Pt 4 & 5 dup 15y M 4, CA 8;7): Oral 4,5); low (Pt 4,6) 6) epilepsy (Pt 4); described in Pt 4: 654 2F Expression 1;9, average (Pt Scoliosis (Pt Motor delay autistic features, Marshall et kb & 479 Listening 6) 4) (Pt 5) hypotonia (Pt 6) al. 2008) kb Comprehension FSIQ: 54 (Pt 10q11.21 1;8 4) dup PPVT AE: 5y Leiter SS: 74 (Pt 5, CA 9) (Pt 4) Pt 6: 20 spoken words at 26m Finelli et 1 8 Mb 25 M NR NR NR Expressive- ID Dysmorphic Delayed Autism; seizures; al. 2004 16p11.2- receptive Ataxic gait diffuse cortical 16p12.2 impairment atrophy dup Ghebranio 1/2 593 kb 41 M NR Speech delay NR Expressive- Mild ID Face NR Seizures; hearing us et al. 16p11.2 receptive hypoplasia; loss; multiple 2007 del disorder high arched congenital anomalies palate Hanson et 60/85* with ~600 kb 3- N NR Phonological NR Language ID (n=8) NR NR ASD (n=20); ADHD al. in press speech or 16p11.2 Adult R processing disorder (n=36) (n=15) language del ^ disorder (n=44)# impairment Hempel et 1 7.7 Mb 13y3 M NR Severe speech Poor Severe ID Dysmorphic Motor delay Feeding difficulties; al. 2009 16p11.2- m delay sucking & expressive hypotonia; fine motor p12.2 del chewing, impairment deficit; hearing loss; 13 CNVs drooling introverted behavior in total Kumar et 5/6 16p11.2 4-14 4 NR NR NR PPVT BNL Nonverbal NR NR Autism (n=4) al. 2008 del M (n=2, SS 74) IQ BNL Seizures (n=1) (mosaic, 1F Delayed 1st (n=2) n=2) words (n=4) Laffin et 1a 16p11.2 3-6 N NR CAS Impaired Comprehension NAD NAD (gross NR al. 2012 del, R & expression motor) 13q13.3 impaired dup, 14q23.2 del Marshall et 2 16p11.2 NR 1 NR Reduced speech Likely oral Receptive- Nonverbal Dysmorphic NR ASD al. 2008 del M intelligibility motor expressive delay IQ: 82 & 1F (n=1) apraxia (n=1) 93 (n=1) 2 16p11.2 NR 1 NR Reduced speech Likely oral Receptive/expre Impaired Dysmorphic Motor delay ASD; epilepsy (n=1) dup M intelligibility motor ssive delay (n=2) (n=1) (n=1) 1F apraxia Nonverbal Scoliosis IQ: 39 (n=1) Newbury 1 16p11.2 14 M Caucasian DVD NR VABS AE: 3y NR Dysmorphic Normal until PDD-NOS et al. 2013 heterozygo 3m for 1.5yrs us del & communication 6q22.31 domain (CA dup (genes 14yrs) TRDN, NKAIN2) Ockeloen 1 16p11.2 13 M NR Speech NR NR Mild Dysmorphic NR et al. 2014 del problems, VPI learning Submucous difficulties cleft Pebrel- 1 1.7 Mb 16 M NR Delayed with NR Delayed ID Ataxia Delayed Neonatal hypotonia; Richard 16p11.2 deterioration ADD; progressive et al. del (gene vision loss; peripheral CLN3 neuropathy 2014 partially included) Raca et al. 2 562 kb NR N NR CAS NAD OWLS: FSIQ: 103 Gross motor Psychosocial Social difficulties 2013 16p11.2 R Listening PIQ: 108 impairment delay Literacy difficulties del, 310 kb Comprehension VIQ: 96 13q13.3 scale SS: 100, dup, 120 Oral Expression kb 14q23.2 scale SS: 92 del 517 kb NR N NR CAS Nonverbal OWLS: FSIQ: 82 Gross motor Normal ADHD 16p11.2 R oral Listening PIQ: 79 impairment Literacy difficulties del apraxia Comprehension VIQ: 90 scale SS: 96, Oral Expression scale SS: 71 Rosenberg 1 1 Mb NR F NR Severe speech NR NR Mild ID Dysmorphic NR NR et al. 2006 16p11.2 delay del Rosenfeld 17/18 with 16p11.2 5m- 8 NR Speech deficit NR Language Below Dysmorphic Delayed Hypotonia (n=7); et al. 2010 speech & del 20y M (including poor deficit average (n=13) (n=17) apraxia (n=2); poor language 6F articulation, (n=17) High palate attention or ADHD deficits c hyper- or (n=3) (n=8); ASD or hyponasal) autistic features 2 non-verbal (n=9); seizures (n=2); hearing loss (n=3)

8/10 with 16p11.2 1-14 7 NR Speech deficit NR Language ID (n=2) Dysmorphic Delayed Hypotonia (n=4); speech & dup M deficit Delayed (n=8) (n=8) seizures (n=1); poor language 1F (n=1) attention or ADHD deficits (n=3); ASD or autistic features (n=1) Schaaf et 3 16p11.2 16 M Hispanic- Speech delay NR Language delay No tested Dysmorphic Delayed al. 2011 del Mexican Significant dysarthria Reduced speech intelligibility 16p11.2 14 M Caucasian Dysarthria NR PPVT SS: 85 DAS-II SS: Dysmorphic Normal Learning disability; del (speech VABS-II General CAPD; PDD-NOS hypernasal, Communication cognitive rapid, choppy) SS: 67 ability (86), Verbal (82), Non-verbal (87), Spatial (95) 16p11.2 7 M Caucasian NR NR PPVT SS: 78 DAS-II SS: Dysmorphic Delayed Autism; ADHD dup, 1.29 VABS-II General Spastic gait, Mb 17p12 Communication cognitive weak fine dup incl. SS: 76 ability (80), motor PMP22 Verbal (94), coordination gene Non-verbal (75), Spatial (72) Shinawi et 14/16 with 16p11.2 7mo- 9 African Speech delay NR Language delay ID (n=2) Dysmorphic Motor delay Autism (n=3); cleft al. 2010 speech/ del 38yrs M American, (n=14 incl. 1 Learning (n=14) (n=8) palate (n=1); ADHD language 5F Caucasian, non-verbal) disability & other behavioural delayb Vietnamese, (n=1) problems (n=6); Hispanic seizures (n=5)

9/10 with 16p11.2 4-27 6 Hispanic, Speech delay NR Language delay ID (n=8) Dysmorphic Motor delay ADHD/other speech/ dup M Caucasian (n=9 incl. 1 (n=9) (n=6) behavioural problems language 3F stutter) (n=6); seizures (n=3); delay hypotonia (n=1); cleft lip +/- palate (n=2) Shiow et 1 600 kb 4 F NR NR NR Language delay; Low average NR Motor delay ADHD al. 2009 16p11.2 impaired to average del; functional 2 bp communication CORO1A del Tabet et al. 3 847 kb 21 M Caucasian/ Severely NR Impaired FSIQ: 47 Dysmorphic Normal Autism 2012 16p11.2 Mauritius delayed expressive (AE: PIQ: 50 early del (28.4- 4yrs) VIQ: 50 development 29.3 Mb) 8.95 Mb 18 M Caucasian/ Non-verbal NR VABS-II FSIQ: <1st Dysmorphic Normal Autism 16p11.2p1 Mauritius communication centile early 2.2 dup domain: AE development (21.3-30.2 11yrs Mb); VWA3A dup at 16p12.1, & NUPR1, LAT, ALDOA dup at 16p11.2 8.95 Mb 18 M Caucasian/ NR NR VABS-II FSIQ: <1st Dysmorphic Normal Autism 16p11.2p1 Mauritius communication centile early 2.2 dup domain: AE development (21.3-30.2 9yrs Mb); VWA3A dup at 16p12.1, & NUPR1, LAT, ALDOA dup at 16p11.2 Weber et 1 895 kb 12 M NR Speech NR Limited ID Fine & gross Delayed Benign infantile al. 2013 16p11.2 problems vocabulary motor convulsions; del; 1.3 limitations paroxysmal Mb kinesigenic 12p11.1 dyskinesia; unable to dup; 31 read & write Mb 8p23.1p11. 2 hmz; 44 Mb 8q22.1q24. 3 hmz Weiss et 7/8 16p11.2 17m- 6 NR Speech delay NR NR FSIQ: 61, 73 NAD Motor delay Autism (n=7); ADHD al. 2008 del 10y M (n=7) (Aut 1,2) (Pt 1-5, Aut (Aut 1,2); seizures 6m 1F PIQ: 61, 75 1,2) (Aut 2) (Aut 1,2) VIQ: 65, 75 (Aut 1,2) 3/4 16p11.2 2y6m 1 NR Speech delay NR NR ID (Pt 4) Spasticity Motor delay Seizures (Pt 4) dup; - M (Pt 2) (Pt 2) 46,XY,16q 9y9m 2F 11.2q12.1 dup (Pt 3) AE: age equivalent. BNL: below normal limits. CA: chronological age. CAS: childhood apraxia of speech. CAPD: Central Auditory Processing Disorder. DAS: Differential Ability Scales. Del: deletion. Dup: duplication. DVD: developmental verbal dyspraxia. F: female. M: male. Hmz: homozygosity. ID: intellectual disability. NAD: no abnormalities detected. NR: not reported. Pt: Patient. OWLS: Oral and Written Language Scales. PDD-NOS: pervasive developmental disorder – not otherwise specified. RDLS: Reynell Developmental Language Scales. SS: standard score. STLP: Schlichting Test for Language Production. VABS: Vineland Adaptive Behaviour Scales. VPI: velopharyngeal insufficiency. a Participant also described in Raca et al. (2013). b 2 participants too young to undergo a speech evaluation. c Gender for the remaining participants not reported. * n not reported by the authors and was calculated using the percentage provided in the paper. ^ Age of oldest participant not clear. # Terms phonological processing and articulation deficit appear to be used interchangeably.

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