Abstract
Speech sound disorders (SSD) manifest as difficulties in phonological memory and awareness, oral motor function, language, vocabulary, reading, and spelling. Families enriched for SSD are rare, and typically display a cluster of deficits. We conducted a genome-wide association study (GWAS) in 435 children from 148 families in the Cleveland Family Speech and Reading study (CFSRS), examining 16 variables representing 6 domains. Replication was conducted using the Avon Longitudinal Study of Parents and Children (ALSPAC). We identified 18 significant loci (combined p < 10−8) that we pursued bioinformatically. We prioritized 5 novel gene regions with likely functional repercussions on neural pathways, including those which colocalized with differentially methylated regions in our sample. Polygenic risk scores for receptive language, expressive vocabulary, phonological awareness, phonological memory, spelling, and reading decoding associated with increasing clinical severity. In summary, neural-genetic influence on SSD is primarily multigenic and acts on genomic regulatory elements, similar to other neurodevelopmental disorders.
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Introduction
Communication disorders are highly prevalent in the United States with approximately one in twelve children ages 3–17 years demonstrating a disorder1. The most common difficulties are a speech problem (5%) or language problem (3.3%). Speech sound disorders (SSD) refer to difficulties producing certain sound past the age that a child is expected to acquire the sound, and include both errors of articulation or phonetic structure (errors due to poor motor abilities associated with the production of speech sounds) and phonological errors (errors in applying linguistic rules to combine sounds to form words). SSD has a prevalence of approximately 16% in children 3 years of age2, with an estimated 3.8% of children persisting with speech delay at 6 years of age3. More than half of these children encounter later academic difficulties in language, reading, and spelling4,5,6,7,8. Because of the clinical heterogeneity of speech problems and their correlation with other communication domains, endophenotypes are key to the study of genetic underpinnings9.
Vocabulary is core to speech acquisition10. Children with difficulties in speech sound development often have difficulties with oral language and later reading and spelling disability2,4,5,6,11. Thus, speech, language, reading, and spelling measures are highly correlated and often have common genetic associations7,8. Moreover, speech and other communication phenotypes follow a developmental trajectory, where some speech and language disorders resolve with age, whereas others persist; genetic influences on the less easily resolved manifestations are generally stronger12,13. Because of the common genetic underpinnings and pathologic associations between speech and other communication phenotypes, it is conceivable that genetic replication interweaves with different communication measures. Indeed, various studies have examined candidate gene associations associated with both binary traits and quantitative endophenotypes, and have identified several strong candidates14, though a clear model of genetic susceptibility has not emerged. Of seven known GWASs, none overlap in their top results (multiple genes with p < 5 × 10−5, see Table 2 in the Graham and Fisher meta-analysis paper13), because they focused on several phenotypes (word reading, vocabulary, receptive and expressive language, nonword repetition, and language impairment (LI) binary trait), or these measures were assessed at different ages (either pre-school or early school-age)15,16,17,18,19,20,21,22. Because these studies only present results from one or a few measures and/or a binary trait, it is difficult to dissect the complexity of shared genetic influences. Most have not focused on children with SSD, particularly measures of articulation. Our sample represents a unique set of deeply phenotyped individuals with information on six domains that form the core of speech and language.
SSDs are likely due to deficits in both motor ability and broader neural dysfunction. While motor deficits contribute to problems in speech production, abnormalities in other neural systems likely influence the formation of phonological representation, which is common to SSD as well as reading and LI. We hypothesize that genomic factors associated with variation in speech production, phonological representation, and language may point to neural pathways common to speech, language, reading, and spelling ability. To address this hypothesis, we examined endophenotypes representing motor speech, vocabulary, phonological memory, phonological awareness, reading, spelling, and language, in order to characterize genetic commonality across these domains and fully characterize the complexity of SSD. We conducted a GWAS in the Cleveland Family Speech and Reading Study (CFSRS), a cohort ascertained through a proband with SSD, and replicated findings in a population-based cohort. We also conducted a methylome-wide study (i.e., MWAS) to determine the functional implications of these genetic associations. We utilized a family-based cohort as our discovery sample because we hypothesized it would be enriched for disease-associated variants23,24. In these analyses, we identified new candidate genes for correlated communication endophenotypes, and bioinformatic annotation of these loci revealed that regulation of neural pathways is associated with variation in these measures.
Results
Study population
The CFSRS sample included 435 subjects from 148 families (Table 1). Of these, 27% had SSD only, 4% had LI only, 16% had SSD + LI without CAS, and 11% had CAS (Table 1) diagnosed by a speech-language pathologist. There was a high rate of comorbidities, especially among the probands (Table 1, Supplementary Table 4). Of the subjects in the ALSPAC sample, the prevalence of speech problems by parental report varied from 4 to 6% (Supplementary Table 5).
Genetic correlation analysis reveals new relationships among endophenotypes
Genetic correlation analysis revealed that while many of the patterns of correlation were consistent with phenotypic correlations we have previously reported8, polygenic correlations enable a deeper understanding of these measures, which will inform the examination of replication of association effects both within the CFSRS data set and with measures from ALSPAC (Fig. 1). For example, while previous studies have demonstrated a strong genetic correlation between reading and spelling measures, polygenic correlation analysis additionally reveals correlations between those skills and Elision. Not surprisingly, expressive and receptive language (measured by the CELF), are strongly correlated with vocabulary (EOWPVT and PPVT) in addition to reading (WRMT-AT and WRMT-ID). Vocabulary is also strongly correlated with listening comprehension (WIAT-LC).
Figure 1 shows cross-trait correlation results for each pair of tests using GCTA’s bivariate REML analysis69. The cross-trait correlation was tested under the null hypothesis of 0 correlation. Circles shown are for results significant at p < 0.05, with increasing diameter/color corresponding with increasing correlation (circles omitted otherwise). Traits: Phonological memory MSW.PPC, MSW, NSW, NSW.PPC), Spelling (TWS), Reading (WRMT-ID, WRMT-AT, WIAT-RC), Language (CELF.E, CELF.R, WIAT.LC), Vocabulary (EOWPVT, PPVT), phonological awareness (Elision).
The most significant findings from GWAS reveal five new candidate genes
Single marker association tests significant at p < 10−5 were examined further and integrated with data on gene expression and regulation, as detailed below. Other GWAS of neuropsychiatric disease and behavioral traits have similarly found that noncoding regions harbor a significant proportion of risk alleles25 (Supplementary Fig. 1).
Of five top loci, all had enhancers or promoters for muscle, brain, and/or neuronal progenitor cells, four out of five had significant methylation and meQTL effects, and three out of five had eQTLs for brain and/or skeletal-muscle tissue (Table 2, Fig. 2, Supplementary Fig. 2, Supplementary Table 6). EpiXcan analysis suggested that the SNP in the chromosome 1 IFI6 region is associated with expression in the DLPF cortex (Elision p = 0.018, TWS p = 0.008; Supplementary Tables 7 and 8). The first region on chromosome 14, including NFKBIA and PPP2R3C, shows significant chromatin interaction mapping in adult cortex tissue. NFKBIA, which codes for a component of the NF-κB pathway, is associated with neurogenesis, neuritogenesis, synaptic plasticity, learning, and memory26. The second region on chromosome 14 includes PP2R3C, which is within the topologically associating domain (TAD) boundary of the NFKBIA locus in the Hippocampus and DLPFC. EpiXcan analysis showed NFKBIZ, a gene in the same pathway as NFKIBA, is also associated with expression in the DLPFC (Elision p = 0.000452, TWS p = 0.004939; Supplementary Tables 7 and 8). Further, there was significant colocalization at the MON1B/SYCE1L locus on chromosome 16, with differential gene expression of SYCE1L in multiple brain tissues and skeletal muscle localizing with our SNP association signature (Supplementary Fig. 3) and borderline significant colocalization with MON1B expression. The SETD3 locus also showed colocalization with gene expression in skeletal muscle and brain tissue (Supplementary Fig. 3).
Figure 2 shows association results for the top loci. p-Values displayed are for CFSRS and are for the test for which the top SNP was observed. Circles show p-values for SNP associations and triangles show p-values for methylation associations (specifically those for which the top SNP is an meQTL). The plot shows the top SNP for each region ±200 kb. a IFI16 region. rs855865 was associated with NSW in CFSRS (p = 7 × 10−6) and with vocabulary (WISC-V) in ALSPAC (p = 0.01). This region also includes an meQTL (rs12124059, p = 4 × 10−8) for methylation marker cg07196514, and this methylation marker (cg07196514) was also associated with NSW (p = 0.018). b NFKBIA region. rs57645874 was associated with Elision in CFSRS (p = 1 × 10−6) and with reading accuracy (NARA-A) in ALSPAC (p = 0.02). This region also contains an meQTL, rs4981288, for cg07166546 (p = 2 × 10−50), and this methylation marker was associated with Elision (p = 3 × 10−5), TWS (p = 0.0005) and WRMT-ID (p = 0.002). c DACT1 region. rs856379 was associated with MSW in CFSRS (p = 3 × 10−6) and with nonword reading (ALSPACread) in ALSPAC (p = 0.036). This SNP is an meQTL for methylation marker cg13972423 (p = 3 × 10−5). d SETD3 region rs1257267 was associated with WRMT-AT in CFSRS (p = 6.58 × 10−6) and with nonsense word repetition (CNrep5) in ALSPAC (p = 0.05). While only 1 SNP replicated between CFSRS and ALSPAC, 14 additional SNPs showed association in CFSRS at p < 10−5. This SNP (rs1257267) is an meQTL for cg18949721 (p = 4 × 10−12), and methylation marker cg18949721 was also associated with WRMT-AT (p = 0.003). e MON1B region. rs4888606 was associated with MSW in CFSRS (p = 9 × 10−6) and with nonword reading (ALSPACread) in ALSPAC (p = 0.046). While only 1 SNP replicated between CFSRS and ALSPAC, 18 additional SNPs showed association in CFSRS at p < 10−5. This SNP (rs4888606) falls in an intron of MON1B and is an meQTL for cg06128999 (p = 4 × 10−23) and cg05007098 (p = 1 × 10−15); these 2 methylation markers were also associated with MSW (p = 0.045 and p = 0.12, respectively). Functional annotation is in Supplementary Fig. 2.
Replication of previous communication disorder loci
In the replication phase, we focused on gene-level replication because of the differences in SNP coverage between our study and the original findings. ATP2C2 was associated with single word reading (WRMT-ID, p = 7.6 × 10−8), nonword reading (WRMT-AT, p = 4.6 × 10−5), and phonological awareness (Elision, p = 4.6 × 10−5), consistent with prior literature27 (Supplementary Figs. 4 and 5). Similarly, CYP19A1 was associated with nonword reading (WRMT-AT, p = 2.8 × 10−5), phonological awareness (p = 3.3 × 10−4), and single-word reading (WRMT-ID, p = 5.0 × 10−4), validating a previous association28. CNTNAP2 was associated with receptive language (CELF-R, p = 5.2 × 10−6), and diadochokinetic rate (DDK, p = 2.9 × 10−5), replicating a previous association27. While SNPs within ROBO1 and ROBO2 were not significantly associated with our measures, SNPs in the intergenic region were associated with single word reading (WRMT-ID, p = 3.6 × 10−6); ROBO1 was originally associated with dyslexia while ROBO2 was originally associated with expressive vocabulary22,29. Finally, SNPs within the DCDC2-KIAA0319-TTRAP and in FOXP2 regions were associated with various traits at p < 0.01. Within the ALSPAC cohort, a different pattern of replication emerged (Supplementary Fig. 6), with sometimes different SNPs and/or different phenotypes than those associated with CFSRS.
In addition, we examined loci (genes and/or SNPs) associated in recently published GWAS studies of language and reading15,16,17,18,19,20,21,22 (Supplementary Data 2 and 3); we restricted our examination to the CFSRS data, since the ALSPAC data were included in some of the original studies. In these analyses, we often observed cross-trait replication, with most genes originally associated with dyslexia, and associated with other traits in our sample. These included ZNF385D16, which was associated with all CFSRS traits at p < 0.005, CDH1321, associated with all CFSRS traits at p < 0.005, GRIN2B17, associated with spelling (TWS), expressive vocabulary (EOWPVT), and phonological awareness (Elision) at p < 0.0005 and all CFSRS traits at p < 0.05, NKAIN17, associated with receptive language (CELF-R, at 9.7 × 10−5 (rs16928927 p = 1 × 10−4) and reading comprehension (WIAT-RC, p = 4 × 10−4), and MACROD219 associated with all CFSRS traits at p < 0.005).
Polygenic risk scores are associated with increasing clinical severity
In Fig. 3, we illustrate polygenic risk scores (PRS) for six endophenotypes representing the major domains that we analyzed (receptive language, expressive vocabulary, phonological awareness, phonological memory, spelling, and reading decoding), by quintile, across the clinical subgroups to illustrate the connection between clinical diagnosis and genetic underpinnings of these traits (all endophenotypes are illustrated in Supplementary Fig. 7). Generally, we found that polygenic load, indicated by increasing risk scores, was associated with clinical severity (p < 1 × 10−8 by ANOVA), with typical children having the lowest scores, followed by children with SSD-only, and children with SSD + LI and CAS having the greatest scores. The exception to this trend is receptive language, where the genetic load is greatest for children with LI, for whom receptive language is a focal deficit. Thus, in general, an increase in PRS scores is associated with greater clinical severity.
We constructed polygenic risk scores for 587 individuals who were both genotyped and had clinical subgroup information available. Polygenic risk scores are displayed by quantile across the clinical subgroups for six endophenotypes representing the major domains (a Receptive language; b Expressive vocabulary; c Phonological awareness; d Phonological memory; e Spelling; f Reading decoding).
Discussion
Communication disorders are genetically complex, manifested by a variety of deficiencies in articulation, vocabulary, receptive and expressive language, phonological awareness, reading decoding and comprehension, and spelling. This study ascertained children through an earlier-presenting clinical disorder and examined several key communication measures, and is thus one of the first studies of its kind. This study is also novel in that it is the first GWAS to include a measure of phonological awareness, as well as a motor speech measure. By analyzing several endophenotypes together, we can draw conclusions about the common genetic basis across these seemingly dissimilar skills. Here, we have identified five new candidate regions, some containing multiple genes, that have connections to neurological function and regulation of neurological pathways. We also found that increased polygenic load is associated with more severe communication disorders. Finally, by examining genetic correlations among these traits, we conclude that different domains of communication have some common genetic influences. All of these aspects together add new clarity regarding the genetic underpinnings of speech and language skills.
First, the novel candidate genes that we have identified all have roles in neurological function as evidenced by expression levels of those genes in brain and/or neural tissue, and associations with other communication and/or psychiatric phenotypes. Colocalization analysis provided the strongest evidence for two loci, MON1B/SYCE1L and SETD3, showing that our association effects localized with gene expression in brain and skeletal tissue. This commonality between communication traits and brain and neural pathways was also demonstrated by a mouse study of vocalization30, and pleiotropy between the brain, learning, and psychiatric phenotypes was recently demonstrated by a large GWAS of brain phenotypes31. The existence of enhancers, promoters, and methylation effects in the associated regions further emphasizes the importance of regulatory effects on these traits. Deletions spanning SETD3 and CCNK have been associated with syndromic neurodevelopmental disorders32 and variants in SETX, within this same family of genes, have been associated with CAS33. In addition, CCNK is in the FOXP2 pathway in brain tissue34,35,36. NFKBIA is involved in the regulation of the NF-κB pathway, which is involved a number of brain-related processes including neurogenesis, neuritogenesis, synaptic plasticity, learning, and memory37. PPP2R3C has been associated with schizophrenia38. IFI6 expression has been associated with autism39 and overexpression of IFI6 in the brain is present in chronic neurodegeneration40. Finally, DACT1 may be involved in excitatory synapse organization and dendrite formation during neuronal differentiation41 and is mainly expressed within the first two trimesters of pregnancy, just before the first evidence of speech processing is observed in preterm neonates42. DACT1 was associated with several endophenotypes in our sample. Interestingly, SETD3, NFKBIA, and IFI6 are all also tied to the immune system, and a recent study identified an excess of T cells in the brains of individuals with autism43.
Second, understanding the genetic architecture across these endophenotypes is essential for understanding how loci are associated with different measures in different study cohorts or across the developmental trajectory. Strong genetic correlations are observed between spelling, reading comprehension and decoding, expressive and receptive language, vocabulary, and phonological awareness. The strongest replications were for a variety of measures collected in CFSRS with ALSPAC from older youth. Consistent with these findings, we previously demonstrated that spelling at later ages has a higher estimated heritability than spelling at school-age12. Measures administered in older youth may also be more sensitive to variations in clinical manifestation of SSD. Examination of the ALSPAC measures suggests that many of those administered at younger ages may have tapped different domains than intended, or may have been less sensitive to later emerging reading and spelling skills. Methods of cohort ascertainment may also be important in comparing our findings to those of other studies. Our families were ascertained through a child with SSD whereas other studies ascertained subjects through LI or dyslexia. These different ascertainment schemes affect both the available measures, as well as the distribution of scores and power to detect association. Since dyslexia emerges later than SSD, longitudinal studies that ascertain through a proband with SSD will be able to capture variants associated with SSD, LI, and dyslexia, as there is high comorbidity. In addition to the plethora of studies ascertaining children at a variety of ages, which has an impact on the heritability of traits7, these studies use a wide variety of measures, even for the same endophenotype. Moreover, these studies have been conducted in populations that speak different languages of varying orthographic transparency, which makes them difficult to compare. As noted by Carrion-Castillo et al.15, most of the novel loci identified through GWAS have been unique to each study, and these aforementioned issues may explain the lack of replication. Thus, examination of the genetic correlation matrix is essential for the interpretation of results across studies, as it is nearly impossible to analyze the same exact traits, as we have demonstrated with our replication study cohort (ALSPAC).
Third, we replicated candidate genes that had been previously primarily associated with reading and/or LI: CNTNAP2, ATP2C2, and CYP19A1. These analyses extend previous findings to show that these genes are associated with articulation (CNTNAP2) and phonological awareness (ATP2C2 and CYP19A1). This further illustrates the pleiotropic nature of these genes. While we did not observe an association with SNPs within the coding regions of ROBO1 and ROBO2, we did observe significant associations with SNPs between these two genes, which may have regulatory influences on ROBO1/ROBO2. We also replicated (p < 5 × 10−3) loci identified in recent GWAS of reading and/or language traits. Similar to another association study between FOXP2 variants and language44, we did not observe a statistically significant association between FOXP2 and measures in CFSRS, though there was a replication of some traits at a less stringent (p < 0.01) level44.
Finally, our analysis of PRSs shows strong associations between these risk scores and clinical outcomes of increasing severity. Because of the strong significance of these findings, this suggests that the genetic architecture of communication disorders are maybe largely polygenic, which may additionally explain the lack of replication and/or genome-wide significance. While other studies have examined PRSs associated with language17,45, ours is the first to examine the polygenic risk associated with other communication endophenotypes. It is noteworthy that our associated SNPs fell outside of gene coding regions but resided in regulatory regions, even having potential regulatory effects themselves as further evidenced by colocalization analysis. This further illustrates the genetic complexity of communication disorders; perhaps the search for single gene dysfunction is misplaced, and rather regulatory functions are more relevant.
This study has several limitations. The sample size of the CFSRS cohort was modest, potentially reducing power. There was no clear correspondence between measures obtained in ALSPAC with those in CFSRS, necessitating consideration of cross-trait replication. We restricted analyses in both cohorts to individuals of European descent because of the low sample size in other ethnic groups, reducing generalizability.
In summary, this first GWAS of communication measures ascertained through families with SSD identified five new candidate genes, all with potential relevance in central nervous system function. Polygenic risk is strongly associated with more severe speech and language outcomes. Careful consideration of genetic correlation among domains of verbal and written language shows that these loci have general effects on communication, not specific to any single domain, suggesting a common genetic architecture. Further research is needed to more closely examine the impact of regulatory variants on these outcomes.
Methods
Subject ascertainment—CFSRS
From the CFSRS46,47,48,49,50,51, we examined 435 individuals from 148 families who had both DNA and endophenotype data available (Table 1). As previously described, families were ascertained through a proband with SSD identified from caseloads of speech-language pathologists in the Greater Cleveland area and referred to the study. All participants met inclusion criteria based on information provided by a parent in an interview or via questionnaire including normal hearing acuity; fewer than six episodes of otitis media prior to age 3; monolingual English speaker; absence of a history of neurological disorders other than childhood apraxia of speech (CAS), such as cerebral palsy or autism spectrum disorder; and a diagnosis of an SSD or suspected CAS by a local speech-language pathologist or neurologist. Diagnosis of CAS, one severe type of SSD, was confirmed by an experienced licensed speech-language pathologist upon enrollment into the study. Socioeconomic status was determined at the initial assessment based on parent education levels and occupations using the Hollingshead Four Factor Index of Social Class52. This study was approved by the Institutional Review Board of Case Medical Center and University Hospitals and all parents provided informed consent and children older than 5 years provided assent.
Communication measures in CFSRS
We studied many endophenotypes covering domains that are common to speech, language, and reading, We examined diadochokinetic rates using the Robbins and Klee Oral Speech Motor Control Protocol53 or Fletcher Time-by-Count Test of Diadochokinetic Syllable Rate54. The merged variable is referred to as DDK. Expressive vocabulary was assessed with the Expressive One Word Picture Vocabulary Test-Revised (EOWPVT55) and receptive vocabulary with the Peabody Picture Vocabulary Test—Third Edition (PPVT56), and phonological memory with the Nonsense Word Repetition (NSW57), Multisyllabic Word Repetition (MSW57), and Rapid Color Naming58 task. In addition to examining the total number of words correct for the MSW and NSW, we also examined the percent phonemes correct for both of these tasks (NSW-PPC and MSW-PPC, respectively). Phonological awareness was assessed using the Elision subtest of the Comprehensive Test of Phonological Processing—Second Edition59, which measures the ability to remove phonological segments from spoken words to form other words. Reading was assessed using the Woodcock Reading Mastery Test-Revised, Word Attack subtest (WRMT-AT) (reading of nonsense words) and Word Identification Subtest (WRMT-ID) (reading of real words), the Reading Comprehension subtest (WIAT-RC), and Listening Comprehension subtest (WIAT-LC) of the Wechsler Individual Achievement Test60. Spelling was assessed on the Test of Written Spelling-3 (TWS) using the total score61. The expressive and receptive language was assessed using the Test of Language Development (TOLD62) and Clinical Evaluation of Language Fundamentals-Revised or Clinical Evaluation of Language Fundamentals-Preschool according to age (CELF63) referred to as the CELF-E (expressive) and CELF-R (receptive), respectively. Additional details about these measures are provided in the Supplementary Note. For each of our tests, we selected the first available assessment for each individual (Supplementary Table 1).
For the following tests—NSW, NSW PPC, MSW, and MSW PPC—we did not have population normed data, therefore, we converted all scores to age-adjusted z-scores using CFSRS controls. Here, controls were defined as individuals without SSD, LI or CAS. To age-adjust we chose the first available observation for each of the four tests for every control within the CFSRS to determine the effect of age. The age-adjusted score is simply the standardized residual of the score with the effect of age and age-squared regressed out (where the age effect is determined by controls and subsequent adjustment is applied to all participants)48,64. Age and age-squared are both used to determine the effect of age, as there is a nonlinear relationship between age and each of the above four tests. If applicable, test scores were transformed to an approximately normal distribution using the Box–Cox power transformation39. Because measures were already age-normed or age-adjusted, age was not included additionally as a covariate in GWAS or other analytical models.
GWAS analysis
DNA was extracted from buffy coats or saliva samples as previously described6. All genotyping was performed using the Illumina Omni 2.5 platform. Standard QC procedures were applied, including filtering based on call rate, Hardy–Weinberg equilibrium (HWE), chromosome (autosomes only), minor allele frequency (MAF), and Mendelian errors. Principal components analysis (PCA) was conducted using markers that attained MAF ≥ 0.01, sample and variant call rate ≥ 0.98 and p ≥ 0.0001 from an exact test of HWE while omitting genomic regions with long-range linkage disequilibrium (LD)65. Genotyped data were later imputed to Phase 3, cosmopolitan reference option, of the 1000 Genomes Project panel using the University of Michigan Imputation server66 which implements minimac367. Following imputation, all markers with imputation quality score R2 < 0.6 and MAF < 0.05 in our population were removed. Samples were processed and typed for the Illumina Methylation450 chip by the CWRU School of Medicine Genomics Core.
Principal components (PC) obtained from PCA and the genetic relationship matrix (GRM) were generated using genotyped markers that met QC criteria. We used PC-AiR and PC-Relate from the Bioconductor package GENESIS version 2.6.168 to generate our PCs and GRM, respectively. PC-AiR accounts for sample relatedness to provide ancestry inference that is not confounded by family structure, while PC-Relate uses the ancestry representative PCs from PC-AiR to provide relatedness estimates due only to the recent family (pedigree) structure.
To examine cross-trait correlation, we used GCTA version 1.24.469 to run a bivariate REML analysis for each pair of tests and tested for genetic correlations equal to 0. GCTA’s bivariate REML analysis estimates the genetic variance of each test and the genetic covariance between the two tests that can be captured by all SNPs70. Here we included all SNPs with MAF ≥ 0.01. The genetic variance/covariance calculated was adjusted for sex and the first two PCs.
We used RVTests, version 2.071 to conduct our GWAS for each of the 16 communication phenotypes, assuming an additive effect of alleles and restricting to all common SNPs with MAF > 0.05. Phenotypes were transformed using a Box-Cox transformation (MASS, R) when applicable (Supplementary Table 2). We specifically relied on RVTest’s Grammar-gamma test72, which performs a linear mixed model association test while allowing for genotype dosages and accounting for family structure using the GRM. Because each of our tests was age-normed we included only sex and the first two PCs as covariates in our regression models.
PRS analysis
In addition, we generated endophenotype-based PRS in the European subset of the CFSRS where genotype data, as well as clinical group data (no disorder, SSD only, language impairment (LI) only, SSD + LI, CAS) were available. This analysis was done to elucidate the connection between the genetic architecture of these endophenotypes and standard clinical diagnosis seen in clinics. Risk scores were derived from association statistics from our CFSRS GWASs and were constructed using PLINK 1.973 (clump and score functions). Regions were considered if at least one variant in the region met the threshold for inclusion as a risk variant (p < 0.001). Clumping of variants was done in selected regions around the variant showing the strongest association in the region, removing other variants in linkage disequilibrium (r2 > 0.5). We used a linear mixed model to model the relationship between PRS and clinical group, controlling for sex and familial relationship (based on family ID). Nested model comparison (the full model with the clinical group included versus the reduced model with clinical group removed) using the chi-squared test was implemented to determine if the clinical group explained a significant amount of variability in polygenic risk. These PRSs were used to examine the hypothesis that an increase in PRS score would associate with more complex clinical phenotypes when comparing SSD only versus SSD + LI and CAS.
Statistical analysis of methylome-wide data
Quality control and normalization of raw methylation data (as Illumina.idat files) were carried out using the Bioconductor package RnBeads version 2.3.3 for R74. We removed methylation probes in non-CpG contexts, with nearby SNPs, on the X and Y chromosomes, and probes with low variability (SD < 0.005), leaving a total of 470,870 CpG markers with detection p value < 0.05. We normalized signal intensity by means of the BMIQ algorithm75, which adjusts for differences between Infinium I and II loci, and adjusted background by the methylumi NOOB procedure, as implemented in RnBeads. Our final data set was scaled to proportion of methylated DNA strand (β) values. Duplicate pairs were verified through concordance of genotypes for 65 SNPs on the Methylation450 chip. The final data set typed for the Methylation450 panel comprised 713 unique individuals, plus 60 duplicate samples.
The source of DNA for the MWAS came from saliva samples. Because our sample included salivary DNA samples, we were unable to adjust for cell-type composition using a blood-sample-based reference. Instead, we conducted principal components analysis (PCA) on genomewide methylation as follows: We selected 287,720 CpG sites with SD ≥ 0.02 across the entire sample and normalized the beta values for each site to mean = 0, SD = 1, creating an m × n matrix X, where m is the number of markers and n the number of samples. The eigenvectors from the matrix X′X/(m − 1), an n × n matrix, were obtained using the eigen() function in R, to be used as PC covariates in methylome-wide association studies (MWAS). We regressed our SSD outcomes on each of the first 20 PCs, and included significantly associated PCs in MWAS. Phenotypes were adjusted for between one and four PCs.
We tested for association between CpG beta values and endophenotypes using the linear mixed model approach of GRAMMAR-Gamma72 as implemented in RVtests71. Because our phenotypes were age-normed, we did not adjust for age, but rather for sex and one to four PCs.
We conducted a targeted cis-methylation QTL analysis over 521 CpG sites within 50 kilobasepairs (kb) of 162 candidate SNPs (Supplementary Data 1), using Matrix eQTL version 2.276 to find the effect of genotype on the extent of methylation in a sample of 597 individuals with both epigenetic and imputed genotype data. All pairs of SNPs and CpG sites within 100 kb were considered to be in cis. Methylation was expressed as M values, where M = log(β/(1 − β)), which extends the range of possible values to (−∞,∞), making the values suitable as an outcome for linear regression.
Replication dataset—ALSPAC
To replicate our GWAS findings, we obtained data from the Avon Longitudinal Study of Parents and Children (ALSPAC). The ALSPAC study was a prospective population-based birth cohort of babies born from >14,000 pregnancies between April 1991–December 1992, who were followed prospectively with a wide battery of developmental tests, parental questionnaires, child-completed questionnaires, and health outcomes77,78,79. Pregnant women residents in Avon, the UK with expected dates of delivery from 1st April 1991 to 31st December 1992 were invited to take part in the study. The initial number of pregnancies enrolled is 14,541 (for these at least one questionnaire has been returned or a “Children in Focus” clinic had been attended by 19/07/99). Of these initial pregnancies, there was a total of 14,676 fetuses, resulting in 14,062 live births and 13,988 children who were alive at 1 year of age. The study website contains details of all the data that is available through a fully searchable data dictionary (http://www.bris.ac.uk/alspac/researchers/data-access/data-dictionary). Blood samples were also collected for biomarker and genetic analyses.
Ethical approval for the study was obtained from the ALSPAC Ethics and Law Committee and Institutional Review Board of Case Medical Center and University Hospitals. Because this was a birth cohort, all children were included, regardless of diagnosis. We obtained both parental report data on speech development in the children, and also communication measures similar to those that we analyzed (see Communication Measures above and Supplementary Table 3). As this was a longitudinal study, different measures were given at different ages, and when the same domain was tested at two different ages, the identical measure was not used. At some ages, only random subsets were selected, so the sample size available from each age is not the same. In Supplementary Table 3, we list the measures given in the CFSRS battery along with the most similar measure given in ALSPAC. Because all the children were the same age when specific assessments were given, no age adjustment was needed. There were no equivalent measures for RAN and Elision.
Genotype QC was performed previously by ALSPAC16. We restricted our ALSPAC sample to unrelated individuals by randomly removing one from a pair of twins, when applicable. PCs were generated using Hail 0.1 software, to accommodate the format of files obtained from ALSPAC, using a standard PCA approach80. In generating the PCs we first removed long-range LD regions and restricted to variants with a MAF > 0.01, an imputation quality score of >0.95, and variants not in LD (r2 < 0.2; following the same process as with PLINK’s –indep-pairwise default procedure). Genetic association testing was performed using linear regression in Hail 0.1 when outcome measures were continuous and using logistic regression in Hail 0.1 when outcome measures were binary. We restricted our analyses to variants with a MAF > 0.01 and an imputation quality score of >0.6; we used a lower MAF threshold because we hypothesized that causal variants might be rarer in a population-based cohort compared to a cohort that was ascertained through a trait of interest. Covariates adjusted for included sex and the first two PCs. Age was not a consideration as ALSPAC is a longitudinal birth cohort study and age differences were negligible for any given measure.
Functional annotation and results integration
In this analysis, we considered CFSRS the discovery sample, since families were ascertained through a child with SSD, and used ALSPAC as the replication sample. We identified associated loci with SNPs significant at p < 10−5 in CFSRS and p < 0.05 in ALSPAC, with effects in the same direction.
Because the majority of our findings are intergenic and/or fall in noncoding regions, we relied on annotation tools FUMA version 1.35d and HaploReg to characterize which genes our variants might affect, as well as variants’ functionality. We utilized FUMA81 for mapping genes to our variants based on genomic proximity, eQTL evidence, and chromatin interactions evidence. Default settings in FUMA were used, with the exception of tissue specificity. We hypothesized that gene expression and regulation would be most relevant in the brain and neural tissues, as well as muscles related to speech. In FUMA, we focused on eQTL and chromatin interaction evidence in our target tissues (brain and muscle). Additional details are found in the Supplement. HaploReg v.4.1 was used to examine the chromatin state evidence predicting whether the variant fell in a promoter or enhancer region. Using HaploReg v4.1 we examined histone marks indicating enhancer/promoter for brain tissues, neural tissues (including neuronal progenitor cells) and skeletal muscle tissue.
In order to further prioritize and synthesize our findings, we annotated associated loci as described above, including annotation of associated effects of these loci in the literature, and incorporated supportive findings from our MWAS (Supplementary Data 1). We generated a simple locus priority score as the sum of the number of times a locus included an enhancer and/or promoter, included an eQTL, was previously associated with a communication disorder and/or neuropsychiatric disorder, showed eQTL or chromatin state evidence specific to brain and/or neural tissues, mapped to a gene that was a FOXP2 target in brain tissue34,35,36, and an meQTL in that region (at p < 5 × 10−5) with an associated methylation site (at p < 0.05) with the same phenotype as the associated GWAS loci, as determined using the bioinformatic resources described above.
We applied the EpiXcan pipeline82 to train gene expression predictors in human brain tissue. For genotypes and gene expression, we used psychENCODE data from the dorsolateral prefrontal cortex (DLPFC)83. We restricted our analysis to 924 Caucasian samples. We initially computed eQTL summary statistics using the R package Matrix eQTL version 2.276, followed by estimation of SNP priors through the qtlBHM Bayesian hierarchical model84 using the Roadmap Epigenomics Project chromatin states for DLPFC (‘BRN_DL_PRFRNTL_CRTX’). In total, 363,955 predictors for 18,425 genes were recruited in the EpiXcan psychENCODE model. We then applied the S-PrediXcan method85 using the EpiXcan psychENCODE model as well as the SNP covariance matrix on the GWAS summary statistics. These analyses were based on genome-wide association results from two phenotypes from our GWAS, TWS, and Elision; these traits were chosen because they had the greatest number of unique significantly associated loci. Detailed results are in Supplementary Tables 7 and 8.
Chromatin interaction mapping was performed in FUMA using Hi-C data from PsychENCODE83 (Hi-C based enhancer-promoter interactions), Schmitt et al.86 (Hi-C based (significant loops) of cell line GSE87112, tissues Dorsolateral Prefrontal Cortex, Hippocampus and Neural progenitor cell) and Giusti-Rodriguez et al.87 (Hi-C data (significant loops after Bonferroni correction (Pbon < 0.001)) of adult and fetal cortex). Chromatin interactions were filtered by FDR < 1 × 10−6.
We primarily focused on loci with priority scores >5, and for loci with priority scores equal to 5, we examined loci with compelling evidence in the communication disorders literature and/or our own methylation data. These loci were then examined using colocalization analysis in LocusFocus88, as described below, which facilitates the exploration of a GWAS signal and the degree of colocalization with eQTLs in relevant tissue.
We used LocusFocus version 1.4.988 to explore our GWAS signals in their degree of colocalization with expression quantitative trait loci (eQTL) for genes within ±200 kb of the lead SNP in the relevant GTEx tissues. The aim of this method is to annotate GWAS-derived associations to the most probable gene(s) and tissue(s) that may be driving that signal. This method uses the Simple Sum method to assess the degree of colocalization of any two given datasets. The Simple Sum region used for calculating colocalization of eQTLs and GWAS signals is ±100 kb of the lead SNP (i.e., GWAS signals and eQTLs within 100 kb of the lead SNP for genes within 200 kb of lead SNP). When applied to GTEx, LocusFocus presents the degree of colocalization of genes nearby the GWAS association for all the tissues selected in an interactive heatmap plot. Here we selected 14 tissues, including all brain tissue available for GTEx v7 (brain_spinal_cord_cervical, nucleus_accumbens_basal_ganglia, cerebellar_hemisphere, hippocampus, caudate_basal_ganglia, anterior_cingulate_cortex, cortex, hypothalamus, amygdala, frontal_cortex, substantia_nigra, putamen_basal_ganglia, cerebellum), as well as, skeletal_muscle. We also brought in psychEncode eQTL data83 (FDR < 0.05 and a filter requiring genes to have an expression > 0.1 fragments per KB per million reads (FPKM) in at least 10 samples) in as a secondary dataset to examine colocalization with our GWAS signal and eQTLs within psychEncode data. Here, we pulled eQTLs, within 100 kb of our lead SNP for genes within 200 kb of our lead SNP.
Examination of previously identified candidate genes for communication disorders
In order to examine whether our GWAS replicated previous findings (either from published GWAS in language and reading phenotypes and/or targeted candidate gene studies of these phenotypes), we took a twofold approach. If the original papers provided rs IDs, we looked up our results at those specific SNPs. If the papers did not provide that level of detail, we instead examined all SNPs with MAF > 5% in the gene regions ±5 kb.
Reporting summary
Further information on research design is available in the Nature Research Reporting Summary linked to this article.
Data availability
Data from the Cleveland Family Speech and Reading study are not available for broad genetic data sharing because study subjects did not provide informed consent for such data sharing, over 80% specifically saying that they wanted to be recontacted for additional use of the data. The IRB governing this study has imposed a restriction stating that the consent forms did not adequately cover the issue of deposition of the data into public repositories and that participants needed to be reconsented. In an effort to reconsent them, we have attempted to recontact these participants on numerous occasions, but have only been marginally successful. Summary statistics are not provided because of concerns that subjects can be identified from summary statistics, based on published literature demonstrating this is possible, and because these phenotypes are sufficiently rare and participants were ascertained in a narrow geographic region. Please contact the corresponding author, Sudha Iyengar, ski@case.edu, to request summary statistics. These can be shared on request but will require an IRB application, and submission of names of individuals who will use the data to our IRB.
Code availability
All software versions are identified within the Methods. If there is no version number, then that software package only has one (current) version. There were no custom scripts created for the analyses conducted in this paper. Only one variable was created in this analysis (DDK) and those methods are fully described with the Measures.
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Acknowledgements
We would like to thank the families who have so generously participated in this study for many years. This research was supported by the Genomics Core Facility of the CWRU School of Medicine’s Genetics and Genome Sciences Department. This work made use of the High-Performance Computing Resource in the Core Facility for Advanced Research Computing at Case Western Reserve University. This work was supported by NIH grant R01DC000528 awarded to Dr. Lewis and R01DC012380 awarded to Dr. Iyengar. We are extremely grateful to all the families who took part in the ALSPAC study, the midwives for their help in recruiting them, and the whole ALSPAC team, which includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, and nurses. The UK Medical Research Council and Wellcome (Grant ref: 217065/Z/19/Z) and the University of Bristol provide core support for ALSPAC. This publication is the work of the authors and Dr. Sudha Iyengar will serve as guarantor for the contents of this paper. GWAS data for ALSPAC was generated at the Genotyping Facilities at Wellcome Sanger Institute.
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C.M.S., P.B., B.L. and S.K.I. conceptualized and designed the study, drafted the initial paper, and reviewed and revised the paper. P.B., R.P.I., H.V.-H., B.T., W.Z., M.O., E.R.C. and P.R. conducted the statistical analyses. R.P.I., H.V.-H. and H.G.T. helped conceptualize the study and critically reviewed the manuscript for important intellectual content. G.M., Y.W., L.F., J.T. and B.L. collected the data and revised and reviewed the paper. All authors approved the final manuscript as submitted. Dr. Igo passed away prior to the final submission of this paper. He provided edits and written comments on the penultimate version in May 2020 and passed away unexpectedly in July 2020. He was responsible for the methylation (MWAS) analyses and provided invaluable guidance on the GWAS analyses.
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Benchek, P., Igo, R.P., Voss-Hoynes, H. et al. Association between genes regulating neural pathways for quantitative traits of speech and language disorders. npj Genom. Med. 6, 64 (2021). https://doi.org/10.1038/s41525-021-00225-5
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DOI: https://doi.org/10.1038/s41525-021-00225-5
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