ABSTRACT
Although it is ubiquitous in genomics, the current human reference genome (GRCh38) is incomplete: It is missing large sections of heterochromatic sequence, and as a singular, linear reference genome, it does not represent the full spectrum of human genetic diversity. To characterize gaps in GRCh38 and human genetic diversity, we developed an algorithm for sequence location approximation using nuclear families (ASLAN) to identify the region of origin of reads that do not align to GRCh38. Using unmapped reads and variant calls from whole-genome sequences (WGSs), ASLAN uses a maximum likelihood model to identify the most likely region of the genome that a subsequence belongs to given the distribution of the subsequence in the unmapped reads and phasings of families. Validating ASLAN on synthetic data and on reads from the alternative haplotypes in the decoy genome, ASLAN localizes >90% of 100-bp sequences with >92% accuracy and â¼1 Mb of resolution. We then ran ASLAN on 100-mers from unmapped reads from WGS from more than 700 families, and compared ASLAN localizations to alignment of the 100-mers to the recently released T2T-CHM13 assembly. We found that many unmapped reads in GRCh38 originate from telomeres and centromeres that are gaps in GRCh38. ASLAN localizations are in high concordance with T2T-CHM13 alignments, except in the centromeres of the acrocentric chromosomes. Comparing ASLAN localizations and T2T-CHM13 alignments, we identified sequences missing from T2T-CHM13 or sequences with high divergence from their aligned region in T2T-CHM13, highlighting new hotspots for genetic diversity.
Subject(s)
Genome, Human , Genomics , Humans , Algorithms , Telomere/genetics , Genetic Variation , Sequence Analysis, DNAABSTRACT
Importance: While research has identified racial and ethnic disparities in access to autism services, the size, extent, and specific locations of these access gaps have not yet been characterized on a national scale. Mapping comprehensive national listings of autism health care services together with the prevalence of autistic children of various races and ethnicities and evaluating geographic regions defined by localized commuting patterns may help to identify areas within the US where families who belong to minoritized racial and ethnic groups have disproportionally lower access to services. Objective: To evaluate differences in access to autism health care services among autistic children of various races and ethnicities within precisely defined geographic regions encompassing all serviceable areas within the US. Design, Setting, and Participants: This population-based cross-sectional study was conducted from October 5, 2021, to June 3, 2022, and involved 530â¯965 autistic children in kindergarten through grade 12. Core-based statistical areas (CBSAs; defined as areas containing a city and its surrounding commuter region), the Civil Rights Data Collection (CRDC) data set, and 51â¯071 autism resources (collected from October 1, 2015, to December 18, 2022) geographically distributed into 912 CBSAs were combined and analyzed to understand variation in access to autism health care services among autistic children of different races and ethnicities. Six racial and ethnic categories (American Indian or Alaska Native, Asian, Black or African American, Hispanic or Latino, Native Hawaiian or other Pacific Islander, and White) assigned by the US Department of Education were included in the analysis. Main Outcomes and Measures: A regularized least-squares regression analysis was used to measure differences in nationwide resource allocation between racial and ethnic groups. The number of autism resources allocated per autistic child was estimated based on the child's racial and ethnic group. To evaluate how the CBSA population size may have altered the results, the least-squares regression analysis was run on CBSAs divided into metropolitan (>50 000 inhabitants) and micropolitan (10 000-50 000 inhabitants) groups. A Mann-Whitney U test was used to compare the model estimated ratio of autism resources to autistic children among specific racial and ethnic groups comprising the proportions of autistic children in each CBSA. Results: Among 530 965 autistic children aged 5 to 18 years, 83.9% were male and 16.1% were female; 0.7% of children were American Indian or Alaska Native, 5.9% were Asian, 14.3% were Black or African American, 22.9% were Hispanic or Latino, 0.2% were Native Hawaiian or other Pacific Islander, 51.7% were White, and 4.2% were of 2 or more races and/or ethnicities. At a national scale, American Indian or Alaska Native autistic children (ß = 0; 95% CI, 0-0; P = .01) and Hispanic autistic children (ß = 0.02; 95% CI, 0-0.06; P = .02) had significant disparities in access to autism resources in comparison with White autistic children. When evaluating the proportion of autistic children in each racial and ethnic group, areas in which Black autistic children (>50% of the population: ß = 0.05; <50% of the population: ß = 0.07; P = .002) or Hispanic autistic children (>50% of the population: ß = 0.04; <50% of the population: ß = 0.07; P < .001) comprised greater than 50% of the total population of autistic children had significantly fewer resources than areas in which Black or Hispanic autistic children comprised less than 50% of the total population. Comparing metropolitan vs micropolitan CBSAs revealed that in micropolitan CBSAs, Black autistic children (ß = 0; 95% CI, 0-0; P < .001) and Hispanic autistic children (ß = 0; 95% CI, 0-0.02; P < .001) had the greatest disparities in access to autism resources compared with White autistic children. In metropolitan CBSAs, American Indian or Alaska Native autistic children (ß = 0; 95% CI, 0-0; P = .005) and Hispanic autistic children (ß = 0.01; 95% CI, 0-0.06; P = .02) had the greatest disparities compared with White autistic children. Conclusions and Relevance: In this study, autistic children from several minoritized racial and ethnic groups, including Black and Hispanic autistic children, had access to significantly fewer autism resources than White autistic children in the US. This study pinpointed the specific geographic regions with the greatest disparities, where increases in the number and types of treatment options are warranted. These findings suggest that a prioritized response strategy to address these racial and ethnic disparities is needed.
Subject(s)
Autistic Disorder , Child , Humans , Male , Female , Cross-Sectional Studies , Health Services Accessibility , Healthcare Disparities , Racial GroupsABSTRACT
While hundreds of thousands of human whole genome sequences (WGS) have been collected in the effort to better understand genetic determinants of disease, these whole genome sequences have less frequently been used to study another major determinant of human health: the human virome. Using the unmapped reads from WGS of over 1000 families, we present insights into the human blood DNA virome, focusing particularly on human herpesvirus (HHV) 6A, 6B, and 7. In addition to extensively cataloguing the viruses detected in WGS of human whole blood and lymphoblastoid cell lines, we use the family structure of our dataset to show that household drives transmission of several viruses, and identify the Mendelian inheritance patterns characteristic of inherited chromsomally integrated human herpesvirus 6 (iciHHV-6). Consistent with prior studies, we find that 0.6% of our dataset's population has iciHHV, and we locate candidate integration sequences for these cases. We document genetic diversity within exogenous and integrated HHV species and within integration sites of HHV-6. Finally, in the first observation of its kind, we present evidence that suggests widespread de novo HHV-6B integration and HHV-7 integration and reactivation in lymphoblastoid cell lines. These findings show that the unmapped read space of WGS is a promising source of data for virology research.
Subject(s)
Herpesvirus 6, Human , Roseolovirus Infections , Humans , Herpesvirus 6, Human/genetics , Virus Integration , Sequence Analysis , Cell LineABSTRACT
Autism is among the most common neurodevelopmental conditions. Timely diagnosis and access to therapeutic resources are essential for positive prognoses, yet long queues and unevenly dispersed resources leave many untreated. Without granular estimates of autism prevalence by geographic area, it is difficult to identify unmet needs and mechanisms to address them. Mining a dataset of 53M children using meaningful geographic regions, we computed autism prevalence across the country. We then performed comparative analysis against 50,000 resources to identify the type and extent of gaps in access to autism services. We find a steady increase in autism diagnoses from K-5, supporting delayed diagnosis of autism, and consistent under-diagnosis of females. We find a significant inverse relationship between prevalence and availability of resources (p < 0.001). While more work is needed to characterize additional trends including racial and ethnicity-based disparities, the identification of resource gaps can direct and prioritize new innovations.
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The unmapped readspace of whole genome sequencing data tends to be large but is often ignored. We posit that it contains valuable signals of both human infection and contamination. Using unmapped and poorly aligned reads from whole genome sequences (WGS) of over 1000 families and nearly 5000 individuals, we present insights into common viral, bacterial, and computational contamination that plague whole genome sequencing studies. We present several notable results: (1) In addition to known contaminants such as Epstein-Barr virus and phiX, sequences from whole blood and lymphocyte cell lines contain many other contaminants, likely originating from storage, prep, and sequencing pipelines. (2) Sequencing plate and biological sample source of a sample strongly influence contamination profile. And, (3) Y-chromosome fragments not on the human reference genome commonly mismap to bacterial reference genomes. Both experiment-derived and computational contamination is prominent in next-generation sequencing data. Such contamination can compromise results from WGS as well as metagenomics studies, and standard protocols for identifying and removing contamination should be developed to ensure the fidelity of sequencing-based studies.
Subject(s)
Bacteriophages , Epstein-Barr Virus Infections , Computational Biology , Genome, Bacterial , Genome, Human , Genome, Viral , Herpesvirus 4, Human/genetics , High-Throughput Nucleotide Sequencing/methods , Humans , Whole Genome SequencingABSTRACT
Artificial Intelligence (A.I.) solutions are increasingly considered for telemedicine. For these methods to serve children and their families in home settings, it is crucial to ensure the privacy of the child and parent or caregiver. To address this challenge, we explore the potential for global image transformations to provide privacy while preserving the quality of behavioral annotations. Crowd workers have previously been shown to reliably annotate behavioral features in unstructured home videos, allowing machine learning classifiers to detect autism using the annotations as input. We evaluate this method with videos altered via pixelation, dense optical flow, and Gaussian blurring. On a balanced test set of 30 videos of children with autism and 30 neurotypical controls, we find that the visual privacy alterations do not drastically alter any individual behavioral annotation at the item level. The AUROC on the evaluation set was 90.0% ±7.5% for unaltered videos, 85.0% ±9.0% for pixelation, 85.0% ±9.0% for optical flow, and 83.3% ±9.3% for blurring, demonstrating that an aggregation of small changes across behavioral questions can collectively result in increased misdiagnosis rates. We also compare crowd answers against clinicians who provided the same annotations for the same videos as crowd workers, and we find that clinicians have higher sensitivity in their recognition of autism-related symptoms. We also find that there is a linear correlation (r = 0.75, p < 0.0001) between the mean Clinical Global Impression (CGI) score provided by professional clinicians and the corresponding score emitted by a previously validated autism classifier with crowd inputs, indicating that the classifier's output probability is a reliable estimate of the clinical impression of autism. A significant correlation is maintained with privacy alterations, indicating that crowd annotations can approximate clinician-provided autism impression from home videos in a privacy-preserved manner.
ABSTRACT
BACKGROUND: Automated emotion classification could aid those who struggle to recognize emotions, including children with developmental behavioral conditions such as autism. However, most computer vision emotion recognition models are trained on adult emotion and therefore underperform when applied to child faces. OBJECTIVE: We designed a strategy to gamify the collection and labeling of child emotion-enriched images to boost the performance of automatic child emotion recognition models to a level closer to what will be needed for digital health care approaches. METHODS: We leveraged our prototype therapeutic smartphone game, GuessWhat, which was designed in large part for children with developmental and behavioral conditions, to gamify the secure collection of video data of children expressing a variety of emotions prompted by the game. Independently, we created a secure web interface to gamify the human labeling effort, called HollywoodSquares, tailored for use by any qualified labeler. We gathered and labeled 2155 videos, 39,968 emotion frames, and 106,001 labels on all images. With this drastically expanded pediatric emotion-centric database (>30 times larger than existing public pediatric emotion data sets), we trained a convolutional neural network (CNN) computer vision classifier of happy, sad, surprised, fearful, angry, disgust, and neutral expressions evoked by children. RESULTS: The classifier achieved a 66.9% balanced accuracy and 67.4% F1-score on the entirety of the Child Affective Facial Expression (CAFE) as well as a 79.1% balanced accuracy and 78% F1-score on CAFE Subset A, a subset containing at least 60% human agreement on emotions labels. This performance is at least 10% higher than all previously developed classifiers evaluated against CAFE, the best of which reached a 56% balanced accuracy even when combining "anger" and "disgust" into a single class. CONCLUSIONS: This work validates that mobile games designed for pediatric therapies can generate high volumes of domain-relevant data sets to train state-of-the-art classifiers to perform tasks helpful to precision health efforts.
ABSTRACT
BACKGROUND: Autism spectrum disorder (ASD) is a widespread neurodevelopmental condition with a range of potential causes and symptoms. Standard diagnostic mechanisms for ASD, which involve lengthy parent questionnaires and clinical observation, often result in long waiting times for results. Recent advances in computer vision and mobile technology hold potential for speeding up the diagnostic process by enabling computational analysis of behavioral and social impairments from home videos. Such techniques can improve objectivity and contribute quantitatively to the diagnostic process. OBJECTIVE: In this work, we evaluate whether home videos collected from a game-based mobile app can be used to provide diagnostic insights into ASD. To the best of our knowledge, this is the first study attempting to identify potential social indicators of ASD from mobile phone videos without the use of eye-tracking hardware, manual annotations, and structured scenarios or clinical environments. METHODS: Here, we used a mobile health app to collect over 11 hours of video footage depicting 95 children engaged in gameplay in a natural home environment. We used automated data set annotations to analyze two social indicators that have previously been shown to differ between children with ASD and their neurotypical (NT) peers: (1) gaze fixation patterns, which represent regions of an individual's visual focus and (2) visual scanning methods, which refer to the ways in which individuals scan their surrounding environment. We compared the gaze fixation and visual scanning methods used by children during a 90-second gameplay video to identify statistically significant differences between the 2 cohorts; we then trained a long short-term memory (LSTM) neural network to determine if gaze indicators could be predictive of ASD. RESULTS: Our results show that gaze fixation patterns differ between the 2 cohorts; specifically, we could identify 1 statistically significant region of fixation (P<.001). In addition, we also demonstrate that there are unique visual scanning patterns that exist for individuals with ASD when compared to NT children (P<.001). A deep learning model trained on coarse gaze fixation annotations demonstrates mild predictive power in identifying ASD. CONCLUSIONS: Ultimately, our study demonstrates that heterogeneous video data sets collected from mobile devices hold potential for quantifying visual patterns and providing insights into ASD. We show the importance of automated labeling techniques in generating large-scale data sets while simultaneously preserving the privacy of participants, and we demonstrate that specific social engagement indicators associated with ASD can be identified and characterized using such data.
Subject(s)
Autism Spectrum Disorder , Mobile Applications , Autism Spectrum Disorder/diagnosis , Child , Computers, Handheld , Fixation, Ocular , Humans , Social ParticipationABSTRACT
As the last decade of human genomics research begins to bear the fruit of advancements in precision medicine, it is important to ensure that genomics' improvements in human health are distributed globally and equitably. An important step to ensuring health equity is to improve the human reference genome to capture global diversity by including a wide variety of alternative haplotypes, sequences that are not currently captured on the reference genome.We present a method that localizes 100 basepair (bp) long sequences extracted from short-read sequencing that can ultimately be used to identify what regions of the human genome non-reference sequences belong to.We extract reads that don't align to the reference genome, and compute the population's distribution of 100-mers found within the unmapped reads. We use genetic data from families to identify shared genetic material between siblings and match the distribution of unmapped k-mers to these inheritance patterns to determine the the most likely genomic region of a k-mer. We perform this localization with two highly interpretable methods of artificial intelligence: a computationally tractable Hidden Markov Model coupled to a Maximum Likelihood Estimator. Using a set of alternative haplotypes with known locations on the genome, we show that our algorithm is able to localize 96% of k-mers with over 90% accuracy and less than 1Mb median resolution. As the collection of sequenced human genomes grows larger and more diverse, we hope that this method can be used to improve the human reference genome, a critical step in addressing precision medicine's diversity crisis.
Subject(s)
Artificial Intelligence , Genome, Human , Computational Biology , Genomics , High-Throughput Nucleotide Sequencing , Humans , Sequence Analysis, DNAABSTRACT
BACKGROUND: Sequencing partial 16S rRNA genes is a cost effective method for quantifying the microbial composition of an environment, such as the human gut. However, downstream analysis relies on binning reads into microbial groups by either considering each unique sequence as a different microbe, querying a database to get taxonomic labels from sequences, or clustering similar sequences together. However, these approaches do not fully capture evolutionary relationships between microbes, limiting the ability to identify differentially abundant groups of microbes between a diseased and control cohort. We present sequence-based biomarkers (SBBs), an aggregation method that groups and aggregates microbes using single variants and combinations of variants within their 16S sequences. We compare SBBs against other existing aggregation methods (OTU clustering and Microphenoor DiTaxa features) in several benchmarking tasks: biomarker discovery via permutation test, biomarker discovery via linear discriminant analysis, and phenotype prediction power. We demonstrate the SBBs perform on-par or better than the state-of-the-art methods in biomarker discovery and phenotype prediction. RESULTS: On two independent datasets, SBBs identify differentially abundant groups of microbes with similar or higher statistical significance than existing methods in both a permutation-test-based analysis and using linear discriminant analysis effect size. . By grouping microbes by SBB, we can identify several differentially abundant microbial groups (FDR <.1) between children with autism and neurotypical controls in a set of 115 discordant siblings. Porphyromonadaceae, Ruminococcaceae, and an unnamed species of Blastocystis were significantly enriched in autism, while Veillonellaceae was significantly depleted. Likewise, aggregating microbes by SBB on a dataset of obese and lean twins, we find several significantly differentially abundant microbial groups (FDR<.1). We observed Megasphaera andSutterellaceae highly enriched in obesity, and Phocaeicola significantly depleted. SBBs also perform on bar with or better than existing aggregation methods as features in a phenotype prediction model, predicting the autism phenotype with an ROC-AUC score of .64 and the obesity phenotype with an ROC-AUC score of .84. CONCLUSIONS: SBBs provide a powerful method for aggregating microbes to perform differential abundance analysis as well as phenotype prediction. Our source code can be freely downloaded from http://github.com/briannachrisman/16s_biomarkers .
Subject(s)
Gastrointestinal Microbiome , Biomarkers , Cluster Analysis , Gastrointestinal Microbiome/genetics , Humans , RNA, Ribosomal, 16S/genetics , SoftwareABSTRACT
BACKGROUND: Machine learning approaches for predicting disease risk from high-dimensional whole genome sequence (WGS) data often result in unstable models that can be difficult to interpret, limiting the identification of putative sets of biomarkers. Here, we design and validate a graph-based methodology based on maximum flow, which leverages the presence of linkage disequilibrium (LD) to identify stable sets of variants associated with complex multigenic disorders. RESULTS: We apply our method to a previously published logistic regression model trained to identify variants in simple repeat sequences associated with autism spectrum disorder (ASD); this L1-regularized model exhibits high predictive accuracy yet demonstrates great variability in the features selected from over 230,000 possible variants. In order to improve model stability, we extract the variants assigned non-zero weights in each of 5 cross-validation folds and then assemble the five sets of features into a flow network subject to LD constraints. The maximum flow formulation allowed us to identify 55 variants, which we show to be more stable than the features identified by the original classifier. CONCLUSION: Our method allows for the creation of machine learning models that can identify predictive variants. Our results help pave the way towards biomarker-based diagnosis methods for complex genetic disorders.
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BACKGROUND: As next-generation sequencing technologies make their way into the clinic, knowledge of their error rates is essential if they are to be used to guide patient care. However, sequencing platforms and variant-calling pipelines are continuously evolving, making it difficult to accurately quantify error rates for the particular combination of assay and software parameters used on each sample. Family data provide a unique opportunity for estimating sequencing error rates since it allows us to observe a fraction of sequencing errors as Mendelian errors in the family, which we can then use to produce genome-wide error estimates for each sample. RESULTS: We introduce a method that uses Mendelian errors in sequencing data to make highly granular per-sample estimates of precision and recall for any set of variant calls, regardless of sequencing platform or calling methodology. We validate the accuracy of our estimates using monozygotic twins, and we use a set of monozygotic quadruplets to show that our predictions closely match the consensus method. We demonstrate our method's versatility by estimating sequencing error rates for whole genome sequencing, whole exome sequencing, and microarray datasets, and we highlight its sensitivity by quantifying performance increases between different versions of the GATK variant-calling pipeline. We then use our method to demonstrate that: 1) Sequencing error rates between samples in the same dataset can vary by over an order of magnitude. 2) Variant calling performance decreases substantially in low-complexity regions of the genome. 3) Variant calling performance in whole exome sequencing data decreases with distance from the nearest target region. 4) Variant calls from lymphoblastoid cell lines can be as accurate as those from whole blood. 5) Whole-genome sequencing can attain microarray-level precision and recall at disease-associated SNV sites. CONCLUSION: Genotype datasets from families are powerful resources that can be used to make fine-grained estimates of sequencing error for any sequencing platform and variant-calling methodology.
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The evolutionary dynamics of SARS-CoV-2 have been carefully monitored since the COVID-19 pandemic began in December 2019. However, analysis has focused primarily on single nucleotide polymorphisms and largely ignored the role of insertions and deletions (indels) as well as recombination in SARS-CoV-2 evolution. Using sequences from the GISAID database, we catalogue over 100 insertions and deletions in the SARS-CoV-2 consensus sequences. We hypothesize that these indels are artifacts of recombination events between SARS-CoV-2 replicates whereby RNA-dependent RNA polymerase (RdRp) re-associates with a homologous template at a different loci ("imperfect homologous recombination"). We provide several independent pieces of evidence that suggest this. (1) The indels from the GISAID consensus sequences are clustered at specific regions of the genome. (2) These regions are also enriched for 5' and 3' breakpoints in the transcription regulatory site (TRS) independent transcriptome, presumably sites of RNA-dependent RNA polymerase (RdRp) template-switching. (3) Within raw reads, these indel hotspots have cases of both high intra-host heterogeneity and intra-host homogeneity, suggesting that these indels are both consequences of de novo recombination events within a host and artifacts of previous recombination. We briefly analyze the indels in the context of RNA secondary structure, noting that indels preferentially occur in "arms" and loop structures of the predicted folded RNA, suggesting that secondary structure may be a mechanism for TRS-independent template-switching in SARS-CoV-2 or other coronaviruses. These insights into the relationship between structural variation and recombination in SARS-CoV-2 can improve our reconstructions of the SARS-CoV-2 evolutionary history as well as our understanding of the process of RdRp template-switching in RNA viruses.
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Background/Introduction: Emotion detection classifiers traditionally predict discrete emotions. However, emotion expressions are often subjective, thus requiring a method to handle compound and ambiguous labels. We explore the feasibility of using crowdsourcing to acquire reliable soft-target labels and evaluate an emotion detection classifier trained with these labels. We hypothesize that training with labels that are representative of the diversity of human interpretation of an image will result in predictions that are similarly representative on a disjoint test set. We also hypothesize that crowdsourcing can generate distributions which mirror those generated in a lab setting. Methods: We center our study on the Child Affective Facial Expression (CAFE) dataset, a gold standard collection of images depicting pediatric facial expressions along with 100 human labels per image. To test the feasibility of crowdsourcing to generate these labels, we used Microworkers to acquire labels for 207 CAFE images. We evaluate both unfiltered workers as well as workers selected through a short crowd filtration process. We then train two versions of a ResNet-152 neural network on soft-target CAFE labels using the original 100 annotations provided with the dataset: (1) a classifier trained with traditional one-hot encoded labels, and (2) a classifier trained with vector labels representing the distribution of CAFE annotator responses. We compare the resulting softmax output distributions of the two classifiers with a 2-sample independent t-test of L1 distances between the classifier's output probability distribution and the distribution of human labels. Results: While agreement with CAFE is weak for unfiltered crowd workers, the filtered crowd agree with the CAFE labels 100% of the time for happy, neutral, sad and "fear + surprise", and 88.8% for "anger + disgust". While the F1-score for a one-hot encoded classifier is much higher (94.33% vs. 78.68%) with respect to the ground truth CAFE labels, the output probability vector of the crowd-trained classifier more closely resembles the distribution of human labels (t=3.2827, p=0.0014). Conclusions: For many applications of affective computing, reporting an emotion probability distribution that accounts for the subjectivity of human interpretation can be more useful than an absolute label. Crowdsourcing, including a sufficient filtering mechanism for selecting reliable crowd workers, is a feasible solution for acquiring soft-target labels.
ABSTRACT
BACKGROUND: Complex human health conditions with etiological heterogeneity like Autism Spectrum Disorder (ASD) often pose a challenge for traditional genome-wide association study approaches in defining a clear genotype to phenotype model. Coalitional game theory (CGT) is an exciting method that can consider the combinatorial effect of groups of variants working in concert to produce a phenotype. CGT has been applied to associate likely-gene-disrupting variants encoded from whole genome sequence data to ASD; however, this previous approach cannot take into account for prior biological knowledge. Here we extend CGT to incorporate a priori knowledge from biological networks through a game theoretic centrality measure based on Shapley value to rank genes by their relevance-the individual gene's synergistic influence in a gene-to-gene interaction network. Game theoretic centrality extends the notion of Shapley value to the evaluation of a gene's contribution to the overall connectivity of its corresponding node in a biological network. RESULTS: We implemented and applied game theoretic centrality to rank genes on whole genomes from 756 multiplex autism families. Top ranking genes with the highest game theoretic centrality in both the weighted and unweighted approaches were enriched for pathways previously associated with autism, including pathways of the immune system. Four of the selected genes HLA-A, HLA-B, HLA-G, and HLA-DRB1-have also been implicated in ASD and further support the link between ASD and the human leukocyte antigen complex. CONCLUSIONS: Game theoretic centrality can prioritize influential, disease-associated genes within biological networks, and assist in the decoding of polygenic associations to complex disorders like autism.
Subject(s)
Algorithms , Game Theory , Gene Regulatory Networks , Genetic Association Studies , Autism Spectrum Disorder/genetics , Genome-Wide Association Study , Humans , Protein Interaction Mapping , Reproducibility of ResultsABSTRACT
We performed a comprehensive assessment of rare inherited variation in autism spectrum disorder (ASD) by analyzing whole-genome sequences of 2,308 individuals from families with multiple affected children. We implicate 69 genes in ASD risk, including 24 passing genome-wide Bonferroni correction and 16 new ASD risk genes, most supported by rare inherited variants, a substantial extension of previous findings. Biological pathways enriched for genes harboring inherited variants represent cytoskeletal organization and ion transport, which are distinct from pathways implicated in previous studies. Nevertheless, the de novo and inherited genes contribute to a common protein-protein interaction network. We also identified structural variants (SVs) affecting non-coding regions, implicating recurrent deletions in the promoters of DLG2 and NR3C2. Loss of nr3c2 function in zebrafish disrupts sleep and social function, overlapping with human ASD-related phenotypes. These data support the utility of studying multiplex families in ASD and are available through the Hartwell Autism Research and Technology portal.
Subject(s)
Autism Spectrum Disorder/genetics , Genetic Predisposition to Disease/genetics , Pedigree , Protein Interaction Maps/genetics , Animals , Child , Databases, Genetic , Disease Models, Animal , Female , Gene Deletion , Guanylate Kinases/genetics , Humans , Inheritance Patterns/genetics , Machine Learning , Male , Nuclear Family , Promoter Regions, Genetic/genetics , Receptors, Mineralocorticoid/genetics , Risk Factors , Tumor Suppressor Proteins/genetics , Whole Genome Sequencing , Zebrafish/geneticsABSTRACT
Studies on autism spectrum disorder (ASD) have amassed substantial evidence for the role of genetics in the disease's phenotypic manifestation. A large number of coding and non-coding variants with low penetrance likely act in a combinatorial manner to explain the variable forms of ASD. However, many of these combined interactions, both additive and epistatic, remain undefined. Coalitional game theory (CGT) is an approach that seeks to identify players (individual genetic variants or genes) who tend to improve the performance-association to a disease phenotype of interest-of any coalition (subset of co-occurring genetic variants) they join. This method has been previously applied to boost biologically informative signal from gene expression data and exome sequencing data but remains to be explored in the context of cooperativity among non-coding genomic regions. We describe our extension of previous work, highlighting non-coding chromosomal regions relevant to ASD using CGT on alteration data of 4595 fully sequenced genomes from 756 multiplex families. Genomes were encoded into binary matrices for three types of non-coding regions previously implicated in ASD and separated into ASD (case) and unaffected (control) samples. A player metric, the Shapley value, enabled determination of individual variant contributions in both sets of cohorts. A total of 30 non-coding positions were found to have significantly elevated player scores and likely represent significant contributors to the genetic coordination underlying ASD. Cross-study analyses revealed that a subset of mutated non-coding regions (all of which are in human accelerated regions (HARs)) and related genes are involved in biological pathways or behavioral outcomes known to be affected in autism, suggesting the importance of single nucleotide polymorphisms (SNPs) within HARs in ASD. These findings support the use of CGT in identifying hidden yet influential non-coding players from large-scale genomic data, to better understand the precise underpinnings of complex neurodevelopmental disorders such as autism.
ABSTRACT
Autism spectrum disorder (ASD) is a heritable neurodevelopmental disorder affecting 1 in 59 children. While noncoding genetic variation has been shown to play a major role in many complex disorders, the contribution of these regions to ASD susceptibility remains unclear. Genetic analyses of ASD typically use unaffected family members as controls; however, we hypothesize that this method does not effectively elevate variant signal in the noncoding region due to family members having subclinical phenotypes arising from common genetic mechanisms. In this study, we use a separate, unrelated outgroup of individuals with progressive supranuclear palsy (PSP), a neurodegenerative condition with no known etiological overlap with ASD, as a control population. We use whole genome sequencing data from a large cohort of 2182 children with ASD and 379 controls with PSP, sequenced at the same facility with the same machines and variant calling pipeline, in order to investigate the role of noncoding variation in the ASD phenotype. We analyze seven major types of noncoding variants: microRNAs, human accelerated regions, hypersensitive sites, transcription factor binding sites, DNA repeat sequences, simple repeat sequences, and CpG islands. After identifying and removing batch effects between the two groups, we trained an â1-regularized logistic regression classifier to predict ASD status from each set of variants. The classifier trained on simple repeat sequences performed well on a held-out test set (AUC-ROC = 0.960); this classifier was also able to differentiate ASD cases from controls when applied to a completely independent dataset (AUC-ROC = 0.960). This suggests that variation in simple repeat regions is predictive of the ASD phenotype and may contribute to ASD risk. Our results show the importance of the noncoding region and the utility of independent control groups in effectively linking genetic variation to disease phenotype for complex disorders.
Subject(s)
Autism Spectrum Disorder/genetics , DNA/genetics , Genetic Variation , Machine Learning , Case-Control Studies , Child , Cohort Studies , Computational Biology , CpG Islands , Female , Gene Regulatory Networks , Genetic Association Studies , Genetic Predisposition to Disease , Humans , Logistic Models , Male , MicroRNAs/genetics , Microsatellite Repeats , Phenotype , Polymorphism, Single Nucleotide , RNA, Untranslated/genetics , Supranuclear Palsy, Progressive/genetics , Whole Genome SequencingABSTRACT
Despite mounting evidence for the strong role of genetics in the phenotypic manifestation of Autism Spectrum Disorder (ASD), the specific genes responsible for the variable forms of ASD remain undefined. ASD may be best explained by a combinatorial genetic model with varying epistatic interactions across many small effect mutations. Coalitional or cooperative game theory is a technique that studies the combined effects of groups of players, known as coalitions, seeking to identify players who tend to improve the performance--the relationship to a specific disease phenotype--of any coalition they join. This method has been previously shown to boost biologically informative signal in gene expression data but to-date has not been applied to the search for cooperative mutations among putative ASD genes. We describe our approach to highlight genes relevant to ASD using coalitional game theory on alteration data of 1,965 fully sequenced genomes from 756 multiplex families. Alterations were encoded into binary matrices for ASD (case) and unaffected (control) samples, indicating likely gene-disrupting, inherited mutations in altered genes. To determine individual gene contributions given an ASD phenotype, a "player" metric, referred to as the Shapley value, was calculated for each gene in the case and control cohorts. Sixty seven genes were found to have significantly elevated player scores and likely represent significant contributors to the genetic coordination underlying ASD. Using network and cross-study analysis, we found that these genes are involved in biological pathways known to be affected in the autism cases and that a subset directly interact with several genes known to have strong associations to autism. These findings suggest that coalitional game theory can be applied to large-scale genomic data to identify hidden yet influential players in complex polygenic disorders such as autism.