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SummaryAfrican populations are the most diverse in the world yet are sorely underrepresented in medical genetics research. Here, we examine the structure of African populations using genetic and comprehensive multigenerational ethnolinguistic data from the Neuropsychiatric Genetics of African Populations-Psychosis study (NeuroGAP-Psychosis) consisting of 900 individuals from Ethiopia, Kenya, South Africa, and Uganda. We find that self-reported language classifications meaningfully tag underlying genetic variation that would be missed with consideration of geography alone, highlighting the importance of culture in shaping genetic diversity. Leveraging our uniquely rich multi-generational ethnolinguistic metadata, we track language transmission through the pedigree, observing the disappearance of several languages in our cohort as well as notable shifts in frequency over three generations. We find suggestive evidence for the rate of language transmission in matrilineal groups having been higher than that for patrilineal ones. We highlight both the diversity of variation within the African continent, as well as how within-Africa variation can be informative for broader variant interpretation; many variants appearing rare elsewhere are common in parts of Africa. The work presented here improves the understanding of the spectrum of genetic variation in African populations and highlights the enormous and complex genetic and ethnolinguistic diversity within Africa.

Polygenic risk scores (PRSs) have been widely explored in precision medicine. However, few studies have thoroughly investigated their best practices in global populations across different diseases. We here utilized data from Global Biobank Meta-analysis Initiative (GBMI) to explore methodological considerations and PRS performance in 9 different biobanks for 14 disease endpoints. Specifically, we constructed PRSs using pruning and thresholding (P + T) and PRS-continuous shrinkage (CS). For both methods, using a European-based linkage disequilibrium (LD) reference panel resulted in comparable or higher prediction accuracy compared with several other non-European-based panels. PRS-CS overall outperformed the classic P + T method, especially for endpoints with higher SNP-based heritability. Notably, prediction accuracy is heterogeneous across endpoints, biobanks, and ancestries, especially for asthma, which has known variation in disease prevalence across populations. Overall, we provide lessons for PRS construction, evaluation, and interpretation using GBMI resources and highlight the importance of best practices for PRS in the biobank-scale genomics era.

Funding Information: The work of the contributing biobanks was supported by numerous grants from governmental and charitable bodies. Biobank-specific acknowledgments and more detailed acknowledgments are included in Data S2. Initiative management, S.B.C. J.C. N.J.C. M.J.D. E.E.K. A.R.M. B.M.N. Y.O. A.V.P. D.A.v.H. R.G.W. C.J.W. W.Z. and S.Z.; individual biobank analysis, A.B. Y.B. B.M.B. C.D.B. S.C. T.-T.C. K.C. S.M.D. M.D. G.H.d.B. Y.D. N.J.D. M.-J.F. Y.-C.A.F. S.F. V.L.F. L.G.F. E.R.G. T.R.G. D.H.G. C.R.G. G.G.-A. S.E.G. L.A.G. C.H. J.B.H. W.E.H. H.H. K.H. N.I. A.I. R.J. M. Kurki, J.K. N.K. E.E.K. J.T.K. M. Kanai, T.L. K.L. M.H.L. S.L. K.L. Y.-F.L. V.L.F. R.J.F.L. E.A.L.-M. A.R.-M. S.M.-G. R.M. R.E.M. H.C.M. A.R.M. Y.M. H.M. S.E.M. I.Y.M. B.M. S.M. K.N. S.N. M.A.N.-A. K.N. Y.O. P.P. A.L.-P. A.P. B.P. S.P. M.H.P. D.J.R. N.R. M.D.R. A.R. C.S. S.S. S.S.S. J.A.S. P.S. I.S. T.T. R.T. K.T. J.U. D.A.v.H. B.V. M.V. Y.V. J.M.V. R.G.W. Y.W. S.J.W. B.N.W. K.-H.H.W. M.Z. X.Z. and S.Z.; individual biobank management, N.A. A.A.T. K.M.A.-D. P.A. K.C.B. M. Boehnke, M. Boezen, C.D.B. A.C. Z.C. C.-Y.C. J.C. N.J.C. S.M.D. S.F. Y.-C.A.F. S.F. E.F. T.G. C.R.G. C.J.G. Y.G. H.H. K.A.H. K.H. S.I.I. N.M.J. N.K. E.E.K. J.T.K. C.L. M.H.L. M.T.M.L. L.L. K.L. Y.-F.L. R.J.F.L. J.L. S.M. Y.M. K.M. I.Y.M. Y.O. C.M.O. A.V.P. B.P. D.J.P. D.J.R. M.D.R. S.S. J.W.S. H.S. K.S. T.T. U.T. R.C.T. D.A.v.H. M.V. R.G.W. D.C.W. C.W. J.W. M.Z. X.Z. and S.Z.; study design and interpretation of results, A.B. M. Boehnke, M. Boezen, B.M.B. T.-T.C. C.-Y.C. M.J.D. G.D.S. N.J.D. S.F. M.-J.F. H.K.F. E.R.G. A.G. T.G. J.B.H. J.H. K.H. R.J. M.K. E.E.K. T.K. C.M.L. V.L.F. E.A.L.-M. A.R.M. S.N. B.M.N. C.M.O. J.J.P. B.P. N.R. H.R. J.A.S. I.S. K.T. D.A.v.H. R.G.W. Y.W. D.C.W. S.J.W. C.J.W. B.N.W. J.W. K.-H.H.W. M.Z. H.Z. J.Z. W.Z. X.Z. and S.Z.; drafted and edited the paper, A.B. M. Boehnke, M. Boezen, M.J.D. G.H.d.B. N.J.D. T.R.G. J.B.H. N.I. N.M.J. M.K. V.L.F. S.M. A.R.M. H.M. S.N. B.M.N. C.M.O. B.P. H.R. C.S. J.A.S. J.W.S. K.T. Y.W. D.C.W. C.J.W. K.-H.H.W. H.Z. J.Z. W.Z. and S.Z.; primary meta-analysis and quality control, M.J.D. H.K.F. M. Kanai, J.K. J.T.K. M. Kurki, M.M. B.M.N. C.J.W. K.-H.H.W. and W.Z.; drug discovery: S.N. T.K. K.-H.H.W. W.Z. and Y.O.; fine mapping, M. Kanai, W.Z. M.J.D. and H.K.F.; polygenic risk score, Y.W. S.N. E.A.L.-M. S.K. K.T. K.L. M. Kanai, W.Z. K.W. M.-J.F. L.B. P.A. P.D. V.L.F. R.M. Y.M. B.B. S.S. J.U. E.R.G. N.J.C. I.S. Y.O. A.R.M. and J.B.H.; proteome-wide Mendelian randomization, H.Z. H.R. A.B. G.H. G.D.S. B.M.B. W.Z. B.M.N. T.R.G. and J.Z.; transcriptome-wide association study, A.B. J.B.H. W.Z. J.Z. M. Kanai, B.P. E.R.G. and N.J.C.; asthma, K.T. W.Z. Y.W. M. Kanai, S.N. Y.O. B.M.N. M.J.D. and A.R.M.; heart failure, K.-H.H.W. N.J.D. B.N.W. I.S. S.E.G. J.B.H. N.J.C. M.P. R.J.F.L. M.J.D. B.M.N. W.Z. W.E.H. and C.J.W.; idiopathic pulmonary fibrosis, J.J.P. W.Z. M.J.D. J.T.K. N.J.C. and J.B.H.; primary open-angle glaucoma, V.L.F. A.B. W.Z. Y.W. K.L. M. Kanai, E.A.L.-M. P.S. R.T. X.Z. S.N. S.S. Y.O. N.I. S.M. H.S. I.S. C.W. A.R.M. E.R.G. N.M.J. N.J.C. and J.B.H.; stroke, I.S. K.-H.H.W. W.H. B.N.W. W.Z. J.E.H. A.P. B.B. A.H.S. M.E.G. R.G.W. K.H. C.K. S.Z. M.J.D. B.M.N. and C.J.W.; venous thromboembolism, B.N.W. I.S. K.-H.H.W. B.B. V.L.F. K.T. M.D. B.N. W.Z. J.A.S. and C.J.W. All authors reviewed the manuscript. M.J.D. is a founder of Maze Therapeutics. B.M.N. is a member of the scientific advisory board at Deep Genomics and a consultant for Camp4 Therapeutics, Takeda Pharmaceutical, and Biogen. The spouse of C.J.W. works at Regeneron Pharmaceuticals. C.-Y.C. is employed by Biogen. C.R.G. owns stock in 23andMe, Inc. T.R.G. has received research funding from various pharmaceutical companies to support the application of Mendelian randomization to drug target prioritization. E.E.K. has received speaker fees from Regeneron, Illumina, and 23andMe and is a member of the advisory board for Galateo Bio. R.E.M. has received speaker fees from Illumina and is a scientific advisor to the Epigenetic Clock Development Foundation. G.D.S. has received research funding from various pharmaceutical companies to support the application of Mendelian randomization to drug target prioritization. K.S. and U.T. are employed by deCODE Genetics/Amgen, Inc. J.Z. has received research funding from various pharmaceutical companies to support the application of Mendelian randomization to drug target prioritization. S.M. is a co-founder of and holds stock in Seonix Bio. Publisher Copyright: © 2022 Biobanks facilitate genome-wide association studies (GWASs), which have mapped genomic loci across a range of human diseases and traits. However, most biobanks are primarily composed of individuals of European ancestry. We introduce the Global Biobank Meta-analysis Initiative (GBMI)—a collaborative network of 23 biobanks from 4 continents representing more than 2.2 million consented individuals with genetic data linked to electronic health records. GBMI meta-analyzes summary statistics from GWASs generated using harmonized genotypes and phenotypes from member biobanks for 14 exemplar diseases and endpoints. This strategy validates that GWASs conducted in diverse biobanks can be integrated despite heterogeneity in case definitions, recruitment strategies, and baseline characteristics. This collaborative effort improves GWAS power for diseases, benefits understudied diseases, and improves risk prediction while also enabling the nomination of disease genes and drug candidates by incorporating gene and protein expression data and providing insight into the underlying biology of human diseases and traits.

PurposeWe aimed to gain insight into frequencies of genetic variants in genes implicated in neurodevelopmental disorder with epilepsy (NDD+E) by investigating large cohorts of patients in a diagnostic setting.MethodsWe analyzed variants in NDD+E using epilepsy gene panel sequencing performed between 2013 and 2017 by two large diagnostic companies. We compared variant frequencies in 6,994 panels to other 8,588 recently published panels as well as exome-widede novovariants in 1,942 individuals with NDD+E and 10,937 controls.ResultsGenes with highest frequencies of ultra-rare variants in NDD+E comprisedSCN1A, KCNQ2, SCN2A, CDKL5, SCN8AandSTXBP1, concordant with the two other epilepsy cohorts we investigated. Only 46% of the analysed 262 dominant and X-linked panel genes contained ultra-rare variants in patients. Among genes with contradictory evidence of association with epilepsyCACNB4, CLCN2, EFHC1, GABRD, MAGI2andSRPX2showed equal frequencies in cases and controls.ConclusionWe show that improvement of panel design increased diagnostic yield over time, but panels still display genes with low or no diagnostic yield. With our data, we hope to improve current diagnostic NDD+E panel design and provide a resource of ultra-rare variants in individuals with NDD+E to the community.

Genetics provides two major opportunities for understanding human disease—as a transformative line of etiological inquiry and as a biomarker for heritable diseases. In psychiatry, biomarkers are very much needed for both research and treatment, given the heterogenous populations identified by current phenomenologically based diagnostic systems. To date, however, useful and valid biomarkers have been scant owing to the inaccessibility and complexity of human brain tissue and consequent lack of insight into disease mechanisms. Genetic biomarkers are therefore especially promising for psychiatric disorders. Genome-wide association studies of common diseases have matured over the last decade, generating the knowledge base for increasingly informative individual-level genetic risk prediction. In this review, we discuss fundamental concepts involved in computing genetic risk with current methods, strengths and weaknesses of various approaches, assessments of utility, and applications to various psychiatric disorders and related traits. Although genetic risk prediction has become increasingly straightforward to apply and common in published studies, there are important pitfalls to avoid. At present, the clinical utility of genetic risk prediction is still low; however, there is significant promise for future clinical applications as the ancestral diversity and sample sizes of genome-wide association studies increase. We discuss emerging data and methods aimed at improving the value of genetic risk prediction for disentangling disease mechanisms and stratifying subjects for epidemiological and clinical studies. For all applications, it is absolutely critical that polygenic risk prediction is applied with appropriate methodology and control for confounding to avoid repeating some mistakes of the candidate gene era.

Human genetic studies have long been vastly Eurocentric, raising a key question about the generalizability of these study findings to other populations. Because humans originated in Africa, these populations retain more genetic diversity, and yet individuals of African descent have been tremendously underrepresented in genetic studies. The diversity in Africa affords ample opportunities to improve fine-mapping resolution for associated loci, discover novel genetic associations with phenotypes, build more generalizable genetic risk prediction models, and better understand the genetic architecture of complex traits and diseases subject to varying environmental pressures. Thus, it is both ethically and scientifically imperative that geneticists globally surmount challenges that have limited progress in African genetic studies to date while meaningfully including African investigators, as greater inclusivity and enhanced research capacity affords enormous opportunities to accelerate genomic discoveries that translate more effectively to all populations. We review the advantages and challenges of studying the genetic architecture of complex traits and diseases in Africa. For example, with greater genetic diversity comes greater ancestral heterogeneity; this higher level of understudied diversity can yield novel genetic findings, but some methods that assume homogeneous population structure and work well in European populations may work less well in the presence of greater diversity and heterogeneity in African populations. Consequently, we advocate for methodological development that will accelerate studies important for all populations, especially those currently underrepresented in genetics.

Background & aimsIndividuals with monogenic disorders of phagocyte function develop chronic colitis that resembles Crohn's disease (CD). We tested for associations between mutations in genes encoding reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidases, neutrophil function, and phenotypes of CD in pediatric patients.MethodsWe performed whole-exome sequence analysis to identify mutations in genes encoding NADPH oxidases (such as CYBA, CYBB, NCF1, NCF2, NCF4, RAC1, and RAC2) using DNA from 543 pediatric patients with inflammatory bowel diseases. Blood samples were collected from an additional 129 pediatric patients with CD and 26 children without IBD (controls); we performed assays for neutrophil activation, reactive oxygen species (ROS) production, and bacteria uptake and killing. Whole-exome sequence analysis was performed using DNA from 46 of the children with CD to examine associations with NADPH gene mutations; RNA sequence analyses were performed using blood cells from 46 children with CD to test for variations in neutrophil gene expression associated with ROS production.ResultsWe identified 26 missense mutations in CYBA, CYBB, NCF1, NCF2, and NCF4. Patients with CD who carried mutations in these genes were 3-fold more likely to have perianal disease (P= .0008) and stricturing complications (P= .002) than children with CD without these mutations. Among patients withCD with none of these mutations, 9% had undergone abdominal surgery; among patients with mutations in these NADPH oxidase genes, 31% had undergone abdominal surgery (P=.0004). A higher proportion of neutrophils from children with CD had low ROS production (47%) than from controls (15%) among the 129 patients tested for ROS (P= .002). Minor alleles of the NADPH genes were detected in 7% of children with CD whose neutrophils produced normal levels of ROS vs 38% of children whose neutrophils produced low levels of ROS (P= .009). Neutrophils that produced low levels of ROS had specific alterations in genes that regulate glucose metabolism and antimicrobial responses.ConclusionsWe identified missense mutations in genes that encode NADPH oxidases in children with CD; these were associated with a more aggressive disease course and reduced ROS production by neutrophils from the patients.

Protein truncating variants (PTVs) are likely to modify gene function and have been linked to hundreds of Mendelian disorders. However, the impact of PTVs on complex traits has been limited by the available sample size of whole-exome sequencing studies (WES). Here we assemble WES data from 100,304 individuals to quantify the impact of rare PTVs on 13 quantitative traits and 10 diseases. We focus on those PTVs that occur in PTV-intolerant (PI) genes, as these are more likely to be pathogenic. Carriers of at least one PI-PTV were found to have an increased risk of autism, schizophrenia, bipolar disorder, intellectual disability and ADHD (P-value (p) range: 5x10-3-9x10-12). In controls, without these disorders, we found that this burden associated with increased risk of mental, behavioral and neurodevelopmental disorders as captured by electronic health record information. Furthermore, carriers of PI-PTVs tended to be shorter (p=2x10-5), have fewer years of education (p=2x10-4) and be younger (p=2x10-7); the latter observation possibly reflecting reduced survival or study participation. While other gene-sets derived from in vivo experiments did not show any associations with PTV-burden, gene sets implicated in GWAS of cardiovascular-related traits and inflammatory bowel disease showed a significant PTV-burden with corresponding traits, mainly driven by established genes involved in familial forms of these disorders. We leveraged population health registries from 14,117 individuals to study the phenome-wide impact of PI-PTVs and identified an increase in the number of hospital visits among PI-PTV carriers. In conclusion, we provide the most thorough investigation to date of the impact of rare deleterious coding variants on complex traits, suggesting widespread pleiotropic risk.

Sequencing-based studies have identified novel risk genes for rare, severe epilepsies and revealed a role of rare deleterious variation in common epilepsies. To identify the shared and distinct ultra-rare genetic risk factors for rare and common epilepsies, we performed a whole-exome sequencing (WES) analysis of 9,170 epilepsy-affected individuals and 8,364 controls of European ancestry. We focused on three phenotypic groups; the rare but severe developmental and epileptic encephalopathies (DEE), and the commoner phenotypes of genetic generalized epilepsy (GGE) and non-acquired focal epilepsy (NAFE). We observed that compared to controls, individuals with any type of epilepsy carried an excess of ultra-rare, deleterious variants in constrained genes and in genes previously associated with epilepsy, with the strongest enrichment seen in DEE and the least in NAFE. Moreover, we found that inhibitory GABAA receptor genes were enriched for missense variants across all three classes of epilepsy, while no enrichment was seen in excitatory receptor genes. The larger gene groups for the GABAergic pathway or cation channels also showed a significant mutational burden in DEE and GGE. Although no single gene surpassed exome-wide significance among individuals with GGE or NAFE, highly constrained genes and genes encoding ion channels were among the top associations, including CACNA1G, EEF1A2, and GABRG2 for GGE and LGI1, TRIM3, and GABRG2 for NAFE. Our study confirms a convergence in the genetics of common and rare epilepsies associated with ultra-rare coding variation and highlights a ubiquitous role for GABAergic inhibition in epilepsy etiology in the largest epilepsy WES study to date.

We present the largest exome sequencing study of autism spectrum disorder (ASD) to date (n=35,584 total samples, 11,986 with ASD). Using an enhanced Bayesian framework to integrate de novo and case-control rare variation, we identify 102 risk genes at a false discovery rate ≤ 0.1. Of these genes, 49 show higher frequencies of disruptive de novo variants in individuals ascertained for severe neurodevelopmental delay, while 53 show higher frequencies in individuals ascertained for ASD; comparing ASD cases with mutations in these groups reveals phenotypic differences. Expressed early in brain development, most of the risk genes have roles in regulation of gene expression or neuronal communication (i.e., mutations effect neurodevelopmental and neurophysiological changes), and 13 fall within loci recurrently hit by copy number variants. In human cortex single-cell gene expression data, expression of risk genes is enriched in both excitatory and inhibitory neuronal lineages, consistent with multiple paths to an excitatory/inhibitory imbalance underlying ASD.

Background Genome-wide association studies (GWASs) have identified >200 genomic regions associated with IBD. These signals are mainly driven by common variants in noncoding regions, making it a challenge to extract biological insight. Targeted sequencing of genes in these regions has successfully identified putative causal variants, often rarer and independent of the initial GWAS hit. These coding variants have led to more direct functional experiments demonstrating causal mechanisms for at least ten genes. Methods To further rare variant-based discovery, we pursued large-scale exome sequencing of more than 30,000 Crohn's disease (CD) cases and population controls from more than 20 centers in the International IBD Genetics Consortium. Sequencing was performed at the Broad Institute using both Nextera (11,125 CD cases) and TWIST (7,442 CD cases) exome captures - and at the Sanger Institute (whole genomes 6,404 CD cases and Agilent exome 3,848 CD cases). Further replication was performed with a sample of 4,359 cases from Kiel sequenced at Regeneron. In each technical experiment, a comparable or larger number of sequenced controls were available for genetic association analysis. Results We conducted meta-analysis of two exome captures at the Broad Institute. To expand on GWAS, we focused on rare and low-frequency coding variants between 0.01% and 10% and estimated roughly 85% of all protein coding variants in this frequency range are reliably analyzed in both exome captures. 119 variants (figure below) were identified with p Conclusion These findings provide novel launch points for mechanistic studies that will further our understanding of disease pathogenesis. For example, SDF2L1 (R161H) flags a gene not previously implicated in IBD but which is reported to regulate feeding-induced ER stress, with a series of CRISPR screens identifying it as an essential regulator of ER homeostasis. Download : Download high-res image (141KB) Download : Download full-size image Effect size versus frequency for significant low frequency coding variants (credit: Hailiang Huang)

Background And Aims The host receptor for severe acute respiratory syndrome coronavirus 2, angiotensin-converting enzyme 2 (ACE2), is highly expressed in small bowel (SB). Our aim was to identify factors influencing intestinal ACE2 expression in Crohn's disease (CD), ulcerative colitis (UC), and non–inflammatory bowel disease (IBD) controls. Methods Using bulk RNA sequencing or microarray transcriptomics from tissue samples (4 SB and 2 colonic cohorts; n = 495; n = 387 UC; n = 94 non-IBD), we analyzed the relationship between ACE2 with demographics and disease activity and prognosis. We examined the outcome of anti–tumor necrosis factor and anti–interleukin-12/interleukin-23 treatment on SB and colonic ACE2 expression in 3 clinical trials. Univariate and multivariate regression models were fitted. Results ACE2 levels were consistently reduced in SB CD and elevated in colonic UC compared with non-IBD controls. Elevated SB ACE2 was also associated with demographic features (age and elevated body mass index) associated with poor coronavirus disease 2019 outcomes. Within CD, SB ACE2 was reduced in patients subsequently developing complicated disease. Within UC, colonic ACE2 was elevated in active disease and in patients subsequently requiring anti–tumor necrosis factor rescue therapy. SB and colonic ACE2 expression in active CD and UC were restored by anti-cytokine therapy, most notably in responders. Conclusions Reduced SB but elevated colonic ACE2 levels in IBD are associated with inflammation and severe disease, but normalized after anti-cytokine therapy, suggesting compartmentalization of ACE2-related biology in SB and colonic inflammation. The restoration of ACE2 expression with anti-cytokine therapy might be important in the context of severe acute respiratory syndrome coronavirus 2 infection and potentially explain reports of reduced morbidity from coronavirus disease 2019 in IBD patients treated with anti-cytokines.

A. Palotie on työryhmän Int IBD Genetics Consortium jäsen. One goal of human genetics is to understand the genetic basis of disease, a challenge for diseases of complex inheritance because risk alleles are few relative to the vast set of benign variants. Risk variants are often sought by association studies in which allele frequencies in case subjects are contrasted with those from population-based samples used as control subjects. In an ideal world we would know population-level allele frequencies, releasing researchers to focus on case subjects. We argue this ideal is possible, at least theoretically, and we outline a path to achieving it in reality. If such a resource were to exist, it would yield ample savings and would facilitate the effective use of data repositories by removing administrative and technical barriers. We call this concept the Universal Control Repository Network (UNICORN), a means to perform association analyses without necessitating direct access to individual-level control data. Our approach to UNICORN uses existing genetic resources and various statistical tools to analyze these data, including hierarchical clustering with spectral analysis of ancestry; and empirical Bayesian analysis along with Gaussian spatial processes to estimate ancestry-specific allele frequencies. We demonstrate our approach using tens of thousands of control subjects from studies of Crohn disease, showing how it controls false positives, provides power similar to that achieved when all control data are directly accessible, and enhances power when control data are limiting or even imperfectly matched ancestrally. These results highlight how UNICORN can enable reliable, powerful, and convenient genetic association analyses without access to the individual-level data.

Background Genomic studies in Autism Spectrum Disorder (ASD) have largely focused on high impact de novo mutations that disrupt protein-coding sequence. Given the size of the noncoding genome and its regulatory role in gene function, it is likely that rare, noncoding variation represents an important component of the genetic architecture of ASD. Characterization of noncoding mutations may also provide insights into the cell types and critical developmental stages involved in ASD. However, there is no obvious noncoding equivalent to protein-truncating variants, thus necessitating an unbiased and statistically rigorous association strategy for noncoding variation that parallels standards set by common variant analyses. Methods Using whole genome sequencing (WGS) of 2,076 individuals (519 cases, unaffected sibling controls, and both parents), we evaluated genomic variation across the spectrum of variant size and frequency. The results of 12 variant discovery algorithms were integrated to identify de novo SNVs, indels, and structural variants (SVs); cross-site validation exceeded 93% for all variant classes. Variants were annotated using an extensive series of noncoding functional annotations and gene sets, including gene-defined regions (e.g. promoters) and regulatory regions (e.g. histone marks), conservation, proximity to gene sets of interest (e.g. FMRP targets), and variant type (e.g. SNVs, indels), resulting in 51,801 combinations of annotation categories. ASD association within each category was assessed using a binomial test to compare variant counts in cases and controls in a Category-Wide Association Study (CWAS). To account for multiple testing, correlations of p-values were assessed between the 51,801 categories from 20,000 sets of simulated variants. Eigenvalue decomposition estimated that 4,211 effective tests explained 99% of the variation. Results A small excess of de novo noncoding variants was observed in cases (1.02-fold), which was not significant after correcting for paternal age. While we identified several variants that were likely causal for an individual, no annotation category was significant after correcting for 4,211 tests in the CWAS. The lowest p-values were observed in coding regions, including missense variation and SVs not detected by previous technologies. Similarly, no category of rare inherited variants demonstrated parental transmission bias or ASD association. Discussion Our results suggest that there is no clear category of rare noncoding variation with equivalent impact on ASD risk as large SVs or protein-disrupting mutations. Furthermore, given the multiple categories of noncoding mutations that may potentially confer ASD risk, identifying noncoding disease associations and quantifying this risk will require a statistically rigorous approach that includes stringent multiple testing correction for this multitude of plausible hypotheses. Analogous to genome-wide association studies of common variation, this approach is likely to identify sound and replicable noncoding associations, but will require substantially larger sample sizes, likely in excess of 5,000 cases.

Attention-Deficit Hyperactivity Disorder (ADHD) is a highly heritable childhood behavioural disorder affecting 3-6% of school-age children, and has a heritability of around 0.80. The SNP heritability, estimating the amount of risk attributed to common genetic variation, has been estimated to 0.22. The difference between SNP heritability and total heritability indicates that the genetic component of ADHD most likely also includes effects of rare variants. The role of ultra-rare deleterious variants has been established for schizophrenia and autism, but the role of these variants in ADHD remains unknown. Here we present results from whole exome sequencing of two cohorts of ADHD cases and controls. A Danish cohort consisting of samples identified in the Danish Newborn Screening Biobank (DNSB) consisting of ~3,170 ADHD cases and ~6,100 controls, and a sample consisting of ~1,200 clinical ascertained ADHD cases from Germany and the Netherlands, and a control group of ~3,000 individuals with German, Dutch and Danish ancestries, giving a grand total of 7,542 cases and 9,100 controls. Preliminary results from the analysis of the DNSB ADHD cohort demonstrate a significant overrepresentation of ultra-rare deleterious variants in evolutionary constrained genes in cases compared to controls (P = 8.21x10-10). We will present results from analyses of the impact of ultra-rare deleterious variation on ADHD risk based on the full sample of ADHD cases and controls. We will especially focus on the burden of these variants in ADHD cases compared to controls in highly evolutionary constrained genes as well as specific gene-sets relevant to ADHD, e.g. “synaptic genes”, “neurite outgrowth genes”, “genes bound by the fragile X mental retardation gene FMRP” and “genes with high brain expression”. Furthermore, we will evaluate, whether ADHD risk genes identified based on common variant analyses also carry an increased burden of ultra-rare deleterious variants, and conduct gene-based association analyses to identify top-ranking genes most frequently hit by rare deleterious variants in ADHD cases compared to controls.

Background Studies of de novo variation, which is identified by exome sequencing parent-offspring families, have successfully identified over 100 genes associated with neurodevelopmental disorders, most notably intellectual disability / developmental delay (ID/DD) or autism spectrum disorders (ASDs). Mutations in the genes first discovered in de novo studies of ASD were specifically enriched in those ASD individuals with comorbid ID/DD, and these genes were commonly assumed to affect both traits. As such, some criticized these studies for failing to separate ID/DD genes from those genes that confer risk to ASD without ID/DD. Winner's curse suggests the effect size for these genes would be greatest in ASD (i.e., the trait it was first discovered in). Through a meta-analysis of de novo variants from 3982 probands ascertained for ASD (892 with comorbid ID/DD) and 5264 probands ascertained for ID/DD (503 with comorbid ASD) we show that, in fact, the reverse is true: previously associated ASD genes are more often mutated in individuals with ID/DD who do not have ASD. Methods We meta-analyzed of 14,048 previously published de novo variants from 9,246 families (father, mother, affected proband). We leveraged detailed phenotyping on 85.9% of the probands to increase power to both identify associated genes and calculate the degree of risk each gene confers for different disorders. Results To identify disease associated genes, we compared the number of observed de novo missense and protein-truncating variants (PTVs) to the number expected from a null mutational model across three sets: ASD+ID/DD, ASD only, and ID/DD only. This yielded a total of 98 significant genes, 8 of which are novel. The contribution of evidence towards each gene's association is overwhelmingly provided by ID/DD compared to ASD (4.9-fold excess; P Discussion Studying de novo variation has been extremely successful for identifying disease-associated genes, with ASD being arguably the flagship trait for this study design. However, the presence of comorbid ID/DD in ASD probands with associated de novo variants begged the question as to how much risk each gene confers to the different disorders. Leveraging detailed phenotyping in a meta-analysis of 3982 ASD and 5264 ID/DD individuals, we identified 98 disease-associated genes, of which only 3 are more strongly associated with ASD than ID/DD. Furthermore, genes previously associated with ASD are more often observed in individuals with ID/DD who themselves do not have ASD. Therefore, researchers should be cautious with using published lists of ASD genes for follow-up functional studies - especially if the goal is to learn about the genetic etiology of core ASD features in the absence of cognitive impairment - namely social and behavioral impairments.

Analysis of de novo CNVs (dnCNVs) from the full Simons Simplex Collection (SSC) (N = 2,591 families) replicates prior findings of strong association with autism spectrum disorders (ASDs) and confirms six risk loci (1q21.1, 3q29, 7q11.23, 16p11.2, 15q11.2-13, and 22q11.2). The addition of published CNV data from the Autism Genome Project (AGP) and exome sequencing data from the SSC and the Autism Sequencing Consortium (ASC) shows that genes within small de novo deletions, but not within large dnCNVs, significantly overlap the high-effect risk genes identified by sequencing. Alternatively, large dnCNVs are found likely to contain multiple modest-effect risk genes. Overall, we find strong evidence that de novo mutations are associated with ASD apart from the risk for intellectual disability. Extending the transmission and de novo association test (TADA) to include small de novo deletions reveals 71 ASD risk loci, including 6 CNV regions (noted above) and 65 risk genes (FDR ≤ 0.1). Through analysis of de novo mutations in autism spectrum disorder (ASD), Sanders et al. find that small deletions, but not large deletions/duplications, contain one critical gene. Combining CNV and sequencing data, they identify 6 loci and 65 genes associated with ASD.

Genome-wide association studies (GWAS) have revealed risk alleles for ulcerative colitis (UC). To understand their cell type specificities and pathways of action, we generate an atlas of 366,650 cells from the colon mucosa of 18 UC patients and 12 healthy individuals, revealing 51 epithelial, stromal, and immune cell subsets, including BEST4⁺ enterocytes, microfold-like cells, and IL13RA2⁺IL11⁺ inflammatory fibroblasts, which we associate with resistance to anti-TNF treatment. Inflammatory fibroblasts, inflammatory monocytes, microfold-like cells, and T cells that co-express CD8 and IL-17 expand with disease, forming intercellular interaction hubs. Many UC risk genes are cell type specific and co-regulated within relatively few gene modules, suggesting convergence onto limited sets of cell types and pathways. Using this observation, we nominate and infer functions for specific risk genes across GWAS loci. Our work provides a framework for interrogating complex human diseases and mapping risk variants to cell types and pathways., National Institutes of Health (U.S.) (Grant 5U24AI118672)

Background The current data indicated that the allelic architecture of complex traits is caused by many common and rare variants. Large GWAS meta-analyses have been successfully applied in the search for common variants affecting the risk of developing psychiatric disorders, in particular schizophrenia and Major Depressive Disorder. However, these studies are designed to examine only the common variant proportion of the genomic landscape whereas high-throughput sequencing allows direct examination of both common and rare alleles. Schizophrenia is one of the most disabling mental disorders; it has a lifetime prevalence of around 1% and a heritability estimated as high as 80%. Although around one third of the heritability can be attributed to common variants, prior studies indicate that rare variants also contribute to its etiology. Methods A collaboration between iPSYCH (The Lundbeck Initiative for Integrative Psychiatric Research, Denmark) and the Broad Institute (in Cambridge, MA, USA) is conducting large scale exome sequencing of major psychiatric disorders, including schizophrenia. DNA is extracted from dried blood spots (DBS) stored at the Danish Neonatal Screening Biobank. The samples can be matched to a wide range of phenotypic information available in Danish registries. Results We present here the analysis of a large collection of schizophrenia individuals recruited in clinical centers (1,866) and from DBS samples (3,710): a total of 5,576 cases and 7,468 controls from Denmark. We follow up in a similarly sized sample from Sweden with 4,969 cases and 6,245 controls. The combined analysis represents the largest exome sequencing study in schizophrenia to date. We have found evidence showing a higher per-person rate of disruptive ultra-rare loss-of-function variants located in constrained genes among schizophrenia cases compared to controls (combined p-value 1.6e-07). Meta-analysis SKAT of rare and ultra-rare variants at gene level has been performed. Discussion The results from burden and enrichment analysis, as well as ranking of mutational load, will be discussed in the larger perspective of findings from both GWAS and other exome analyses in schizophrenia.

The future beckons to us. Whither do we go and what shall be our endeavor? … We have hard work ahead. There is no resting for any one of us till we redeem our pledge in full.—Jawaharlal Nehru (“Tryst with Destiny”)