Christine R Stevens

• Broad Institute of MIT and Harvard

Genetic mutations that yield defective cystic fibrosis transmembrane regulator (CFTR) protein cause cystic fibrosis, a life-limiting autosomal recessive Mendelian disorder. A protective role of CFTR loss-of-function mutations in inflammatory bowel disease (IBD) has been suggested, but its evidence has been inconclusive and contradictory. Here, leve...

Genomic scientists have long been promised cheaper DNA sequencing, but deep whole genomes are still costly, especially when considered for large cohorts in population-level studies. More affordable options include microarrays + imputation, whole exome sequencing (WES), or low-pass whole genome sequencing (WGS) + imputation. WES + array + imputation...

Investigating the role of host genetic factors in COVID-19 severity and susceptibility can inform our understanding of the underlying biological mechanisms that influence adverse outcomes and drug development. Here we present a second updated genome-wide association study (GWAS) on COVID-19 severity and infection susceptibility to SARS-CoV-2 from t...

Short-read genome sequencing (GS) holds the promise of becoming the primary diagnostic approach for the assessment of autism spectrum disorder (ASD) and fetal structural anomalies (FSAs). However, few studies have comprehensively evaluated its performance against current standard-of-care diagnostic tests: karyotype, chromosomal microarray (CMA), an...

Investigating the role of host genetic factors in COVID-19 severity and susceptibility can inform our understanding of the underlying biological mechanisms that influence adverse outcomes and drug development. Here we present a second updated genome-wide association study (GWAS) on COVID-19 severity and infection susceptibility to SARS-CoV-2 from t...

Background Crohn’s disease (CD) can affect any segment of the digestive tract but is most often localized in the ileal, ileocolonic, and colorectal regions of the intestines. It is believed that the chronic inflammation in CD is a result of an imbalance between the epithelial barrier, the immune system, and the intestinal microbiota. The aim of the...

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...

Structural variants (SVs) rearrange large segments of DNA 1 and can have profound consequences in evolution and human disease 2,3 . As national biobanks, disease-association studies, and clinical genetic testing have grown increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD) 4 have become...

Background & aims: Primary sclerosing cholangitis (PSC) is a rare bile duct disease strongly associated with inflammatory bowel disease (IBD). Whole-exome sequencing (WES) has contributed to understanding the molecular basis of very early-onset IBD, but rare protein-altering genetic variants have not been identified for early-onset PSC. We perform...

Whether or not populations diverge with respect to the genetic contribution to risk of specific complex diseases is relevant to understanding the evolution of susceptibility and origins of health disparities. Here, we describe a large-scale whole-genome sequencing study of inflammatory bowel disease encompassing 1,774 affected individuals and 1,644...

Background and Aims The largest cause of mortality in patients with inflammatory bowel disease (IBD) remains thrombo-embolic disease (TED). Recent reports have demonstrated that both monogenic and polygenic factors contribute to TED and 10% of ‘healthy’ subjects are genetically at high risk for TED. Our aim was to utilize whole exome sequencing (WE...

Objective Both the gut microbiome and host genetics are known to play significant roles in the pathogenesis of IBD. However, the interaction between these two factors and its implications in the aetiology of IBD remain underexplored. Here, we report on the influence of host genetics on the gut microbiome in IBD. Design To evaluate the impact of ho...

Structural variants (SVs) rearrange large segments of DNA1 and can have profound consequences in evolution and human disease2,3. As national biobanks, disease-association studies, and clinical genetic testing have grown increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD)4 have become int...

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 analytical framework to integrate de novo and case-control rare variation, we identify 102 risk genes at a false discovery rate of 0.1 or less. Of these genes, 49 show higher frequencies of disruptiv...

The exome sequences of approximately 8,000 children with autism spectrum disorder (ASD) and/or attention deficit hyperactivity disorder (ADHD) and 5,000 controls were analyzed, finding that individuals with ASD and individuals with ADHD had a similar burden of rare protein-truncating variants in evolutionarily constrained genes, both significantly...

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+ enter...

[This corrects the article DOI: 10.1371/journal.pgen.1007329.].

Structural variants (SVs) rearrange large segments of the genome and can have profound consequences for evolution and human diseases. As national biobanks, disease association studies, and clinical genetic testing grow increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD) have become integ...

Attention deficit/hyperactivity disorder (ADHD) is a highly heritable childhood behavioral disorder affecting 5% of children and 2.5% of adults. Common genetic variants contribute substantially to ADHD susceptibility, but no variants have been robustly associated with ADHD. We report a genome-wide association meta-analysis of 20,183 individuals dia...

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...

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 analytical framework to integrate de novo and case-control rare variation, we identify 102 risk genes at a false discovery rate of 0.1 or less. Of these genes, 49 show higher frequencies of disruptiv...

We present the largest exome sequencing study to date focused on rare variation in autism spectrum disorder (ASD) (n=35,584). Integrating de novo and case-control variation with an enhanced Bayesian framework incorporating evolutionary constraint against mutation, we implicate 99 genes in ASD risk at a false discovery rate (FDR) ≤ 0.1. Of these 99...

As part of a broader collaborative network of exome sequencing studies, we developed a jointly called data set of 5,685 Ashkenazi Jewish exomes. We make publicly available a resource of site and allele frequencies, which should serve as a reference for medical genetics in the Ashkenazim (hosted in part at https://ibd.broadinstitute.org, also availa...

Autism spectrum disorder (ASD) is a highly heritable and heterogeneous group of neurodevelopmental phenotypes diagnosed in more than 1% of children. Common genetic variants contribute substantially to ASD susceptibility, but to date no individual variants have been robustly associated with ASD. With a marked sample size increase from a unique Danis...

Sensory stimuli drive the maturation and function of the mammalian nervous system in part through the activation of gene expression networks that regulate synapse development and plasticity. These networks have primarily been studied in mice, and it is not known whether there are species- or clade-specific activity-regulated genes that control feat...

As part of a broader collaborative network of exome sequencing studies, we developed a jointly called data set of 5,685 Ashkenazi Jewish exomes. We make publicly available a resource of site and allele frequencies, which should serve as a reference for medical genetics in the Ashkenazim. We estimate that 30% of protein-coding alleles present in the...

Nature Communications 7 Article number: 12342 10.1038/ncomms12342 ( 2016 ); Published 9 August 2016 ; Updated 13 September 2016 The HTML version of this Article incorrectly listed the authors of the UK IBD Genetics Consortium and the NIDDK IBD Genetics Consortium individually in the main author list.

Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortiu...

Protein-truncating variants protective against human disease provide in vivo validation of therapeutic targets. Here we used targeted sequencing to conduct a search for protein-truncating variants conferring protection against inflammatory bowel disease exploiting knowledge of common variants associated with the same disease. Through replication ge...

Supplementary Figures 1-8, Supplementary Tables 1-3, Supplementary Notes 1-3 and Supplementary References

Prioritizing protective protein truncating variants identified in the targeted sequencing data set

Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) sequence data for 60,706 individuals of diverse ethnicities generated as part of the Exome Aggregation Consortium (...

Aims: Dysregulated nitric oxide (NO) signaling contributes to the pathogenesis of hypertension, a prevalent and often sex-specific risk factor for cardiovascular disease. We previously reported that mice deficient in the α1 subunit of the NO receptor soluble guanylate cyclase (sGCα1 (-/-) mice) display sex- and strain-specific hypertension: male b...

We conducted a search for protein truncating variants conferring protection against inflammatory bowel disease exploiting knowledge of common variants associated with the same disease. We found that a protein truncating variant (rs36095412, p.R179X, genotyped in 11,148 ulcerative colitis patients and 295,446 controls, MAF = up to 0.78%) in RNF186,...

The genetic architecture of autism spectrum disorder involves the interplay of common and rare variants and their impact on hundreds of genes. Using exome sequencing, here we show that analysis of rare coding variation in 3,871 autism cases and 9,937 ancestry-matched or parental controls implicates 22 autosomal genes at a false discovery rate (FDR)...

Spontaneously arising (de novo) mutations have an important role in medical genetics. For diseases with extensive locus heterogeneity, such as autism spectrum disorders (ASDs), the signal from de novo mutations is distributed across many genes, making it difficult to distinguish disease-relevant mutations from background variation. Here we provide...

More than 80% of Crohn's disease (CD) patients will require surgery. Surgery is not curative and rates of re-operation are high. Identification of genetic variants associated with repeat surgery would allow risk stratification of patients who may benefit from early aggressive therapy and/or post-operative prophylactic treatment. CD patients who had...

Copy number variation (CNV) is an important determinant of human diversity and plays important roles in susceptibility to disease. Most studies of CNV carried out to date have made use of chromosome microarray and have had a lower size limit for detection of about 30 kilobases (kb). With the emergence of whole-exome sequencing studies, we asked whe...

Genome-wide association studies and follow-up meta-analyses in Crohn's disease (CD) and ulcerative colitis (UC) have recently identified 163 disease-associated loci that meet genome-wide significance for these two inflammatory bowel diseases (IBD). These discoveries have already had a tremendous impact on our understanding of the genetic architectu...

P-values versus Missingness. We used 5500 genes to make this plot. For each gene, we calculate the -log 10 p-values and the odds ratio of missingness in case and control. The red line is the fitted line of these 5500 observations. (TIF)

The required sample sizes by applying meta- and mega-analysis. (PDF)

Classification tree results for heterozygote calls. (PDF)

Distribution of the genomic control factor . By permuting case/control status 100 times the distribution of is obtained based on the 1000 largest genes. The red line shows the mean of the permutation distribution and the green line shows obtained from the data using (A) Broad SKAT p-values obtained without eigenvectors; (B) Broad SKAT p-values, wit...

Genes with p-value from the SKAT or Burden Test. (XLSX)

PCA from common variants, low frequency variants and both type of variants for Baylor samples. Eigen-vectors are obtained by applying PCA to all common variants that have no missingness (14,702 variants) (A), all low frequency variants that have no missingness (8783 variants) (B), and both type of variants (C). The colors are obtained by clustering...

PCA of Baylor and Broad samples together. first eigen-vector versus second eigen-vector for Broad and Baylor samples. (TIF)

MAF Comparison: Baylor versus Broad. We compare the MAF for 72,758 shared non-synonymous variants in the two data sets. (TIF)

Depth Comparison: Baylor versus Broad. We compare the average sample depth for all non-synonymous variants in the two data sets. (TIF)

Genomic control and based on different types of PC adjustment. (PDF)

The p-values of genes which have two or more de novo nonsense or missense mutations as reported in [5]. (XLSX)

Histogram of p-values for SKAT and Burden Test. (A) and (B) are SKAT p-values for Broad and Baylor samples, respectively. (C) and (D) are Burden test p-values for Broad and Baylor samples, respectively. Green vertical lines are the 25%, 50% and 75% quantiles of p-values. (TIF)

Comparison of seven individuals called by both Baylor and Broad under different filters. (PDF)

The p-values of 114 ASD genes. (XLSX)

Additional Information Regarding Methods. Part A gives additional information about sequencing, including data generation and quality control. Part B gives the mathematical exposition of mega- and meta-analysis. Part C provides details for association analysis. (PDF)

We report on results from whole-exome sequencing (WES) of 1,039 subjects diagnosed with autism spectrum disorders (ASD) and 870 controls selected from the NIMH repository to be of similar ancestry to cases. The WES data came from two centers using different methods to produce sequence and to call variants from it. Therefore, an initial goal was to...

Although genetic lesions responsible for some mendelian disorders can be rapidly discovered through massively parallel sequencing of whole genomes or exomes, not all diseases readily yield to such efforts. We describe the illustrative case of the simple mendelian disorder medullary cystic kidney disease type 1 (MCKD1), mapped more than a decade ago...

To characterize the role of rare complete human knockouts in autism spectrum disorders (ASDs), we identify genes with homozygous or compound heterozygous loss-of-function (LoF) variants (defined as nonsense and essential splice sites) from exome sequencing of 933 cases and 869 controls. We identify a 2-fold increase in complete knockouts of autosom...

Despite significant heritability of autism spectrum disorders (ASDs), their extreme genetic heterogeneity has proven challenging for gene discovery. Studies of primarily simplex families have implicated de novo copy number changes and point mutations, but are not optimally designed to identify inherited risk alleles. We apply whole-exome sequencing...

Whole-exome sequencing (WES), which analyzes the coding sequence of most annotated genes in the human genome, is an ideal approach to studying fully penetrant autosomal-recessive diseases, and it has been very powerful in identifying disease-causing mutations even when enrollment of affected individuals is limited by reduced survival. In this study...

zCall is a variant caller specifically designed for calling rare single-nucleotide polymorphisms from array-based technology. This caller is implemented as a post-processing step after a default calling algorithm has been applied. The algorithm uses the intensity profile of the common allele homozygote cluster to define the location of the other tw...

Male mice deficient in the α 1 subunit of soluble guanylate cyclase, a nitric oxide (NO) receptor, are hypertensive when on a 129S6 (S6) background (sGC α 1 - / - S 6 ) but not when on a C57BL/6 (B6) background (sGC α 1 - / - B 6 ) , suggesting that hypertension associated with sGCα 1 -deficiency is modulated by genetic factors. Genetic linkage ana...

Nitric oxide (NO) plays an essential role in regulating hypertension and blood flow by inducing relaxation of vascular smooth muscle. Male mice deficient in a NO receptor component, the α1 subunit of soluble guanylate cyclase (sGCα1), are prone to hypertension in some, but not all, mouse strains, suggesting that additional genetic factors contribut...

Pedigrees of the 16 AGRE families. Whole exome sequencing was performed on patients indicated with an arrow. Shaded symbols indicate affected individuals. (TIF)

Whole-exome sequencing performance. Average read depth and coverage for each exome are presented. The transition-to-transversion ratios (Ti/Tv) were as expected for coding sequences. (DOCX)

The rate of validation by Sequenom genotyping correlated with sequencing depth. Pearson's correlation = 0.532, P = 0.001×10−30, t-test. (TIF)

Candidate autism genes that contain compound heterozygous variants. (DOCX)