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• Single-cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation

  GABAergic interneurons are essential for neural circuit function and their loss or dysfunction is implicated in human neuropsychiatric disease. In vitro methods for interneuron generation hold promise for studying human cellular and functional properties and ultimately therapeutic cell replacement. We used a protocol for generating cortical interneurons from hESCs and analyzed the properties and maturation timecourse of cell types using single-cell RNAseq (data available at GEO under: GSE93802 on March 10 2017). Transcriptomic profiles of the hESC-derived interneurons were compared to several different populations of cells from mid-gestation human neocortex that showed differing levels of PAX6 and SOX2 expression. For this study, 104 samples of 100 human neocortical cells each, have been sorted based on SOX2 and PAX6 expression, mRNA recovered from the fixed cells by FRISCR, and transcriptomic profiles generated by SmartSeq2. The RNA-seq data from the 104 100-cell samples is included in this dbGaP study.

  Study phs001276

• Human Liver Cohort (HLC)

  The Human Liver Cohort (HLC) study aimed to characterize the genetic architecture of gene expression in human liver using genotyping, gene expression profiling, and enzyme activity measurements of Cytochrom P450. The HLC was assembled from a total of 780 liver samples screened. DNA samples were genotyped on the Affymetrix 500K SNP and Illumina 650Y SNP genotyping arrays. Only data from those samples which were collected postmortem are accessible through this submission. These 228 samples represent a subset of the 427 samples included in the Human Liver Cohort Publication (Schadt, Molony et al. 2008, PMID: 18462017). RNA samples were profiled on a custom Agilent 44,000 feature microarray composed of 39,280 oligonucleotide probes targeting transcripts representing 34,266 known and predicted genes, including high-confidence, noncoding RNA sequences. Gene Expression data for the samples from which it could be obtained is available in GEO under accession number GSE9588. Results and networks will be made available for download from Sage Bionetworks.

  Study phs000253

• Genetic Studies in the Hutterites

  We conducted genetic studies of disease-associated quantitative phenotypes, including microbiome and gene expression studies, and common diseases, such as asthma and Alzheimer's disease, by genotyping and/or sequencing in the Hutterites, a founder population of European descent. The Hutterites who have participated in our studies live on communal farms in South Dakota and are related to each other through multiple lines of descent in a 3,657-person, 13-generation pedigree with 64 founders. The small number of founding genomes reduces genetic heterogeneity whereas their communal lifestyle ensures that non-genetic factors are remarkably uniform between individuals. Our sample includes >1,600 subjects who have participated in our studies of fertility (since 1982), asthma, cardiovascular disease and other complex phenotypes (since 1993), microbiome studies (since 2011), and/or immune response (since 2012). The variable 'Total number of consented subjects' reflects the count of subjects with individual level phenotype and genotype data in dbGaP.

  Study phs000185

• L1-Seq and Genome-Wide SNP Genotyping in a Multiethnic Asian Population

  Insertions of the human-specific subfamily of LINE-1 (L1) retrotransposon are highly polymorphic across individuals and can critically influence the human transcriptome. We hypothesized that L1 insertions could represent genetic variants determining important human phenotypic traits, and performed an integrated analysis of L1 elements and single nucleotide polymorphisms (SNPs) in several human populations. We found that a large fraction of L1s were in high linkage disequilibrium (LD) with their surrounding genomic regions and that they were well-tagged by SNPs. However, L1 variants were only partially captured by SNPs on standard SNP arrays, so that their potential phenotypic impact would be frequently missed by SNP array-based genome-wide association studies. We next identified potential phenotypic effects of L1s by looking for signatures of natural selection linked to L1 insertions; significant extended haplotype homozygosity (EHH) was detected around several L1 insertions. This suggests that some of these L1 insertions may have been the target of recent positive selection.

  Study phs000732

• DNA Methylation Studies in CREW Cohorts (URECA and COAST)

  Children's Respiratory Environment Workgroup (CREW) is an NIH-funded project consisting of 12 individual U.S. cohorts and three scientific centers working together to identify phenotypes and causes of childhood asthma. CREW includes data from a large number of children and their families, with broad diversity in terms of ethnicity, family characteristics, neighborhoods and geographic locations. In this study, we identified differentially methylated regions from whole-genome bisulfite sequencing (WGBS) in nasal epithelial cells from 39 children of European or African ancestries, and with or without allergic asthma. Study participants were from two of the CREW cohorts: the Urban Environment and Childhood Asthma (URECA) cohort and the Childhood Origins of Asthma (COAST) cohort.The URECA children are also participants of a larger genetic study, in which DNA samples are derived from blood. That data is presented in the "Whole Genome Sequencing in the Inner City Asthma Consortium (ICAC) Cohorts - phs002921" study.

  Study phs003321

• Unraveling the Genetic Architecture of Diabetic Retinopathy in South India

  This study aims to understand the genetic architecture of diabetic retinopathy in the South Indian population by examining participants with South Indian ancestry and type 2 diabetes (T2D) from two sources: the Sankara Nethralaya-Diabetic Retinopathy Epidemiology and Molecular Genetic Study (SN-DREAMS) and prospective recruitment at Sankara Nethralaya affiliates. A total of 2393 patients were recruited and included in the genetic analysis, with 1588 patients having no diabetic retinopathy (DR) serving as the controls and 805 patients with any level of DR serving as the cases. Enrolled individuals had genome-wide genotyping from DNA extracted from blood samples. In addition, whole genome sequencing (WGS) was performed on 31 members from 2 families. Clinical data, such as age, duration of diabetes, and hemoglobin A1C (HbA1c) were recorded for study participants. Diabetic retinopathy was assessed by clinical exam and/or fundus photography. The grading of diabetic retinopathy followed the International Clinical Diabetic Retinopathy Severity Scale.

  Study phs002116

• Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

  While many genetic variants have been associated with risk for human diseases, how these variants affect gene expression in various cell types remains largely unknown. To address this gap, the DICE [Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics] project was established. Considering all human immune cell types and conditions studied, we identified cis-eQTLs for a total of 12,254 unique genes, which represent 61% of all protein-coding genes expressed in these cell types. Strikingly, a large fraction (41%) of these genes showed a strong cis-association with genotype only in a single cell type. We also found that biological sex is associated with major differences in immune cell gene expression in a highly cell-specific manner. These datasets will help reveal the effects of disease risk-associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis.

  Study phs001703

• Type I Interferon Exacerbates Mycobacterium Tuberculosis Induced Human Macrophage Death

  In this study, we tested whether type I interferons (IFN-I), namely IFN-alpha and IFN-beta, may promote Mycobacterium tuberculosis (Mtb) pathogenesis by exacerbating cell death of human monocyte-derived macrophages (MDM) infected with Mtb. We differentiated the MDM under two different published methods (see Document Method.pdf for Table 1 of Methods). To determine if MDM infected with Mtb upregulates IFN-I transcripts, signaling factors, or IFN-I stimulated genes (ISGs), the MDM were infected with Mtb or treated with an activator of stimulator of IFN genes (STING), diamidobenzimidazole (di-ABZI). STING activation acted as a positive control for IFN-I induction and ISG upregulation. Indeed, di-ABZI treated MDM differentiated under both methods upregulated ISGs 24 hpi. At 24 hour post treatment, MDM differentiated under one method, but not under another method, upregulated ISGs, such as ISG15, IFITM3, and CXCL10, upon Mtb infection. MDM differentiated under both methods upregulated ISGs upon di-ABZI treatment.

  Study phs003607

• Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer

  Mismatch repair (MMR) deficient cancer evolves through the continuous erosion of coding homopolymers in target genes. Curiously, the MMR genes MSH6 and MSH3 also contain coding homopolymers and these are frequent mutational targets in MMR-deficient cancers. The impact of incremental MMR mutations on MMR-deficient colorectal cancer evolution is unknown. We show that microsatellite instability modulates DNA repair by toggling hypermutable mononucleotide homopolymer runs in MSH6 and MSH3 through stochastic frameshift switching. Spontaneous mutation and reversion modulates subclonal mutation rate, mutation bias, and clonal HLA and neoantigen diversity. Patient-derived organoids corroborate these observations and show that in the absence of immune selection MMR homopolymer sequences drift back into reading frame, suggesting a fitness cost of elevated mutation rates. Combined experimental and simulation studies demonstrate that subclonal immune selection favours incremental MMR mutations. Overall, our data demonstrate that MMR-deficient colorectal cancers fuel intratumour heterogeneity by adapting subclonal mutation rate and diversity to immune selection.

  Study EGAS50000000297

• Spatially resolved niche and tumor microenvironmental alterations in gastric cancer peritoneal metastases

  Peritoneal metastases (PM) in gastric cancer (GC) portend a poor prognosis, yet our understanding of tumor microenvironmental (TME) characteristics associated with GCPM remain limited. Here, we analyzed intrinsic genomic alterations and transcriptomic programs predictive of GCPM in a prospective cohort of 248 patients, identifying CDH1, PIGR, and ELF3 mutations as predictors. By inspecting the spatial dynamics of the TME, we find that tumor compartment infiltration of pro-tumorigenic cell types such as inflammatory cancer-associated fibroblasts (CAFs) predict peritoneal recurrence. Next, in a cross-sectional study of 205 samples from 55 patients, distinct pathways and immune compositions in GCPM relative to liver metastases highlight the TME's significance in transcoelomic metastases. Notably, several putative therapeutic targets exhibited distinct expression patterns between PTs and PMs. Our findings highlight transcriptomic variations and niche reprogramming in the GCPM peritoneal environment, revealing roles of myeloid dendritic cells, effector memory CD8+ T cells, and CAFs in metastatic progression.

  Study EGAS50000000501