WebGWAS: A web server for instant GWAS on arbitrary phenotypes.

Complex disease genetics is a key area of research for reducing disease and improving human health. Genome-wide association studies (GWAS) help in this research by identifying regions of the genome that contribute to complex disease risk. However, GWAS are computationally intensive and require access to individual-level genetic and health information, which presents concerns about privacy and imposes costs on researchers seeking to study complex diseases.

Connectome-based symptom mapping and related gene expression in children with autism and/or attention-deficit/hyperactivity disorder.

Clinical, neuroimaging and genomics evidence have increasingly underscored a degree of overlap between autism and attention-deficit/hyperactivity disorder (ADHD). This study explores the specific contribution of their core symptoms to shared biology in a sample of N=166 verbal children (6-12 years) with rigorously-established primary diagnoses of either autism or ADHD (without autism). We investigated the associations between inter-individual differences in clinician-based dimensional measures of autism and ADHD symptoms and whole-brain low motion intrinsic functional connectivity (iFC).

Social and Polygenic Risk Factors for Time to Comorbid Diagnoses in Individuals with Substance Use Disorders: A Phenome-Wide Survival Analysis.

Importance: Persons with substance use disorders (SUD) often suffer from additional comorbidities, including psychiatric conditions and physical health problems. Researchers have explored this overlap in electronic health records (EHR) using phenome wide association studies (PheWAS) to characterize how different indicators are related to all conditions in an individual's EHR. However, analyses have been largely cross-sectional in nature.

Investigating the pathogenicity of the recessive p.A251T variant in monogenic diabetes using iPSC-derived beta-like cells.

Monogenic diabetes, formerly called Maturity-Onset Diabetes of the Young (MODY), involves single-gene mutations, typically with dominant inheritance, and has been associated with variants in 14 genes. Among these, mutations are the most common, and their diagnosis allows the use of alternative therapies, including sulfonylureas. In an earlier study, we described a variant displaying recessive transmission, p.

Genetic Architecture of Postpartum Psychosis: From Common to Rare Genetic Variation.

Postpartum psychosis is a severe psychiatric condition marked by the abrupt onset of psychosis, mania, or psychotic depression following childbirth. Despite evidence for a strong genetic basis, the roles of common and rare genetic variation remain poorly understood. Leveraging data from Swedish national registers and genomic data from the All of Us Research Program, we estimated family-based heritability at 55% and WGS-based heritability at 37%, with an overrepresentation on the X chromosome.

Dominant negative mutations cause ADA2 deficiency in heterozygous carriers.

Human ADA2 deficiency (DADA2) is an inborn error of immunity with a broad clinical phenotype which encompasses vasculopathy including livedo racemosa and lacunar strokes, as well as hemato-immunological features. Diagnosis is based on the combination of decreased serum ADA2 activity and the identification of biallelic deleterious alleles in the gene. DADA2 carriers harbor a single pathogenic variant in and are mostly considered healthy and asymptomatic.

Deriving Mendelian Randomization-based Causal Networks of Brain Imaging Phenotypes and Bipolar Disorder.

Neuroanatomical variation in individuals with bipolar disorder (BD) has been previously described in observational studies. However, the causal dynamics of these relationships remain unexplored. We performed Mendelian Randomization of 297 structural and functional neuroimaging phenotypes from the UK BioBank and BD using genome-wide association study summary statistics.

Single-Nucleus Atlas of Cell-Type Specific Genetic Regulation in the Human Brain.

Genetic risk variants for common diseases are predominantly located in non-coding regulatory regions and modulate gene expression. Although bulk tissue studies have elucidated shared mechanisms of regulatory and disease-associated genetics, the cellular specificity of these mechanisms remains largely unexplored. This study presents a comprehensive single-nucleus multi-ancestry atlas of genetic regulation of gene expression in the human prefrontal cortex, comprising 5.

HLA EPLET Frequencies Are Similar in Six Population Groups and Are Expressed by the Most Common HLA Alleles.

The degree of immunological compatibility between donors and recipients greatly impacts allograft survival. In the United States kidney allocation system, HLA antigen-level matching has been shown to cause ethnic disparities and thus, has been de-emphasised. However, priority points are still awarded for antigen-level zero-ABDR matching, zero-DR matching and one-DR matching.

Familial RPL26 Variant Causing Congenital Anomalies Without Hematological Features of Diamond Blackfan Anemia.

Diamond Blackfan anemia (DBA) is an autosomal dominant disorder with a heterogeneous clinical presentation which may include macrocytic anemia typically presenting in the first year of life, growth retardation, and congenital malformations in 30%-50% of patients. This phenotypic variability is partially explained by genotype-phenotype correlations, with several ribosomal protein genes implicated in this disorder. Most cases are due to de novo variants, but familial occurrences highlight variable expressivity and reduced penetrance.

Emerging role of genetics in kidney transplantation.

The advent of more affordable genomic analytical pipelines has facilitated the expansion of genetic studies in kidney transplantation. Advances in genetic sequencing have allowed for a greater understanding of the genetic basis of chronic kidney disease, which has helped to guide transplant management and address issues related to living donation in specific disease settings. Recent efforts have shown significant effects of genetic ancestry and donor APOL1 risk genotypes in determining worse allograft outcomes and increased donation risks.

Genome of root celery and population genomic analysis reveal the complex breeding history of celery.

Celery (Apium graveolens L.) is an important vegetable crop in the Apiaceae family. It comprises three botanical varieties: common celery with solid and succulent petioles, celeriac or root celery with enlarged and fleshy hypocotyls and smallage or leaf celery with slender, leafy and usually hollow petioles.

Religion, spirituality, and DNA methylation in HPA-axis genes among Hispanic/Latino adults.

Aim: Investigate associations between religion and spirituality (R&S) and DNA methylation of four HPA-axis genes (i.e. 14 CpG sites) among 992 adults from the Hispanic Community Health Study/Study of Latinos cohorts.

Risks of grade reclassification among patients with Gleason grade group 1 prostate cancer and PI-RADS 5 findings on prostate MRI.

Background And Objective: As most Prostate Imaging Reporting and Data System (PI-RADS) 5 lesions on MRI harbor Gleason grade (GG) group ≥2 disease on biopsy, optimal management of patients with imaging-biopsy discordance remains unclear. To estimate grade misclassification, we evaluated the incidence of Gleason upgrading among patients with GG1 disease in the setting of a PI-RADS 5 lesion.

Methods: We conducted a single-institution retrospective analysis to identify patients with GG1 prostate cancer on fusion biopsy with MRI demonstrating ≥1 PI-RADS 5 lesion.

Domain adaptation in small-scale and heterogeneous biological datasets.

Machine-learning models are key to modern biology, yet models trained on one dataset are often not generalizable to other datasets from different cohorts or laboratories due to both technical and biological differences. Domain adaptation, a type of transfer learning, alleviates this problem by aligning different datasets so that models can be applied across them. However, most state-of-the-art domain adaptation methods were designed for large-scale data such as images, whereas biological datasets are smaller and have more features, and these are also complex and heterogeneous.

Facilitators and Barriers to Increasing Equity in Cystic Fibrosis Newborn Screening Algorithms.

Background: Newborn screening (NBS) for cystic fibrosis (CF) was universally implemented in the United States in 2010 to improve disease outcomes. Despite universal screening, disparities in outcomes currently exist between people with CF (PwCF) with Black/African, Asian, Indigenous, and Latino/Hispanic ancestry in comparison to PwCF of European ancestry. This is in part because CFTR panels used for newborn screening are often based on variants common in European ancestries leading to higher rates of false negatives for PwCF from minoritized racial and ethnic groups.

In Silico-Designed G-Quadruplex Targeting Peptide Attenuates VEGF-A Expression, Preventing Angiogenesis in Cancer Cells.

Vascular endothelial growth factor-A (VEGF-A) is a growth factor and pluripotent cytokine that promotes angiogenesis in cancer cells, transitioning to an angiogenic phenotype. The binding of VEGF-A protein to VEGF receptors (VEGFR-1 and VEGFR-2) initiates a cascade of events that stimulates angiogenesis by facilitating the migration and enhancing the permeability of endothelial cells. The proximal promoter of the VEGF gene encompasses a 36-base pair region (from -85 to -50) that can form a stable G-quadruplex (G4) structure in specific conditions.

ECHINOCOCCUS MULTILOCULARIS IN NEW YORK WILDLIFE: DISTRIBUTION AND GENETIC DIVERSITY OF AN EMERGING PATHOGEN.

Echinococcus is a genus of cestode parasites of paramount veterinary and medical importance globally. Two species, Echinococcus granulosus sensu lato and Echinococcus multilocularis, are endemic to North America and are the etiologic agents of cystic echinococcosis and alveolar echinococcosis, respectively. North America is currently experiencing an epidemiological shift in the state of transmission, distribution, and prevalence of E.

Pan-cancer analysis of biallelic inactivation in tumor suppressor genes identifies KEAP1 zygosity as a predictive biomarker in lung cancer.

The canonical model of tumor suppressor gene (TSG)-mediated oncogenesis posits that loss of both alleles is necessary for inactivation. Here, through allele-specific analysis of sequencing data from 48,179 cancer patients, we define the prevalence, selective pressure for, and functional consequences of biallelic inactivation across TSGs. TSGs largely assort into distinct classes associated with either pan-cancer (Class 1) or lineage-specific (Class 2) patterns of selection for biallelic loss, although some TSGs are predominantly monoallelically inactivated (Class 3/4).

Eleven Grand Challenges for Inflammatory Bowel Disease Genetics and Genomics.

The past 2 decades have witnessed extraordinary advances in our understanding of the genetic factors influencing inflammatory bowel disease (IBD), providing a foundation for the approaching era of genomic medicine. On behalf of the NIDDK IBD Genetics Consortium, we herein survey 11 grand challenges for the field as it embarks on the next 2 decades of research utilizing integrative genomic and systems biology approaches. These involve elucidation of the genetic architecture of IBD (how it compares across populations, the role of rare variants, and prospects of polygenic risk scores), in-depth cellular and molecular characterization (fine-mapping causal variants, cellular contributions to pathology, molecular pathways, interactions with environmental exposures, and advanced organoid models), and applications in personalized medicine (unmet medical needs, working toward molecular nosology, and precision therapeutics).

Islands of genomic stability in the face of genetically unstable metastatic cancer.

Introduction: Metastatic cancer affects millions of people worldwide annually and is the leading cause of cancer-related deaths. Most patients with metastatic disease are not eligible for surgical resection, and current therapeutic regimens have varying success rates, some with 5-year survival rates below 5%. Here, we test the hypothesis that metastatic cancer can be genetically targeted by exploiting single base substitution mutations unique to individual cells that occur as part of normal aging prior to transformation.