A catalogue of chromosome counts for Phylum Nematoda.

Nematodes are important biological models in genetics and genomics, with research driven by basic biological as well as applied questions. The presence of holocentric chromosomes, clades with frequent polyploidy and the phenomenon of programmed DNA elimination make nematode karyotypic diversity of particular interest. Here we present a catalogue of published karyotypes of nematode species, rationalising and normalising descriptions from the previous 135 years.

The genome sequence of the planthopper, (Germar, 1821).

We present a genome assembly from an individual male (planthopper; Arthropoda; Insecta; Hemiptera; Delphacidae). The genome sequence has a total length of 957.80 megabases.

Taxonomy Identifiers (TaxId) for Biodiversity Genomics: a guide to getting TaxId for submission of data to public databases.

Biodiversity genomics critically depends on correct taxonomic identification of the sample from which data are derived. Tracking of that taxonomic information through systems that archive data and report on genome sequencing efforts. For submission of data to the International Nucleotide Sequence Database Collaboration (INSDC) databases (DNA DataBank of Japan [DDBJ], European Nucleotide Archive [ENA] and National Center for Biotechnology Information [NCBI]), samples and data derived from them must be assigned a species-level NCBI Taxonomy taxonomic identifier (TaxId, sometimes referred to as taxId or txid).

Integrating Genomic Data with the Development of CRISPR-Based Point-of-Care-Testing for Bacterial Infections.

Purpose Of Review: Bacterial infections and antibiotic resistance contribute to global mortality. Despite many infections being preventable and treatable, the lack of reliable and accessible diagnostic tools exacerbates these issues. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based diagnostics has emerged as a promising solution.

Engineering structural variants to interrogate genome function.

Structural variation, such as deletions, duplications, inversions and complex rearrangements, can have profound effects on gene expression, genome stability, phenotypic diversity and disease susceptibility. Structural variants can encompass up to millions of bases and have the potential to rearrange substantial segments of the genome. They contribute considerably more to genetic diversity in human populations and have larger effects on phenotypic traits than point mutations.

Long-term tracking of haematopoietic clonal dynamics and mutations in non-human primate undergoing transplantation of lentivirally barcoded haematopoietic stem and progenitor cells.

Haematopoietic stem and progenitor cell (HSPC) autologous gene therapies are promising treatment for a variety of blood disorders. Investigation of the long-term HSPC clonal dynamics and other measures of safety and durability following lentiviral-mediated gene therapies in predictive models are crucial for assessing risks and benefits in order to inform decisions regarding wider utilization. We established an autologous lentivirally barcoded HSPC transplantation model in rhesus macaque (RM), a model offering insights into haematopoiesis and gene therapies with direct relevance to human.

Profiling immune cell tissue niches in the spatial -omics era.

Immune responses require complex, spatially coordinated interactions between immune cells and their tissue environment. For decades, we have imaged tissue sections to visualize a limited number of immune-related macromolecules in situ, functioning as surrogates for cell types or processes of interest. However, this inevitably provides a limited snapshot of the tissue's immune landscape.

Identification of complex Plasmodium falciparum genetic backgrounds circulating in Africa: a multicountry genomic epidemiology analysis.

Background: The population structure of the malaria parasite Plasmodium falciparum can reveal underlying adaptive evolutionary processes. Selective pressures to maintain complex genetic backgrounds can encourage inbreeding, producing distinct parasite clusters identifiable by population structure analyses.

Methods: We analysed population structure in 3783 P falciparum genomes from 21 countries across Africa, provided by the MalariaGEN Pf7 dataset.

Crucial role of biosensors in the detection of helminth biomarkers in public health programmes.

Helminthiases are highly prevalent but neglected infections that affect more than 1·5 billion people worldwide. Considering the worldwide prevalence of helminthiases, WHO has declared them a public health concern since 2001, necessitating rigorous control and elimination efforts. However, only a few reliable point-of-care diagnostic tests are available for assessing the effectiveness of public health interventions targeting helminthiases, thus increasing the risk of suboptimal outcomes, misallocation of resources, and emergence of drug-resistant helminths.

Microbial occurrence and symbiont detection in a global sample of lichen metagenomes.

In lichen research, metagenomes are increasingly being used for evaluating symbiont composition and metabolic potential, but the overall content and limitations of these metagenomes have not been assessed. We reassembled over 400 publicly available metagenomes, generated metagenome-assembled genomes (MAGs), constructed phylogenomic trees, and mapped MAG occurrence and frequency across the data set. Ninety-seven percent of the 1,000 recovered MAGs were bacterial or the fungal symbiont that provides most cellular mass.

A chromosomal reference genome sequence for the malaria mosquito, , Theobald, 1903.

We present a genome assembly from an individual female (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae) from Lopé, Gabon. The genome sequence is 225.7 megabases in span.

Curating genomic disease-gene relationships with Gene2Phenotype (G2P).

Genetically determined disorders are highly heterogenous in clinical presentation and underlying molecular mechanism. The evidence underpinning these conditions in the peer-reviewed literature requires robust critical evaluation for diagnostic use. Here, we present a structured curation process for Gene2Phenotype (G2P).

Identifying barriers and opportunities to facilitate the uptake of whole genome sequencing in paediatric haematology and oncology practice.

Background: The clinical utility of whole genome sequencing (WGS) in paediatric cancer has been demonstrated in recent years. WGS has been routinely available in the National Health Service (NHS) England for all children with cancer in England since 2021, but its uptake has been variable geographically. To explore the underlying barriers to routine use of WGS in this population across England and more widely in the United Kingdom (UK) and the Republic of Ireland (ROI), a one-day workshop was held in Cambridge, United Kingdom in October 2022.

Fine-mapping and molecular characterisation of primary sclerosing cholangitis genetic risk loci.

Genome-wide association studies of primary sclerosing cholangitis have identified 23 susceptibility loci. The majority of these loci reside in non-coding regions of the genome and are thought to exert their effect by perturbing the regulation of nearby genes. Here, we aim to identify these genes to improve the biological understanding of primary sclerosing cholangitis, and nominate potential drug targets.

Large-Scale Pharmacogenomics Analysis of Patients With Cancer Within the 100,000 Genomes Project Combining Whole-Genome Sequencing and Medical Records to Inform Clinical Practice.

Purpose: As part of the 100,000 Genomes Project, we set out to assess the potential viability and clinical impact of reporting genetic variants associated with drug-induced toxicity for patients with cancer recruited for whole-genome sequencing (WGS) as part of a genomic medicine service.

Methods: Germline WGS from 76,805 participants was analyzed for pharmacogenetic (PGx) variants in four genes (, , , ) associated with toxicity induced by five drugs used in cancer treatment (capecitabine, fluorouracil, mercaptopurine, thioguanine, irinotecan). Linking genomic data with prescribing and hospital incidence records, a phenome-wide association study (PheWAS) was performed to identify whether phenotypes indicative of adverse drug reactions (ADRs) were enriched in drug-exposed individuals with the relevant PGx variants.

Bacteria divide to conquer antibiotics.

High-level resistance to methicillin requires a distinct form of cell division.

Contemporary epidemiology of hospitalised heart failure with reduced versus preserved ejection fraction in England: a retrospective, cohort study of whole-population electronic health records.

Background: Heart failure is common, complex, and often associated with coexisting chronic medical conditions and a high mortality. We aimed to assess the epidemiology of people admitted to hospital with heart failure with reduced ejection fraction (HFrEF) and heart failure with preserved ejection fraction (HFpEF), including the period covering the COVID-19 pandemic, which was previously not well characterised.

Methods: In this retrospective, cohort study, we used whole-population electronic health records with 57 million individuals in England to identify patients hospitalised with heart failure as the primary diagnosis in any consultant episode of an in-patient admission to a National Health Service (NHS) hospital.