Wellcome Sanger Institute

Ganaie F.A., Beall B.W., Yu J., van der Linden M., McGee L., Satzke C., Manna S., Lo S.W., Bentley S.D., Ravenscroft N., Nahm M.H.

SUMMARY Streptococcus pneumoniae (the “pneumococcus”) is a significant human pathogen. The key determinant of pneumococcal fitness and virulence is its ability to produce a protective polysaccharide (PS) capsule, and anti-capsule antibodies mediate serotype-specific opsonophagocytic killing of bacteria. Notably, immunization with pneumococcal conjugate vaccines (PCVs) has effectively reduced the burden of disease caused by serotypes included in vaccines but has also spurred a relative upsurge in the prevalence of non-vaccine serotypes. Recent advancements in serotyping and bioinformatics surveillance tools coupled with high-resolution analytical techniques have enabled the discovery of numerous new capsule types, thereby providing a fresh perspective on the dynamic pneumococcal landscape. This review offers insights into the current pneumococcal seroepidemiology highlighting important serotype shifts in different global regions in the PCV era. It also comprehensively summarizes newly discovered serotypes from 2007 to 2024, alongside updates on revised chemical structures and the de-novo determinations of structures for previously known serotypes. Furthermore, we spotlight emerging evidence on non-pneumococcal Mitis-group strains that express capsular PS that are serologically and biochemically related to the pneumococcal capsule types. We further discuss the implications of these recent findings on capsule nomenclature, pneumococcal carriage detection, and future PCV design. The review maps out the current status and also outlines the course for future research and vaccine strategies, ensuring a continued effective response to the evolving pneumococcal challenge.

Matentzoglu N., Bello S.M., Stefancsik R., Alghamdi S.M., Anagnostopoulos A.V., Balhoff J.P., Balk M.A., Bradford Y.M., Bridges Y., Callahan T.J., Caufield H., Cuzick A., Carmody L.C., Caron A.R., de Souza V., et. al.

Abstract Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.

Leong I.U., Cabrera C.P., Cipriani V., Ross P.J., Turner R.M., Stuckey A., Sanghvi S., Pasko D., Moutsianas L., Odhams C.A., Elgar G.S., Chan G., Giess A., Walker S., Foulger R.E., et. al.

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 ( DPYD , NUDT15 , TPMT , UGT1A1 ) 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. In a subset of 7,081 patients with cancer, DPYD variants were reported back to clinicians and outcomes were collected. RESULTS We identified clinically relevant PGx variants across the four genes in 62.7% of participants in our cohort. Extending this to annual prescription numbers in England for the drugs affected by these PGx variants, approximately 14,540 patients per year could potentially benefit from a reduced dose or alternative drug to reduce the risk of ADRs. Validating PGx associations in a real-world data set, we found a significant association between PGx variants in DPYD and toxicity-related phenotypes in patients treated with capecitabine or fluorouracil. Reported DPYD variants were deemed informative for clinical decision making in a majority of cases. CONCLUSION Reporting PGx variants from germline WGS relevant to patients with cancer alongside primary findings related to their cancer can be clinically informative, informing prescribing to reduce the risk of ADRs. Extending the range of actionable variants to those found in patients of non-European ancestry is important and will extend the potential clinical impact.

Zaremba B., Fallahshahroudi A., Schneider C., Schmidt J., Sarropoulos I., Leushkin E., Berki B., Van Poucke E., Jensen P., Senovilla-Ganzo R., Hervas-Sotomayor F., Trost N., Lamanna F., Sepp M., García-Moreno F., et. al.

Innovations in the pallium likely facilitated the evolution of advanced cognitive abilities in birds. We therefore scrutinized its cellular composition and evolution using cell type atlases from chicken, mouse, and nonavian reptiles. We found that the avian pallium shares most inhibitory neuron types with other amniotes. Whereas excitatory neuron types in amniote hippocampal regions show evolutionary conservation, those in other pallial regions have diverged. Neurons in the avian mesopallium display gene expression profiles akin to the mammalian claustrum and deep cortical layers, while certain nidopallial cell types resemble neurons in the piriform cortex. Lastly, we observed substantial gene expression convergence between the dorsally located hyperpallium and ventrally located nidopallium during late development, suggesting that topological location does not always dictate gene expression programs determining functional properties in the adult avian pallium.

Oberstaller J., Xu S., Naskar D., Zhang M., Wang C., Gibbons J., Pires C.V., Mayho M., Otto T.D., Rayner J.C., Adams J.H.

Malaria parasites are highly divergent from model eukaryotes. Large-scale genome engineering methods effective in model organisms are frequently inapplicable, and systematic studies of gene function are few. We generated more than 175,000 transposon insertions in the Plasmodium knowlesi genome, averaging an insertion every 138 base pairs, and used this “supersaturation” mutagenesis to score essentiality for 98% of genes. The density of mutations allowed mapping of putative essential domains within genes, providing a completely new level of genome annotation for any Plasmodium species. Although gene essentiality was largely conserved across P. knowlesi , Plasmodium falciparum , and rodent malaria model Plasmodium berghei , a large number of shared genes are differentially essential, revealing species-specific adaptations. Our results indicated that Plasmodium essential gene evolution was conditionally linked to adaptive rewiring of metabolic networks for different hosts.

McIntyre J., Morrison A., Maitland K., Berger D., Price D.R., Dougan S., Grigoriadis D., Tracey A., Holroyd N., Bull K., Rose Vineer H., Glover M.J., Morgan E.R., Nisbet A.J., McNeilly T.N., et. al.

The parasitic nematode Teladorsagia circumcincta is one of the most important pathogens of sheep and goats in temperate climates worldwide and can rapidly evolve resistance to drugs used to control it. To understand the genetics of drug resistance, we have generated a highly contiguous genome assembly for the UK T. circumcincta isolate, MTci2. Assembly using PacBio long-reads and Hi-C long-molecule scaffolding together with manual curation resulted in a 573 Mb assembly (N50 = 84 Mb, total scaffolds = 1,286) with five autosomal and one sex-linked chromosomal-scale scaffolds consistent with its karyotype. The genome resource was further improved via annotation of 22,948 genes, with manual curation of over 3,200 of these, resulting in a robust and near complete resource (96.3% complete protein BUSCOs) to support basic and applied research on this important veterinary pathogen. Genome-wide analyses of drug resistance, combining evidence from three distinct experiments, identified selection around known candidate genes for benzimidazole, levamisole and ivermectin resistance, as well as novel regions associated with ivermectin and moxidectin resistance. These insights into contemporary and historic genetic selection further emphasise the importance of contiguous genome assemblies in interpreting genome-wide genetic variation associated with drug resistance and identifying key loci to prioritise in developing diagnostic markers of anthelmintic resistance to support parasite control.

Gutiérrez-Abril J., Gundem G., Fiala E., Liosis K., Farnoud N., Leongamornlert D., Amallraja A., Arango Ossa J.E., Domenico D., Levine M.F., Medina-Martínez J.S., Stockfisch E., You D., Walsh M.F., Jasinski S., et. al.

Portal E.A., Farley C., Iannetelli T., Coelho J., Efstratiou A., Bentley S.D., Chalker V.J., Spiller O.B.

Background: Streptococcus agalactiae (Group B Streptococcus, GBS) is a leading cause of neonatal sepsis in high-income countries. While intrapartum antibiotic screening reduces this risk, increasing resistance to macrolides and lincosamides in Europe since the 1990s has limited therapeutic options for penicillin-allergic patients. Reports of reduced beta-lactam susceptibility in GBS further emphasise the need for robust antimicrobial resistance (AMR) surveillance. However, broth microdilution (BMD) methods are unsuitable for large-scale antimicrobial susceptibility testing (AST). Objective: To demonstrate that agar-dilution AST provides equivalent results to broth dilution methods, with superior capacity for high-throughput screening. Methods: Agar-dilution and microdilution AST methods were compared using a panel of 24 characterised susceptible and resistant GBS strains for benzylpenicillin, chloramphenicol, clindamycin, erythromycin, gentamicin, levofloxacin, tetracycline, and vancomycin. Minimum inhibitory concentration (MIC) agreements were evaluated, and resistance profile correlations were assessed using Cohen’s kappa values. Results: Agar-dilution demonstrated >90% agreement with BMD MIC for most antimicrobials, except vancomycin (87.5%), erythromycin (83.33%), and tetracycline (52.78%). Cohen’s kappa values indicated strong agreement (0.88–1.00) for resistance determination. Agar-dilution avoided “trailing growth” issues associated with BMD and facilitated easier detection of non-GBS contaminants. Conclusions: Agar-dilution is a valid method for high-throughput AMR surveillance of retrospective cohorts (96 isolates per plate) and is critical for identifying emerging GBS resistance trends and informing therapeutic guidelines. However, due to the large number of plates required per antimicrobial, it is impractical for routine clinical diagnostics.

Cai Z., Apolinário S., Baião A.R., Pacini C., Sousa M.D., Vinga S., Reddel R.R., Robinson P.J., Garnett M.J., Zhong Q., Gonçalves E.

Al-Ajli F.O., Formenti G., Fedrigo O., Tracey A., Sims Y., Howe K., Al-Karkhi I.M., Althani A.A., Jarvis E.D., Rahman S., Ayub Q.

The taxonomic classification of a falcon population found in the Mongolian Altai region in Asia has been heavily debated for two centuries and previous studies have been inconclusive, hindering a more informed conservation approach. Here, we generated a chromosome-level gyrfalcon reference genome using the Vertebrate Genomes Project (VGP) assembly pipeline. Using whole genome sequences of 49 falcons from different species and populations, including “Altai” falcons, we analyzed their population structure, admixture patterns, and demographic history. We find that the Altai falcons are genomic mosaics of saker and gyrfalcon ancestries, and carry distinct W and mitochondrial haplotypes that cluster with the lanner falcon. The Altai maternally-inherited haplotypes diverged 422,000 years before present (290,000–550,000 YBP) from the ancestor of sakers and gyrfalcons, both of which, in turn, split 109,000 YBP (70,000–150,000 YBP). The Altai W chromosome has 31 coding variants in 29 genes that may possibly influence important structural, behavioral, and reproductive traits. These findings provide insights into the question of Altai falcons as a candidate distinct species.

Li Y., Lim C., Dismuke T., Malawsky D.S., Oasa S., Bruce Z.C., Offenhäuser C., Baumgartner U., D’Souza R.C., Edwards S.L., French J.D., Ock L.S., Nair S., Sivakumaran H., Harris L., et. al.

OLIG2-expressing tumor stem cells have been shown to drive recurrence in Sonic Hedgehog (SHH)-subgroup medulloblastoma (MB) and patients urgently need specific therapies to target this tumor cell population. Here, we investigate the therapeutic potential of the brain-penetrant orally bioavailable, OLIG2 inhibitor CT-179, using SHH-MB explant organoids, PDX and GEM SHH-MB models. We find that CT-179 disrupts OLIG2 dimerization, phosphorylation and DNA binding and alters tumor cell-cycle kinetics, increasing differentiation and apoptosis. CT-179 prolongs survival in SHH-MB PDX and GEM models and potentiates radiotherapy (RT) in vivo. Single cell transcriptomic studies (scRNA-seq) confirm that CT-179 increases differentiation and implicate Cdk4 up-regulation in maintaining proliferation during treatment. Consistent with CDK4 mediating CT-179 resistance, CT-179 combines effectively with the CDK4/6 inhibitor palbociclib, further prolonging survival in vivo. These data support therapeutic targeting of OLIG2+ tumor stem cells in regimens for SHH-driven MB, to improve response, delay recurrence and ultimately improve MB patient outcomes. Previously, OLIG2-expressing stems cells have been identified as having a role in medulloblastoma recurrence. Here, the authors investigate the effects of targeting this OLIG2+ stem cell population in Sonic Hedgehog (SHH) medulloblastoma using CT-179, an OLIG2 inhibitor.

Kregar L.D., Williams N., Lee J., Mitchell E., Laurenti E., Nangalia J., Campbell P.

Abstract Ageing is the decline in an organism's function over time, driven by internal and external stresses. Key features of ageing include genomic instability, telomere shortening, epigenetic changes, and loss of proteostasis, and they tend to worsen and compound with age. However, how do these molecular changes manifest in the observed systemic changes seen in ageing is unclear. Somatic mutations contribute to cancer but are thought to have a limited role in ageing, as the genome tolerates rare random errors. Yet, some mutations confer a fitness advantage to the cell, allowing it to overproliferate relative to other cells. To what extent does a clone's founding cell also confer a phenotype, which is inherited by the expanding clone is incompletely understood. It would be interesting to see if constant mutation rates coupled with slow but exponential clonal expansion leads to a sizable proportion of cells that also carry a stable phenotype, which could result in tissue ageing at a systemic level. We sequenced whole genomes and methylomes of single human hematopoietic stem cells (HSCs) from several healthy individuals of different ages and patients with hematologic malignancies. Based on the patterns of shared and cell-specific somatic mutations, we built phylogenies of HSCs for each individual. To establish whether loss or gain of methylation, both mono and bi-allelic, was heritable across cell division, we developed a method that recapitulates this process in a population of related cells. We analysed approximately 25 million CpG sites per individual, and find that methylation is highly heritable at the majority of sites. Moreover, the method allows us to accurately time when methylation changes occurred as methylation changes are assigned to a branch, which represents a common ancestor of the descendant cells, and the branches of a phylogeny can be linked to a developmental period, thus disentangling their evolutionary history. We observe that methylation changes are remarkably stable as we found that thousands of such changes are acquired before germ layer formation and are stably inherited until old age. Interestingly, the same regions across individuals acquire these pre-gastrulation changes that are maintained indefinitely. Moreover, we found the rates of methylation change are several folds higher than the rates of somatic mutations and that methylation changes are stochastic and allele-specific. Lastly, we find that some of these changes precede the neoplasm’s clone, which suggests they might play a role in function. By comparing normal healthy individuals of different ages with cancer patients, we have been able to unravel the process of normal ageing from disease development at an unprecedented scale and granularity. Citation Format: Lori D Kregar, Nicholas Williams, Joe Lee, Emily Mitchell, Elisa Laurenti, Jyoti Nangalia, Peter Campbell. Characteristics of methylation heritability in human somatic cells [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Methylation, Clonal Hematopoiesis, and Cancer; 2025 Feb 1-4; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2025;85(3 Suppl):Abstract nr PR002.

Bellis K.L., Dissanayake O.M., Harrison E.M., Aggarwal D.

Community-acquired (CA), community-onset methicillin-resistant Staphylococcus aureus (CO-MRSA) infection presents a significant public health challenge, even where MRSA rates are historically lower. Despite successes in reducing hospital-onset MRSA, CO-MRSA rates are increasing globally, with a need to understand this trend, and the potential risk factors for re-emergence.

Brown M.R., Gonzalez de La Rosa P., Blaxter M.

Abstract Summary tidk (short for telomere identification toolkit), uses a simple, fast algorithm to scan long DNA reads for the presence of short tandemly repeated DNA in runs, and to aggregate them based on canonical DNA string representation. These are telomeric repeat candidates. Our algorithm is shown to be accurate in genomes for which the telomeric repeat unit is known and is tested across a wide variety of newly assembled genomes to uncover new telomeric repeat units. Tools are provided to identify telomeric repeats de novo, scan genomes for known telomeric repeats, and to visualize telomeric repeats on the assembly. tidk is implemented in Rust and is available as a command line tool which can be compiled using the Rust toolchain or downloaded as a binary from bioconda. Availability the tidk Rust crate is freely available under the MIT license (https://crates.io/crates/tidk), and the source code is available at https://github.com/tolkit/telomeric-identifier. Supplementary information Supplementary data are available at Bioinformatics online.

Pinglay S., Lalanne J., Daza R.M., Kottapalli S., Quaisar F., Koeppel J., Garge R.K., Li X., Lee D.S., Shendure J.

Studying the functional consequences of structural variants (SVs) in mammalian genomes is challenging because (i) SVs arise much less commonly than single-nucleotide variants or small indels and (ii) methods to generate, map, and characterize SVs in model systems are underdeveloped. To address these challenges, we developed Genome-Shuffle-seq, a method that enables the multiplex generation and mapping of thousands of SVs (deletions, inversions, translocations, and extrachromosomal circles) throughout mammalian genomes. We also demonstrate the co-capture of SV identity with single-cell transcriptomes, facilitating the measurement of SV impact on gene expression. We anticipate that Genome-Shuffle-seq will be broadly useful for the systematic exploration of the functional consequences of SVs on gene expression, the chromatin landscape, and three-dimensional nuclear architecture, while also initiating a path toward a minimal mammalian genome.