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Hepatitis B virus (HBV) integration events are profiled in liver tissues from hepatocellular carcinoma patients using a high-throughput HBV integration sequencing method and bioinformatics. HBV is often found to integrate in mitochondrial DNA.

Dennis et al. investigate potential breast cancer associations with rare germline copy number variants (CNVs) by conducting a genome-wide analysis in a large breast cancer case-control dataset. The authors detected associations with exonic deletions in established breast cancer susceptibility genes and suggestive associations for a number of non-coding CNVs.

Phaeochromocytomas and paragangliomas (PPGL) are rare endocrine tumours that can affect paediatric patients as well as adults. In this first international Consensus Statement on PPGL in paediatric patients, the authors discuss the diagnosis, management and long-term surveillance of these tumours in children and adolescents.

Research addressing sustainability issues is more effective if ‘co-produced’ by academics and non-academics, but definitions of co-production vary. This Perspective presents four knowledge co-production principles for sustainability research and guides on how to engage in co-productive practices.

The risk of germline copy number variants (CNVs) in BRCA1 and BRCA2 pathogenic variant carriers in breast cancer is assessed, with CNVs overlapping SULT1A1 decreasing breast cancer risk in BRCA1 carriers.

TRACERx Lung: Intratumoral transcriptional heterogeneity, which often hinders the development of clinically useful RNA-expression-biased biomarkers for cancer, can now be overcome with an approach for the identification of clonal expression biomarkers.

Multiregion spatial histology, exome and transcriptome data from patients with non-small cell lung cancer suggest that cancer subclones from immune cold regions diversify later than subclones from immune hot regions

The Red List of Ecosystems is a headline indicator in the Kunming-Montreal Global Biodiversity Framework. This Progress illustrates how the Red List of Ecosystems can be used by Parties to the Framework to contribute to its implementation and monitoring.

The analysis of T-cell antigens in long-term survivors of pancreatic ductal adenocarcinoma suggests that neoantigen immunogenicity and quality, not purely quantity, correlate with survival.

The Human BioMolecular Atlas Program (HuBMAP) presents its production phase: the generation of spatial maps of functional tissue units across organs from diverse populations and the creation of tools and infrastructure to advance biomedical research.

Multiple transcriptome approaches, including single-cell sequencing, demonstrate that escape from X chromosome inactivation is widespread and occasionally variable between cells, chromosomes, and tissues, resulting in sex-biased expression of at least 60 genes and potentially contributing to sex-specific differences in health and disease.

A complex Nuclear Receptor Element (cNRE) of 32 base pairs that emerged from a viral infection drives the quail Slow Myosin Heavy Chain III (SMyHC III) promoter preferential expression to the atria.

Wagner et al. carry out a longitudinal seroepidemiological study of SARS-CoV-2 antibodies in a cohort of adults from a large company in Vienna, Austria. In individuals positive for S1-reactive antibodies at baseline, RBD-specific antibodies are most likely to persist for six months and correlate most closely with SARS-CoV-2 neutralizing ability.

Inglese et al. develop a predictive model that computes multi-regional statistical morpho-functional mesoscopic traits from T1-weighted magnetic resonance imaging scans. Their model reliably discriminates people with Alzheimer’s disease-related pathologies from those without.

The findings of a World Health Organization expert working group that is developing animal models to test vaccines and therapeutic agents for the treatment of COVID-19, and their relevance for preclinical testing, are reviewed.

The genome of the Southern Ocean phytoplankton Fragilariopsis cylindrus differs markedly from the genomes of its more temperate relatives, with divergent alleles being differentially expressed in environmentally specific conditions such as freezing and darkness.

Antibodies elicited by a triple homologous or heterologous vaccination regimen or following natural SARS-CoV-2 infection combined with a two-dose vaccine course, result in highest neutralization capacity against the Omicron variant BA.1.

Dube et al. generated an atlas of human brain circular RNA (circRNA) expression in individuals with and without Alzheimer disease (AD). They demonstrated circRNA expression correlates with AD severity, even before substantial clinical symptom onset.

Pulmonary venous tumor cells disseminating before tumor resection are heterogeneous, predict relapse and seed future metastasis of lung cancer

Standard-of-care management of renal cell carcinoma (RCC) relies on surgery for low-risk localized disease and systemic treatment for poor-prognosis metastatic tumours, but patients with high-risk localized tumours and with metastatic disease that has a good-to-intermediate prognosis are in a grey area for treatment. In this Review, the authors provide a comprehensive overview of the current knowledge on surgery and systemic treatment in the management of metastatic and localized RCC.

Zhou et al. utilise deep learning to improve polygenic risk analysis for Alzheimer’s disease. Their computational approach outperforms existing statistical methods and helps to identify potential biological mechanisms of Alzheimer’s disease risk.

Subsurface heat transfer from the subtropical Atlantic Ocean to high latitudes during the mid-to-late Pliocene may have been responsible for a delay in the intensification of Northern Hemisphere glaciations, according to sedimentary proxy records and numerical modelling.

In this Consensus Statement, the authors present results from an international multi-stakeholder consensus conducted by the PIONEER consortium to identify the most important questions in the field of prostate cancer that could be addressed using big data.

Azevedo et al. conduct a machine learning-based analysis of structural MRI data from multiple cohorts. The authors identify Alzheimer’s disease-like neuroimaging phenotypes associated with poorer cognitive performance in a healthy UK Biobank cohort, potentially highlighting a population at risk of Alzheimer’s disease.

Cholangiocarcinoma (CCA) comprises heterogeneous biliary malignant tumours, and their incidence is increasing worldwide. This expert Consensus Statement, endorsed by the ENS-CCA, summarizes the latest advances in CCA, including classification, genetics and treatment, and provides recommendations for CCA management and priorities across basic, translational and clinical research.

Doan et al. characterize and assess the stability of film matrix embedded Adeno-Associated Virus 9 (AAV9) vectors during storage and transport at ambient temperatures. High and low viscosity formulations of AAV9 stored at 25 °C maintain titer for 6 months.

In this Perspective article, members of the European Reference Network on Rare and Complex Connective Tissue and Musculoskeletal Diseases discuss clinical and organizational challenges in this community caused by the COVID-19 pandemic and what lessons might be learned for the future.

The incidence of early-onset colorectal cancer (in patients <50 years old) is increasing at an alarming rate. This Review highlights potential risk factors and putative mechanisms that drive this disease, and suggests likely areas for fruitful research, including diet, stress and antibiotics.

The ability to realize quantum systems for quantum technology relies on protocols capable of generating robust quantum states. The authors propose two protocols to generate arbitrary NOON states, one is deterministic, the other is probabilistic, and discuss their implementation in ultra-cold atom systems.

Lakis et al. report novel findings related to the epigenetic landscape of pancreatic neuroendocrine cancer. This relatively large cohort provides functional insights into the epigenetic wiring of pancreatic neuroendocrine tumor sub-types with the potential ability to stratify tumours of different prognosis.

Using a high throughput, random bacterial peptide display approach applied to patient serum samples, Haynes, Kamath, Bozekowski et al identify the antigens and epitopes that elicit a SARS-CoV-2 humoral response. They identify differences depending on disease severity and further in silico analysis suggests decreased epitope signal for Q677P but not for D614G mutant SARSCoV-2 strains.

Evidence from in vitro experiments, animal models and humans is revisited and highlights the potential role of the blood-brain barrier in mediating the effects of non-invasive brain stimulation in AD.

The diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene glacial cycles, leading to a remarkable diversity of species and ecosystems. This rich biodiversity is under threat from anthropogenic drivers, such as climate change, invasive species, land use changes, overexploitation, or pathogen (re)emergence. The inventory, characterisation, and study of biodiversity at inter- and intra-specific levels using genomics is crucial to promote its preservation and recovery by informing biodiversity conservation policies, management measures, and research. The participation of researchers from Portuguese institutions in the European Reference Genome Atlas (ERGA) initiative and its pilot effort to generate reference genomes for European biodiversity has reinforced the establishment of Biogenome Portugal. This nascent institutional network will connect the national community of researchers in genomics. Here, we describe the Portuguese contribution to ERGA’s pilot effort, which will generate high-quality reference genomes of six species from Portugal that are endemic, iconic, and/or endangered and include plants, insects, and vertebrates (fish, birds, and mammals) from mainland Portugal or the Azores islands. In addition, we outline the objectives of Biogenome Portugal, which aims to (i) promote scientific collaboration, (ii) contribute to advanced training, (iii) stimulate the participation of institutions and researchers based in Portugal in international biodiversity genomics initiatives, and (iv) contribute to the transfer of knowledge to stakeholders and engaging the public to preserve biodiversity. This initiative will strengthen biodiversity genomics research in Portugal and fuel the genomic inventory of Portuguese eukaryotic species. Such efforts will be critical to the conservation of the country’s rich biodiversity and will contribute to ERGA’s goal of generating reference genomes for European species.