Integrated Mapping of Establishment Risk for Emerging Vector-Borne Infections: A Case Study of Canine Leishmaniasis in Southwest France

BACKGROUND: Zoonotic visceral leishmaniasis is endemic in the Mediterranean Basin, where the dog is the main reservoir host. The disease's causative agent, Leishmania infantum, is transmitted by blood-feeding female sandflies. This paper reports an integrative study of canine leishmaniasis in a region of France spanning the southwest Massif Central and the northeast Pyrenees, where the vectors are the sandflies Phlebotomus ariasi and P. perniciosus. METHODS: Sandflies were sampled in 2005 using sticky traps placed uniformly over an area of approximately 100 by 150 km. High- and low-resolution satellite data for the area were combined to construct a model of the sandfly data, which was then used to predict sandfly abundance throughout the area on a pixel by pixel basis (resolution of c. 1 km). Using literature- and expert-derived estimates of other variables and parameters, a spatially explicit R(0) map for leishmaniasis was constructed within a Geographical Information System. R(0) is a measure of the risk of establishment of a disease in an area, and it also correlates with the amount of control needed to stop transmission. CONCLUSIONS: To our knowledge, this is the first analysis that combines a vector abundance prediction model, based on remotely-sensed variables measured at different levels of spatial resolution, with a fully mechanistic process-based temperature-dependent R(0) model. The resulting maps should be considered as proofs-of-principle rather than as ready-to-use risk maps, since validation is currently not possible. The described approach, based on integrating several modeling methods, provides a useful new set of tools for the study of the risk of outbreaks of vector-borne diseases

The ICR639 CPG NGS validation series: A resource to assess analytical sensitivity of cancer predisposition gene testing [version 1; referees: 2 approved]

The analytical sensitivity of a next generation sequencing (NGS) test reflects the ability of the test to detect real sequence variation. The evaluation of analytical sensitivity relies on the availability of gold-standard, validated, benchmarking datasets. For NGS analysis the availability of suitable datasets has been limited. Most laboratories undertake small scale evaluations using in-house data, and/or rely on in silico generated datasets to evaluate the performance of NGS variant detection pipelines. Cancer predisposition genes (CPGs), such as BRCA1 and BRCA2, are amongst the most widely tested genes in clinical practice today. Hundreds of providers across the world are now offering CPG testing using NGS methods. Validating and comparing the analytical sensitivity of CPG tests has proved difficult, due to the absence of comprehensive, orthogonally validated, benchmarking datasets of CPG pathogenic variants. To address this we present the ICR639 CPG NGS validation series. This dataset comprises data from 639 individuals. Each individual has sequencing data generated using the TruSight Cancer Panel (TSCP), a targeted NGS assay for the analysis of CPGs, together with orthogonally generated data showing the presence of at least one CPG pathogenic variant per individual. The set consists of 645 pathogenic variants in total. There is strong representation of the most challenging types of variants to detect, with 339 indels, including 16 complex indels and 24 with length greater than five base pairs and 74 exon copy number variations (CNVs) including 23 single exon CNVs. The series includes pathogenic variants in 31 CPGs, including 502 pathogenic variants in BRCA1 or BRCA2, making this an important comprehensive validation dataset for providers of BRCA1 and BRCA2 NGS testing. We have deposited the TSCP FASTQ files of the ICR639 series in the European Genome-phenome Archive (EGA) under accession number EGAD00001004134

Sarcoma and the 100,000 Genomes Project: our experience and changes to practice

The largest whole genome sequencing (WGS) endeavour involving cancer and rare diseases was initiated in the UK in 2015 and ran for 5 years. Despite its rarity, sarcoma ranked third overall among the number of patients' samples sent for sequencing. Herein, we recount the lessons learned by a specialist sarcoma centre that recruited close to 1000 patients to the project, so that we and others may learn from our experience. WGS data was generated from 597 patients, but samples from the remaining approximately 400 patients were not sequenced. This was largely accounted for by unsuitability due to extensive necrosis, secondary to neoadjuvant radiotherapy or chemotherapy, or being placed in formalin. The number of informative genomes produced was reduced further by a PCR amplification step. We showed that this loss of genomic data could be mitigated by sequencing whole genomes from needle core biopsies. Storage of resection specimens at 4 °C for up to 96 h overcame the challenge of freezing tissue out of hours including weekends. Removing access to formalin increased compliance to these storage arrangements. With over 70 different sarcoma subtypes described, WGS was a useful tool for refining diagnoses and identifying novel alterations. Genomes from 350 of the cohort of 597 patients were analysed in this study. Overall, diagnoses were modified for 3% of patients following review of the WGS findings. Continued refinement of the variant-calling bioinformatic pipelines is required as not all alterations were identified when validated against histology and standard of care diagnostic tests. Further research is necessary to evaluate the impact of germline mutations in patients with sarcoma, and sarcomas with evidence of hypermutation. Despite 50% of the WGS exhibiting domain 1 alterations, the number of patients with sarcoma who were eligible for clinical trials remains small, highlighting the need to revaluate clinical trial design

Characteristics and outcomes of neonatal SARS-CoV-2 infection in the UK: a prospective national cohort study using active surveillance.

BACKGROUND: Babies differ from older children with regard to their exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, data describing the effect of SARS-CoV-2 in this group are scarce, and guidance is variable. We aimed to describe the incidence, characteristics, transmission, and outcomes of SARS-CoV-2 infection in neonates who received inpatient hospital care in the UK. METHODS: We carried out a prospective UK population-based cohort study of babies with confirmed SARS-CoV-2 infection in the first 28 days of life who received inpatient care between March 1 and April 30, 2020. Infected babies were identified through active national surveillance via the British Paediatric Surveillance Unit, with linkage to national testing, paediatric intensive care audit, and obstetric surveillance data. Outcomes included incidence (per 10 000 livebirths) of confirmed SARS-CoV-2 infection and severe disease, proportions of babies with suspected vertically and nosocomially acquired infection, and clinical outcomes. FINDINGS: We identified 66 babies with confirmed SARS-CoV-2 infection (incidence 5·6 [95% CI 4·3-7·1] per 10 000 livebirths), of whom 28 (42%) had severe neonatal SARS-CoV-2 infection (incidence 2·4 [1·6-3·4] per 10 000 livebirths). 16 (24%) of these babies were born preterm. 36 (55%) babies were from white ethnic groups (SARS-CoV-2 infection incidence 4·6 [3·2-6·4] per 10 000 livebirths), 14 (21%) were from Asian ethnic groups (15·2 [8·3-25·5] per 10 000 livebirths), eight (12%) were from Black ethnic groups (18·0 [7·8-35·5] per 10 000 livebirths), and seven (11%) were from mixed or other ethnic groups (5·6 [2·2-11·5] per 10 000 livebirths). 17 (26%) babies with confirmed infection were born to mothers with known perinatal SARS-CoV-2 infection, two (3%) were considered to have possible vertically acquired infection (SARS-CoV-2-positive sample within 12 h of birth where the mother was also positive). Eight (12%) babies had suspected nosocomially acquired infection. As of July 28, 2020, 58 (88%) babies had been discharged home, seven (11%) were still admitted, and one (2%) had died of a cause unrelated to SARS-CoV-2 infection. INTERPRETATION: Neonatal SARS-CoV-2 infection is uncommon in babies admitted to hospital. Infection with neonatal admission following birth to a mother with perinatal SARS-CoV-2 infection was unlikely, and possible vertical transmission rare, supporting international guidance to avoid separation of mother and baby. The high proportion of babies from Black, Asian, or minority ethnic groups requires investigation. FUNDING: UK National Institute for Health Research Policy Research Programme

Effects of environmental change on genetic diversity and distribution pf phelbotomus ariasi, a vector of visceral leishmaniasis in Southwest Europe

Leishmania infantum is the causative agent of zoonotic visceral leishmaniasis (ZVL) in the Mediterranean region, with the domestic dog as the main reservoir host. Phlebotomus (Larroussius) ariasi is the principal vector in cooler, forested ecotopes in southwest Europe, which suggests that it might be subject to environmental and geographical isolation. However, the population genetics of P. ariasi had been little studied before this thesis, which investigated how the population differentiation of this vector might affect its ability to spread northwards, or persist in the Mediterranean region, in response to climate and habitat change. Thirty-six spatio-temporal populations of P. ariasi were molecularly characterized across its range, predominantly from southwest France but including geographical outgroups from Spain, Portugal and North Africa. Phylogenetic and population genetic assessments were made based on five DNA sequences: mitochondrial cytochrome b, nuclear elongation factor-la and apyrase, plus two anonymous nuclear loci, AAm20 and AAm24. The results demonstrated the absence of cryptic sibling species of P. ariasi and the selective neutrality of each locus. Mitochondrial DNA revealed a historical phylogeographic structure, which was consistent with Pleistocene climate change driving multiple haplogroup divergences within glacial refuges and phalanx-like population expansions in interglacial periods. Nuclear loci mostly showed isolation by distance, but some supported restricted gene flow between the Pyrenees and the Massif Central, France, as indicated by cytochrome b. A glacial refuge may have existed north of the Pyrenees. The genetic diversity observed in the northeast Pyrenees, France, permitted an assessment of the effects of broadleaf forest fragmentation on the differentiation of P. ariasi. No conclusive evidence was found to support contemporary genetic substructuring or impoverishment associated with a recent increase in forest fragmentation. The salivary peptide apyrase revealed a geographical pattern of polymorphism consistent with the other selectively neutral loci. A range of selection tests indicated that apyrase was not evolving under positive directional or balancing selection and, therefore, a genetic arms race with the mammalian host and/or Leishmania parasite was not supported. The approach taken provides a proof of principle for helping to assess apyrase and other salivary peptides as vaccine candidates against leishmaniasis

Reducing Single-Use Plastics in Medicine Packaging Roundtable Report 2022

On December 1st 2021, YewMaker hosted a virtual roundtable on 'Reducing Single-Use Plastics in Medicines Packaging' with 58 participants from the Sustainable Medicines Partnership stakeholder groups. The Roundtable Report was completed in April 2022 and is downloadable at the link below

CARTtools v1.0.0

First release of CARTtool

The ICR1000 UK exome series: a resource of gene variation in an outbred population [version 1; referees: 2 approved]

To enhance knowledge of gene variation in outbred populations, and to provide a dataset with utility in research and clinical genomics, we performed exome sequencing of 1,000 UK individuals from the general population and applied a high-quality analysis pipeline that includes high sensitivity and specificity for indel detection. Each UK individual has, on average, 21,978 gene variants including 160 rare (0.1%) variants not present in any other individual in the series. These data provide a baseline expectation for gene variation in an outbred population. Summary data of all 295,391 variants we detected are included here and the individual exome sequences are available from the European Genome-phenome Archive as the ICR1000 UK exome series. Furthermore, samples and other phenotype and experimental data for these individuals are obtainable through application to the 1958 Birth Cohort committee

Accurate clinical detection of exon copy number variants in a targeted NGS panel using DECoN.

Background: Targeted next generation sequencing (NGS) panels are increasingly being used in clinical genomics to increase capacity, throughput and affordability of gene testing. Identifying whole exon deletions or duplications (termed exon copy number variants, 'exon CNVs') in exon-targeted NGS panels has proved challenging, particularly for single exon CNVs.  Methods: We developed a tool for the Detection of Exon Copy Number variants (DECoN), which is optimised for analysis of exon-targeted NGS panels in the clinical setting. We evaluated DECoN performance using 96 samples with independently validated exon CNV data. We performed simulations to evaluate DECoN detection performance of single exon CNVs and to evaluate performance using different coverage levels and sample numbers. Finally, we implemented DECoN in a clinical laboratory that tests BRCA1 and BRCA2 with the TruSight Cancer Panel (TSCP). We used DECoN to analyse 1,919 samples, validating exon CNV detections by multiplex ligation-dependent probe amplification (MLPA).  Results: In the evaluation set, DECoN achieved 100% sensitivity and 99% specificity for BRCA exon CNVs, including identification of 8 single exon CNVs. DECoN also identified 14/15 exon CNVs in 8 other genes. Simulations of all possible BRCA single exon CNVs gave a mean sensitivity of 98% for deletions and 95% for duplications. DECoN performance remained excellent with different levels of coverage and sample numbers; sensitivity and specificity was >98% with the typical NGS run parameters. In the clinical pipeline, DECoN automatically analyses pools of 48 samples at a time, taking 24 minutes per pool, on average. DECoN detected 24 BRCA exon CNVs, of which 23 were confirmed by MLPA, giving a false discovery rate of 4%. Specificity was 99.7%.  Conclusions: DECoN is a fast, accurate, exon CNV detection tool readily implementable in research and clinical NGS pipelines. It has high sensitivity and specificity and acceptable false discovery rate. DECoN is freely available at www.icr.ac.uk/decon

Proffered Papers and Posters Presented at the Seventh International Symposium on Hereditary Breast and Ovarian Cancer—BrcA: From the Personal to the Population

The comprehensive assessment of inherited mutations in cancer susceptibility genes helps to optimize clinical decision-making [...