A genome-wide SNP genotyping resource for tropical pine tree species

We performed gene and genome targeted SNP discovery towards the development of a genome-wide, multispecies genotyping array for tropical pines. Pooled RNA-seq data from shoots of seedlings from five tropical pine species was used to identify transcript-based SNPs resulting in 1.3 million candidate Affymetrix SNP probe sets. In addition, we used a custom 40 K probe set to perform capture-seq in pooled DNA from 81 provenances representing the natural ranges of six tropical pine species in Mexico and Central America resulting in 563 K candidate SNP probe sets. Altogether, 300 K RNA-seq (72%) and 120 K capture-seq (28%) derived SNP probe sets were tiled on a 420 K screening array that was used to genotype 576 trees representing the 81 provenances and commercial breeding material. Based on the screening array results, 50 K SNPs were selected for commercial SNP array production including 20 K polymorphic SNPs for P. patula, P. tecunumanii, P. oocarpa and P. caribaea, 15 K for P. greggii and P. maximinoi, 13 K for P. elliottii and 8K for P. pseudostrobus. We included 9.7 K ancestry informative SNPs that will be valuable for species and hybrid discrimination. Of the 50 K SNP markers, 25% are polymorphic in only one species, while 75% are shared by two or more species. The Pitro50K SNP chip will be useful for population genomics and molecular breeding in this group of pine species that, together with their hybrids, represent the majority of fast-growing tropical and subtropical pine plantations globally.DATA AVAILABILITY STATEMENT : The pooled targeted capture sequencing data have been made available via NCBI SRA BioProject accession PRJNA742386. RNA-seq data are available via NCBI SRA BioProject accessions PRJNA416697 (P. tecunumanii), PRJNA416698 (P. patula), PRJNA685280 (P. oocarpa), PRJNA685281 (P. greggii) and PRJNA685282 (P. maximinoi). Metadata and probe set sequences used for markers selected for the 50 K commercial array are available as Supporting Information (Table S5). Genotype data set used for PCA and STRUCTURE analysis is available in Supporting Information (Table S6).http://www.wileyonlinelibrary.com/journal/men2022-08-12hj2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Risk of Arterial and Venous Thrombotic Events Among Patients with COVID-19:A Multi-National Collaboration of Regulatory Agencies from Canada, Europe, and United States

Purpose: Few studies have examined how the absolute risk of thromboembolism with COVID-19 has evolved over time across different countries. Researchers from the European Medicines Agency, Health Canada, and the United States (US) Food and Drug Administration established a collaboration to evaluate the absolute risk of arterial (ATE) and venous thromboembolism (VTE) in the 90 days after diagnosis of COVID-19 in the ambulatory (eg, outpatient, emergency department, nursing facility) setting from seven countries across North America (Canada, US) and Europe (England, Germany, Italy, Netherlands, and Spain) within periods before and during COVID-19 vaccine availability. Patients and Methods: We conducted cohort studies of patients initially diagnosed with COVID-19 in the ambulatory setting from the seven specified countries. Patients were followed for 90 days after COVID-19 diagnosis. The primary outcomes were ATE and VTE over 90 days from diagnosis date. We measured country -level estimates of 90 -day absolute risk (with 95% confidence intervals) of ATE and VTE. Results: The seven cohorts included 1,061,565 patients initially diagnosed with COVID-19 in the ambulatory setting before COVID19 vaccines were available (through November 2020). The 90 -day absolute risk of ATE during this period ranged from 0.11% (0.09- 0.13%) in Canada to 1.01% (0.97-1.05%) in the US, and the 90 -day absolute risk of VTE ranged from 0.23% (0.21-0.26%) in Canada to 0.84% (0.80-0.89%) in England. The seven cohorts included 3,544,062 patients with COVID-19 during vaccine availability (beginning December 2020). The 90 -day absolute risk of ATE during this period ranged from 0.06% (0.06-0.07%) in England to 1.04% (1.01-1.06%) in the US, and the 90 -day absolute risk of VTE ranged from 0.25% (0.24-0.26%) in England to 1.02% (0.99- 1.04%) in the US. Conclusion: There was heterogeneity by country in 90 -day absolute risk of ATE and VTE after ambulatory COVID-19 diagnosis both before and during COVID-19 vaccine availability. Plain Language Summary: Cohort studies of patients diagnosed with COVID-19 in both the ambulatory and hospital settings have suggested that SARS-CoV-2 infection promotes hypercoagulability that could lead to arterial or venous thromboembolism. However, few studies have examined how the risk of thromboembolism with COVID-19 has evolved over time across different countries. A new collaboration was established among the regulatory authorities of Canada, Europe, and the US within the International Coalition of Medicines Regulatory Authorities to evaluate the 90 -day risk of both arterial and venous thromboembolism after initial diagnosis of COVID-19 in the ambulatory or hospital setting from seven countries across North America (Canada, US) and Europe (England, Germany, Italy, Netherlands, and Spain) within periods before and during COVID-19 vaccine availability. The study found that there was variability in the risk of both arterial and venous thromboembolism by month across the countries among patients initially diagnosed with COVID-19 in the ambulatory or hospital setting. Differences in the healthcare systems, prevalence of comorbidities in the study cohorts, and approaches to the case definitions of thromboembolism likely contributed to the variability in estimates of thromboembolism risk across the countries

Cumulative Burden of Colorectal Cancer-Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer.

BACKGROUND & AIMS: Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC. METHODS: We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants. RESULTS: Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28-4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80-3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 × 10-5). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61-5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70-3.00). Sensitivity analyses were consistent with these findings. CONCLUSIONS: In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be more strongly associated with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive measures

The association between anastomotic leakage and health-related quality of life after colorectal cancer surgery

Aim: Colorectal anastomotic leakage (AL) is a serious complication. Studies on the impact of AL on health-related quality of life (HRQoL) are scarce. We aimed to investigate the association between AL and HRQoL in colorectal cancer patients up to 2 years after diagnosis, and to evaluate whether AL is associated with a clinically relevant decrease in HRQoL over time. Methods: Patients diagnosed with Stage I–III colorectal cancer undergoing elective surgical resection with primary anastomosis between 2010 and 2017 were included. HRQoL was evaluated using the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire C30, represented by the summary score, and analysed at diagnosis and at 6 months and 2 years post-diagnosis. Multivariable linear regression was performed to assess the association between AL and HRQoL, while multivariable logistic regression was used to investigate the association between AL and a clinically relevant HRQoL decrease (≥10 points) during follow-up compared to the time of diagnosis. Results: In total, 1197 patients were included of whom 63 (5%) developed AL. AL was not associated with HRQoL at 6 months post-diagnosis nor at 2 years post-diagnosis. However, having AL was associated with an increased risk of a clinically relevant decrease in HRQoL at 6 months post-diagnosis (OR 3.65, 95% CI 1.62–8.21) but not at 2 years after diagnosis (OR 1.91, 95% CI 0.62–5.93). Conclusion: Although AL was not associated with HRQoL at 6 months or 2 years post-diagnosis, AL was a determinant of a clinically relevant decrease in HRQoL at 6 months after diagnosis. Future work should identify feasible and effective strategies to prevent declines in QoL in this patient population

Risk of Arterial and Venous Thrombotic Events Among Patients with COVID-19:A Multi-National Collaboration of Regulatory Agencies from Canada, Europe, and United States

Purpose: Few studies have examined how the absolute risk of thromboembolism with COVID-19 has evolved over time across different countries. Researchers from the European Medicines Agency, Health Canada, and the United States (US) Food and Drug Administration established a collaboration to evaluate the absolute risk of arterial (ATE) and venous thromboembolism (VTE) in the 90 days after diagnosis of COVID-19 in the ambulatory (eg, outpatient, emergency department, nursing facility) setting from seven countries across North America (Canada, US) and Europe (England, Germany, Italy, Netherlands, and Spain) within periods before and during COVID-19 vaccine availability. Patients and Methods: We conducted cohort studies of patients initially diagnosed with COVID-19 in the ambulatory setting from the seven specified countries. Patients were followed for 90 days after COVID-19 diagnosis. The primary outcomes were ATE and VTE over 90 days from diagnosis date. We measured country -level estimates of 90 -day absolute risk (with 95% confidence intervals) of ATE and VTE. Results: The seven cohorts included 1,061,565 patients initially diagnosed with COVID-19 in the ambulatory setting before COVID19 vaccines were available (through November 2020). The 90 -day absolute risk of ATE during this period ranged from 0.11% (0.09- 0.13%) in Canada to 1.01% (0.97-1.05%) in the US, and the 90 -day absolute risk of VTE ranged from 0.23% (0.21-0.26%) in Canada to 0.84% (0.80-0.89%) in England. The seven cohorts included 3,544,062 patients with COVID-19 during vaccine availability (beginning December 2020). The 90 -day absolute risk of ATE during this period ranged from 0.06% (0.06-0.07%) in England to 1.04% (1.01-1.06%) in the US, and the 90 -day absolute risk of VTE ranged from 0.25% (0.24-0.26%) in England to 1.02% (0.99- 1.04%) in the US. Conclusion: There was heterogeneity by country in 90 -day absolute risk of ATE and VTE after ambulatory COVID-19 diagnosis both before and during COVID-19 vaccine availability. Plain Language Summary: Cohort studies of patients diagnosed with COVID-19 in both the ambulatory and hospital settings have suggested that SARS-CoV-2 infection promotes hypercoagulability that could lead to arterial or venous thromboembolism. However, few studies have examined how the risk of thromboembolism with COVID-19 has evolved over time across different countries. A new collaboration was established among the regulatory authorities of Canada, Europe, and the US within the International Coalition of Medicines Regulatory Authorities to evaluate the 90 -day risk of both arterial and venous thromboembolism after initial diagnosis of COVID-19 in the ambulatory or hospital setting from seven countries across North America (Canada, US) and Europe (England, Germany, Italy, Netherlands, and Spain) within periods before and during COVID-19 vaccine availability. The study found that there was variability in the risk of both arterial and venous thromboembolism by month across the countries among patients initially diagnosed with COVID-19 in the ambulatory or hospital setting. Differences in the healthcare systems, prevalence of comorbidities in the study cohorts, and approaches to the case definitions of thromboembolism likely contributed to the variability in estimates of thromboembolism risk across the countries

Priority III

The Priority III Priority Setting Partnership identified priorities for future research around how we plan, do and share the results of rapid reviews in the context of healthcare using a modified JLA approac

What are the most important unanswered research questions on rapid review methodology? A James Lind Alliance research methodology Priority Setting Partnership: the Priority III study protocol

The value of rapid reviews in informing health care decisions is more evident since the onset of the coronavirus disease 2019 (COVID-19) pandemic. While systematic reviews can be completed rapidly, rapid reviews are usually a type of evidence synthesis in which components of the systematic review process may be simplified or omitted to produce information more efficiently within constraints of time, expertise, funding or any combination thereof. There is an absence of high-quality evidence underpinning some decisions about how we plan, do and share rapid reviews. We will conduct a modified James Lind Alliance Priority Setting Partnership to determine the top 10 unanswered research questions about how we plan, do and share rapid reviews in collaboration with patients, public, reviewers, researchers, clinicians, policymakers and funders. An international steering group consisting of key stakeholder perspectives (patients, the public, reviewers, researchers, clinicians, policymakers and funders) will facilitate broad reach, recruitment and participation across stakeholder groups. An initial online survey will identify stakeholders' perceptions of research uncertainties about how we plan, do and share rapid reviews. Responses will be categorised to generate a long list of questions. The list will be checked against systematic reviews published within the past three years to identify if the question is unanswered. A second online stakeholder survey will rank the long list in order of priority. Finally, a virtual consensus workshop of key stakeholders will agree on the top 10 unanswered questions. Research prioritisation is an important means for minimising research waste and ensuring that research resources are targeted towards answering the most important questions. Identifying the top 10 rapid review methodology research priorities will help target research to improve how we plan, do and share rapid reviews and ultimately enhance the use of high-quality synthesised evidence to inform health care policy and practice