The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features...

Additional file 9: Supplementary Fig. 4. Pan-genome profiles of ureolytic isolates. Pan-genome (blue) and core-genome (red) sizes were predicted based on all the strains of individual species.

Additional file 7: Supplementary Fig. 2. Microbial metabolites inside and outside of the dialysis bags. A. The identified metabolites inside the dialysis bags; B. A heatmap of the metabolite profiles at each incubation time both inside and outside of the dialysis bags; C. Correlation of metabolite profiles between insides and outside the dialysis bags.

Additional file 1: Text S1. Dietary assessment and creation of the MedDiet scores. Table S1. Components and scoring of the MEDAS and MEDAS Continuous Mediterranean diet scores. Table S2. Components and scoring of the PYRAMID Mediterranean diet adherence score. Table S3. ICD-9 and ICD-10 codes for dementia diagnosis. Figure S1. Participant flowchart. Table S4. Risk of incident dementia according to Mediterranean diet adherence, with analyses restricted to individuals with a minimum of 2 dietary reports....

Additional file 1: Text S1. Dietary assessment and creation of the MedDiet scores. Table S1. Components and scoring of the MEDAS and MEDAS Continuous Mediterranean diet scores. Table S2. Components and scoring of the PYRAMID Mediterranean diet adherence score. Table S3. ICD-9 and ICD-10 codes for dementia diagnosis. Figure S1. Participant flowchart. Table S4. Risk of incident dementia according to Mediterranean diet adherence, with analyses restricted to individuals with a minimum of 2 dietary reports....

Additional file 3. Sampling frame for recruitment.

Additional file 1. Read codes to be used to identify patients with CVD from GP records (obtained from QRISK®-3 for comparability of models).

Additional file 2. MESH Search Terms. This document provides the MESH search terms that were included specifically in the MEDLINE database and altered to fit the other databases.

Additional file 1: Supplementary Table1. Full search strategy. Supplementary Table 2. List of excluded full textstudies with reasons for exclusion. Supplementary Table 3. Fulldetails of AMSTAR2 results

Additional file 1: Figure S1. Flow diagram showing the selection of eligible pregnancies from the CPRD pregnancy register.

Additional file 8: Figure S4. Risk factors associated with polypharmacy during the first trimester of pregnancy.

Additional file 9: Figure S5. Risk factors associated with polypharmacy during the entire pregnancy period.

Additional file 9: Figure S3. Lipid traits – tissue/cell type associations estimated by DESE according to GTEx gene-level and GTEx transcript-level selective expression.

Additional file 11: Figure S4. Comparison of PheWAS results in UKB and MVP for the LDL-C PGS, HDL-C PGS, TC PGS, TG PGS and nonHDL-C PGS.

Additional file 14: Figure S6. PheWAS meta-analysis results for the trans-ethnic TC PGS in UK Biobank and MVP.

Additional file 3: Table S1. 24-h cough monitoring: Cough count [1/hour]. Table S2. 24-h cough frequency: Subgroup analyses by baseline cough count (Bayesian mixed model). Table S3. 24-h cough frequency: Responder rates for different change thresholds. Table S4. VAS cough severity: Responder rates. Table S5. Treatment-emergent adverse events observed in > 5% of patients. Table S6. Cough frequency: Subgroup analyses by occurrence of taste-related adverse events (Bayesian mixed model). Table S7. Cough severity (VAS): Subgroup...

Additional file 1. PRISMA-ScR Checklist.

Additional file 1: Supplemental Table S1. HARP2 Study: Logit-Poisson Hurdle Model.

Background: While international guidelines recommend medication reviews as part of the management of multimorbidity, evidence on how to implement reviews in practice in primary care is lacking. The MyComrade (MultimorbiditY Collaborative Medication Review And Decision Making) intervention is an evidence-based, theoretically informed novel intervention which aims to support the conduct of medication reviews for patients with multimorbidity in primary care. Aim: The pilot study aimed to assess the feasibility of a defnitive trial of the...

Short Summary Severe acute respiratory syndrome coronavirus 2 infection from the Omicron variant in children/adolescents is less severe than infection from the Delta variant. Those 6 to <18 years also have less severe disease than those <6 years old. Background There are limited data assessing coronavirus 2019 (COVID-19) disease severity in children/adolescents infected with the Omicron variant. Methods We identified children and adolescents <18 years of age with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)...

In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24...

In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24...

Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning...

Supplementary Material 3

Supplementary Material 1