Additional file 1: Supplemental Methods. Table S1. Inclusion and exclusion criteria. Table S2. Outcome of the cognitive test battery. Table S3. Imaging protocol and sequence parameters. Table S4. Correlation of biomarkers to cognitive domains and brain morphology. Table S5. Extended clinical characteristics of NfL quartiles. Table S6. Extended clinical characteristics of pTau quartiles. Table S7. Mediation analysis of parameters affecting serum levels of Ln(NfL). Table S8. Mediation analysis of parameters affecting serum levels of Ln(pTau)....

Additional file 1. The additional file provides statistical comparison of gene expression between wildtype and Cx3cr1GFP/GFP mice at the different time points, control data for human FoxP3 staining, the growth rate of ARPE-19 to compare with Crisp/Cas treated ARPE-19 cells and uncropped dot plots.

Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the...

Additional file 1. The additional file provides statistical comparison of gene expression between wildtype and Cx3cr1GFP/GFP mice at the different time points, control data for human FoxP3 staining, the growth rate of ARPE-19 to compare with Crisp/Cas treated ARPE-19 cells and uncropped dot plots.

Additional file 11: Material and Methods.

Additional file 11: Material and Methods.

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...

Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. 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 tumor types, we integrated...

The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding...

The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding...

Additional file 1: Supplementary preclinical and clinical information.

Additional file 1: Supplementary preclinical and clinical information.

Additional file 1: Table S1. Included publication in analysis of the research question. Table S2. Excluded references and reason for exclusion.

Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the...

Supplementary Material 1

Supplementary Material 1

Additional file 1: Supplemental Methods. Table S1. Inclusion and exclusion criteria. Table S2. Outcome of the cognitive test battery. Table S3. Imaging protocol and sequence parameters. Table S4. Correlation of biomarkers to cognitive domains and brain morphology. Table S5. Extended clinical characteristics of NfL quartiles. Table S6. Extended clinical characteristics of pTau quartiles. Table S7. Mediation analysis of parameters affecting serum levels of Ln(NfL). Table S8. Mediation analysis of parameters affecting serum levels of Ln(pTau)....

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...

Supplemental Material, sj-docx-1-cpt-10.1177_10742484221146375 for Up-Titration of Sacubitril/Valsartan Among Patients With Heart Failure and Preserved Ejection Fraction by Koichiro Matsumura, Takeshi Ijichi, Junko Morimoto, Kensuke Takabayashi, Mitsunori Miho, Keisuke Ueno, Eijiro Yagi, Toru Takase, Masafumi Ueno and Gaku Nakazawa in Journal of Cardiovascular Pharmacology and Therapeutics

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...

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...

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...

Additional file 1: Supplementary material. Description of assay parallelism and pre-analytical stability.

Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. 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 tumor types, we integrated...