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...

qPCR primers, model parameter estimates

Supplemental material, sj-doc-1-msj-10.1177_13524585231155639 for Cerebrospinal fluid–related tissue damage in multiple sclerosis patients with iron rim lesions by Matthias Wittayer, Claudia E Weber, Maximilian Kittel, Michael Platten, Lucas Schirmer, Hayrettin Tumani, Achim Gass and Philipp Eisele in Multiple Sclerosis Journal

Supplemental material, sj-docx-3-tan-10.1177_17562864221143834 for Parkinson’s disease or multiple system atrophy: potential separation by quantitative susceptibility mapping by Franz Marxreiter, Vera Lambrecht, Angelika Mennecke, Jannis Hanspach, Jelena Jukic, Martin Regensburger, Juergen Herrler, Alexander German, Jan Kassubek, Georg Grön, Hans-Peter Müller, Frederik B. Laun, Arnd Dörfler, Juergen Winkler and Manuel A. Schmidt in Therapeutic Advances in Neurological Disorders

Supplemental material, sj-docx-1-eso-10.1177_23969873231164728 for Genetic liability to migraine and functional outcome after ischemic stroke by Mengmeng Wang, Iyas Daghlas, Zhizhong Zhang, Dan Ye, Shun Li and Dandan Liu in European Stroke Journal

Supplemental material, sj-docx-3-tan-10.1177_17562864221143834 for Parkinson’s disease or multiple system atrophy: potential separation by quantitative susceptibility mapping by Franz Marxreiter, Vera Lambrecht, Angelika Mennecke, Jannis Hanspach, Jelena Jukic, Martin Regensburger, Juergen Herrler, Alexander German, Jan Kassubek, Georg Grön, Hans-Peter Müller, Frederik B. Laun, Arnd Dörfler, Juergen Winkler and Manuel A. Schmidt in Therapeutic Advances in Neurological Disorders

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-msj-10.1177_13524585231151212 for Cognition in patients with neuromyelitis optica spectrum disorders: A prospective multicentre study of 217 patients (CogniNMO-Study) by Martin W Hümmert, Carlotta Stern, Friedemann Paul, Ankelien Duchow, Judith Bellmann-Strobl, Ilya Ayzenberg, Carolin Schwake, Ingo Kleiter, Kerstin Hellwig, Sven Jarius, Brigitte Wildemann, Makbule Senel, Achim Berthele, Katrin Giglhuber, Felix Luessi, Matthias Grothe, Luisa Klotz, Rasmus Schülke, Stefan Gingele, Jürgen H Faiss, Annette Walter, Clemens Warnke, Florian Then Bergh, Orhan Aktas, Marius Ringelstein, Jan-Patrick...

Statistical analyses

Supplemental material, sj-docx-2-msj-10.1177_13524585231155639 for Cerebrospinal fluid–related tissue damage in multiple sclerosis patients with iron rim lesions by Matthias Wittayer, Claudia E Weber, Maximilian Kittel, Michael Platten, Lucas Schirmer, Hayrettin Tumani, Achim Gass and Philipp Eisele in Multiple Sclerosis Journal

Supplemental material, sj-docx-2-msj-10.1177_13524585231155639 for Cerebrospinal fluid–related tissue damage in multiple sclerosis patients with iron rim lesions by Matthias Wittayer, Claudia E Weber, Maximilian Kittel, Michael Platten, Lucas Schirmer, Hayrettin Tumani, Achim Gass and Philipp Eisele in Multiple Sclerosis Journal

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...

Containing all supplementary tables, figures as well as additional methods

Supplementary Figures S1-S11

Supplemental material, sj-docx-1-msj-10.1177_13524585231151212 for Cognition in patients with neuromyelitis optica spectrum disorders: A prospective multicentre study of 217 patients (CogniNMO-Study) by Martin W Hümmert, Carlotta Stern, Friedemann Paul, Ankelien Duchow, Judith Bellmann-Strobl, Ilya Ayzenberg, Carolin Schwake, Ingo Kleiter, Kerstin Hellwig, Sven Jarius, Brigitte Wildemann, Makbule Senel, Achim Berthele, Katrin Giglhuber, Felix Luessi, Matthias Grothe, Luisa Klotz, Rasmus Schülke, Stefan Gingele, Jürgen H Faiss, Annette Walter, Clemens Warnke, Florian Then Bergh, Orhan Aktas, Marius Ringelstein, Jan-Patrick...

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...

Statistical analyses

qPCR primers, model parameter estimates

Supplemental material, sj-doc-1-msj-10.1177_13524585231155639 for Cerebrospinal fluid–related tissue damage in multiple sclerosis patients with iron rim lesions by Matthias Wittayer, Claudia E Weber, Maximilian Kittel, Michael Platten, Lucas Schirmer, Hayrettin Tumani, Achim Gass and Philipp Eisele in Multiple Sclerosis Journal

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...

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-eso-10.1177_23969873231164728 for Genetic liability to migraine and functional outcome after ischemic stroke by Mengmeng Wang, Iyas Daghlas, Zhizhong Zhang, Dan Ye, Shun Li and Dandan Liu in European Stroke Journal

Containing all supplementary tables, figures as well as additional methods