Additional file 1. Supplementary Figures S1-S17.

Additional file 1. Supplementary Figures S1-S17.

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...

Higher adherence to the Mediterranean diet during pregnancy is related to a lower risk of preterm birth and to better offspring cardiometabolic health. DNA methylation may be an underlying biological mechanism. We evaluated whether maternal adherence to the Mediterranean diet was associated with offspring cord blood DNA methylation. We meta-analysed epigenome-wide association studies (EWAS) of maternal adherence to the Mediterranean diet during pregnancy and offspring cord blood DNA methylation in 2802 mother–child pairs from five...

Additional file 1: Fig S1. Validation ofvideo-based exposure to a zebrafish predator. Fig S2. Principal component analysis (PCA) of RNA-seq performed in7 dpf larvae. Fig S3. RNA-seq vsqPCR correlation values.

Additional file 2: Script 1. Script limma_sva.r.

Additional file 4: Figure S1. Protein quantitative assay development. (A) Histogram showing the number of proteins quantified in each group. In red are proteins quantified in at least 4 out of 7 patients which were included in the statistical analysis. (B) Peptide identity confirmation between parallel reaction monitoring (PRM) elution profiles of endogenous peptides and internal standards. Transitions showing interferences were removed (middle panel, marked arrow) and those measurements considered to be under the limit...

Additional file 1: Fig S1. Validation ofvideo-based exposure to a zebrafish predator. Fig S2. Principal component analysis (PCA) of RNA-seq performed in7 dpf larvae. Fig S3. RNA-seq vsqPCR correlation values.

Additional file 2: Script 1. Script limma_sva.r.

Higher adherence to the Mediterranean diet during pregnancy is related to a lower risk of preterm birth and to better offspring cardiometabolic health. DNA methylation may be an underlying biological mechanism. We evaluated whether maternal adherence to the Mediterranean diet was associated with offspring cord blood DNA methylation. We meta-analysed epigenome-wide association studies (EWAS) of maternal adherence to the Mediterranean diet during pregnancy and offspring cord blood DNA methylation in 2802 mother–child pairs from five...

Additional file 2: Figure S1. BraLan3 genome assembly and annotation quality comparison. Drer, Ggal, Mmus, Hsap, Bflo and Bbel correspond to the latest available genome assemblies for zebrafish, chicken, mouse, human, Florida amphioxus (B. floridae) and an Asian amphioxus (B. belcheri), respectively (see Methods). Blan2 corresponds to the latest genome reference for the European amphioxus previous to this publication [8] and Blan3 corresponds to BraLan3, the genome reference for the European amphioxus presented in this...

Additional file 3. Supplementary Note 1.

Additional file 4. Review history.

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...

Neuronal microexons represent the most highly conserved class of alternative splicing events and their timed expression shapes neuronal biology, including neuronal commitment and differentiation. The six-nt microexon 34ʹ is included in the neuronal form of TAF1 mRNA, which encodes the largest subunit of the basal transcription factor TFIID. In this study, we investigate the tissue distribution of TAF1-34ʹ mRNA and protein and the mechanism responsible for its neuronal-specific splicing. Using isoform-specific RNA probes and antibodies,...

Additional file 8: Figure S2. Prediction ability of the protein signatures when considering partially chemosensitive patients and clinical variables. (A) Retention time drift of TKT, LAMC1, FUCO and CRP endogenous peptides for all samples analysed. (B) Receiver operating curves of the two best protein combination. TKT + LAMC1 + FUCO with an AUC of 0.76 (95% CI 0.64—0.87) and TKT + LAMC1 + CRP with an AUC of 0.75 (95% CI 0.64–0.86). (C) Receiver operating...

Additional file 8: Figure S2. Prediction ability of the protein signatures when considering partially chemosensitive patients and clinical variables. (A) Retention time drift of TKT, LAMC1, FUCO and CRP endogenous peptides for all samples analysed. (B) Receiver operating curves of the two best protein combination. TKT + LAMC1 + FUCO with an AUC of 0.76 (95% CI 0.64—0.87) and TKT + LAMC1 + CRP with an AUC of 0.75 (95% CI 0.64–0.86). (C) Receiver operating...

The testis produces gametes through spermatogenesis and evolves rapidly at both the morphological and molecular level in mammals1-6, probably owing to the evolutionary pressure on males to be reproductively successful7. However, the molecular evolution of individual spermatogenic cell types across mammals remains largely uncharacterized. Here we report evolutionary analyses of single-nucleus transcriptome data for testes from 11 species that cover the three main mammalian lineages (eutherians, marsupials and monotremes) and birds (the evolutionary outgroup), and...

Additional file 9. Review history.

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...

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...

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 testis produces gametes through spermatogenesis and evolves rapidly at both the morphological and molecular level in mammals1-6, probably owing to the evolutionary pressure on males to be reproductively successful7. However, the molecular evolution of individual spermatogenic cell types across mammals remains largely uncharacterized. Here we report evolutionary analyses of single-nucleus transcriptome data for testes from 11 species that cover the three main mammalian lineages (eutherians, marsupials and monotremes) and birds (the evolutionary outgroup), and...

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...