The pan-cancer analysis of whole genomes The expansion of whole-genome sequencing studies from individual ICGC and TCGA working groups presented the opportunity to undertake a meta-analysis of genomic features across tumour types. To achieve this, the PCAWG Consortium was established. A Technical Working Group implemented the informatics analyses by aggregating the raw sequencing data from different working groups that studied individual tumour types, aligning the sequences to the human genome and delivering a set of high-quality somatic mutation calls for downstream analysis (Extended Data Fig. 1). Given the recent meta-analysis
Factors that influence mental health help seeking among adults 55+ years were examined prospectively. A discriminant analysis significantly differentiated between 120 older adults needing and seeking services and a comparison group of 120 older adults not needing services. Prior to having sought help, help seekers demonstrated poorer psychological well-being, reported more physical health problems, reported a higher level of unpleasant stressful events, and perceived greater deficits in the amount of social support available to them in time of need. The vast majority of these older help seekers sought help for their mental health problems from a medical doctor rather than from a mental health center or clinic or from a minister. Significantly more help seekers than nonseekers experienced stressful events involving bereavement, social and economic loss, and new physical illness.
Laboratory selection experiments are alluring in their simplicity, power, and ability to inform us about how evolution works. A longstanding challenge facing evolution experiments with metazoans is that significant generational turnover takes a long time. In this work, we present data from a unique system of experimentally evolved laboratory populations of Drosophila melanogaster that have experienced three distinct life-history selection regimes. The goal of our study was to determine how quickly populations of a certain selection regime diverge phenotypically from their ancestors, and how quickly they converge with independently derived populations that share a selection regime. Our results indicate that phenotypic divergence from an ancestral population occurs rapidly, within dozens of generations, regardless of that population's evolutionary history. Similarly, populations sharing a selection treatment converge on common phenotypes in this same time frame, regardless of selection pressures those populations may have experienced in the past. These patterns of convergence and divergence emerged much faster than expected, suggesting that intermediate evolutionary history has transient effects in this system. The results we draw from this system are applicable to other experimental evolution projects, and suggest that many relevant questions can be sufficiently tested on shorter timescales than previously thought.
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 telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXX trunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXX trunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
The evolution of genomic research and its integration into clinical practice, as they become international—even global—endeavors, has brought us to a place where scientists and clinicians may now only ignore the rules governing international data sharing at their own peril. Open data policies, on the one hand, increasingly require custodians of others’ genomic data to make it as widely available as feasible, including to researchers in other countries. Data protection law, on the other, has become a significant hurdle to the sharing of personal data across jurisdictional borders. The space between these two competing duties is narrowing. In contrast with the other texts in this volume, which explore the present and future of data sharing and data protection, this article’s focus is on the past. It centres on the historical development of the data protection rules regarding the international transfer of personal data up to the present. The article’s aim is to bring into focus the underlying objectives that have influenced and that will continue to influence the way that data protection rules are applied to the fields of genomics and health, as well as future developments in data protection generally. The first part of this article describes the development of international data-sharing data protection rules since 1970. The second considers difficulties in applying general data protection rules to the specific context of genomics and health. The third and final part compares the options available to comply with the international transfer restrictions set out in the standard-setting EU General Data Protection Regulation from a genomics perspective.
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 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.
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