FracPaQ: A MATLAB™ toolbox for the quantification of fracture patterns

The patterns of fractures in deformed rocks are rarely uniform or random. Fracture orientations, sizes, and spatial distributions often exhibit some kind of order. In detail, relationships may exist among the different fracture attributes, e.g. small fractures dominated by one orientation, larger fractures by another. These relationships are important because the mechanical (e.g. strength, anisotropy) and transport (e.g. fluids, heat) properties of rock depend on these fracture attributes and patterns. This paper describes FracPaQ, a new open source, cross-platform toolbox to quantify fracture patterns, including distributions in fracture attributes and their spatial variation. Software has been developed to quantify fracture patterns from 2-D digital images, such as thin section micrographs, geological maps, outcrop or aerial photographs or satellite images. The toolbox comprises a suite of MATLAB™ scripts based on previously published quantitative methods for the analysis of fracture attributes: orientations, lengths, intensity, density and connectivity.An estimate of permeability in 2-D is made using a parallel plate model. The software provides an objective and consistent methodology for quantifying fracture patterns and their variations in 2-D across a wide range of length scales, rock types and tectonic settings. The implemented methods presented are inherently scale independent, and a key task where applicable is analysing and integrating quantitative fracture pattern data from micro-to macro-scales. The toolbox was developed in MATLAB™ and the source code is publicly available on GitHub™ and the Mathworks™ FileExchange. The code runs on any computer with MATLAB installed, including PCs with Microsoft Windows, Apple Macs with Mac OS X, and machines running different flavours of Linux. The application, source code and sample input files are available in open repositories in the hope that other developers and researchers will optimise and extend the functionality for the benefit of the wider community

Effects of crystallographic anisotropy on fracture development and acoustic emission in quartz

Transgranular microcracking is fundamental for the initiation and propagation of all fractures in rocks. The geometry of these microcracks is primarily controlled by the interaction of the imposed stress field with the mineral elastic properties. However, the effects of anisotropic elastic properties of minerals on brittle fracture are not well understood. This study examines the effects of elastic anisotropy of quartz on the geometry of brittle fracture and related acoustic emissions (AE) developed during indentation experiments on single crystals at ambient pressure and temperature. A Hertzian cone crack developed during blunt indentation of a single crystal of flawless Brazilian quartz parallel to the c axis shows geometric deviation away from predictions based on the isotropic case, consistent with trigonal symmetry. The visible cone crack penetration depth varies from 3 to 5 mm and apical angle from 53 to 40. Electron backscatter diffraction (EBSD) mapping of the crack tip shows that fracturing initiates along a ~40 μm wide process zone, comprising damage along overlapping en echelon high-index crystallographic planes, shown by discrete bands of reduced electron backscatter pattern (EBSP) quality (band contrast).Coalescence of these surfaces results in a stepped fracture morphology. Monitoring of AE during indentation reveals that the elastic anisotropy of quartz has a significant effect on AE location and focal mechanisms. Ninety-four AE events were recorded during indentation and show an increasing frequency with increasing load. They correspond to the development of subsidiary concentric cracks peripheral to the main cone crack. The strong and complex anisotropy in seismic velocity (~28% Vp, ~43% Vs with trigonal symmetry) resulted in inaccurate and high uncertainty in AE locations using Geiger location routine with an isotropic velocity model. This problem was overcome by using a relative (master event) location algorithm that only requires a priori knowledge of the velocity structure within the source volume. The AE location results correlate reasonably well to the extent of the observed cone crack. Decomposition of AE source mechanisms of the Geiger relocated events shows dominantly end-member behavior between tensile and compressive vector dipole events, with some double-couple-dominated events and no purely tensile or compressive events. The same events located by the master event algorithm yield greater percentage of vector dipole components and no double-couple events, indicating that AE source mechanism solutions can depend on AE location accuracy, and therefore, relocation routine that is utilized. Calculations show that the crystallographic anisotropy of quartz causes apparent deviation of the moment tensors away from double-couple and pure tensile/compressive sources consistent with the observations. Preliminary modeling of calcite anisotropy shows a response distinct from quartz, indicating that the effects of anisotropy on interpreting AE are complex and require detailed further study

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

New shock microstructures in titanite (CaTiSiO5) from the peak ring of the Chicxulub impact structure, Mexico

Accessory mineral geochronometers such as apatite, baddeleyite, monazite, xenotime and zircon are increasingly being recognized for their ability to preserve diagnostic microstructural evidence of hypervelocity-impact processes. To date, little is known about the response of titanite to shock metamorphism, even though it is a widespread accessory phase and a U–Pb geochronometer. Here we report two new mechanical twin modes in titanite within shocked granitoid from the Chicxulub impact structure, Mexico. Titanite grains in the newly acquired core from the International Ocean Discovery Program Hole M0077A preserve multiple sets of polysynthetic twins, most commonly with composition planes (K1) = ~ { 1 ¯ 11 } , and shear direction (η1) = , and less commonly with the mode K1 = {130}, η1 = ~ . In some grains, {130} deformation bands have formed concurrently with the deformation twins, indicating dislocation slip with Burgers vector b = can be active during impact metamorphism. Titanite twins in the modes described here have not been reported from endogenically deformed rocks; we, therefore, propose this newly identified twin form as a result of shock deformation. Formation conditions of the twins have not been experimentally calibrated, and are here empirically constrained by the presence of planar deformation features in quartz (12 ± 5 and ~ 17 ± 5 GPa) and the absence of shock twins in zircon (< 20 GPa). While the lower threshold of titanite twin formation remains poorly constrained, identification of these twins highlight the utility of titanite as a shock indicator over the pressure range between 12 and 17 GPa. Given the challenges to find diagnostic indicators of shock metamorphism to identify both ancient and recent impact evidence on Earth, microstructural analysis of titanite is here demonstrated to provide a new tool for recognizing impact deformation in rocks where other impact evidence may be erased, altered, or did not manifest due to generally low (< 20 GPa) shock pressure

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe

Author Correction: The landscape of viral associations in human cancers

author correctio