Stratigraphy and paleoenvironments of the Cretaceous rocks, North and South Pender Islands, British Columbia

The bedrock of North and South Pender Islands, the southernmost islands of British Columbia's Gulf Islands chain, is formed entirely by six formations of the Late Cretaceous Nanaimo Group. These six formations are, from oldest to youngest, the Extens ion- Protection, Cedar District, DeCourcy, Northumberland, Geoffrey, and Spray Formations, A composite section of maximum thicknesses for these formations totals approximately 11,600 feet. The formations, however, vary in thickness significantly along strike. These formations represent four cycles of deltaic progradation, the youngest and oldest of which are incompletely exposed. The Extension-Protection Formation is considered to be the upper part of a west- to northwest-prograding delta complex, the lower part of which is not exposed within the thesis area, The fluvial conglomerates of the Extension-Protection Formation, inferred to be topset beds, are overlain on South Pender Island by an interval of shallow marine arkosic and ljthic sandstones, This shallow marine interval pinches out to the northwest and is absent on North Fender Island. The mineralogy of the conglomerates and sandstones suggests that the ExtensionProtection Formation was derived from the pre- Cretaceous rocks of Vancouver Island. The Extension-Protection Formation intertongues with and grades into the Cedar District /DeCourcy delta. Prodelta muds of the lower Cedar District Formation are overlain by distal bar turbidites. The turbid ite deposits are conformably overlain by arkosic delta-front sheet sands or river mouth bars of the lower DeCourcy Formation. Continued basin subsidence, possibly combined with lower sedirnentation rates, caused a transgression over the lower DeCourcy Formation and a return to prodelta deposition of the upper Cedar District Formation. The upper Cedar District and upper DeCourcy Formations follow a depositional cycle similar to that of the lower Cedar District and lower DeCourcy Formations, with the exception that fluvial conglomerates inferred to be topset beds intertongue with and overlie the shallow marine delta-front sheet sands or river mouth bars. Paleocurrent data, lateral thinning and facies changes, and mineralogy suggest that the Cedar District/DeCourcy delta sediments were derived from a source, to the northwest on Vancouver Is land, which was composed of the Vancouver Group and the Island Intrusions. The vertical succession of prodelta muds, distal bar turbidites,. delta-front sheet sands or river mouth bars, and fluvial conglomerates is the same for the Northumberland/Geoffrey deltaic cycle as for the upper Cedar District /DeCourcy deltaic cycle. Paleocurrent data, lateral thinning and facies changes, and mineralogy suggest that the Northumberland/Geoffrey delta sediments were derived from a source area to the northwest, which was either the same source area as that of the Cedar District /DeCourcy delta, or one similar to it, The Spray Formation, the lower part of the youngest deltaic cycle exposed in the thesis area, consists of distal bar turbidites. The Northumberland/Geoffrey delta intertongues with the Spray Formation, although this intertonguing may be related to the overlying Gabriola Formation, At least three episodes of faulting have deformed the rocks of North and South Pender Islands, forming the Kulleet Syncline and other subordinate folds, The major faults trend west-northwest, with minor faults trending northwest to northeast

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

HudsonJonPark1975.pdf

The bedrock of North and South Pender Islands, the southernmost islands of British Columbia's Gulf Islands chain, is formed entirely by six formations of the Late Cretaceous Nanaimo Group. These six formations are, from oldest to youngest, the Extens ion- Protection, Cedar District, DeCourcy, Northumberland, Geoffrey, and Spray Formations, A composite section of maximum thicknesses for these formations totals approximately 11,600 feet. The formations, however, vary in thickness significantly along strike. These formations represent four cycles of deltaic progradation, the youngest and oldest of which are incompletely exposed. The Extension-Protection Formation is considered to be the upper part of a west- to northwest-prograding delta complex, the lower part of which is not exposed within the thesis area, The fluvial conglomerates of the Extension-Protection Formation, inferred to be topset beds, are overlain on South Pender Island by an interval of shallow marine arkosic and ljthic sandstones, This shallow marine interval pinches out to the northwest and is absent on North Fender Island. The mineralogy of the conglomerates and sandstones suggests that the ExtensionProtection Formation was derived from the pre- Cretaceous rocks of Vancouver Island. The Extension-Protection Formation intertongues with and grades into the Cedar District /DeCourcy delta. Prodelta muds of the lower Cedar District Formation are overlain by distal bar turbidites. The turbid ite deposits are conformably overlain by arkosic delta-front sheet sands or river mouth bars of the lower DeCourcy Formation. Continued basin subsidence, possibly combined with lower sedirnentation rates, caused a transgression over the lower DeCourcy Formation and a return to prodelta deposition of the upper Cedar District Formation. The upper Cedar District and upper DeCourcy Formations follow a depositional cycle similar to that of the lower Cedar District and lower DeCourcy Formations, with the exception that fluvial conglomerates inferred to be topset beds intertongue with and overlie the shallow marine delta-front sheet sands or river mouth bars. Paleocurrent data, lateral thinning and facies changes, and mineralogy suggest that the Cedar District/DeCourcy delta sediments were derived from a source, to the northwest on Vancouver Is land, which was composed of the Vancouver Group and the Island Intrusions. The vertical succession of prodelta muds, distal bar turbidites,. delta-front sheet sands or river mouth bars, and fluvial conglomerates is the same for the Northumberland/Geoffrey deltaic cycle as for the upper Cedar District /DeCourcy deltaic cycle. Paleocurrent data, lateral thinning and facies changes, and mineralogy suggest that the Northumberland/Geoffrey delta sediments were derived from a source area to the northwest, which was either the same source area as that of the Cedar District /DeCourcy delta, or one similar to it, The Spray Formation, the lower part of the youngest deltaic cycle exposed in the thesis area, consists of distal bar turbidites. The Northumberland/Geoffrey delta intertongues with the Spray Formation, although this intertonguing may be related to the overlying Gabriola Formation, At least three episodes of faulting have deformed the rocks of North and South Pender Islands, forming the Kulleet Syncline and other subordinate folds, The major faults trend west-northwest, with minor faults trending northwest to northeast

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The bedrock of North and South Pender Islands, the southernmost islands of British Columbia's Gulf Islands chain, is formed entirely by six formations of the Late Cretaceous Nanaimo Group. These six formations are, from oldest to youngest, the Extens ion- Protection, Cedar District, DeCourcy, Northumberland, Geoffrey, and Spray Formations, A composite section of maximum thicknesses for these formations totals approximately 11,600 feet. The formations, however, vary in thickness significantly along strike. These formations represent four cycles of deltaic progradation, the youngest and oldest of which are incompletely exposed. The Extension-Protection Formation is considered to be the upper part of a west- to northwest-prograding delta complex, the lower part of which is not exposed within the thesis area, The fluvial conglomerates of the Extension-Protection Formation, inferred to be topset beds, are overlain on South Pender Island by an interval of shallow marine arkosic and ljthic sandstones, This shallow marine interval pinches out to the northwest and is absent on North Fender Island. The mineralogy of the conglomerates and sandstones suggests that the ExtensionProtection Formation was derived from the pre- Cretaceous rocks of Vancouver Island. The Extension-Protection Formation intertongues with and grades into the Cedar District /DeCourcy delta. Prodelta muds of the lower Cedar District Formation are overlain by distal bar turbidites. The turbid ite deposits are conformably overlain by arkosic delta-front sheet sands or river mouth bars of the lower DeCourcy Formation. Continued basin subsidence, possibly combined with lower sedirnentation rates, caused a transgression over the lower DeCourcy Formation and a return to prodelta deposition of the upper Cedar District Formation. The upper Cedar District and upper DeCourcy Formations follow a depositional cycle similar to that of the lower Cedar District and lower DeCourcy Formations, with the exception that fluvial conglomerates inferred to be topset beds intertongue with and overlie the shallow marine delta-front sheet sands or river mouth bars. Paleocurrent data, lateral thinning and facies changes, and mineralogy suggest that the Cedar District/DeCourcy delta sediments were derived from a source, to the northwest on Vancouver Is land, which was composed of the Vancouver Group and the Island Intrusions. The vertical succession of prodelta muds, distal bar turbidites,. delta-front sheet sands or river mouth bars, and fluvial conglomerates is the same for the Northumberland/Geoffrey deltaic cycle as for the upper Cedar District /DeCourcy deltaic cycle. Paleocurrent data, lateral thinning and facies changes, and mineralogy suggest that the Northumberland/Geoffrey delta sediments were derived from a source area to the northwest, which was either the same source area as that of the Cedar District /DeCourcy delta, or one similar to it, The Spray Formation, the lower part of the youngest deltaic cycle exposed in the thesis area, consists of distal bar turbidites. The Northumberland/Geoffrey delta intertongues with the Spray Formation, although this intertonguing may be related to the overlying Gabriola Formation, At least three episodes of faulting have deformed the rocks of North and South Pender Islands, forming the Kulleet Syncline and other subordinate folds, The major faults trend west-northwest, with minor faults trending northwest to northeast

Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks.

We examined common variation in asthma risk by conducting a meta-analysis of worldwide asthma genome-wide association studies (23,948 asthma cases, 118,538 controls) of individuals from ethnically diverse populations. We identified five new asthma loci, found two new associations at two known asthma loci, established asthma associations at two loci previously implicated in the comorbidity of asthma plus hay fever, and confirmed nine known loci. Investigation of pleiotropy showed large overlaps in genetic variants with autoimmune and inflammatory diseases. The enrichment in enhancer marks at asthma risk loci, especially in immune cells, suggested a major role of these loci in the regulation of immunologically related mechanisms

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

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