scholarly journals Geographic assessment of cancer genome profiling studies

2019 ◽  
Author(s):  
Paula Carrio Cordo ◽  
Elise Acheson ◽  
Qingyao Huang ◽  
Michael Baudis
Keyword(s):  
Environmental Influence ◽  
Treatment Options ◽  
Medical Knowledge ◽  
Cancer Genome ◽  
Coarse Grained ◽  
Genomic Variants ◽  
Genome Profiling ◽  
Provenance Data ◽  
Somatic Genome ◽  
Correlated Factors

Cancers arise from the accumulation of somatic genome mutations, which can be influenced by inherited genomic variants and external factors such as environmental or lifestyle-related exposure. Due to the heterogeneity of cancers, precise information about the genomic composition of germline and malignant tissues has to be correlated with morphological, clinical and extrinsic features to advance medical knowledge and treatment options. With global differences in cancer frequencies and disease types, geographic data is of importance to understand the interplay between genetic ancestry and environmental influence in cancer incidence, progression and treatment outcome.In this study, we analysed the current landscape of oncogenomic screening publications for geographic information content and quality, to address underrepresented study populations and thereby to fill prominent gaps in our understanding of interactions between somatic variations, population genetics and environmental factors in oncogenesis. We conclude that while the use of proxy derived geographic annotations can be useful for coarse-grained associations, the study of geo-correlated factors in cancer causation and progression will benefit from standardized geographic provenance annotations. Additionally, publication derived geographic provenance data allowed us to highlight stark inequality in the geographies of cancer genome profiling, with a near lack of sizeable studies from Africa and other large regions.

scholarly journals Geographic assessment of cancer genome profiling studies

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Paula Carrio-Cordo ◽  
Elise Acheson ◽  
Qingyao Huang ◽  
Michael Baudis
Keyword(s):  
Environmental Influence ◽  
Treatment Options ◽  
Medical Knowledge ◽  
Cancer Genome ◽  
Coarse Grained ◽  
Genomic Variants ◽  
Genome Profiling ◽  
Provenance Data ◽  
Somatic Genome ◽  
Correlated Factors

Abstract Cancers arise from the accumulation of somatic genome mutations, which can be influenced by inherited genomic variants and external factors such as environmental or lifestyle-related exposure. Due to the heterogeneity of cancers, precise information about the genomic composition of germline and malignant tissues has to be correlated with morphological, clinical and extrinsic features to advance medical knowledge and treatment options. With global differences in cancer frequencies and disease types, geographic data is of importance to understand the interplay between genetic ancestry and environmental influence in cancer incidence, progression and treatment outcome. In this study, we analyzed the current landscape of oncogenomic screening publications for geographic information content and quality, to address underrepresented study populations and thereby to fill prominent gaps in our understanding of interactions between somatic variations, population genetics and environmental factors in oncogenesis. We conclude that while the use of proxy-derived geographic annotations can be useful for coarse-grained associations, the study of geo-correlated factors in cancer causation and progression will benefit from standardized geographic provenance annotations. Additionally, publication-derived geographic provenance data allowed us to highlight stark inequality in the geographies of cancer genome profiling, with a near lack of sizable studies from Africa and other large regions.

scholarly journals MO37-5 Efficacy of liquid biopsy testing for comprehensive cancer genome profiling in 88 cases

2021 ◽  
Vol 32 ◽  
pp. S322
Author(s):  
Nobuhiro Shibata ◽  
Shogen Boku ◽  
Yoshimi Shinomiya ◽  
Hironaga Satake
Keyword(s):  
Liquid Biopsy ◽  
Cancer Genome ◽  
Genome Profiling

scholarly journals Holistic cancer genome profiling for every patient

2020 ◽  
Author(s):  
Serena Nik-Zainal ◽  
Yasin Memari ◽  
Helen R. Davies
Keyword(s):  
Cancer Genome ◽  
Genome Profiling

scholarly journals Along-strike variations in sediment provenance within the Nanaimo basin reveal mechanisms of forearc basin sediment influx events

Lithosphere ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 180-197 ◽  
Author(s):  
Daniel S. Coutts ◽  
William A. Matthews ◽  
Rebecca G. Englert ◽  
Morgan D. Brooks ◽  
Marie-Pier Boivin ◽  
...  
Keyword(s):  
Detrital Zircon ◽  
Coarse Grained ◽  
Sediment Provenance ◽  
Data Set ◽  
Coast Mountains ◽  
The North ◽  
Provenance Data ◽  
Thrust System ◽  
Spatio Temporal ◽  
Forearc Basins

Abstract The along-strike variability in sediment provenance within the Nanaimo basin is important for understanding the tectonic evolution of North America’s Late Cretaceous Pacific margin, providing context for paleogeographic reconstructions. Here, we provide 35 point-counted sandstone samples and 22 new detrital zircon samples from the Nanaimo basin. These new detrital zircon samples compose a portion of a basin-wide data set (N = 49, n = 10,942) that is leveraged to discern spatio-temporal changes in sediment provenance. Provenance data demonstrates that the majority of Nanaimo basin strata were sourced from regions within and east of the Coast Mountains Batholith, while only the southernmost Nanaimo basin, exposed in the San Juan Islands, was supplied sediment from the North Cascade thrust system. Additionally, near-identical age modes and synchronous changes in detrital zircon facies are used to hypothesize a correlation between the Nanaimo Group and the protolith of the Swakane Gneiss. These observations, along with previously identified events in the Cordillera, are used to define two basin-wide events that affected the Nanaimo basin: the first at 84 Ma and the second at 72 Ma. The first event is correlated to the onset of Kula-Farallon spreading, which affected basin subsidence, introduced Proterozoic detrital zircon to the central and southern Nanaimo basin, and uplifted the North Cascade thrust system. The second basin-wide event, which is speculated to have been driven by increased rates of subduction and obliquity, resulted in localized high-flux events in the arc, increased exhumation of the Cascade Crystalline Core, underplating of the Swakane Gneiss, and coarse-grained sedimentation across the basin. The data presented here provides added context for the evolution of the basin and provides insight into the protracted geodynamics of forearc basins undergoing oblique subduction.

scholarly journals PD3-2-3 The short-time results of the OncoGuide NCC Oncopanel System for use in cancer genome profiling at a single institute

2021 ◽  
Vol 32 ◽  
pp. S326
Author(s):  
Shusei Tominaga ◽  
Kiyotsugu Iede ◽  
Takesi Chihara ◽  
Amane Yamauchi
Keyword(s):  
Cancer Genome ◽  
Genome Profiling ◽  
Short Time

MVSC: A Multi-variation Simulator of Cancer Genome

2020 ◽  
Vol 23 (4) ◽  
pp. 326-333
Author(s):  
Ning Li ◽  
Jialiang Yang ◽  
Wen Zhu ◽  
Ying Liang
Keyword(s):  
Next Generation Sequencing ◽  
Genome Structure ◽  
Cancer Genome ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Genomic Variants ◽  
Software Packages ◽  
Tumor Genome ◽  
Generation Sequencing

Background: Many forms of variations exist in the genome, which are the main causes of individual phenotypic differences. The detection of variants, especially those located in the tumor genome, still faces many challenges due to the complexity of the genome structure. Thus, the performance assessment of variation detection tools using next-generation sequencing platforms is urgently needed. Method: We have created a software package called the Multi-Variation Simulator of Cancer genomes (MVSC) to simulate common genomic variants, including single nucleotide polymorphisms, small insertion and deletion polymorphisms, and structural variations (SVs), which are analogous to human somatically acquired variations. Three sets of variations embedded in genomic sequences in different periods were dynamically and sequentially simulated one by one. Results: In cancer genome simulation, complex SVs are important because this type of variation is characteristic of the tumor genome structure. Overlapping variations of different sizes can also coexist in the same genome regions, adding to the complexity of cancer genome architecture. Our results show that MVSC can efficiently simulate a variety of genomic variants that cannot be simulated by existing software packages. Conclusion: The MVSC-simulated variants can be used to assess the performance of existing tools designed to detect SVs in next-generation sequencing data, and we also find that MVSC is memory and time-efficient compared with similar software packages.

scholarly journals Pliocene–Pleistocene basin evolution along the Garlock fault zone, Pilot Knob Valley, California

Geosphere ◽  
2020 ◽  
Vol 16 (5) ◽  
pp. 1208-1224
Author(s):  
William M. Rittase ◽  
J. Douglas Walker ◽  
Joe Andrew ◽  
Eric Kirby ◽  
Elmira Wan
Keyword(s):  
Volcanic Field ◽  
Coarse Grained ◽  
Fine Grained ◽  
Grain Sizes ◽  
The North ◽  
Source Regions ◽  
Provenance Data ◽  
Garlock Fault ◽  
Depositional Patterns ◽  
Fourth Member

Abstract Exposed Pliocene–Pleistocene terrestrial strata provide an archive of the spatial and temporal development of a basin astride the sinistral Garlock fault in California. In the southern Slate Range and Pilot Knob Valley, an ∼2000-m-thick package of Late Cenozoic strata has been uplifted and tilted to the northeast. We name this succession the formation of Pilot Knob Valley and provide new chronologic, stratigraphic, and provenance data for these rocks. The unit is divided into five members that record different source areas and depositional patterns: (1) the lowest exposed strata are conglomeratic rocks derived from Miocene Eagle Crags volcanic field to the south and east across the Garlock fault; (2) the second member consists mostly of fine-grained rocks with coarser material derived from both southern and northern sources; and (3) the upper three members are primarily coarse-grained conglomerates and sandstones derived from the adjacent Slate Range to the north. Tephrochronologic data from four ash samples bracket deposition of the second member to 3.6–3.3 Ma and the fourth member to between 1.1 and 0.6 Ma. A fifth tephrochronologic sample from rocks south of the Garlock fault near Christmas Canyon brackets deposition of a possible equivalent to the second member of the formation of Pilot Knob Valley at ca. 3.1 Ma. Although the age of the base of the lowest member is not directly dated, regional stratigraphic and tectonic associations suggest that the basin started forming ca. 4–5 Ma. By ca. 3.6 Ma, the northward progradation fanglomerate sourced in the Eagle Crags region waned, and subsequent deposition occurred in shallow lacustrine systems. At ca. 3.3 Ma, southward progradation of conglomerates derived from the Slate Range began. Circa 1.1 Ma, continued southward progradation of fanglomerate with Slate Range sources is characterized by a shift to coarser grain sizes, interpreted to reflect uplift of the Slate Range. Overall, basin architecture and the temporal evolution of different source regions were controlled by activity on three regionally important faults—the Garlock, the Marine Gate, and the Searles Valley faults. The timing and style of motions on these faults appear to be directly linked to patterns of basin development.

Must Physicians Reveal Their Wounds?

1996 ◽  
Vol 5 (2) ◽  
pp. 204-213 ◽  
Author(s):  
Barry R. Furrow
Keyword(s):  
Side Effects ◽  
Treatment Options ◽  
Medical Knowledge ◽  
Patient Relationship ◽  
Physician Patient Relationship ◽  
Specialized Knowledge ◽  
Physician Patient ◽  
The Relationship

The physician–patient relationship is anchored in trust. Historically the relationship has been a paternalistic one, with the patient expected to trust the physician's training and skills in doing what is “best” for the patient. But medical knowledge has expanded, as have treatment options and knowledge of the risks of treatment. The physician must now possess volumes of specialized knowledge about procedures and treatments, side effects and alternatives, drugs and their contraindications. Information has become a companion to trust. The patient, while still dependent on the physician's expertise, now wants information about choices and hazards in treatment. Expanded choice has made the patient a consumer of healthcare and its risks rather than a passive recipient of treatment from the professional.

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