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- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:10, s. 1113-1120
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Tidskriftsartikel (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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4. |
- Cherniack, Martin, et al.
(författare)
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Syndromes from segmental vibration and nerve entrapment : observations on case definitions for carpal tunnel syndrome
- 2008
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Ingår i: International Archives of Occupational and Environmental Health. - Berlin : Springer-Vlg. - 0340-0131 .- 1432-1246. ; 81:5, s. 661-669
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: The purpose of this paper is to assess the overlap and stability of two different case definitions of carpal tunnel syndrome CTS. The analysis considers the association between different case definitions and objective tests (sensory nerve conduction velocities, SNCVs and vibrotactile perception thresholds, TTS), and the natural history of CTS, in the context of two vibration-exposed cohorts. Methods: Clinical CTS cases were defined in two ways: (1) by the study physician using fixed criteria, and; (2) by questionnaire and hand diagram. SNCV in median and ulnar nerves was measured for digital, transpalmar, and transcarpal segments, and conventionally as from wrist-digit. Skin temperature was assessed as a point measurement by thermistor and regionally by thermal imaging. VTTs were determined at the bilateral fingertips of the third and fifth digits using a tactometer meeting the requirements of ISO 13091-1 (ISO 2001). The subjects were cohorts of shipyard workers in 2001 and 2004, and dental hygienists in 2002 and 2004. Results: Results are reported for 214 shipyard workers in 2001 and 135 in 2004, and for 94 dental hygienists in 2002 and 66 in 2004. In 2001, 50% of shipyard workers were diagnosed as CTS cases by at least one of the diagnostic schemes, but only 20% were positive by both criteria. Among study physician diagnosed cases, 64% were CTS negative in 2001, 76% were negative in 2004, 13% were positive in both years, 22% became negative after being positive, and 11% became positive after being negative. For only study physician diagnosed CTS did VTTs differ between cases differ and non-cases in digit 3; there was no such distinction in digit 5. The dental hygienists had little CTS. Conclusion: Clinical case definitions of CTS based on diagrams and self-assessment, and clinical evaluation have limited overlap. Combining clinical criteria to create a more narrow or specific case definition of CTS does not appear to predict SNCV. The natural history of CTS suggests a protean disorder with considerable flux in case status over time.
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5. |
- Cherniack, Martin, et al.
(författare)
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The effect of different warming methods on sensory nerve conduction velocity in shipyard workers occupationally exposed to hand-arm vibration.
- 2008
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Ingår i: International archives of occupational and environmental health. - : Springer Science and Business Media LLC. - 1432-1246 .- 0340-0131. ; 81:8, s. 1045-58
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: Segmental sensory nerve conduction velocity (SNCV) was measured from the wrists to the hands and digits in a population of 134 (126 men and 8 women) vibration-exposed shipyard workers following systemic warming using a bicycle ergometer. Results were compared to earlier nerve conduction tests, identical in execution, except that the warming process was segmental and cutaneous. The study was designed to investigate whether SNCVs, which were selectively slow in the fingers after segmental cutaneous (skin surface) warming, would be affected differently by systemic warming. METHODS: Wrist-palm, palm-proximal digit, and digital sensory nerve segments were assessed antidromically by stimulating at the wrist with recording electrodes placed distally. The same subjects were cutaneously warmed in 2001 to >or=31 degrees C and were systemically warmed 28 months later in 2004 by ramped sustained exercise to 100 W for 12 min. Skin temperatures were measured by traditional thermistry and by infrared thermal images taken over the hand and wrist surfaces. RESULTS: When systemic warming was compared to segmental cutaneous warming, SNCVs were increased by 15.1% in the third digit and 20.4% in the fifth digit of the dominant hand. Respective increases in the non-dominant hand were 11.0% and 19.4%. A strong association between increased surface skin temperature and faster SNCV, which had been observed after segmental cutaneous warming, was largely eliminated for both digit and palmar anatomic segments after systemic warming. Significant differences in SNCV between vibration-exposed and non-exposed workers, which had been observed after segmental cutaneous warming, were eliminated after systemic warming. Systemic warming had only a small effect on the wrist-palm (transcarpal) segmental SNCVs. CONCLUSIONS: Reduced SNCV in the digits was observed in vibration-exposed and non-exposed workers. Substituting exercise-induced systemic warming for segmental cutaneous warming significantly increased SNCV in the digits and appeared to reduce differences in SNCV between vibration-exposed and non-exposed workers. These findings persisted despite a substantial time interval between tests, during which the subjects continued to work. There may be more general implications for diagnosing clinical conditions in industrial workers, such as the carpal tunnel syndrome and the hand-arm vibration syndrome.
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- Cherniack, Martin, et al.
(författare)
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The Hand-Arm Vibration International Consortium (HAVIC) : prospective studies on the relationship between power tool exposure and health effects.
- 2007
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Ingår i: Journal of Occupational and Environmental Medicine. - 1076-2752 .- 1536-5948. ; 49:3, s. 289-301
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: The Hand-Arm Vibration International Consortium (HAVIC) is a collaboration of investigators from Europe and North America studying health effects from hand-arm vibration (HAV). Features include prospective design, cross-cohort exposure, and health assessment methods. METHODS: Two new cohorts (dental hygienists and dental hygiene students), two existing cohorts (Finnish forest workers, and Swedish truck cab assemblers), and a previous population (US shipyard workers) are included. Instruments include surveys, quantitative medical tests, physical examination, and work simulation and data logging to assess exposure. New methods were developed for nerve conduction and data logging. RESULTS: Findings on the relationship between nerve conduction and skin temperature in HAV-exposed subjects resulted in a new approach to subject warming. CONCLUSIONS: Integrating established cohorts has advantages over de novo cohort construction. Complex laboratory tests can be successfully adapted for field use.
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