| 1. |
- Campbell, PJ, et al.
(författare)
-
Pan-cancer analysis of whole genomes
- 2020
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
-
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.
|
|
| 2. |
|
|
| 3. |
|
|
| 4. |
|
|
| 5. |
|
|
| 6. |
|
|
| 7. |
|
|
| 8. |
|
|
| 9. |
|
|
| 10. |
|
|
| 11. |
|
|
| 12. |
|
|
| 13. |
|
|
| 14. |
|
|
| 15. |
|
|
| 16. |
|
|
| 17. |
|
|
| 18. |
|
|
| 19. |
- Cazzola, E., et al.
(författare)
-
On the electron agyrotropy during rapid asymmetric magnetic island coalescence in presence of a guide field
- 2016
-
Ingår i: Geophysical Research Letters. - : Blackwell Publishing. - 0094-8276 .- 1944-8007. ; 43:15, s. 7840-7849
-
Tidskriftsartikel (refereegranskat)abstract
- We present an analysis of the properties of the electron velocity distribution during island coalescence in asymmetric reconnection with and without guide field. In a previous study, three main domains were identified, in the case without guide field, as X, D, and M regions featuring different reconnection evolutions. These regions are also identified here in the case with guide field. We study the departure from isotropic and gyrotropic behavior by means of different robust detection algorithms proposed in the literature. While in the case without guide field these metrics show an overall agreement, when the guide field is present, a discrepancy in the agyrotropy within some relevant regions is observed, such as at the separatrices and inside magnetic islands. Moreover, in light of the new observations from the Multiscale MagnetoSpheric mission, an analysis of the electron velocity phase-space in these domains is presented.
|
|
| 20. |
- Cazzola, E., et al.
(författare)
-
On the electron dynamics during island coalescence in asymmetric magnetic reconnection
- 2015
-
Ingår i: Physics of Plasmas. - : American Institute of Physics (AIP). - 1070-664X .- 1089-7674. ; 22:9
-
Tidskriftsartikel (refereegranskat)abstract
- We present an analysis of the electron dynamics during rapid island merging in asymmetric magnetic reconnection. We consider a doubly periodic system with two asymmetric transitions. The upper layer is an asymmetric Harris sheet of finite width perturbed initially to promote a single reconnection site. The lower layer is a tangential discontinuity that promotes the formation of many X-points, separated by rapidly merging islands. Across both layers, the magnetic field and the density have a strong jump, but the pressure is held constant. Our analysis focuses on the consequences of electron energization during island coalescence. We focus first on the parallel and perpendicular components of the electron temperature to establish the presence of possible anisotropies and non-gyrotropies. Thanks to the direct comparison between the two different layers simulated, we can distinguish three main types of behavior characteristic of three different regions of interest. The first type represents the regions where traditional asymmetric reconnections take place without involving island merging. The second type of regions instead shows reconnection events between two merging islands. Finally, the third regions identify the regions between two diverging island and where typical signature of reconnection is not observed. Electrons in these latter regions additionally show a flat-top distribution resulting from the saturation of a two-stream instability generated by the two interacting electron beams from the two nearest reconnection points. Finally, the analysis of agyrotropy shows the presence of a distinct double structure laying all over the lower side facing the higher magnetic field region. This structure becomes quadrupolar in the proximity of the regions of the third type. The distinguishing features found for the three types of regions investigated provide clear indicators to the recently launched Magnetospheric Multiscale NASA mission for investigating magnetopause reconnection involving multiple islands.
|
|
| 21. |
|
|
| 22. |
- Gerstung, M, et al.
(författare)
-
Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes
- 2015
-
Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6, s. 5901-
-
Tidskriftsartikel (refereegranskat)abstract
- Cancer is a genetic disease, but two patients rarely have identical genotypes. Similarly, patients differ in their clinicopathological parameters, but how genotypic and phenotypic heterogeneity are interconnected is not well understood. Here we build statistical models to disentangle the effect of 12 recurrently mutated genes and 4 cytogenetic alterations on gene expression, diagnostic clinical variables and outcome in 124 patients with myelodysplastic syndromes. Overall, one or more genetic lesions correlate with expression levels of ~20% of all genes, explaining 20–65% of observed expression variability. Differential expression patterns vary between mutations and reflect the underlying biology, such as aberrant polycomb repression for ASXL1 and EZH2 mutations or perturbed gene dosage for copy-number changes. In predicting survival, genomic, transcriptomic and diagnostic clinical variables all have utility, with the largest contribution from the transcriptome. Similar observations are made on the TCGA acute myeloid leukaemia cohort, confirming the general trends reported here.
|
|
| 23. |
|
|
| 24. |
- Hagleitner, M M, et al.
(författare)
-
Clinical spectrum of immunodeficiency, centromeric instability and facial dysmorphism (ICF syndrome).
- 2008
-
Ingår i: Journal of medical genetics. - : BMJ. - 1468-6244. ; 45:2, s. 93-9
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Immunodeficiency, centromeric instability and facial dysmorphism (ICF syndrome) is a rare autosomal recessive disease characterised by facial dysmorphism, immunoglobulin deficiency and branching of chromosomes 1, 9 and 16 after PHA stimulation of lymphocytes. Hypomethylation of DNA of a small fraction of the genome is an unusual feature of ICF patients which is explained by mutations in the DNA methyltransferase gene DNMT3B in some, but not all, ICF patients. OBJECTIVE: To obtain a comprehensive description of the clinical features of this syndrome as well as genotype-phenotype correlations in ICF patients. METHODS: Data on ICF patients were obtained by literature search and additional information by means of questionnaires to corresponding authors. Results and CONCLUSIONS: 45 patients all with proven centromeric instability were included in this study. Facial dysmorphism was found to be a common characteristic (n = 41/42), especially epicanthic folds, hypertelorism, flat nasal bridge and low set ears. Hypo- or agammaglobulinaemia was demonstrated in nearly all patients (n = 39/44). Opportunistic infections were seen in several patients, pointing to a T cell dysfunction. Haematological malignancy was documented in two patients. Life expectancy of ICF patients is poor, especially those with severe infections in infancy or chronic gastrointestinal problems and failure to thrive. Early diagnosis of ICF is important since early introduction of immunoglobulin supplementation can improve the course of the disease. Allogeneic stem cell transplantation should be considered as a therapeutic option in patients with severe infections or failure to thrive. Only 19 of 34 patients showed mutations in DNMT3B, suggesting genetic heterogeneity. No genotype-phenotype correlation was found between patients with and without DNMT3B mutations.
|
|
| 25. |
- Innocenti, M. E., et al.
(författare)
-
Switch-off slow shock/rotational discontinuity structures in collisionless magnetic reconnection : What to look for in satellite observations
- 2017
-
Ingår i: Geophysical Research Letters. - : American Geophysical Union (AGU). - 0094-8276 .- 1944-8007. ; 44:8, s. 3447-3455
-
Tidskriftsartikel (refereegranskat)abstract
- In Innocenti et al. (2015) we have observed and characterized for the first time Petschek-like switch-off slow shock/rotational discontinuity (SO-SS/RD) compound structures in a 2-D fully kinetic simulation of collisionless magnetic reconnection. Observing these structures in the solar wind or in the magnetotail would corroborate the possibility that Petschek exhausts develop in collisionless media as a result of single X point collisionless reconnection. Here we highlight their signatures in simulations with the aim of easing their identification in observations. The most notable signatures include a four-peaked ion current profile in the out-of-plane direction, associated ion distribution functions, increased electron and ion anisotropy downstream the SS, and increased electron agyrotropy downstream the RDs.
|
|
| 26. |
|
|
| 27. |
|
|
| 28. |
|
|
| 29. |
|
|
| 30. |
|
|
| 31. |
|
|
| 32. |
|
|
| 33. |
|
|
| 34. |
|
|
| 35. |
|
|
| 36. |
- Tehranchi, Ramin, et al.
(författare)
-
Aberrant mitochondrial iron distribution and maturation arrest characterize early erythroid precursors in low-risk myelodysplastic syndromes
- 2005
-
Ingår i: Blood. - : American Society of Hematology. - 1528-0020 .- 0006-4971. ; 106:1, s. 247-253
-
Tidskriftsartikel (refereegranskat)abstract
- Early erythroblasts from patients with refractory anemia (RA) and RA with ringed sideroblasts (RARS) show constitutive mitochondrial release of cytochrome c. Moreover, mature erythroblasts in RARS, but not in RA, display aberrant accumulation of mitochondrial ferritin (MtF). We analyzed cytochrome c release, MtF expression, and gene expression during erythrold differentiation in bone marrow cells from myelodysplastic syndrome (MDS) patients and healthy controls. Whereas none or few cultured erythrold cells from healthy individuals and RA patients expressed MtF, those from RARS patients showed MtF expression at an early stage, when cells were CD34(+) and without morphologic signs of erythroid differentiation. The proportion of RARS erythroblasts that were MtF(+) increased further upon in vitro maturation. Moreover, a significant overexpression of mRNA encoding cytochrome c, and proapoptotic Bid and Bax, was seen in freshly isolated cells from MDS patients. Genes involved in erythroid differentiation were also dysregulated in MDS cells. Importantly, GATA-1 expression increased during normal erythroid maturation, but remained low in MDS cultures, indicating a block of erythroid maturation at the transcriptional level. In conclusion, aberrant MtF expression in RARS erythroblasts occurs at a very early stage of erythrold differentiation and is paralleled by an up-regulation of genes involved in this process.
|
|
| 37. |
|
|
| 38. |
|
|
| 39. |
- Zhou, M., et al.
(författare)
-
Coalescence of Macroscopic Flux Ropes at the Subsolar Magnetopause : Magnetospheric Multiscale Observations
- 2017
-
Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 119:5
-
Tidskriftsartikel (refereegranskat)abstract
- We report unambiguous in situ observation of the coalescence of macroscopic flux ropes by the magnetospheric multiscale (MMS) mission. Two coalescing flux ropes with sizes of similar to 1 R-E were identified at the subsolar magnetopause by the occurrence of an asymmetric quadrupolar signature in the normal component of the magnetic field measured by the MMS spacecraft. An electron diffusion region (EDR) with a width of four local electron inertial lengths was embedded within the merging current sheet. The EDR was characterized by an intense parallel electric field, significant energy dissipation, and suprathermal electrons. Although the electrons were organized by a large guide field, the small observed electron pressure nongyrotropy may be sufficient to support a significant fraction of the parallel electric field within the EDR. Since the flux ropes are observed in the exhaust region, we suggest that secondary EDRs are formed further downstream of the primary reconnection line between the magnetosheath and magnetospheric fields.
|
|
| 40. |
|
|
| 41. |
|
|
| 42. |
|
|
| 43. |
|
|
| 44. |
|
|
| 45. |
- Cazzola, E., et al.
(författare)
-
On the ions acceleration via collisionless magnetic reconnection in laboratory plasmas
- 2016
-
Ingår i: Physics of Plasmas. - : American Institute of Physics (AIP). - 1070-664X .- 1089-7674. ; 23:11
-
Tidskriftsartikel (refereegranskat)abstract
- This work presents an analysis of the ion outflow from magnetic reconnection throughout fully kinetic simulations with typical laboratory plasma values. A symmetric initial configuration for the density and magnetic field is considered across the current sheet. After analyzing the behavior of a set of nine simulations with a reduced mass ratio and with a permuted value of three initial electron temperatures and magnetic field intensity, the best ion acceleration scenario is further studied with a realistic mass ratio in terms of the ion dynamics and energy budget. Interestingly, a series of shock wave structures are observed in the outflow, resembling the shock discontinuities found in recent magnetohydrodynamic simulations. An analysis of the ion outflow at several distances from the reconnection point is presented, in light of possible laboratory applications. The analysis suggests that magnetic reconnection could be used as a tool for plasma acceleration, with applications ranging from electric propulsion to production of ion thermal beams.
|
|
| 46. |
|
|
| 47. |
- Engert, Andreas, et al.
(författare)
-
The European Hematology Association Roadmap for European Hematology Research : a consensus document
- 2016
-
Ingår i: Haematologica. - Pavia, Italy : Ferrata Storti Foundation (Haematologica). - 0390-6078 .- 1592-8721. ; 101:2, s. 115-208
-
Tidskriftsartikel (refereegranskat)abstract
- The European Hematology Association (EHA) Roadmap for European Hematology Research highlights major achievements in diagnosis and treatment of blood disorders and identifies the greatest unmet clinical and scientific needs in those areas to enable better funded, more focused European hematology research. Initiated by the EHA, around 300 experts contributed to the consensus document, which will help European policy makers, research funders, research organizations, researchers, and patient groups make better informed decisions on hematology research. It also aims to raise public awareness of the burden of blood disorders on European society, which purely in economic terms is estimated at (sic)23 billion per year, a level of cost that is not matched in current European hematology research funding. In recent decades, hematology research has improved our fundamental understanding of the biology of blood disorders, and has improved diagnostics and treatments, sometimes in revolutionary ways. This progress highlights the potential of focused basic research programs such as this EHA Roadmap. The EHA Roadmap identifies nine 'sections' in hematology: normal hematopoiesis, malignant lymphoid and myeloid diseases, anemias and related diseases, platelet disorders, blood coagulation and hemostatic disorders, transfusion medicine, infections in hematology, and hematopoietic stem cell transplantation. These sections span 60 smaller groups of diseases or disorders. The EHA Roadmap identifies priorities and needs across the field of hematology, including those to develop targeted therapies based on genomic profiling and chemical biology, to eradicate minimal residual malignant disease, and to develop cellular immunotherapies, combination treatments, gene therapies, hematopoietic stem cell treatments, and treatments that are better tolerated by elderly patients.
|
|
| 48. |
- Fenaux, P, et al.
(författare)
-
A randomized phase 3 study of lenalidomide versus placebo in RBC transfusion-dependent patients with Low-/Intermediate-1-risk myelodysplastic syndromes with del5q
- 2011
-
Ingår i: Blood. - : American Society of Hematology. - 1528-0020 .- 0006-4971. ; 118:14, s. 3765-3776
-
Tidskriftsartikel (refereegranskat)abstract
- This phase 3, randomized, double-blind study assessed the efficacy and safety of lenalidomide in 205 red blood cell (RBC) transfusion-dependent patients with International Prognostic Scoring System Low-/Intermediate-1-risk del5q31 myelodysplastic syndromes. Patients received lenalidomide 10 mg/day on days 1-21 (n = 69) or 5 mg/day on days 1-28 (n = 69) of 28-day cycles; or placebo (n = 67). Crossover to lenalidomide or higher dose was allowed after 16 weeks. More patients in the lenalidomide 10- and 5-mg groups achieved RBC-transfusion independence (TI) for ≥ 26 weeks (primary endpoint) versus placebo (56.1% and 42.6% vs 5.9%; both P < .001). Median duration of RBC-TI was not reached (median follow-up, 1.55 years), with 60% to 67% of responses ongoing in patients without progression to acute myeloid leukemia (AML). Cytogenetic response rates were 50.0% (10 mg) versus 25.0% (5 mg; P = .066). For the lenalidomide groups combined, 3-year overall survival and AML risk were 56.5% and 25.1%, respectively. RBC-TI for ≥ 8 weeks was associated with 47% and 42% reductions in the relative risks of death and AML progression or death, respectively (P = .021 and .048). The safety profile was consistent with previous reports. Lenalidomide is beneficial and has an acceptable safety profile in transfusion-dependent patients with Low-/Intermediate-1-risk del5q myelodysplastic syndrome. This trial was registered at www.clinicaltrials.gov as #NCT00179621.
|
|
| 49. |
|
|
| 50. |
- Hellström-Lindberg, E, et al.
(författare)
-
The role of JAK2 mutations in RARS and other MDS
- 2008
-
Ingår i: Hematology. American Society of Hematology. Education Program. - : American Society of Hematology. - 1520-4391. ; , s. 52-9
-
Tidskriftsartikel (refereegranskat)abstract
- Acquired sideroblastic anemia with unilineage dysplasia (WHO RARS) is a clonal stem cell disorder characterized by erythroid dysplasia, mitochondrial accumulation of mitochondrial ferritin, defective erythroid maturation and anemia. A fraction of these patients also show elevated platelet counts; since 2001 this has been defined as RARS with marked thrombocytosis (RARS-T). It has recently been described that around half of RARS-T patients, along with a small subset of other MDS and mixed myelodysplastic/ myeloproliferative disorders, carry the JAK2 mutation, and that MPL mutations are found in single patients. Clinically, RARS-T patients show features of both RARS, essential thrombocythmia (ET) and to some extent also myelofibrosis. However, the degree of anemia and overall survival is more similar to RARS than myeloproliferative disorders. The occurrence of JAK2 mutations and features of ET in RARS is too frequent to be the result of chance only, and it is possible that this link may provide a key to an increased understanding of the genetic abnormalities causing ring sideroblast formation.
|
|
