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1.	Abbasi, R., et al. (författare) A Search for IceCube Sub-TeV Neutrinos Correlated with Gravitational-wave Events Detected By LIGO/Virgo 2023 Ingår i: Astrophysical Journal. - : Institute of Physics Publishing (IOPP). - 1538-4357 .- 0004-637X. ; 959:2 Tidskriftsartikel (refereegranskat)abstract The LIGO/Virgo collaboration published the catalogs GWTC-1, GWTC-2.1, and GWTC-3 containing candidate gravitational-wave (GW) events detected during its runs O1, O2, and O3. These GW events can be possible sites of neutrino emission. In this paper, we present a search for neutrino counterparts of 90 GW candidates using IceCube DeepCore, the low-energy infill array of the IceCube Neutrino Observatory. The search is conducted using an unbinned maximum likelihood method, within a time window of 1000 s, and uses the spatial and timing information from the GW events. The neutrinos used for the search have energies ranging from a few GeV to several tens of TeV. We do not find any significant emission of neutrinos, and place upper limits on the flux and the isotropic-equivalent energy emitted in low-energy neutrinos. We also conduct a binomial test to search for source populations potentially contributing to neutrino emission. We report a nondetection of a significant neutrino-source population with this test.
2.	Abbasi, R., et al. (författare) IceCat-1: The IceCube Event Catalog of Alert Tracks 2023 Ingår i: Astrophysical Journal, Supplement Series. - : IOP Publishing Ltd. - 1538-4365 .- 0067-0049. ; 269:1 Tidskriftsartikel (refereegranskat)abstract We present a catalog of likely astrophysical neutrino track-like events from the IceCube Neutrino Observatory. IceCube began reporting likely astrophysical neutrinos in 2016, and this system was updated in 2019. The catalog presented here includes events that were reported in real time since 2019, as well as events identified in archival data samples starting from 2011. We report 275 neutrino events from two selection channels as the first entries in the catalog, the IceCube Event Catalog of Alert Tracks, which will see ongoing extensions with additional alerts. The Gold and Bronze alert channels respectively provide neutrino candidates with a 50% and 30% probability of being astrophysical, on average assuming an astrophysical neutrino power-law energy spectral index of 2.19. For each neutrino alert, we provide the reconstructed energy, direction, false-alarm rate, probability of being astrophysical in origin, and likelihood contours describing the spatial uncertainty in the alert's reconstructed location. We also investigate a directional correlation of these neutrino events with gamma-ray and X-ray catalogs, including 4FGL, 3HWC, TeVCat, and Swift-BAT.
3.	Abbasi, R., et al. (författare) Search for Galactic Core-collapse Supernovae in a Decade of Data Taken with the IceCube Neutrino Observatory 2024 Ingår i: Astrophysical Journal. - : Institute of Physics Publishing (IOPP). - 1538-4357 .- 0004-637X. ; 961:1 Tidskriftsartikel (refereegranskat)abstract The IceCube Neutrino Observatory has been continuously taking data to search for O(0.5–10) s long neutrino bursts since 2007. Even if a Galactic core-collapse supernova is optically obscured or collapses to a black hole instead of exploding, it will be detectable via the O(10) MeV neutrino burst emitted during the collapse. We discuss a search for such events covering the time between 2008 April 17 and 2019 December 31. Considering the average data taking and analysis uptime of 91.7% after all selection cuts, this is equivalent to 10.735 yr of continuous data taking. In order to test the most conservative neutrino production scenario, the selection cuts were optimized for a model based on an 8.8 solar mass progenitor collapsing to an O–Ne–Mg core. Conservative assumptions on the effects of neutrino oscillations in the exploding star were made. The final selection cut was set to ensure that the probability to detect such a supernova within the Milky Way exceeds 99%. No such neutrino burst was found in the data after performing a blind analysis. Hence, a 90% C.L. upper limit on the rate of core-collapse supernovae out to distances of ≈25 kpc was determined to be 0.23 yr−1. For the more distant Magellanic Clouds, only high neutrino luminosity supernovae will be detectable by IceCube, unless external information on the burst time is available. We determined a model-independent limit by parameterizing the dependence on the neutrino luminosity and the energy spectrum.
4.	Abbasi, R., et al. (författare) Search for neutrino lines from dark matter annihilation and decay with IceCube 2023 Ingår i: Physical Review D. - : American Physical Society. - 2470-0010 .- 2470-0029. ; 108:10 Tidskriftsartikel (refereegranskat)abstract Dark matter particles in the Galactic Center and halo can annihilate or decay into a pair of neutrinos producing a monochromatic flux of neutrinos. The spectral feature of this signal is unique and it is not expected from any astrophysical production mechanism. Its observation would constitute a dark matter smoking gun signal. We performed the first dedicated search with a neutrino telescope for such signal, by looking at both the angular and energy information of the neutrino events. To this end, a total of five years of IceCube's DeepCore data has been used to test dark matter masses ranging from 10 GeV to 40 TeV. No significant neutrino excess was found and upper limits on the annihilation cross section, as well as lower limits on the dark matter lifetime, were set. The limits reached are of the order of 10-24 cm3/s for an annihilation and up to 1027 s for decaying dark matter. Using the same data sample we also derive limits for dark matter annihilation or decay into a pair of Standard Model charged particles.
5.	Abbasi, R., et al. (författare) Measurement of atmospheric neutrino mixing with improved IceCube DeepCore calibration and data processing 2023 Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 108:1 Tidskriftsartikel (refereegranskat)abstract We describe a new data sample of IceCube DeepCore and report on the latest measurement of atmospheric neutrino oscillations obtained with data recorded between 2011-2019. The sample includes significant improvements in data calibration, detector simulation, and data processing, and the analysis benefits from a sophisticated treatment of systematic uncertainties, with significantly greater level of detail since our last study. By measuring the relative fluxes of neutrino flavors as a function of their reconstructed energies and arrival directions we constrain the atmospheric neutrino mixing parameters to be sin2θ23=0.51±0.05 and Δm322=2.41±0.07×10-3 eV2, assuming a normal mass ordering. The errors include both statistical and systematic uncertainties. The resulting 40% reduction in the error of both parameters with respect to our previous result makes this the most precise measurement of oscillation parameters using atmospheric neutrinos. Our results are also compatible and complementary to those obtained using neutrino beams from accelerators, which are obtained at lower neutrino energies and are subject to different sources of uncertainties.
6.	Abbasi, R., et al. (författare) Search for 10-1000 GeV Neutrinos from Gamma-Ray Bursts with IceCube 2024 Ingår i: Astrophysical Journal. - : Institute of Physics (IOP). - 1538-4357 .- 0004-637X. ; 964:2 Tidskriftsartikel (refereegranskat)abstract We present the results of a search for 10-1000 GeV neutrinos from 2268 gamma-ray bursts (GRBs) over 8 yr of IceCube-DeepCore data. This work probes burst physics below the photosphere where electromagnetic radiation cannot escape. Neutrinos of tens of giga electronvolts are predicted in sub-photospheric collision of free-streaming neutrons with bulk-jet protons. In a first analysis, we searched for the most significant neutrino-GRB coincidence using six overlapping time windows centered on the prompt phase of each GRB. In a second analysis, we conducted a search for a group of GRBs, each individually too weak to be detectable, but potentially significant when combined. No evidence of neutrino emission is found for either analysis. The most significant neutrino coincidence is for Fermi-GBM GRB bn 140807500, with a p-value of 0.097 corrected for all trials. The binomial test used to search for a group of GRBs had a p-value of 0.65 after all trial corrections. The binomial test found a group consisting only of GRB bn 140807500 and no additional GRBs. The neutrino limits of this work complement those obtained by IceCube at tera electronvolt to peta electronvolt energies. We compare our findings for the large set of GRBs as well as GRB 221009A to the sub-photospheric neutron-proton collision model and find that GRB 221009A provides the most constraining limit on baryon loading. For a jet Lorentz factor of 300 (800), the baryon loading on GRB 221009A is lower than 3.85 (2.13) at a 90% confidence level.
7.	Abbasi, R., et al. (författare) Search for Continuous and Transient Neutrino Emission Associated with IceCube's Highest-energy Tracks: An 11 yr Analysis 2024 Ingår i: Astrophysical Journal. - 1538-4357 .- 0004-637X. ; 964:1 Tidskriftsartikel (refereegranskat)abstract IceCube alert events are neutrinos with a moderate-to-high probability of having astrophysical origin. In this study, we analyze 11 yr of IceCube data and investigate 122 alert events and a selection of high-energy tracks detected between 2009 and the end of 2021. This high-energy event selection (alert events + high-energy tracks) has an average probability of >= 0.5 of being of astrophysical origin. We search for additional continuous and transient neutrino emission within the high-energy events' error regions. We find no evidence for significant continuous neutrino emission from any of the alert event directions. The only locally significant neutrino emission is the transient emission associated with the blazar TXS 0506+056, with a local significance of 3 sigma, which confirms previous IceCube studies. When correcting for 122 test positions, the global p-value is 0.156 and compatible with the background hypothesis. We constrain the total continuous flux emitted from all 122 test positions at 100 TeV to be below 1.2 x 10-15 (TeV cm2 s)-1 at 90% confidence assuming an E -2 spectrum. This corresponds to 4.5% of IceCube's astrophysical diffuse flux. Overall, we find no indication that alert events in general are linked to lower-energetic continuous or transient neutrino emission.
8.	Abbasi, R., et al. (författare) Citizen science for IceCube: Name that Neutrino 2024 Ingår i: European Physical Journal Plus. - 2190-5444. ; 139:6 Tidskriftsartikel (refereegranskat)abstract Name that Neutrino is a citizen science project where volunteers aid in classification of events for the IceCube Neutrino Observatory, an immense particle detector at the geographic South Pole. From March 2023 to September 2023, volunteers did classifications of videos produced from simulated data of both neutrino signal and background interactions. Name that Neutrino obtained more than 128,000 classifications by over 1800 registered volunteers that were compared to results obtained by a deep neural network machine-learning algorithm. Possible improvements for both Name that Neutrino and the deep neural network are discussed.
9.	Abbasi, R., et al. (författare) Search for decoherence from quantum gravity with atmospheric neutrinos 2024 Ingår i: Nature Physics. - 1745-2481 .- 1745-2473. ; 20:6, s. 913-920 Tidskriftsartikel (refereegranskat)abstract Neutrino oscillations at the highest energies and longest baselines can be used to study the structure of spacetime and test the fundamental principles of quantum mechanics. If the metric of spacetime has a quantum mechanical description, its fluctuations at the Planck scale are expected to introduce non-unitary effects that are inconsistent with the standard unitary time evolution of quantum mechanics. Neutrinos interacting with such fluctuations would lose their quantum coherence, deviating from the expected oscillatory flavour composition at long distances and high energies. Here we use atmospheric neutrinos detected by the IceCube South Pole Neutrino Observatory in the energy range of 0.5-10.0 TeV to search for coherence loss in neutrino propagation. We find no evidence of anomalous neutrino decoherence and determine limits on neutrino-quantum gravity interactions. The constraint on the effective decoherence strength parameter within an energy-independent decoherence model improves on previous limits by a factor of 30. For decoherence effects scaling as E2, our limits are advanced by more than six orders of magnitude beyond past measurements compared with the state of the art. Interactions of atmospheric neutrinos with quantum-gravity-induced fluctuations of the metric of spacetime would lead to decoherence. The IceCube Collaboration constrains such interactions with atmospheric neutrinos.
10.	Abbasi, R., et al. (författare) Characterization of the astrophysical diffuse neutrino flux using starting track events in IceCube 2024 Ingår i: Physical Review D - Particles, Fields, Gravitation and Cosmology. - 2470-0010 .- 2470-0029. ; 110:2 Tidskriftsartikel (refereegranskat)abstract A measurement of the diffuse astrophysical neutrino spectrum is presented using IceCube data collected from 2011-2022 (10.3 years). We developed novel detection techniques to search for events with a contained vertex and exiting track induced by muon neutrinos undergoing a charged-current interaction. Searching for these starting track events allows us to not only more effectively reject atmospheric muons but also atmospheric neutrino backgrounds in the southern sky, opening a new window to the sub-100 TeV astrophysical neutrino sky. The event selection is constructed using a dynamic starting track veto and machine learning algorithms. We use this data to measure the astrophysical diffuse flux as a single power law flux (SPL) with a best-fit spectral index of γ=2.58-0.09+0.10 and per-flavor normalization of φper-flavorAstro=1.68-0.22+0.19×10-18×GeV-1 cm-2 s-1 sr-1 (at 100 TeV). The sensitive energy range for this dataset is 3-550 TeV under the SPL assumption. This data was also used to measure the flux under a broken power law, however we did not find any evidence of a low energy cutoff.
11.	Abbasi, R., et al. (författare) Improved modeling of in-ice particle showers for IceCube event reconstruction 2024 Ingår i: Journal of Instrumentation. - 1748-0221. ; 19:6 Tidskriftsartikel (refereegranskat)abstract The IceCube Neutrino Observatory relies on an array of photomultiplier tubes to detect Cherenkov light produced by charged particles in the South Pole ice. IceCube data analyses depend on an in-depth characterization of the glacial ice, and on novel approaches in event reconstruction that utilize fast approximations of photoelectron yields. Here, a more accurate model is derived for event reconstruction that better captures our current knowledge of ice optical properties. When evaluated on a Monte Carlo simulation set, the median angular resolution for in-ice particle showers improves by over a factor of three compared to a reconstruction based on a simplified model of the ice. The most substantial improvement is obtained when including effects of birefringence due to the polycrystalline structure of the ice. When evaluated on data classified as particle showers in the high-energy starting events sample, a significantly improved description of the events is observed.
12.	Feng, S H, et al. (författare) Dense sampling of bird diversity increases power of comparative genomics (vol 587, pg 252, 2020) 2021 Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 592:7856, s. E24-E24 Tidskriftsartikel (refereegranskat)abstract A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03473-8.
13.	Orlando, Ludovic, et al. (författare) Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse 2013 Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 499:7456, s. 74- Tidskriftsartikel (refereegranskat)abstract The rich fossil record of equids has made them a model for evolutionary processes(1). Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP)(2,3). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. prze-walskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0-4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus(4,5). We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski's and domestic horse populations diverged 38-72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski's horse investigated. This supports the contention that Przewalski's horses represent the last surviving wild horse population(6). We find similar levels of genetic variation among Przewalski's and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski's horse. Such regions could correspond to loci selected early during domestication.
14.	Feng, Shaohong, et al. (författare) Dense sampling of bird diversity increases power of comparative genomics 2020 Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833 Tidskriftsartikel (refereegranskat)abstract Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
15.	Hudson, Thomas J., et al. (författare) International network of cancer genome projects 2010 Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7291, s. 993-998 Tidskriftsartikel (refereegranskat)abstract The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.
16.	Wang, F, et al. (författare) Author Correction: Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level 2022 Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1, s. 6748- Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
17.	Ahmadian, Afshin, et al. (författare) Genetic instability in the 9q22.3 region is a late event in the development of squamous cell carcinoma. 1998 Ingår i: Oncogene. - : Springer Science and Business Media LLC. - 0950-9232 .- 1476-5594. ; 17:14 Tidskriftsartikel (refereegranskat)abstract Squamous cell carcinoma (SCC) of the skin represents a group of neoplasms which is associated with exposure to UV light. Recently, we obtained data suggesting that invasive skin cancer and its precursors derive from one original neoplastic clone. Here, the analysis were extended by loss of heterozygosity (LOH) analysis in the chromosome 9q22.3 region. A total of 85 samples, taken from twenty-two sections of sun-exposed sites, corresponding to normal epidermis, morphological normal cells with positive immuno-staining for the p53 protein (p53 patches), dysplasias, cancer in situ (CIS) and squamous cell carcinomas (SCC) of the skin were analysed. Overall, about 70% of p53 patches had mutations in the p53 gene but not LOH in the p53 gene or 9q22.3 region. Approximately 70% of the dysplasias showed p53 mutations of which about 40% had LOH in the p53 region but not in the 9q22.3 region. In contrast, about 65% of SCC and CIS displayed LOH in the 9q22.3 region, as well as frequent (80%) mutations and/or LOH in the p53 gene. These findings strongly suggest that alterations in the p53 gene is an early event in the progression towards SCC, whereas malignant development involves LOH and alterations in at least one (or several) tumor suppressor genes located in chromosome 9q22.3.
18.	Ahmadian, A, et al. (författare) Genetic instability in the 9q22.3 region is a late event in thedevelopment of squamous cell carcinoma. 1998 Ingår i: Oncogene. ; 17, s. 1837- Tidskriftsartikel (refereegranskat)
19.	Berne, B, et al. (författare) Decreased p53 expression in chronically sunexposed human skin after topical photoprotection. 1998 Ingår i: Photodermatology, Photoimmunology & Photomedicine. ; 14, s. 148- Tidskriftsartikel (refereegranskat)
20.	Cepeda, D., et al. (författare) CDK-mediated activation of the SCFFBXO28 ubiquitin ligase promotes MYC-driven transcription and tumourigenesis and predicts poor survival in breast cancer 2013 Ingår i: EMBO Molecular Medicine. - : EMBO. - 1757-4676 .- 1757-4684. ; 5:7, s. 999-1018 Tidskriftsartikel (refereegranskat)abstract SCF (Skp1/Cul1/F-box) ubiquitin ligases act as master regulators of cellular homeostasis by targeting key proteins for ubiquitylation. Here, we identified a hitherto uncharacterized F-box protein, FBXO28 that controls MYC-dependent transcription by non-proteolytic ubiquitylation. SCFFBXO28 activity and stability are regulated during the cell cycle by CDK1/2-mediated phosphorylation of FBXO28, which is required for its efficient ubiquitylation of MYC and downsteam enhancement of the MYC pathway. Depletion of FBXO28 or overexpression of an F-box mutant unable to support MYC ubiquitylation results in an impairment of MYC-driven transcription, transformation and tumourigenesis. Finally, in human breast cancer, high FBXO28 expression and phosphorylation are strong and independent predictors of poor outcome. In conclusion, our data suggest that SCFFBXO28 plays an important role in transmitting CDK activity to MYC function during the cell cycle, emphasizing the CDK-FBXO28-MYC axis as a potential molecular drug target in MYC-driven cancers, including breast cancer. FBXO28 is identified as part of a SCF complex acting as a regulator of tumor cell proliferation and an important modifier of MYC function. FBXO28 may be a new prognostic factor in breast cancer and a new potential drug target in MYC- driven tumors.
21.	Dos Remedios, CG, et al. (författare) Correction to: The Sydney Heart Bank: improving translational research while eliminating or reducing the use of animal models of human heart disease 2018 Ingår i: Biophysical reviews. - : Springer Science and Business Media LLC. - 1867-2450 .- 1867-2469. ; 10:3, s. 941- Tidskriftsartikel (refereegranskat)
22.	Gopalakrishnan, Shyam, et al. (författare) The population genomic legacy of the second plague pandemic 2022 Ingår i: Current Biology. - : Elsevier. - 0960-9822 .- 1879-0445. ; 32:21, s. 4743-4751.e6 Tidskriftsartikel (refereegranskat)abstract Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%–40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th–19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.
23.	Guo, Zhongmin, et al. (författare) Analysis of intratumoral heterogeneity of chromosome 3p deletions and genetic evidence of polyclonal origin of cervical squamous carcinoma. 2001 Ingår i: Modern Pathol. ; 14, s. 54- Tidskriftsartikel (refereegranskat)
24.	Guo, Z, et al. (författare) Clonality of precursors of cervical cancer and their genetic links to invasive cancer 2000 Ingår i: Mod Pathol. ; 13, s. 606- Tidskriftsartikel (refereegranskat)
25.	Guo, ZM, et al. (författare) Comparison of chromosome 3p deletions between cervical precancers synchronous with and without invasive cancer 2000 Ingår i: Int J Cancer. ; 86, s. 518- Tidskriftsartikel (refereegranskat)
26.	Gustafsson, A. C., et al. (författare) HPV-related cancer susceptibility and p53 codon 72 polymorphism 2001 Ingår i: Acta Dermato-Venereologica. - : Medical Journals Sweden AB. - 0001-5555 .- 1651-2057. ; 81, s. 125- Tidskriftsartikel (refereegranskat)abstract Conflicting results regarding the association of a polymorphism at codon 72 of the p53 tumour suppressor gene and susceptibility to develop human papilloma virus (HPV)-associated cervical cancer have been published over the last year, implicating differences in ethnic background, sample origin, sample size and/or detection assay, The material for this study was collected in the identical geographical region as for 2 previous reports with contradictory results regarding the association of codon 72 genotype with squamous cell cancer (SCC), We have used an alternative detection assay, based on pyrosequencing technology, that interrogates the variable position by the accuracy of DNA polymerase. In addition to cervical clinical specimens from SCC, HPV16- and HPV18-infected adenocarcinoma cases as well as cervical intraepithelial neoplasia (CM) were investigated. No significant association was found between p53 codon 72 genotype and the risk to develop adenocarcinoma, SCC or CIN in the Swedish population.
27.	Hedrum, A, et al. (författare) Sequence-based analysis of the human p53 gene based on microdissection oftumor biopsy samples. 1994 Ingår i: Biotechniques. ; 17, s. 118- Tidskriftsartikel (refereegranskat)
28.	Hu, X, et al. (författare) HPV typing and HPV E6 sequence variations in synchronous lesions of squamous cell carcinoma from Swedish patients. 1999 Ingår i: Int J Cancer. ; 24, s. 34- Tidskriftsartikel (refereegranskat)
29.	Jarvis, Erich D., et al. (författare) Whole-genome analyses resolve early branches in the tree of life of modern birds 2014 Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331 Tidskriftsartikel (refereegranskat)abstract To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
30.	Ling, G, et al. (författare) Epidermal p53 response and repair of thymine dimers in human skin after asingle dose of ultraviolet radiation: effects of photoprotection. 2001 Ingår i: Acta Derm.-Venereol.. ; 81, s. 81- Tidskriftsartikel (refereegranskat)
31.	Persson, AE, et al. (författare) Analysis of p53 mutations in single cells obtained from histologicaltissue sections. 2000 Ingår i: Anal. Biochem.. ; 287, s. 25- Tidskriftsartikel (refereegranskat)
32.	Persson, A. E., et al. (författare) Analysis of p53 mutations in single cells obtained from histological tissue sections 2000 Ingår i: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 287:1, s. 25-31 Tidskriftsartikel (refereegranskat)abstract We have previously reported on direct sequence analysis of the p53 gene in laser-dissected single cells from tissue sections, where each allele of two fragments (exons 7 and 8) could be accurately analyzed in only 14% of the cells due to the high frequency of exon and allele dropout. Here in an effort to minimize this problem, we have investigated various approaches for sample preparation and gene amplification. By pinpointing some critical steps in the procedure, we could increase the number of investigated exons and substantially improve the genetic analysis of single cells obtained from histochemically stained frozen tissue sections. The biggest improvement was achieved by minimizing DNA degradation using EDTA as a nuclease inhibitor in all sample preparation steps. Efforts to increase primer annealing, by increasing the concentration of template and primers, in addition to prolonging the annealing and extension times, also improved the amplification efficiency. With these measures we can now amplify six individual exons of the p53 gene (exons 4-9) in 70% of the cells and in 50% of these cells both alleles are amplified. This allows application of the method in various investigations such as within the held of tumor pathology.
33.	Pontén, E, et al. (författare) A complex DICER1 syndrome phenotype associated with a germline pathogenic variant affecting the RNase IIIa domain of DICER1 2022 Ingår i: Journal of medical genetics. - 1468-6244. ; 59:2, s. 141-146 Tidskriftsartikel (refereegranskat)
34.	Ponten, F, et al. (författare) Epithelial-stromal interactions in basal cell cancer: the PDGF system. 1994 Ingår i: J Invest Dermatol. ; 102, s. 304- Tidskriftsartikel (refereegranskat)
35.	Pontén, F, et al. (författare) Genomic analysis of single cells from human basal cell cancer using laser-assisted capture microscopy. 1997 Ingår i: Mutation research. - 0027-5107 .- 1873-135X. ; 382:1-2 Tidskriftsartikel (refereegranskat)abstract In this study, we show that direct mutational analysis of genomic DNA can be performed on single somatic cells extracted from a frozen, immunohistochemically stained tissue section using laser-assisted capture microscopy. Eighty-nine single tumor cells were separately dissected from one case of human basal cell cancer (BCC) and p53 mutations were analyzed by direct semi-automated sequencing of PCR fragments. Amplification was obtained for at least one of the two analyzed exons from approximately 50% of the single tumor cells. Identical p53 mutations were found in widely spread areas of the tumor, suggesting a clonal proliferation originating from one cell. Interestingly, comparison between results of immunohistochemistry and genetic analysis of the single cells revealed the same p53 mutations irrespective of the p53 immunoreactivity. We propose that this approach has a great potential to allow investigation of genotypic differences in single cells and more specifically to resolve important and fundamental questions determining cancer heterogeneity.
36.	Ponten, F, et al. (författare) Genomic analysis of single cells from human basal cell cancer using laser-assisted capture microscopy 1997 Ingår i: Mutation Research Genomics. ; 382, s. 45- Tidskriftsartikel (refereegranskat)
37.	Pontén, F, et al. (författare) Molecular pathology in basal cell cancer with p53 as a genetic marker. 1997 Ingår i: Oncogene. - : Springer Science and Business Media LLC. - 0950-9232 .- 1476-5594. ; 15:9 Tidskriftsartikel (refereegranskat)abstract Human basal cell cancer (BCC) has unique growth characteristics with virtual inability to metastasize. We investigated clonality and genetic progression using p53 mutations as marker. Sampling was done through microdissection of frozen immunohistochemically stained 16 microm slices of tumors. From 11 BCC tumors 78 samples were analysed. Direct DNA sequencing of exons 5-8 was performed, haplotypes were determined after cloning of p53 exons and loss of heterozygosity (LOH) ascertained by microsatellite analysis. All tumors had p53 mutations and in a majority both p53 alleles were affected, commonly through missense mutations. Microdissection of small parts (50-100 cells) of individual tumors showed BCC to be composed of a dominant cell clone and prone to genetic progression with appearance of subclones with a second and even third p53 mutation. Samples from normal immunohistochemically negative epidermis always showed wild type sequence, except for a case of previously unknown germline p53 mutation. Our analysis also included p53 immunoreactive patches i.e. morphologically normal epidermis with a compact pattern of p53 immunoreactivity. Mutations within those were never the same as in the adjacent BCC. This detailed study of only one gene thus uncovered a remarkable heterogeneity within a tumor category famous for its benign clinical behavior.
38.	Ponten, F, et al. (författare) Molecular pathology in basal cell cancer with p53 as a genetic marker 1997 Ingår i: Oncogene. ; 15, s. 1059- Tidskriftsartikel (refereegranskat)
39.	Ponten, F, et al. (författare) Ultraviolet light induces expression of p53 and p21 in human skin; effect of sunscreen and constitutive p21 expression in skin appendages 1995 Ingår i: Journal of Investigative Dermatology. ; 105, s. 402- Tidskriftsartikel (refereegranskat)
40.	Rasmussen, Morten, et al. (författare) Ancient human genome sequence of an extinct Palaeo-Eskimo 2010 Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 463:7282, s. 757-762 Tidskriftsartikel (refereegranskat)abstract We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20×, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.
41.	Ren, Z. P., et al. (författare) Benign clonal keratinocyte patches with p53 mutations show no genetic link to synchronous squamous cell precancer or cancer in human skin 1997 Ingår i: American Journal of Pathology. - : American Society for Investigative Pathology and the Association for Molecular Pathology. - 0002-9440 .- 1525-2191. ; 150:5, s. 1791-803 Tidskriftsartikel (refereegranskat)abstract Ultraviolet light, which is the major etiology of human skin cancer, will cause mutations in the p53 gene. We and others have found that such mutations occur in more than one-half of non-melanoma squamous cell cancer and precancer. Immunostaining for p53 has disclosed a characteristic compact pattern not only in cancer/precancer but also in areas of microscopically normal epidermis termed p53 patches. By microdissection, sequence analysis of the p53 gene, and analysis of loss of heterozygosity (LOH) at the site of this gene, we have now extended previous data to ascertain whether these p53 patches are precursors of simultaneously present squamous cell cancer or its morphologically recognized precancerous stages (dysplasia, carcinoma in situ). In none of 11 instances with co-existence of a p53 patch with dysplasia or in situ or invasive cancer were the mutations identical. We conclude that p53 patches, estimated to be approximately 100,000 times as common as dysplasia, have a very small or even no precancerous potential. Their common presence demonstrates that human epidermis contains a large number of p53 mutations apparently without detrimental effect. The only result of the mutation may be a clandestine benign clonal keratinocyte proliferation. The importance of p53 mutations for such benign cell multiplication on one band and malignant transformation on the other is unclear. Although the spectrum, type, and multiplicity of mutations were similar in both types of proliferative responses, there was a clear difference with respect to LOH. No LOH was found in 17 p53 patches. By contrast 11 of 30 precancers/cancers had LOH.
42.	Ren, Z-P, et al. (författare) Benign clonal keratinocyte patches with p53 mutations show no genetic link to synchronous squamous cell precancer or cancer in human skin 1997 Ingår i: American Journal of Pathology. ; 150, s. 1791- Tidskriftsartikel (refereegranskat)
43.	Ren, Z-P, et al. (författare) Human epidermal cancer and accompanying precursors have identical p53 mutations different from p53 mutations in adjacent areas of clonally expanded non-neoplastic keratinocytes 1996 Ingår i: Oncogene. ; 12, s. 765- Tidskriftsartikel (refereegranskat)
44.	Ren, Z-P, et al. (författare) Reconstruction of the two-dimensional distribution of p53 positive staining patches in sun-exposed morphologically normal skin 1997 Ingår i: Int J Oncol. ; 11, s. 111-115 Tidskriftsartikel (refereegranskat)
45.	Ren, Z-P, et al. (författare) Two distinct p53 immunohistochemical patterns in human squamous-cell skin cancer, precursors and normal epidermis 1996 Ingår i: Int J Cancer. ; 69, s. 174-179 Tidskriftsartikel (refereegranskat)
46.	Williams, Cecilia, 1969-, et al. (författare) A high frequency of sequence alterations is due to formalin fixation of archival specimens. 1999 Ingår i: American Journal of Pathology. - 0002-9440 .- 1525-2191. ; 155:5 Tidskriftsartikel (refereegranskat)abstract Genomic analysis of archival tissues fixed in formalin is of fundamental importance in biomedical research, and numerous studies have used such material. Although the possibility of polymerase chain reaction (PCR)-introduced artifacts is known, the use of direct sequencing has been thought to overcome such problems. Here we report the results from a controlled study, performed in parallel on frozen and formalin-fixed material, where a high frequency of nonreproducible sequence alterations was detected with the use of formalin-fixed tissues. Defined numbers of well-characterized tumor cells were amplified and analyzed by direct DNA sequencing. No nonreproducible sequence alterations were found in frozen tissues. In formalin-fixed material up to one mutation artifact per 500 bases was recorded. The chance of such artificial mutations in formalin-fixed material was inversely correlated with the number of cells used in the PCR-the fewer cells, the more artifacts. A total of 28 artificial mutations were recorded, of which 27 were C-T or G-A transitions. Through confirmational sequencing of independent amplification products artifacts can be distinguished from true mutations. However, because this problem was not acknowledged earlier, the presence of artifacts may have profoundly influenced previously reported mutations in formalin-fixed material, including those inserted into mutation databases.
47.	Williams, C, et al. (författare) A high frequency of sequence alterations is due to formalin fixation ofarchival specimens [see comments] 1999 Ingår i: Am. J. Pathol.. ; 155, s. 1467- Tidskriftsartikel (refereegranskat)
48.	Williams, Cecilia, 1969-, et al. (författare) Clones of normal keratinocytes and a variety of simultaneously present epidermal neoplastic lesions contain a multitude of p53 gene mutations in a xeroderma pigmentosum patient. 1998 Ingår i: Cancer Research. - 0008-5472 .- 1538-7445. ; 58:11 Tidskriftsartikel (refereegranskat)abstract A patient with xeroderma pigmentosum group C was extensively examined for mutations in the p53 gene in normal skin exposed to varying degrees of sunlight and in excisional biopsies of basal cell cancer, squamous cell cancer, and squamous cell dysplasia. Seventy-three samples were analyzed by microdissection of small cell clusters, followed by PCR and direct DNA sequencing. In skin taken from areas that most likely had never been exposed to the sun, no mutations were found. However, in skin exposed to the sun, we observed a multitude of mutations in the p53 gene. UV light-induced mutations were found in all types of lesions, as well as in clusters of morphologically normal epidermal cells. Twenty-nine distinct mutations were found in exons 5-8, all missense or nonsense, of which 27 (93%) were UV-specific C --> T or CC --> TT transitions at dipyrimidine sites of the nontranscribed strand. Two types of normal skin areas containing p53 mutations were observed: areas that stain strongly with p53 antibody (p53 patches) and those that do not stain. Because no silent or intron mutations were found in these cell clusters, the alterations in the p53 gene of morphologically normal cells are likely to have resulted in a selective growth advantage. The poor correlation between mutations and morphological phenotypes demonstrates that p53 mutations alone do not determine the phenotypes observed.
49.	Agaton, C., et al. (författare) Affinity proteomics for systematic protein profiling of chromosome 21 gene products in human tissues 2003 Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 2, s. 405- Tidskriftsartikel (refereegranskat)abstract Here we show that an affinity proteomics strategy using affinity-purified antibodies raised against recombinant human protein fragments can be used for chromosome-wide protein profiling. The approach is based on affinity reagents raised toward bioinformatics-designed protein epitope signature tags corresponding to unique regions of individual gene loci. The genes of human chromosome 21 identified by the genome efforts were investigated, and the success rates for de novo cloning, protein production, and antibody generation were 85, 76, and 56%, respectively. Using human tissue arrays, a systematic profiling of protein expression and subcellular localization was undertaken for the putative gene products. The results suggest that this affinity proteomics strategy can be used to produce a proteome atlas, describing distribution and expression of proteins in normal tissues as well as in common cancers and other forms of diseased tissues.
50.	Asplund, A, et al. (författare) Mosaic pattern of maternal and paternal keratinocyte clones in normal human epidermis revealed by analysis of X-chromosome inactivation 2001 Ingår i: Journal of Investigative Dermatology. ; 117, s. 128- Tidskriftsartikel (refereegranskat)

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