| 1. |
- Thomas, HS, et al.
(författare)
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- 2019
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swepub:Mat__t
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| 2. |
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| 3. |
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| 4. |
- Middeldorp, Christel M., et al.
(författare)
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The Early Growth Genetics (EGG) and EArly Genetics and Lifecourse Epidemiology (EAGLE) consortia : design, results and future prospects
- 2019
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Ingår i: European Journal of Epidemiology. - : Springer Science and Business Media LLC. - 0393-2990 .- 1573-7284. ; 34:3, s. 279-300
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Tidskriftsartikel (refereegranskat)abstract
- The impact of many unfavorable childhood traits or diseases, such as low birth weight and mental disorders, is not limited to childhood and adolescence, as they are also associated with poor outcomes in adulthood, such as cardiovascular disease. Insight into the genetic etiology of childhood and adolescent traits and disorders may therefore provide new perspectives, not only on how to improve wellbeing during childhood, but also how to prevent later adverse outcomes. To achieve the sample sizes required for genetic research, the Early Growth Genetics (EGG) and EArly Genetics and Lifecourse Epidemiology (EAGLE) consortia were established. The majority of the participating cohorts are longitudinal population-based samples, but other cohorts with data on early childhood phenotypes are also involved. Cohorts often have a broad focus and collect(ed) data on various somatic and psychiatric traits as well as environmental factors. Genetic variants have been successfully identified for multiple traits, for example, birth weight, atopic dermatitis, childhood BMI, allergic sensitization, and pubertal growth. Furthermore, the results have shown that genetic factors also partly underlie the association with adult traits. As sample sizes are still increasing, it is expected that future analyses will identify additional variants. This, in combination with the development of innovative statistical methods, will provide detailed insight on the mechanisms underlying the transition from childhood to adult disorders. Both consortia welcome new collaborations. Policies and contact details are available from the corresponding authors of this manuscript and/or the consortium websites.
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| 5. |
- Eiteneer, D., et al.
(författare)
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Depth-Resolved Composition and Electronic Structure of Buried Layers and Interfaces in a LaNiO3/SrTiO3 Superlatticefroni Soft- and Hard-X-ray Standing-Wave Angle-Resolved Photoemission
- 2016
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Ingår i: Journal of Electron Spectroscopy and Related Phenomena. - : Elsevier BV. - 0368-2048 .- 1873-2526. ; 211, s. 70-81
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Tidskriftsartikel (refereegranskat)abstract
- LaNiO3 (LNO) is an intriguing member of the rare-earth nickelates in exhibiting a metal-insulator transition for a critical film thickness of about 4 unit cells [Son et al., Appl. Phys. Lett. 96, 062114 (2010)]; however, such thin films also show a transition to a metallic state in superlattices with SrTiO3 (STO) [Son et al., Appl. Phys. Lett. 97, 202109 (2010)]. In order to better understand this transition, we have studied a strained LNO/STO superlattice with 10 repeats of [4 unit-cell LNO/3 unit-cell STO] grown on an (LaAlO3)(0.3)(Sr2AlTaO6)(0.7) substrate using soft x-ray standing-wave-excited angle-resolved photoemission (SWARPES), together with soft- and hard- x-ray photoemission-measurements of core levels and densities-of-states valence spectra. The experimental results are compared with state-of-the-art density functional theory (DFT) calculations of band structures and densities of states. Using core-level rocking curves and x-ray optical modeling to assess the position of the standing wave, SWARPES measurements are carried out for various incidence angles and used to determine interface-specific changes in momentum-resolved electronic structure. We further show that the momentum-resolved behavior of the Ni 3d e(g) and t(2g) states near the Fermi level, as well as those at the bottom of the valence bands, is very similar to recently published SWARPES results for a related La0.7Sr0.3MnO3/SrTiO3 superlattice that was-studied using the same technique (Gray et al., Europhysics Letters 104, 17004 (2013)), which further validates this experimental approach and our conclusions. Our conclusions are also supported in several ways by comparison to DFT calculations for the parent materials and the superlattice, including layer-resolved density-of-states results.
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| 6. |
- Keqi, A., et al.
(författare)
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Electronic structure of the dilute magnetic semiconductor Ga1-xMnxP from hard x-ray photoelectron spectroscopy and angle-resolved photoemission
- 2018
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Ingår i: Physical Review B. - 2469-9950 .- 2469-9969. ; 97:15
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Tidskriftsartikel (refereegranskat)abstract
- We have investigated the electronic structure of the dilute magnetic semiconductor (DMS) Ga0.98Mn0.02P and compared it to that of an undoped GaP reference sample, using hard x-ray photoelectron spectroscopy (HXPS) and hard x-ray angle-resolved photoemission spectroscopy (HARPES) at energies of about 3 keV. We present experimental data, as well as theoretical calculations, to understand the role of the Mn dopant in the emergence of ferromagnetism in this material. Both core-level spectra and angle-resolved or angle-integrated valence spectra are discussed. In particular, the HARPES experimental data are compared to free-electron final-state model calculations and to more accurate one-step photoemission theory. The experimental results show differences between Ga0.98Mn0.02P and GaP in both angle-resolved and angle-integrated valence spectra. The Ga0.98Mn0.02P bands are broadened due to the presence of Mn impurities that disturb the long-range translational order of the host GaP crystal. Mn-induced changes of the electronic structure are observed over the entire valence band range, including the presence of a distinct impurity band close to the valence-band maximum of the DMS. These experimental results are in good agreement with the one-step photoemission calculations and a prior HARPES study of Ga0.97Mn0.03As and GaAs [Gray et al., Nat. Mater. 11, 957 (2012)], demonstrating the strong similarity between these two materials. The Mn 2p and 3s core-level spectra also reveal an essentially identical state in doping both GaAs and GaP.
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| 7. |
- Conlon, C. S., et al.
(författare)
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Hard x-ray standing-wave photoemission insights into the structure of an epitaxial Fe/MgO multilayer magnetic tunnel junction
- 2019
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Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 126:7
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Tidskriftsartikel (refereegranskat)abstract
- The Fe/MgO magnetic tunnel junction is a classic spintronic system, with current importance technologically and interest for future innovation. The key magnetic properties are linked directly to the structure of hard-to-access buried interfaces, and the Fe and MgO components near the surface are unstable when exposed to air, making a deeper probing, nondestructive, in-situ measurement ideal for this system. We have thus applied hard x-ray photoemission spectroscopy (HXPS) and standing-wave (SW) HXPS in the few kilo-electron-volt energy range to probe the structure of an epitaxially grown MgO/Fe superlattice. The superlattice consists of 9 repeats of MgO grown on Fe by magnetron sputtering on an MgO(001) substrate, with a protective Al2O3 capping layer. We determine through SW-HXPS that 8 of the 9 repeats are similar and ordered, with a period of 33 +/- 4 angstrom, with the minor presence of FeO at the interfaces and a significantly distorted top bilayer with ca. 3 times the oxidation of the lower layers at the top MgO/Fe interface. There is evidence of asymmetrical oxidation on the top and bottom of the Fe layers. We find agreement with dark-field scanning transmission electron microscope (STEM) and x-ray reflectivity measurements. Through the STEM measurements, we confirm an overall epitaxial stack with dislocations and warping at the interfaces of ca. 5 angstrom. We also note a distinct difference in the top bilayer, especially MgO, with possible Fe inclusions. We thus demonstrate that SW-HXPS can be used to probe deep buried interfaces of novel magnetic devices with few-angstrom precision.
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| 8. |
- Osoegawa, Kazutoyo, et al.
(författare)
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Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop
- 2019
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Ingår i: Human Immunology. - : ELSEVIER SCIENCE INC. - 0198-8859 .- 1879-1166. ; 80:4, s. 228-236
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Tidskriftsartikel (refereegranskat)abstract
- The 17th International HLA and Immunogenetics Workshop (IHIW) organizers conducted a Pilot Study (PS) in which 13 laboratories (15 groups) participated to assess the performance of the various sequencing library preparation protocols, NGS platforms and software in use prior to the workshop. The organizers sent 50 cell lines to each of the 15 groups, scored the 15 independently generated sets of NGS HLA genotyping data, and generated "consensus" HLA genotypes for each of the 50 cell lines. Proficiency Testing (PT) was subsequently organized using four sets of 24 cell lines, selected from 48 of 50 PS cell lines, to validate the quality of NGS HLA typing data from the 34 participating IHIW laboratories. Completion of the PT program with a minimum score of 95% concordance at the HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 loci satisfied the requirements to submit NGS HLA typing data for the 17th IHIW projects. Together, these PS and PT efforts constituted the 17th IHIW Quality Control project. Overall PT concordance rates for HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1, HLA-DRB3, HLA-DRB4 and HLA-DRB5 were 98.1%, 97.0% and 98.1%, 99.0%, 98.6%, 98.8%, 97.6%, 96.0%, 99.1%, 90.0% and 91.7%, respectively. Across all loci, the majority of the discordance was due to allele dropout. The high cost of NGS HLA genotyping per experiment likely prevented the retyping of initially failed HLA loci. Despite the high HLA genotype concordance rates of the software, there remains room for improvement in the assembly of more accurate consensus DNA sequences by NGS HLA genotyping software.
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| 9. |
- Newell, Felicity, et al.
(författare)
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Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets
- 2019
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge of key drivers and therapeutic targets in mucosal melanoma is limited due to the paucity of comprehensive mutation data on this rare tumor type. To better understand the genomic landscape of mucosal melanoma, here we describe whole genome sequencing analysis of 67 tumors and validation of driver gene mutations by exome sequencing of 45 tumors. Tumors have a low point mutation burden and high numbers of structural variants, including recurrent structural rearrangements targeting TERT, CDK4 and MDM2. Significantly mutated genes are NRAS, BRAF, NF1, KIT, SF3B1, TP53, SPRED1, ATRX, HLA-A and CHD8. SF3B1 mutations occur more commonly in female genital and anorectal melanomas and CTNNB1 mutations implicate a role for WNT signaling defects in the genesis of some mucosal melanomas. TERT aberrations and ATRX mutations are associated with alterations in telomere length. Mutation profiles of the majority of mucosal melanomas suggest potential susceptibility to CDK4/6 and/or MEK inhibitors.
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| 10. |
- van der Valk, Ralf J P, et al.
(författare)
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A novel common variant in DCST2 is associated with length in early life and height in adulthood.
- 2015
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Ingår i: Human molecular genetics. - : Oxford University Press (OUP). - 1460-2083 .- 0964-6906. ; 24:4, s. 1155-68
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Tidskriftsartikel (refereegranskat)abstract
- Common genetic variants have been identified for adult height, but not much is known about the genetics of skeletal growth in early life. To identify common genetic variants that influence fetal skeletal growth, we meta-analyzed 22 genome-wide association studies (Stage 1; N = 28 459). We identified seven independent top single nucleotide polymorphisms (SNPs) (P < 1 × 10(-6)) for birth length, of which three were novel and four were in or near loci known to be associated with adult height (LCORL, PTCH1, GPR126 and HMGA2). The three novel SNPs were followed-up in nine replication studies (Stage 2; N = 11 995), with rs905938 in DC-STAMP domain containing 2 (DCST2) genome-wide significantly associated with birth length in a joint analysis (Stages 1 + 2; β = 0.046, SE = 0.008, P = 2.46 × 10(-8), explained variance = 0.05%). Rs905938 was also associated with infant length (N = 28 228; P = 5.54 × 10(-4)) and adult height (N = 127 513; P = 1.45 × 10(-5)). DCST2 is a DC-STAMP-like protein family member and DC-STAMP is an osteoclast cell-fusion regulator. Polygenic scores based on 180 SNPs previously associated with human adult stature explained 0.13% of variance in birth length. The same SNPs explained 2.95% of the variance of infant length. Of the 180 known adult height loci, 11 were genome-wide significantly associated with infant length (SF3B4, LCORL, SPAG17, C6orf173, PTCH1, GDF5, ZNFX1, HHIP, ACAN, HLA locus and HMGA2). This study highlights that common variation in DCST2 influences variation in early growth and adult height.
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