| 1. |
- Docherty, Anna R, et al.
(författare)
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GWAS Meta-Analysis of Suicide Attempt: Identification of 12 Genome-Wide Significant Loci and Implication of Genetic Risks for Specific Health Factors.
- 2023
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Ingår i: The American journal of psychiatry. - : American Psychiatric Association Publishing. - 1535-7228 .- 0002-953X. ; 180:10, s. 723-738
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Tidskriftsartikel (refereegranskat)abstract
- Suicidal behavior is heritable and is a major cause of death worldwide. Two large-scale genome-wide association studies (GWASs) recently discovered and cross-validated genome-wide significant (GWS) loci for suicide attempt (SA). The present study leveraged the genetic cohorts from both studies to conduct the largest GWAS meta-analysis of SA to date. Multi-ancestry and admixture-specific meta-analyses were conducted within groups of significant African, East Asian, and European ancestry admixtures.This study comprised 22 cohorts, including 43,871 SA cases and 915,025 ancestry-matched controls. Analytical methods across multi-ancestry and individual ancestry admixtures included inverse variance-weighted fixed-effects meta-analyses, followed by gene, gene-set, tissue-set, and drug-target enrichment, as well as summary-data-based Mendelian randomization with brain expression quantitative trait loci data, phenome-wide genetic correlation, and genetic causal proportion analyses.Multi-ancestry and European ancestry admixture GWAS meta-analyses identified 12 risk loci at p values <5×10-8. These loci were mostly intergenic and implicated DRD2, SLC6A9, FURIN, NLGN1, SOX5, PDE4B, and CACNG2. The multi-ancestry SNP-based heritability estimate of SA was 5.7% on the liability scale (SE=0.003, p=5.7×10-80). Significant brain tissue gene expression and drug set enrichment were observed. There was shared genetic variation of SA with attention deficit hyperactivity disorder, smoking, and risk tolerance after conditioning SA on both major depressive disorder and posttraumatic stress disorder. Genetic causal proportion analyses implicated shared genetic risk for specific health factors.This multi-ancestry analysis of suicide attempt identified several loci contributing to risk and establishes significant shared genetic covariation with clinical phenotypes. These findings provide insight into genetic factors associated with suicide attempt across ancestry admixture populations, in veteran and civilian populations, and in attempt versus death.
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| 2. |
- Mullins, Niamh, et al.
(författare)
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Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors
- 2022
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Ingår i: Biological Psychiatry. - : Elsevier. - 0006-3223 .- 1873-2402. ; 91:3, s. 313-327
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Suicide is a leading cause of death worldwide, and nonfatal suicide attempts, which occur far more frequently, are a major source of disability and social and economic burden. Both have substantial genetic etiology, which is partially shared and partially distinct from that of related psychiatric disorders.METHODS: We conducted a genome-wide association study (GWAS) of 29,782 suicide attempt (SA) cases and 519,961 controls in the International Suicide Genetics Consortium (ISGC). The GWAS of SA was conditioned on psychiatric disorders using GWAS summary statistics via multitrait-based conditional and joint analysis, to remove genetic effects on SA mediated by psychiatric disorders. We investigated the shared and divergent genetic architectures of SA, psychiatric disorders, and other known risk factors.RESULTS: Two loci reached genome-wide significance for SA: the major histocompatibility complex and an intergenic locus on chromosome 7, the latter of which remained associated with SA after conditioning on psychiatric disorders and replicated in an independent cohort from the Million Veteran Program. This locus has been implicated in risk-taking behavior, smoking, and insomnia. SA showed strong genetic correlation with psychiatric disorders, particularly major depression, and also with smoking, pain, risk-taking behavior, sleep disturbances, lower educational attainment, reproductive traits, lower socioeconomic status, and poorer general health. After conditioning on psychiatric disorders, the genetic correlations between SA and psychiatric disorders decreased, whereas those with nonpsychiatric traits remained largely unchanged.CONCLUSIONS: Our results identify a risk locus that contributes more strongly to SA than other phenotypes and suggest a shared underlying biology between SA and known risk factors that is not mediated by psychiatric disorders.
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| 3. |
- Richards, Stephen, et al.
(författare)
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The genome of the model beetle and pest Tribolium castaneum.
- 2008
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Ingår i: Nature. - 1476-4687. ; 452:7190, s. 949-55
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Tidskriftsartikel (refereegranskat)abstract
- Tribolium castaneum is a representative of earth’s most numerous eukaryotic order, a powerful model organism for the study of generalized insect development, and also an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved an ability to interact with a diverse chemical environment as evidenced by large expansions in odorant and gustatory receptors, as well as p450 and other detoxification enzymes. Developmental patterns in Tribolium are more representative of other arthropods than those found in Drosophila, a fact represented in gene content and function. For one, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, and some are expressed in the growth zone crucial for axial elongation in short germ development. Systemic RNAi in T. castaneum appears to use mechanisms distinct from those found in C. elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
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| 4. |
- Auer-Grumbach, Michaela, et al.
(författare)
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Rare Variants in MME, Encoding Metalloprotease Neprilysin, Are Linked to Late-Onset Autosomal-Dominant Axonal Polyneuropathies
- 2016
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 99:3, s. 607-623
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Tidskriftsartikel (refereegranskat)abstract
- Axonal polyneuropathies are a frequent cause of progressive disability in the elderly. Common etiologies comprise diabetes mellitus, paraproteinaemia, and inflammatory disorders, but often the underlying causes remain elusive. Late-onset axonal Charcot-Marie-Tooth neuropathy (CMT2) is an autosomal-dominantly inherited condition that manifests in the second half of life and is genetically largely unexplained. We assumed age-dependent penetrance of mutations in a so far unknown gene causing late-onset CMT2. We screened 51 index case subjects with late-onset CMT2 for mutations by whole-exome (WES) and Sanger sequencing and subsequently queried WES repositories for further case subjects carrying mutations in the identified candidate gene. We studied nerve pathology and tissue levels and function of the abnormal protein in order to explore consequences of the mutations. Altogether, we observed heterozygous rare loss-of-function and missense mutations in MME encoding the metalloprotease neprilysin in 19 index case subjects diagnosed with axonal polyneuropathies or neurodegenerative conditions involving the peripheral nervous system. MME mutations segregated in an autosomal-dominant fashion with age-related incomplete penetrance and some affected individuals were isolated case subjects. We also found that MME mutations resulted in strongly decreased tissue availability of neprilysin and impaired enzymatic activity. Although neprilysin is known to degrade beta-amyloid, we observed no increased amyloid deposition or increased incidence of dementia in individuals with MME mutations. Detection of MME mutations is expected to increase the diagnostic yield in late-onset polyneuropathies, and it will be tempting to explore whether substances that can elevate neprilysin activity could be a rational option for treatment.
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| 5. |
- Eklof, Daniel, et al.
(författare)
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Mysterious SiB3: Identifying the Relation between alpha- and beta-SiB3
- 2019
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Ingår i: ACS Omega. - : AMER CHEMICAL SOC. - 2470-1343. ; 4:20, s. 18741-18759
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Tidskriftsartikel (refereegranskat)abstract
- Binary silicon boride SiB3 has been reported to occur in two forms, as disordered and nonstoichiometric alpha-SiB3-x, which relates to the alpha-rhombohedral phase of boron, and as strictly ordered and stoichiometric beta-SiB3. Similar to other boron-rich icosahedral solids, these SiB3 phases represent potentially interesting refractory materials. However, their thermal stability, formation conditions, and thermodynamic relation are poorly understood. Here, we map the formation conditions of alpha-SiB3-x and beta-SiB3 and analyze their relative thermodynamic stabilities. alpha-SiB3-x is metastable (with respect to beta-SiB3 and Si), and its formation is kinetically driven. Pure polycrystalline bulk samples may be obtained within hours when heating stoichiometric mixtures of elemental silicon and boron at temperatures 1200-1300 degrees C. At the same time, alpha-SiB3-x decomposes into SiB6 and Si, and optimum time-temperature synthesis conditions represent a trade-off between rates of formation and decomposition. The formation of stable beta-SiB3 was observed after prolonged treatment (days to weeks) of elemental mixtures with ratios Si/B = 1:11:4 at temperatures 1175-1200 degrees C. The application of high pressures greatly improves the kinetics of SiB3 formation and allows decoupling of SiB3 formation from decomposition. Quantitative formation of beta-SiB3 was seen at 1100 degrees C for samples pressurized to 5.5-8 GPa. beta-SiB3 decomposes peritectoidally at temperatures between 1250 and 1300 degrees C. The highly ordered nature of beta-SiB3 is reflected in its Raman spectrum, which features narrow and distinct lines. In contrast, the Raman spectrum of alpha-SiB3-x is characterized by broad bands, which show a clear relation to the vibrational modes of isostructural, ordered B6P. The detailed composition and structural properties of disordered alpha-SiB3-x were ascertained by a combination of single-crystal X-ray diffraction and Si-29 magic angle spinning NMR experiments. Notably, the compositions of polycrystalline bulk samples (obtained at T amp;lt;= 1200 degrees C) and single crystal samples (obtained from Si-rich molten Si-B mixtures at T amp;gt; 1400 degrees C) are different, SiB2.93(7) and SiB2.64(2), respectively. The incorporation of Si in the polar position of B-12 icosahedra results in highly strained cluster units. This disorder feature was accounted for in the refined crystal structure model by splitting the polar position into three sites. The electron-precise composition of alpha-SiB3-x is SiB2.5 and corresponds to the incorporation of, on average, two Si atoms in each B-12 icosahedron. Accordingly, alpha-SiB3-x constitutes a mixture of B10Si2 and B11Si clusters. The structural and phase stability of alpha-SiB3-x were explored using a first-principles cluster expansion. The most stable composition at 0 K is SiB2.5, which however is unstable with respect to the decomposition beta-SiB3 + Si. Modeling of the configurational and vibrational entropies suggests that alpha-SiB3-x only becomes more stable than beta-SiB3 at temperatures above its decomposition into SiB6 and Si. Hence, we conclude that alpha-SiB3-x is metastable at all temperatures. Density functional theory electronic structure calculations yield band gaps of similar size for electron-precise alpha-SiB2.5 and beta-SiB3, whereas alpha-SiB3 represents a p-type conductor.
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| 6. |
- Eklöf, Daniel, et al.
(författare)
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Mysterious SiB3 : Identifying the Relation between α- and β-SiB3
- 2019
-
Ingår i: ACS Omega. - : American Chemical Society (ACS). - 2470-1343. ; 4:20, s. 18741-18759
-
Tidskriftsartikel (refereegranskat)abstract
- Binary silicon boride SiB3 has been reported to occur in two forms, as disordered and nonstoichiometric alpha-SiB3-x, which relates to the alpha-rhombohedral phase of boron, and as strictly ordered and stoichiometric beta-SiB3. Similar to other boron-rich icosahedral solids, these SiB3 phases represent potentially interesting refractory materials. However, their thermal stability, formation conditions, and thermodynamic relation are poorly understood. Here, we map the formation conditions of alpha-SiB3-x and beta-SiB3 and analyze their relative thermodynamic stabilities. alpha-SiB3-x is metastable (with respect to beta-SiB3 and Si), and its formation is kinetically driven. Pure polycrystalline bulk samples may be obtained within hours when heating stoichiometric mixtures of elemental silicon and boron at temperatures 1200-1300 degrees C. At the same time, alpha-SiB3-x decomposes into SiB6 and Si, and optimum time-temperature synthesis conditions represent a trade-off between rates of formation and decomposition. The formation of stable beta-SiB3 was observed after prolonged treatment (days to weeks) of elemental mixtures with ratios Si/B = 1:11:4 at temperatures 1175-1200 degrees C. The application of high pressures greatly improves the kinetics of SiB3 formation and allows decoupling of SiB3 formation from decomposition. Quantitative formation of beta-SiB3 was seen at 1100 degrees C for samples pressurized to 5.5-8 GPa. beta-SiB3 decomposes peritectoidally at temperatures between 1250 and 1300 degrees C. The highly ordered nature of beta-SiB3 is reflected in its Raman spectrum, which features narrow and distinct lines. In contrast, the Raman spectrum of alpha-SiB3-x is characterized by broad bands, which show a clear relation to the vibrational modes of isostructural, ordered B6P. The detailed composition and structural properties of disordered alpha-SiB3-x were ascertained by a combination of single-crystal X-ray diffraction and Si-29 magic angle spinning NMR experiments. Notably, the compositions of polycrystalline bulk samples (obtained at T <= 1200 degrees C) and single crystal samples (obtained from Si-rich molten Si-B mixtures at T > 1400 degrees C) are different, SiB2.93(7) and SiB2.64(2), respectively. The incorporation of Si in the polar position of B-12 icosahedra results in highly strained cluster units. This disorder feature was accounted for in the refined crystal structure model by splitting the polar position into three sites. The electron-precise composition of alpha-SiB3-x is SiB2.5 and corresponds to the incorporation of, on average, two Si atoms in each B-12 icosahedron. Accordingly, alpha-SiB3-x constitutes a mixture of B10Si2 and B11Si clusters. The structural and phase stability of alpha-SiB3-x were explored using a first-principles cluster expansion. The most stable composition at 0 K is SiB2.5, which however is unstable with respect to the decomposition beta-SiB3 + Si. Modeling of the configurational and vibrational entropies suggests that alpha-SiB3-x only becomes more stable than beta-SiB3 at temperatures above its decomposition into SiB6 and Si. Hence, we conclude that alpha-SiB3-x is metastable at all temperatures. Density functional theory electronic structure calculations yield band gaps of similar size for electron-precise alpha-SiB2.5 and beta-SiB3, whereas alpha-SiB3 represents a p-type conductor.
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| 7. |
- Eklöf, Daniel, et al.
(författare)
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Transport Properties of Ag-doped ZnSb
- 2021
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Ingår i: Zeitschrift für Anorganische und Allgemeines Chemie. - : Wiley. - 0044-2313 .- 1521-3749. ; 647:2-3, s. 34-40
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Tidskriftsartikel (refereegranskat)abstract
- The intermetallic compound ZnSb is a (II-V) narrow gap semiconductor with interesting thermoelectric properties. Electrical resistivity, Hall coefficient, thermopower and thermal conductivity were measured up to 400 K on Ag-doped samples with concentrations 0.2, 0.5, 1, 2, and 3 at.%, which were consolidated to densities in excess of 99.5 % by spark plasma sintering. The work confirms a huge improvement of the thermoelectric Figure-of-merit, ZT, upon Ag doping. The optimum doping level is near 0.5 at.% Ag and results in ZT values around 1.05 at 390 K. The improvement stems from a largely decreased resistivity, which in turn relates to an increase of the hole charge carrier concentration by two orders of magnitude. It is argued that Ag can replace minute concentrations of Zn (on the order of 0.2 at.%) in the crystal structure which enhances the intrinsic impurity band of ZnSb. Excess Ag was found to segregate in grain boundaries. So the best performing material may be considered as a composite Zn similar to 0.998Ag similar to 0.002Sb/Ag-similar to 0.003.
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| 8. |
- Fang, Li Tai, et al.
(författare)
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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1151-1160
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Tidskriftsartikel (refereegranskat)abstract
- Tumor-normal paired DNA samples from a breast cancer cell line and a matched lymphoblastoid cell line enable calibration of clinical sequencing pipelines and benchmarking 'tumor-only' or 'matched tumor-normal' analyses. The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.
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| 9. |
- Fischer, Andreas, et al.
(författare)
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Synthesis, Structure, and Properties of the Electron-Poor II-V Semiconductor ZnAs
- 2014
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 53:16, s. 8691-8699
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Tidskriftsartikel (refereegranskat)abstract
- ZnAs was synthesized at 6 GPa and 1273 K utilizing multianvil highpressure techniques and structurally characterized by single-crystal and powder X-ray 7 diffraction (space group Pbca (No. 61), a = 5.6768(2) angstrom, b = 7.2796(2) angstrom, c = 7.5593(2) angstrom, Z = 8). The compound is isostructural to ZnSb (CdSb type) and displays multicenter bonded rhomboid rings Zn2As2, which are connected to each other by classical two-center, two-electron bonds. At ambient pressure ZnAs is metastable with respect to Zn3As2 and ZnAs2. When heating at a rate of 10 K/min decomposition takes place at similar to 700 K. Diffuse reflectance measurements reveal a band gap of 0.9 eV. Electrical resistivity, thermopower, and thermal conductivity were measured in the temperature range of 2-400 K and compared to thermoelectric ZnSb. The room temperature values of the resistivity and thermopower are similar to 1 Omega cm and +27 mu V/K, respectively. These values are considerably higher and lower, respectively, compared to Zn Sb. Above 150 K the thermal conductivity attains low values, around 2 W/m.K, which is similar to that of ZnSb. The heat capacity of ZnAs was measured between 2 and 300 K and partitioned into a Debye and two Einstein contributions with temperatures of theta(D) = 234 K, theta(E1) = 95 K, and theta(E2) = 353 K. Heat capacity and thermal conductivity of ZnSb and ZnAs show very similar features, which possibly relates to their common electron-poor bonding properties.
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| 10. |
- Foox, Jonathan, et al.
(författare)
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The SEQC2 epigenomics quality control (EpiQC) study
- 2021
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundCytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA’s Epigenomics Quality Control Group.ResultsEach sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms.ConclusionsThe data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.
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