| 1. |
- Docherty, Anna R, et al.
(author)
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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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In: The American journal of psychiatry. - : American Psychiatric Association Publishing. - 1535-7228 .- 0002-953X. ; 180:10, s. 723-738
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Journal article (peer-reviewed)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.
(author)
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Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors
- 2022
-
In: Biological Psychiatry. - : Elsevier. - 0006-3223 .- 1873-2402. ; 91:3, s. 313-327
-
Journal article (peer-reviewed)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.
(author)
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The genome of the model beetle and pest Tribolium castaneum.
- 2008
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In: Nature. - 1476-4687. ; 452:7190, s. 949-55
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Journal article (peer-reviewed)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. |
- Watson, Hunna J., et al.
(author)
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Common Genetic Variation and Age of Onset of Anorexia Nervosa
- 2022
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In: BIOLOGICAL PSYCHIATRY: GLOBAL OPEN SCIENCE. - : Elsevier BV. - 2667-1743. ; 2:4, s. 368-378
-
Journal article (peer-reviewed)abstract
- BACKGROUND: Genetics and biology may influence the age of onset of anorexia nervosa (AN). The aims of this study were to determine whether common genetic variation contributes to age of onset of AN and to investigate the genetic associations between age of onset of AN and age at menarche.METHODS: A secondary analysis of the Psychiatric Genomics Consortium genome-wide association study (GWAS) of AN was performed, which included 9335 cases and 31,981 screened controls, all from European ancestries. We conducted GWASs of age of onset, early-onset AN (,13 years), and typical-onset AN, and genetic correlation, genetic risk score, and Mendelian randomization analyses.RESULTS: Two loci were genome-wide significant in the typical-onset AN GWAS. Heritability estimates (single nucleotide polymorphism-h2) were 0.01-0.04 for age of onset, 0.16-0.25 for early-onset AN, and 0.17-0.25 for typical-onset AN. Early-and typical-onset AN showed distinct genetic correlation patterns with putative risk factors for AN. Specifically, early-onset AN was significantly genetically correlated with younger age at menarche, and typical-onset AN was significantly negatively genetically correlated with anthropometric traits. Genetic risk scores for age of onset and early-onset AN estimated from independent GWASs significantly predicted age of onset. Mendelian randomization analysis suggested a causal link between younger age at menarche and early -onset AN.CONCLUSIONS: Our results provide evidence consistent with a common variant genetic basis for age of onset and implicate biological pathways regulating menarche and reproduction.
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| 5. |
- Auer-Grumbach, Michaela, et al.
(author)
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Rare Variants in MME, Encoding Metalloprotease Neprilysin, Are Linked to Late-Onset Autosomal-Dominant Axonal Polyneuropathies
- 2016
-
In: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 99:3, s. 607-623
-
Journal article (peer-reviewed)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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| 6. |
- Eklof, Daniel, et al.
(author)
-
Mysterious SiB3: Identifying the Relation between alpha- and beta-SiB3
- 2019
-
In: ACS Omega. - : AMER CHEMICAL SOC. - 2470-1343. ; 4:20, s. 18741-18759
-
Journal article (peer-reviewed)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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| 7. |
- Eklöf, Daniel, et al.
(author)
-
Mysterious SiB3 : Identifying the Relation between α- and β-SiB3
- 2019
-
In: ACS Omega. - : American Chemical Society (ACS). - 2470-1343. ; 4:20, s. 18741-18759
-
Journal article (peer-reviewed)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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| 8. |
- Eklöf, Daniel, et al.
(author)
-
Transport Properties of Ag-doped ZnSb
- 2021
-
In: Zeitschrift für Anorganische und Allgemeines Chemie. - : Wiley. - 0044-2313 .- 1521-3749. ; 647:2-3, s. 34-40
-
Journal article (peer-reviewed)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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| 9. |
- Fang, Li Tai, et al.
(author)
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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
- 2021
-
In: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1151-1160
-
Journal article (peer-reviewed)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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| 10. |
- Fischer, Andreas, et al.
(author)
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Synthesis, Structure, and Properties of the Electron-Poor II-V Semiconductor ZnAs
- 2014
-
In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 53:16, s. 8691-8699
-
Journal article (peer-reviewed)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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| 11. |
- Foox, Jonathan, et al.
(author)
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The SEQC2 epigenomics quality control (EpiQC) study
- 2021
-
In: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 22:1
-
Journal article (peer-reviewed)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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| 12. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
-
In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 13. |
- Leblond, Claire S, et al.
(author)
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Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of autism spectrum disorders.
- 2012
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In: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 8:2
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Journal article (peer-reviewed)abstract
- Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental disorders with a complex inheritance pattern. While many rare variants in synaptic proteins have been identified in patients with ASD, little is known about their effects at the synapse and their interactions with other genetic variations. Here, following the discovery of two de novo SHANK2 deletions by the Autism Genome Project, we identified a novel 421 kb de novo SHANK2 deletion in a patient with autism. We then sequenced SHANK2 in 455 patients with ASD and 431 controls and integrated these results with those reported by Berkel et al. 2010 (n=396 patients and n=659 controls). We observed a significant enrichment of variants affecting conserved amino acids in 29 of 851 (3.4%) patients and in 16 of 1,090 (1.5%) controls (P=0.004, OR=2.37, 95% CI=1.23-4.70). In neuronal cell cultures, the variants identified in patients were associated with a reduced synaptic density at dendrites compared to the variants only detected in controls (P=0.0013). Interestingly, the three patients with de novo SHANK2 deletions also carried inherited CNVs at 15q11-q13 previously associated with neuropsychiatric disorders. In two cases, the nicotinic receptor CHRNA7 was duplicated and in one case the synaptic translation repressor CYFIP1 was deleted. These results strengthen the role of synaptic gene dysfunction in ASD but also highlight the presence of putative modifier genes, which is in keeping with the "multiple hit model" for ASD. A better knowledge of these genetic interactions will be necessary to understand the complex inheritance pattern of ASD.
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| 14. |
- Oldoni, Emanuela, et al.
(author)
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Tackling the translational challenges of multi-omics research in the realm of European personalised medicine : A workshop report
- 2022
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In: Frontiers in Molecular Biosciences. - : Frontiers Media S.A.. - 2296-889X. ; 9
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Journal article (peer-reviewed)abstract
- Personalised medicine (PM) presents a great opportunity to improve the future of individualised healthcare. Recent advances in -omics technologies have led to unprecedented efforts characterising the biology and molecular mechanisms that underlie the development and progression of a wide array of complex human diseases, supporting further development of PM. This article reflects the outcome of the 2021 EATRIS-Plus Multi-omics Stakeholder Group workshop organised to 1) outline a global overview of common promises and challenges that key European stakeholders are facing in the field of multi-omics research, 2) assess the potential of new technologies, such as artificial intelligence (AI), and 3) establish an initial dialogue between key initiatives in this space. Our focus is on the alignment of agendas of European initiatives in multi-omics research and the centrality of patients in designing solutions that have the potential to advance PM in long-term healthcare strategies.
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| 15. |
- Palmkvist, Jenny, et al.
(author)
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Marin videokartering runt Tärnö 2019 : Inventering av marina värden
- 2019
-
Reports (other academic/artistic)abstract
- Medins Havs- och Vattenkonsulter AB har på uppdrag av Länsstyrelsen i Blekinge län utfört en marin dropvideoinventering med fokus på bottenstruktur och associerad biota i området runt Tärnö, Karlshamns kommun. Totalt insamlades data från 100 videotransekter utslumpade i tre djupintervall. Från varje videotransekt bestämdes täckningsgraden av substrattyp samt vegetation och fauna. Baserat på dessa data gjordes en klassning av naturtyp och prioriterade bevarandevärden.I den nordvästra delen av området i de mindre vindexponerade områdena mellan öarna, dominerade mjuka substrat i form av lera/silt/gyttja, sand och grus. I den södra och östra delen av området som ligger i ett mer vindexponerat läge dominerades bottnarna av hårda substrat. Totalt påträffades 20 olika taxa/grupper av kärlväxter eller alger. På fem transekter påträffades ingen fastsittande vegetation eller djur utan endast lösliggande fintrådiga alger på mjukbotten. Som djupast noterades enstaka kärlväxter ner till ca 9 meters djup och enstaka blåstångsplantor ner till ca 13 meters djup.Vegetationen dominerades i hela området av fastsittande fintrådiga alger. Även lösdrivande fintrådiga alger noterades på flertalet filmer i höga tätheter i huvudsak i den norra delen av området. Fleråriga alger såsom såg- och blåstång samt kräkel noterades på 4,1 % av den undersökta ytan med huvudsaklig förekomst i den norra delen av området. Ålgräs dominerade kärlväxtförekomsten och noterades på 16 transekter med en genomsnittlig täckningsgrad på 51 %. Som djupast konstaterades sammanhängande ålgräsängar ner till 7,6 meter. Utöver ålgräs observerades kärlväxter såsom borstnate, hårsärv och kransalgen havsrufse. Blåmusslor var det vanligast förekommande djuret och påträffades på 41 transekter. På 11 av transekterna var täckningsgraden över 10 % vilket utgör gränsen för att kunna klassas som en musselbank enligt Natura 2000.Skärgårdsområdet runt Tärnö är varierat med både utsatta och skyddade delar och därmed förekommer flera olika naturtyper. Den dominerande naturtypen, vilken framför allt förekom i den södra och östligaste delen av området som ligger exponerat för vind och vågor, klassades enligt definitionen i Natura 2000 som ”1170 - Rev” med olika underkategorier. I de exponerade områdena fanns även enstaka transekter med dominerande mjukbotten vilka klassades som ”1110 - Sublittorala sandbankar”. I området vid de trädlösa småöarna öster om Harö definierades naturtypen som ”1620 - Skär i Östersjön”. I den nordvästra delen av området som är mindre exponerat från väder och vind har naturtypen vid flera av transekterna klassats som ”1160 - Vikar och sund” med olika underkategorier. Vid flera av de undersökta provytorna identifierades preciserade bevarandevärden vilka visas i tabeller och kartor. Sammantaget bedöms det undersökta området hysa flera olika naturtyper med höga naturvärden.
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| 16. |
- Pinto, Dalila, et al.
(author)
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Convergence of Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders.
- 2014
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In: American journal of human genetics. - : Elsevier BV. - 1537-6605 .- 0002-9297. ; 94:5, s. 677-694
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Journal article (peer-reviewed)abstract
- Rare copy-number variation (CNV) is an important source of risk for autism spectrum disorders (ASDs). We analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0× 10(-5)) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability (odds ratio = 12.62, p = 2.7× 10(-15), ∼3% of ASD subjects). Pathogenic CNVs, often showing variable expressivity, included rare de novo and inherited events at 36 loci, implicating ASD-associated genes (CHD2, HDAC4, and GDI1) previously linked to other neurodevelopmental disorders, as well as other genes such as SETD5, MIR137, and HDAC9. Consistent with hypothesized gender-specific modulators, females with ASD were more likely to have highly penetrant CNVs (p = 0.017) and were also overrepresented among subjects with fragile X syndrome protein targets (p = 0.02). Genes affected by de novo CNVs and/or loss-of-function single-nucleotide variants converged on networks related to neuronal signaling and development, synapse function, and chromatin regulation.
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| 17. |
- Ren, Luyao, et al.
(author)
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
- 2023
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In: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24:1
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Journal article (peer-reviewed)abstract
- BACKGROUND: Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as they are limited to benchmark regions. Therefore, it is important to develop DNA reference materials that enable the assessment of variant detection performance across the entire genome.RESULTS: We established a DNA reference material suite from four immortalized cell lines derived from a family of parents and monozygotic twins. Comprehensive reference datasets of 4.2 million small variants and 15,000 structural variants were integrated and certified for evaluating the reliability of germline variant calls inside the benchmark regions. Importantly, the genetic built-in-truth of the Quartet family design enables estimation of the precision of variant calls outside the benchmark regions. Using the Quartet reference materials along with study samples, batch effects are objectively monitored and alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Moreover, the matched RNA and protein reference materials and datasets from the Quartet project enables cross-omics validation of variant calls from multiomics data.CONCLUSIONS: The Quartet DNA reference materials and reference datasets provide a unique resource for objectively assessing the quality of germline variant calls throughout the whole-genome regions and improving the reliability of large-scale genomic profiling.
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| 18. |
- Scherer, Petra, et al.
(author)
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An introduction to TWG25: Inclusive mathematics education – challenges for students with special needs
- 2023
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In: <em>Proceedings of the Thirteenth Congress of the European Society for Research in Mathematics Education (CERME13)</em>. - 9789637031045 ; , s. 4524-4531
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Conference paper (peer-reviewed)abstract
- Inclusive mathematics education is a complex and multifaceted, under-researched area where research often requires collaboration between various fields of study – mathematics education, special education, pedagogy, psychology, etc. The Thematic Working Group ‘TWG25 – Challenges for Students with Special Needs’, established in 2019, is one of the platforms opening up space for collaborative research in this area. This means that TWG25 embraces research in very different fields of mathematics, research from the point of view of teachers, pupils, teacher education and classroom practices at all school levels from preschool education to upper secondary, even university level. The presented papers and posters give the opportunity to share but also to grow aware of what the field of inclusive mathematics education involves in an international context. Apart from the topics of the single papers and posters more general questions of inclusive mathematics are discussed in this introduction.
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| 19. |
- Schneider, Anselm, et al.
(author)
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State Governance Beyond the 'Shadow of Hierarchy' : A social mechanisms perspective on governmental CSR policies
- 2019
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In: Organization Studies. - : SAGE Publications. - 0170-8406 .- 1741-3044. ; 40:8, s. 1147-1168
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Journal article (peer-reviewed)abstract
- The extent to which state authorities can regulate the externalities and the behaviour of multinational corporations (MNCs) is limited. This is especially true when MNCs operate in or do business with fragile states that lack the willingness and/or resources to effectively and legitimately regulate businesses. However, MNCs often engage in private regulation to remedy some of the problems that unregulated business behaviour creates. In this article we examine what limits the effectiveness and legitimacy of the contributions made by MNCs to global governance. We explore the mechanisms that state authorities in functioning states can use to overcome these barriers as well as the boundary conditions of these mechanisms at both company and government levels. We provide a framework for governmental CSR policies and describe the ways in which functioning states engage in governance beyond the 'shadow of hierarchy' and directly or indirectly influence business conduct beyond the territory in which their legal regulations can be enforced.
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| 20. |
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| 21. |
- Vethe, Heidrun, et al.
(author)
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Distinct protein signature of hypertension-induced damage in the renal proteome of the two-kidney, one-clip rat model
- 2015
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In: Journal of Hypertension. - 0263-6352 .- 1473-5598. ; 33:1, s. 126-135
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Journal article (peer-reviewed)abstract
- BACKGROUND:Hypertensive nephrosclerosis is one of the most frequent causes of chronic kidney failure. Proteome analysis potentially improves the pathophysiological understanding and diagnostic precision of this disorder. In the present exploratory study, we investigated experimental nephrosclerosis in the two-kidney, one-clip (2K1C) hypertensive rat model.METHODS:The renal cortex proteome from juxtamedullary cortex and outer cortex of 2K1C male Wistar-Hannover rats (n = 4) was compared with the sham-operated controls (n = 6), using mass spectrometry-based quantitative proteomics. We combined a high abundant plasma protein depletion strategy with an extended liquid chromatographic gradient to improve peptide and protein identification. Immunohistology was used for independent confirmation of abundance.RESULTS:We identified 1724 proteins, of which 1434 were quantified with at least two unique peptides. Comparative proteomics revealed 608 proteins, including the platelet-derived growth factor receptor-β signalling pathway, with different abundances between the non-clipped kidney of hypertensive 2K1C rats and the corresponding kidney of the normotensive controls (P < 0.05, absolute fold change ≥1.5). Among the most significantly altered proteins in the whole cortex were periostin, transgelin, and creatine kinase B-type. Relative abundance of periostin alone allowed clear classification of 2K1C and controls. Enrichment of periostin in 2K1C rats was verified by immunohistology, showing positivity especially around the fibrotic vessels.CONCLUSION:The proteome is altered in hypertension-induced kidney damage. We propose periostin, especially in combination with transgelin and creatine kinase B-type, as possible proteomic classifier to distinguish hypertensive nephrosclerosis from the normal tissue. This classifier needs to be further validated with respect to early diagnosis of fibrosis, prognosis, and its potential as a novel molecular target for pharmacological interventions.
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| 22. |
- Xiao, Wenming, et al.
(author)
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
- 2021
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In: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1141-1150
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Journal article (peer-reviewed)abstract
- Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing. Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.
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| 23. |
- Zhao, Yongmei, et al.
(author)
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Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study
- 2021
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In: Scientific Data. - : Springer Nature. - 2052-4463. ; 8:1
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Journal article (peer-reviewed)abstract
- With the rapid advancement of sequencing technologies, next generation sequencing (NGS) analysis has been widely applied in cancer genomics research. More recently, NGS has been adopted in clinical oncology to advance personalized medicine. Clinical applications of precision oncology require accurate tests that can distinguish tumor-specific mutations from artifacts introduced during NGS processes or data analysis. Therefore, there is an urgent need to develop best practices in cancer mutation detection using NGS and the need for standard reference data sets for systematically measuring accuracy and reproducibility across platforms and methods. Within the SEQC2 consortium context, we established paired tumor-normal reference samples and generated whole-genome (WGS) and whole-exome sequencing (WES) data using sixteen library protocols, seven sequencing platforms at six different centers. We systematically interrogated somatic mutations in the reference samples to identify factors affecting detection reproducibility and accuracy in cancer genomes. These large cross-platform/site WGS and WES datasets using well-characterized reference samples will represent a powerful resource for benchmarking NGS technologies, bioinformatics pipelines, and for the cancer genomics studies.
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