| 1. |
- Wang, Anqi, et al.
(författare)
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Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants
- 2023
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Ingår i: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 55:12, s. 2065-2074
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Tidskriftsartikel (refereegranskat)abstract
- The transferability and clinical value of genetic risk scores (GRSs) across populations remain limited due to an imbalance in genetic studies across ancestrally diverse populations. Here we conducted a multi-ancestry genome-wide association study of 156,319 prostate cancer cases and 788,443 controls of European, African, Asian and Hispanic men, reflecting a 57% increase in the number of non-European cases over previous prostate cancer genome-wide association studies. We identified 187 novel risk variants for prostate cancer, increasing the total number of risk variants to 451. An externally replicated multi-ancestry GRS was associated with risk that ranged from 1.8 (per standard deviation) in African ancestry men to 2.2 in European ancestry men. The GRS was associated with a greater risk of aggressive versus non-aggressive disease in men of African ancestry (P = 0.03). Our study presents novel prostate cancer susceptibility loci and a GRS with effective risk stratification across ancestry groups.
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| 2. |
- Abrahams, I., et al.
(författare)
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A Combined Total Scattering and Simulation Approach to Analyzing Defect Structure in Bi3YO6
- 2010
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Ingår i: Chemistry of Materials. - : American Chemical Society (ACS). - 1520-5002 .- 0897-4756. ; 22:15, s. 4435-4445
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Tidskriftsartikel (refereegranskat)abstract
- The defect structure and electrical properties of the fast oxide ion-conducting solid electrolyte delta-Bi3YO6 have been studied using a combination of total neutron scattering analysis, energy minimization methods, and AC impedance spectroscopy. Conventional structural analysis using the Rietveld method reveals the oxide ions to be distributed over three crystallographic sites at room temperature, with a small change in this distribution at 800 degrees C. Analysis of short-range correlations using a total neutron scattering approach yields information on Bi and Y coordination environments. Careful analysis of the angular distribution functions derived from reverse Monte Carlo modeling of the total scattering data reveals physical evidence for a predominance of vacancy ordering in this system. This ordering is confirmed as the lowest energy configuration in parallel energy minimization simulations.
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| 3. |
- Anney, Richard, et al.
(författare)
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A genome-wide scan for common alleles affecting risk for autism.
- 2010
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 19:20, s. 4072-4082
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Tidskriftsartikel (refereegranskat)abstract
- Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.
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| 4. |
- Buffart, L. M., et al.
(författare)
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Effects and moderators of coping skills training on symptoms of depression and anxiety in patients with cancer : Aggregate data and individual patient data meta-analyses
- 2020
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Ingår i: Clinical Psychology Review. - : Elsevier BV. - 0272-7358 .- 1873-7811. ; 80
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Forskningsöversikt (refereegranskat)abstract
- PURPOSE: This study evaluated the effects of coping skills training (CST) on symptoms of depression and anxiety in cancer patients, and investigated moderators of the effects.METHODS: Overall effects and intervention-related moderators were studied in meta-analyses of pooled aggregate data from 38 randomized controlled trials (RCTs). Patient-related moderators were examined using linear mixed-effect models with interaction tests on pooled individual patient data (n = 1953) from 15 of the RCTs.RESULTS: CST had a statistically significant but small effect on depression (g = -0.31,95% confidence interval (CI) = -0.40;-0.22) and anxiety (g = -0.32,95%CI = -0.41;-0.24) symptoms. Effects on depression symptoms were significantly larger for interventions delivered face-to-face (p = .003), led by a psychologist (p = .02) and targeted to patients with psychological distress (p = .002). Significantly larger reductions in anxiety symptoms were found in younger patients (pinteraction < 0.025), with the largest reductions in patients <50 years (β = -0.31,95%CI = -0.44;-0.18) and no significant effects in patients ≥70 years. Effects of CST on depression (β = -0.16,95%CI = -0.25;-0.07) and anxiety (β = -0.24,95%CI = -0.33;-0.14) symptoms were significant in patients who received chemotherapy but not in patients who did not (pinteraction < 0.05).CONCLUSIONS: CST significantly reduced symptoms of depression and anxiety in cancer patients, and particularly when delivered face-to-face, provided by a psychologist, targeted to patients with psychological distress, and given to patients who were younger and received chemotherapy.
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| 5. |
- Casey, Jillian P, et al.
(författare)
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A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder.
- 2012
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Ingår i: Human Genetics. - : Springer Science and Business Media LLC. - 0340-6717 .- 1432-1203. ; 131:4, s. 565-579
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Tidskriftsartikel (refereegranskat)abstract
- Autism spectrum disorder (ASD) is a highly heritable disorder of complex and heterogeneous aetiology. It is primarily characterized by altered cognitive ability including impaired language and communication skills and fundamental deficits in social reciprocity. Despite some notable successes in neuropsychiatric genetics, overall, the high heritability of ASD (~90%) remains poorly explained by common genetic risk variants. However, recent studies suggest that rare genomic variation, in particular copy number variation, may account for a significant proportion of the genetic basis of ASD. We present a large scale analysis to identify candidate genes which may contain low-frequency recessive variation contributing to ASD while taking into account the potential contribution of population differences to the genetic heterogeneity of ASD. Our strategy, homozygous haplotype (HH) mapping, aims to detect homozygous segments of identical haplotype structure that are shared at a higher frequency amongst ASD patients compared to parental controls. The analysis was performed on 1,402 Autism Genome Project trios genotyped for 1 million single nucleotide polymorphisms (SNPs). We identified 25 known and 1,218 novel ASD candidate genes in the discovery analysis including CADM2, ABHD14A, CHRFAM7A, GRIK2, GRM3, EPHA3, FGF10, KCND2, PDZK1, IMMP2L and FOXP2. Furthermore, 10 of the previously reported ASD genes and 300 of the novel candidates identified in the discovery analysis were replicated in an independent sample of 1,182 trios. Our results demonstrate that regions of HH are significantly enriched for previously reported ASD candidate genes and the observed association is independent of gene size (odds ratio 2.10). Our findings highlight the applicability of HH mapping in complex disorders such as ASD and offer an alternative approach to the analysis of genome-wide association data.
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| 6. |
- Chatterjee, S., et al.
(författare)
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Protein Paucimannosylation Is an Enriched N-Glycosylation Signature of Human Cancers
- 2019
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 19:21-22
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Tidskriftsartikel (refereegranskat)abstract
- While aberrant protein glycosylation is a recognized characteristic of human cancers, advances in glycoanalytics continue to discover new associations between glycoproteins and tumorigenesis. This glycomics‐centric study investigates a possible link between protein paucimannosylation, an under‐studied class of human N‐glycosylation [Man1‐3GlcNAc2Fuc0‐1], and cancer. The paucimannosidic glycans (PMGs) of 34 cancer cell lines and 133 tissue samples spanning 11 cancer types and matching non‐cancerous specimens are profiled from 467 published and unpublished PGC‐LC‐MS/MS N‐glycome datasets collected over a decade. PMGs, particularly Man2‐3GlcNAc2Fuc1, are prominent features of 29 cancer cell lines, but the PMG level varies dramatically across and within the cancer types (1.0–50.2%). Analyses of paired (tumor/non‐tumor) and stage‐stratified tissues demonstrate that PMGs are significantly enriched in tumor tissues from several cancer types including liver cancer (p = 0.0033) and colorectal cancer (p = 0.0017) and is elevated as a result of prostate cancer and chronic lymphocytic leukaemia progression (p < 0.05). Surface expression of paucimannosidic epitopes is demonstrated on human glioblastoma cells using immunofluorescence while biosynthetic involvement of N‐acetyl‐β‐hexosaminidase is indicated by quantitative proteomics. This intriguing association between protein paucimannosylation and human cancers warrants further exploration to detail the biosynthesis, cellular location(s), protein carriers, and functions of paucimannosylation in tumorigenesis and metastasis.
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| 7. |
- Leonard, Hampton L., et al.
(författare)
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The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data
- 2023
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Ingår i: npj Parkinson's Disease. - : Springer Science and Business Media LLC. - 2373-8057. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Open science and collaboration are necessary to facilitate the advancement of Parkinson’s disease (PD) research. Hackathons are collaborative events that bring together people with different skill sets and backgrounds to generate resources and creative solutions to problems. These events can be used as training and networking opportunities, thus we coordinated a virtual 3-day hackathon event, during which 49 early-career scientists from 12 countries built tools and pipelines with a focus on PD. Resources were created with the goal of helping scientists accelerate their own research by having access to the necessary code and tools. Each team was allocated one of nine different projects, each with a different goal. These included developing post-genome-wide association studies (GWAS) analysis pipelines, downstream analysis of genetic variation pipelines, and various visualization tools. Hackathons are a valuable approach to inspire creative thinking, supplement training in data science, and foster collaborative scientific relationships, which are foundational practices for early-career researchers. The resources generated can be used to accelerate research on the genetics of PD.
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| 8. |
- Leszczynska, M., et al.
(författare)
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Oxide ion distribution, vacancy ordering and electrical behaviour in the Bi3NbO7-Bi3YbO6 pseudo-binary system
- 2014
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Ingår i: Journal of Materials Chemistry A. - : Royal Society of Chemistry (RSC). - 2050-7488 .- 2050-7496. ; 2:43, s. 18624-18634
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Tidskriftsartikel (refereegranskat)abstract
- Oxide ion distribution, vacancy ordering and electrical conductivity has been examined in the Nb/Yb double substituted bismuth oxide based system Bi3Nb1-xYbxO7-x, using X-ray and neutron powder diffraction, reverse Monte Carlo modelling of total neutron scattering data and a. c. impedance spectroscopy. Transference number measurements confirm the system to be predominantly ionically conducting above ca. 450 degrees C. Niobium rich compositions show incommensurate ordering of the fluorite subcell, while increasing ytterbium content results in a commensurate fluorite, with fully disordered cation and anion sublattices. Oxide ion distribution shows both compositional and thermal dependencies. The latter is discussed with respect to its effect on the thermal variation of cubic lattice parameter. Substitution of bismuth by niobium and ytterbium in the cation sublattice of bismuth oxide leads to the creation of Frenkel interstitial oxide ions, which increase the tetrahedral vacancy concentration. The high vacancy concentration is confirmed in both Rietveld and RMC analyses of neutron data. Examination of vacancy ordering, in the x - 0.6 composition, indicates a favouring of vacancy pair alignment.
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| 9. |
- Leszczynska, M., et al.
(författare)
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Thermal Variation of Structure and Electrical Conductivity in Bi4YbO7.5
- 2013
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Ingår i: Chemistry of Materials. - : American Chemical Society (ACS). - 1520-5002 .- 0897-4756. ; 25:3, s. 326-336
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Tidskriftsartikel (refereegranskat)abstract
- The thermal behavior of the oxide ion-conducting solid electrolyte Bi4YbO7.5 was investigated using a combination of variable temperature X-ray and neutron powder diffraction, thermal analysis (DTA and TGA), and ac impedance spectroscopy. The title compound shows a fluorite-type structure throughout the measured temperature range (20-850 degrees C), with a phase separation at ca. 600 degrees C into a cubic delta-type phase and an orthorhombic phase of assumed stoichiometry Bi17Yb7O36. This type of transition is a relatively common feature in bismuth oxide-based systems and can limit their practical application. Here, the transition was carefully studied using isothermal measurements, which showed that it is accompanied by changes in oxide-ion stoichiometry, as well as significant disorder in the oxide ion sublattice in the delta-type phase. These results correlate with the observed electrical behavior. Analysis of the total neutron scattering through reverse Monte Carlo (RMC) modeling reveals details of the coordination environments for both cations. The oxide-ion vacancy distribution seems to be consistent with a favoring of vacancy pairs, although vacancy pairs exhibit the highest frequency as they have the maximum likelihood. A vacancy ordering model based on three vacancies per cell is presented.
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| 10. |
- Leszczynska, M., et al.
(författare)
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Total scattering analysis of cation coordination and vacancy pair distribution in Yb substituted delta-Bi2O3
- 2013
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Ingår i: Journal of Physics Condensed Matter. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 25:45
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Tidskriftsartikel (refereegranskat)abstract
- Reverse Monte Carlo (RMC) modelling of neutron total scattering data, combined with conventional Rietveld analysis of x-ray and neutron data, has been used to describe the cation coordination environments and vacancy pair distribution in the oxide ion conducting electrolyte Bi3YbO6. The thermal variation of the cubic fluorite unit cell volume, monitored by variable temperature x-ray and neutron experiments, reveals significant curvature, which is explained by changes in the oxide ion distribution. There is a significant increase in tetrahedral oxide ion vacancy concentration relative to delta-Bi2O3, due to the creation of Frenkel defects associated with the Yb3+ cation. The tetrahedral oxide ion vacancy concentration increases from room temperature to 800 degrees C, but little change is observed in the vacancy pair distribution with temperature. The vacancy pair distributions at both temperatures are consistent with a favouring of vacancy pairs.
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