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Article ; Online: Early Spread of SARS-CoV-2 in the Icelandic Population. Reply.

Gudbjartsson, Daniel F / Stefansson, Kari

2020 Volume 383, Issue 22, Page(s) 2184–2185

MeSH term(s)	COVID-19 ; Coronavirus Infections/epidemiology ; Humans ; Iceland/epidemiology ; Pandemics ; Pneumonia, Viral/epidemiology ; SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-11-04
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	207154-x
ISSN	1533-4406 ; 0028-4793
ISSN (online)	1533-4406
ISSN	0028-4793
DOI	10.1056/NEJMc2027653
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Article: Early Spread of SARS-CoV-2 in the Icelandic Population. Reply

Gudbjartsson, Daniel F / Stefansson, Kari

N. Engl. j. med

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #910306
Database	COVID19

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Article ; Online: A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes.

Sigurpalsdottir, Brynja D / Stefansson, Olafur A / Holley, Guillaume / Beyter, Doruk / Zink, Florian / Hardarson, Marteinn Þ / Sverrisson, Sverrir Þ / Kristinsdottir, Nina / Magnusdottir, Droplaug N / Magnusson, Olafur Þ / Gudbjartsson, Daniel F / Halldorsson, Bjarni V / Stefansson, Kari

Genome biology

2024 Volume 25, Issue 1, Page(s) 69

Abstract: Background: Long-read sequencing can enable the detection of base modifications, such as CpG methylation, in single molecules of DNA. The most commonly used methods for long-read sequencing are nanopore developed by Oxford Nanopore Technologies (ONT) ... ...

Abstract	Background: Long-read sequencing can enable the detection of base modifications, such as CpG methylation, in single molecules of DNA. The most commonly used methods for long-read sequencing are nanopore developed by Oxford Nanopore Technologies (ONT) and single molecule real-time (SMRT) sequencing developed by Pacific Bioscience (PacBio). In this study, we systematically compare the performance of CpG methylation detection from long-read sequencing. Results: We demonstrate that CpG methylation detection from 7179 nanopore-sequenced DNA samples is highly accurate and consistent with 132 oxidative bisulfite-sequenced (oxBS) samples, isolated from the same blood draws. We introduce quality filters for CpGs that further enhance the accuracy of CpG methylation detection from nanopore-sequenced DNA, while removing at most 30% of CpGs. We evaluate the per-site performance of CpG methylation detection across different genomic features and CpG methylation rates and demonstrate how the latest R10.4 flowcell chemistry and base-calling algorithms improve methylation detection from nanopore sequencing. Additionally, we show how the methylation detection of 50 SMRT-sequenced genomes compares to nanopore sequencing and oxBS. Conclusions: This study provides the first systematic comparison of CpG methylation detection tools for long-read sequencing methods. We compare two commonly used computational methods for the detection of CpG methylation in a large number of nanopore genomes, including samples sequenced using the latest R10.4 nanopore flowcell chemistry and 50 SMRT sequenced samples. We provide insights into the strengths and limitations of each sequencing method as well as recommendations for standardization and evaluation of tools designed for genome-scale modified base detection using long-read sequencing.
MeSH term(s)	Humans ; DNA Methylation ; Sequence Analysis, DNA/methods ; Genome, Human ; High-Throughput Nucleotide Sequencing/methods ; DNA
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2024-03-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-024-03207-9
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Article ; Online: Comment on "Evaluating the cardiovascular safety of sclerostin inhibition using evidence from meta-analysis of clinical trials and human genetics".

Hólm, Hilma / Sulem, Patrick / Tragante, Vinicius / Thorsteinsdottir, Unnur / Gudbjartsson, Daniel F / Stefansson, Kari

Science translational medicine

2021 Volume 13, Issue 622, Page(s) eabe8497

Abstract: Genetic data do not provide evidence for SOST inhibition causing cardiovascular disease. ...

Abstract	Genetic data do not provide evidence for SOST inhibition causing cardiovascular disease.
MeSH term(s)	Adaptor Proteins, Signal Transducing/genetics ; Cardiovascular Diseases/genetics ; Human Genetics ; Humans
Chemical Substances	Adaptor Proteins, Signal Transducing
Language	English
Publishing date	2021-12-01
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	2518854-9
ISSN	1946-6242 ; 1946-6234
ISSN (online)	1946-6242
ISSN	1946-6234
DOI	10.1126/scitranslmed.abe8497
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Zs.A 6941: Show issues

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Article ; Online: GWAS of Hematuria.

Gagliano Taliun, Sarah A / Sulem, Patrick / Sveinbjornsson, Gardar / Gudbjartsson, Daniel F / Stefansson, Kari / Paterson, Andrew D / Barua, Moumita

Clinical journal of the American Society of Nephrology : CJASN

2022 Volume 17, Issue 5, Page(s) 672–683

Abstract: Background and objectives: Glomerular hematuria has varied causes but can have a genetic basis, including Alport syndrome and IgA nephropathy.: Design, setting, participants, & measurements: We used summary statistics to identify genetic variants ... ...

Abstract	Background and objectives: Glomerular hematuria has varied causes but can have a genetic basis, including Alport syndrome and IgA nephropathy. Design, setting, participants, & measurements: We used summary statistics to identify genetic variants associated with hematuria in White British UK Biobank participants. Individuals with glomerular hematuria were enriched by excluding participants with genitourinary conditions. A strongly associated locus on chromosome 2 ( Results: In total, 16,866 hematuria cases and 391,420 controls were included. Cases had higher urinary albumin-creatinine compared with controls (women: 13.01 mg/g [8.05-21.33] versus 12.12 mg/g [7.61-19.29]; Conclusions: Our study identifies six loci associated with hematuria, including independent variants in Podcast: This article contains a podcast at https://www.asn-online.org/media/podcast/CJASN/2022_04_26_CJN13711021.mp3.
MeSH term(s)	Male ; Humans ; Female ; Hematuria/genetics ; Collagen Type IV/genetics ; Genome-Wide Association Study ; Nephritis, Hereditary/genetics ; Kidney Glomerulus ; Autoantigens/genetics ; LDL-Receptor Related Proteins/genetics ; Membrane Transport Proteins/genetics
Chemical Substances	Collagen Type IV ; Autoantigens ; SORL1 protein, human ; LDL-Receptor Related Proteins ; Membrane Transport Proteins
Language	English
Publishing date	2022-04-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2226665-3
ISSN	1555-905X ; 1555-9041
ISSN (online)	1555-905X
ISSN	1555-9041
DOI	10.2215/CJN.13711021
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Zs.A 6584: Show issues

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Article ; Online: Predicting the presence of coronary plaques featuring high-risk characteristics using polygenic risk scores and targeted proteomics in patients with suspected coronary artery disease.

Møller, Peter Loof / Rohde, Palle Duun / Dahl, Jonathan Nørtoft / Rasmussen, Laust Dupont / Nissen, Louise / Schmidt, Samuel Emil / McGilligan, Victoria / Gudbjartsson, Daniel F / Stefansson, Kari / Holm, Hilma / Bentzon, Jacob Fog / Bøttcher, Morten / Winther, Simon / Nyegaard, Mette

Genome medicine

2024 Volume 16, Issue 1, Page(s) 40

Abstract: Background: The presence of coronary plaques with high-risk characteristics is strongly associated with adverse cardiac events beyond the identification of coronary stenosis. Testing by coronary computed tomography angiography (CCTA) enables the ... ...

Abstract	Background: The presence of coronary plaques with high-risk characteristics is strongly associated with adverse cardiac events beyond the identification of coronary stenosis. Testing by coronary computed tomography angiography (CCTA) enables the identification of high-risk plaques (HRP). Referral for CCTA is presently based on pre-test probability estimates including clinical risk factors (CRFs); however, proteomics and/or genetic information could potentially improve patient selection for CCTA and, hence, identification of HRP. We aimed to (1) identify proteomic and genetic features associated with HRP presence and (2) investigate the effect of combining CRFs, proteomics, and genetics to predict HRP presence. Methods: Consecutive chest pain patients (n = 1462) undergoing CCTA to diagnose obstructive coronary artery disease (CAD) were included. Coronary plaques were assessed using a semi-automatic plaque analysis tool. Measurements of 368 circulating proteins were obtained with targeted Olink panels, and DNA genotyping was performed in all patients. Imputed genetic variants were used to compute a multi-trait multi-ancestry genome-wide polygenic score (GPS Results: HRPs were detected in 165 (11%) patients, and 15 input features were associated with HRP presence. Prediction of HRP presence based on CRFs yielded a mean area under the receiver operating curve (AUC) ± standard error of 73.2 ± 0.1, versus 69.0 ± 0.1 for proteomics and 60.1 ± 0.1 for GPS Conclusions: In patients with suspected CAD, incorporating genetic data with either clinical or proteomic data improves the prediction of high-risk plaque presence. Trial registration: https://clinicaltrials.gov/ct2/show/NCT02264717 (September 2014).
MeSH term(s)	Humans ; Coronary Artery Disease/diagnosis ; Coronary Artery Disease/genetics ; Genetic Risk Score ; Proteomics ; Coronary Angiography/methods ; Plaque, Atherosclerotic/genetics ; Plaque, Atherosclerotic/complications ; Risk Factors
Language	English
Publishing date	2024-03-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2484394-5
ISSN	1756-994X ; 1756-994X
ISSN (online)	1756-994X
ISSN	1756-994X
DOI	10.1186/s13073-024-01313-8
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Article ; Online: Cartilage Acidic Protein 1 in Plasma Associates With Prevalent Osteoarthritis and Predicts Future Risk as Well as Progression to Joint Replacements: Results From the UK Biobank Resource.

Styrkarsdottir, Unnur / Lund, Sigrun H / Thorleifsson, Gudmar / Saevarsdottir, Saedis / Gudbjartsson, Daniel F / Thorsteinsdottir, Unnur / Stefansson, Kari

Arthritis & rheumatology (Hoboken, N.J.)

2022 Volume 75, Issue 4, Page(s) 544–552

Abstract: Objective: The level of cartilage acidic protein 1 (CRTAC1) in plasma was recently discovered to be associated with osteoarthritis (OA) risk and progression to joint replacement in Iceland. This study was undertaken to validate these findings in an ... ...

Abstract	Objective: The level of cartilage acidic protein 1 (CRTAC1) in plasma was recently discovered to be associated with osteoarthritis (OA) risk and progression to joint replacement in Iceland. This study was undertaken to validate these findings in an independent population. Methods: In this study, 1,462 plasma proteins were measured in 54,265 participants from the UK Biobank on the Olink Explore platform. We analyzed the association of plasma proteins with prevalent OA, incident OA, and progression to joint replacement. We assessed the specificity of OA association through comparison of associations with inflammatory joint diseases and with previous joint replacement. Results: The CRTAC1 protein showed the strongest association with prevalent knee OA (odds ratio [OR] 1.34 [95% confidence interval (95% CI) 1.27, 1.41]) and was associated with hip OA (OR 1.19 [95% CI 1.11, 1.28]). It predicted incident diagnosis of OA in the knee (hazard ratio [HR] 1.40 [95% CI 1.35, 1.46]) and hip (HR 1.25 [95% CI 1.19, 1.31]), as well as progression to joint replacement (HR 1.20 [95% CI 1.08, 1.33] for the knee and HR 1.22 [95% CI 1.08, 1.38] for the hip), while no association was found with inflammatory joint diseases. Individuals in the highest quintile of risk based on CRTAC1 level, age, sex, and body mass index had a 10-fold risk of knee or hip OA within 5 years compared to those in the lowest quintile. Adding aggrecan core protein (ACAN) and neurocan core protein (NCAN) to the model improved the prediction of OA but not joint replacement. Furthermore, we replicated the association of CUB domain-containing protein 1 with prior joint replacement. Conclusion: Plasma CRTAC1 is a specific biomarker for OA and a predictor of OA risk and progression to joint replacement. Adding ACAN and NCAN protein levels to the CRTAC1 model improved the prediction of OA.
MeSH term(s)	Humans ; Arthroplasty, Replacement ; Calcium-Binding Proteins ; Cartilage ; Osteoarthritis, Hip/epidemiology ; Osteoarthritis, Hip/surgery ; Osteoarthritis, Knee/epidemiology ; Osteoarthritis, Knee/surgery ; United Kingdom/epidemiology
Chemical Substances	Calcium-Binding Proteins ; CRTAC1 protein, human
Language	English
Publishing date	2022-12-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2756371-6
ISSN	2326-5205 ; 2326-5191
ISSN (online)	2326-5205
ISSN	2326-5191
DOI	10.1002/art.42376
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Article ; Online: Polygenic risk scores associate with blood pressure traits across the lifespan.

Øvretveit, Karsten / Ingeström, Emma M L / Spitieris, Michail / Tragante, Vinicius / Wade, Kaitlin H / Thomas, Laurent F / Wolford, Brooke N / Wisløff, Ulrik / Gudbjartsson, Daniel F / Holm, Hilma / Stefansson, Kari / Brumpton, Ben M / Hveem, Kristian

European journal of preventive cardiology

2023 Volume 31, Issue 6, Page(s) 644–654

Abstract: Aims: Hypertension is a major modifiable cause of morbidity and mortality that affects over 1 billion people worldwide. Blood pressure (BP) traits have a strong genetic component that can be quantified with polygenic risk scores (PRSs). To date, the ... ...

Abstract	Aims: Hypertension is a major modifiable cause of morbidity and mortality that affects over 1 billion people worldwide. Blood pressure (BP) traits have a strong genetic component that can be quantified with polygenic risk scores (PRSs). To date, the performance of BP PRSs has mainly been assessed in adults, and less is known about polygenic hypertension risk in childhood. Methods and results: Multiple PRSs for systolic BP (SBP), diastolic BP (DBP), and pulse pressure were developed using either genome-wide significant weights, pruning and thresholding, or Bayesian regression. Among 87 total PRSs, the top performer for each trait was applied in independent cohorts of children and adult to assess genotype-phenotype associations and disease risk across the lifespan. Differences between those with low (1st decile), average (2nd-9th decile), and high (10th decile) PRS emerge in the first years of life and are maintained throughout adulthood. These diverging BP trajectories also seem to affect cardiovascular and renal disease risk, with increased risk observed among those in the top decile and reduced risk among those in the bottom decile of the polygenic risk distribution compared with the rest of the population. Conclusion: Genetic risk factors are associated with BP traits across the lifespan, beginning in the first years of life. Given the importance of exposure time in disease pathogenesis and the early rise in BP levels among those genetically susceptible, PRSs may help identify high-risk individuals prior to hypertension onset, facilitate primordial prevention, and reduce the burden of this public health challenge.
MeSH term(s)	Adult ; Child ; Humans ; Blood Pressure ; Genetic Risk Score ; Longevity ; Bayes Theorem ; Hypertension/epidemiology ; Genetic Predisposition to Disease ; Risk Factors
Language	English
Publishing date	2023-11-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2626011-6
ISSN	2047-4881 ; 2047-4873
ISSN (online)	2047-4881
ISSN	2047-4873
DOI	10.1093/eurjpc/zwad365
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Article ; Online: DanMAC5: a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals.

Banasik, Karina / Møller, Peter L / Techlo, Tanya R / Holm, Peter C / Walters, G Bragi / Ingason, Andrés / Rosengren, Anders / Rohde, Palle D / Kogelman, Lisette J A / Westergaard, David / Siggaard, Troels / Chmura, Piotr J / Chalmer, Mona A / Magnússon, Ólafur Þ / Þórisson, Guðmundur Á / Stefánsson, Hreinn / Guðbjartsson, Daníel F / Stefánsson, Kári / Olesen, Jes /

Winther, Simon / Bøttcher, Morten / Brunak, Søren / Werge, Thomas / Nyegaard, Mette / Hansen, Thomas F

BMC genomic data

2023 Volume 24, Issue 1, Page(s) 30

Abstract: Objectives: Allele counts of sequence variants obtained by whole genome sequencing (WGS) often play a central role in interpreting the results of genetic and genomic research. However, such variant counts are not readily available for individuals in the ...

Abstract	Objectives: Allele counts of sequence variants obtained by whole genome sequencing (WGS) often play a central role in interpreting the results of genetic and genomic research. However, such variant counts are not readily available for individuals in the Danish population. Here, we present a dataset with allele counts for sequence variants (single nucleotide variants (SNVs) and indels) identified from WGS of 8,671 (5,418 females) individuals from the Danish population. The data resource is based on WGS data from three independent research projects aimed at assessing genetic risk factors for cardiovascular, psychiatric, and headache disorders. To enable the sharing of information on sequence variation in Danish individuals, we created summarized statistics on allele counts from anonymized data and made them available through the European Genome-phenome Archive (EGA, https://identifiers.org/ega. Dataset: EGAD00001009756 ) and in a dedicated browser, DanMAC5 (available at www.danmac5.dk ). The summary level data and the DanMAC5 browser provide insight into the allelic spectrum of sequence variants segregating in the Danish population, which is important in variant interpretation. Data description: Three WGS datasets with an average coverage of 30x were processed independently using the same quality control pipeline. Subsequently, we summarized, filtered, and merged allele counts to create a high-quality summary level dataset of sequence variants.
MeSH term(s)	Female ; Humans ; Polymorphism, Single Nucleotide/genetics ; Genome ; Whole Genome Sequencing/methods ; Genomics ; Denmark
Language	English
Publishing date	2023-05-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2730-6844
ISSN (online)	2730-6844
DOI	10.1186/s12863-023-01132-7
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Article ; Online: Response by Björnsson et al to Letter Regarding Article, "Large-Scale Screening for Monogenic and Clinically Defined Familial Hypercholesterolemia in Iceland".

Björnsson, Eythór / Thorgeirsson, Gudmundur / Helgadóttir, Anna / Gudbjartsson, Daníel F / Hólm, Hilma / Thorsteinsdóttir, Unnur / Sulem, Patrick / Stefánsson, Kári

Arteriosclerosis, thrombosis, and vascular biology

2021 Volume 42, Issue 1, Page(s) e46–e47

MeSH term(s)	Cholesterol, LDL ; Humans ; Hyperlipoproteinemia Type II/diagnosis ; Hyperlipoproteinemia Type II/epidemiology ; Hyperlipoproteinemia Type II/genetics ; Iceland/epidemiology
Chemical Substances	Cholesterol, LDL
Language	English
Publishing date	2021-12-22
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	1221433-4
ISSN	1524-4636 ; 1079-5642
ISSN (online)	1524-4636
ISSN	1079-5642
DOI	10.1161/ATVBAHA.121.317201
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