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Article ; Online: Genetic analysis: moving between linkage and association.

Smith, Albert Vernon

Cold Spring Harbor protocols

2012 Volume 2012, Issue 2, Page(s) 174–182

Abstract: The approaches to identifying genes and genomic regions associated with human disease can be grouped into two categories: linkage analysis and genetic association analysis. Linkage analysis is useful for diseases of high penetrance that run strongly ... ...

Abstract	The approaches to identifying genes and genomic regions associated with human disease can be grouped into two categories: linkage analysis and genetic association analysis. Linkage analysis is useful for diseases of high penetrance that run strongly within families, but is limited in its ability to detect situations where there are multiple genes with smaller effects. An alternative is genetic association studies, which were initially performed on small numbers of candidate genes. This approach identified relatively few genes that were consistently associated with disease, but it is now possible to do a genetic association for the whole genome, making this approach more powerful. In practice, the two types of analysis are often interlinked. This article provides information on the tools needed to perform both genetic linkage and genetic association analysis.
MeSH term(s)	Disease/genetics ; Genetic Association Studies/methods ; Genetic Linkage ; Humans
Language	English
Publishing date	2012-02-01
Publishing country	United States
Document type	Journal Article
ISSN	1559-6095
ISSN (online)	1559-6095
DOI	10.1101/pdb.top067819
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Article: Manipulating HapMap Data Using HaploView.

Smith, Albert Vernon

CSH protocols

2008 Volume 2008, Page(s) pdb.prot5025

Abstract: INTRODUCTIONThe primary goal of the International Haplotype Map Project has been to develop a haplotype map of the human genome that describes the common patterns of genetic variation, in order to accelerate the search for the genetic causes of human ... ...

Abstract	INTRODUCTIONThe primary goal of the International Haplotype Map Project has been to develop a haplotype map of the human genome that describes the common patterns of genetic variation, in order to accelerate the search for the genetic causes of human disease. Within the project, ~3.9 million distinct single-nucleotide polymorphisms (SNPs) have been genotyped in 270 individuals from four worldwide populations. The project data are available for unrestricted public use at the HapMap website. This site, which is the primary portal to genotype data produced by the project, offers bulk downloads of the data set, as well as interactive data browsing and analysis tools that are not available elsewhere. Advanced users who wish to exercise fine control over the display of regions of high linkage disequilibrium (LD) or who wish to experiment with new algorithms for tag-SNP picking may wish to analyze HapMap data using the HaploView program. This program works well in combination with the HapMap website genome browser. A big advantage of HaploView over the genome browser is that it displays simultaneous high- and low-power views of regions of LD, and gives immediate feedback during scrolling and zooming operations. This protocol describes the use of HaploView to manipulate HapMap data.
Language	English
Publishing date	2008-07-01
Publishing country	United States
Document type	Journal Article
DOI	10.1101/pdb.prot5025
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Article: Browsing HapMap Data Using the Genome Browser.

Smith, Albert Vernon

CSH protocols

2008 Volume 2008, Page(s) pdb.prot5023

Abstract	INTRODUCTIONThe primary goal of the International Haplotype Map Project has been to develop a haplotype map of the human genome that describes the common patterns of genetic variation, in order to accelerate the search for the genetic causes of human disease. Within the project, ~3.9 million distinct single-nucleotide polymorphisms (SNPs) have been genotyped in 270 individuals from four worldwide populations. The project data are available for unrestricted public use at the HapMap website. This site, which is the primary portal to genotype data produced by the project, offers bulk downloads of the data set, as well as interactive data browsing and analysis tools that are not available elsewhere. Research into the genetic contributions to a human disease commonly focuses on candidate genes identified from linkage and/or association studies, as well as from pathways suspected to be involved in a particular disease process. In studying candidate genes, a researcher will want to know whether there are any common SNPs in the immediate vicinity, what those SNPs' alleles are, and the relative frequencies of the alleles in the population. The researcher will also be particularly interested in coding SNPs, whose alleles change the amino acid sequence of the gene product and therefore might represent functional variations. This protocol provides details on how to use the genome browser to navigate to and explore HapMap data for a gene or region of interest.
Language	English
Publishing date	2008-07-01
Publishing country	United States
Document type	Journal Article
DOI	10.1101/pdb.prot5023
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Article: Retrieving HapMap Data via Bulk Download.

Smith, Albert Vernon

CSH protocols

2008 Volume 2008, Page(s) pdb.prot5027

Abstract	INTRODUCTIONThe primary goal of the International Haplotype Map Project has been to develop a haplotype map of the human genome that describes the common patterns of genetic variation, in order to accelerate the search for the genetic causes of human disease. Within the project, ~3.9 million distinct single-nucleotide polymorphisms (SNPs) have been genotyped in 270 individuals from four worldwide populations. The project data are available for unrestricted public use at the HapMap Web site. This site, which is the primary portal to genotype data produced by the project, offers bulk downloads of the data set, as well as interactive data browsing and analysis tools that are not available elsewhere. Bulk downloads of chromosome- or genome-wide data provide text dumps of the entire HapMap data set. Although complete, such downloads do not provide any filtering or selection services. This protocol describes the retrieval of HapMap data via bulk download.
Language	English
Publishing date	2008-07-01
Publishing country	United States
Document type	Journal Article
DOI	10.1101/pdb.prot5027
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Article: Generating HapMap Data Text Reports Using the Genome Browser.

Smith, Albert Vernon

CSH protocols

2008 Volume 2008, Page(s) pdb.prot5024

Abstract	INTRODUCTIONThe primary goal of the International Haplotype Map Project has been to develop a haplotype map of the human genome that describes the common patterns of genetic variation, in order to accelerate the search for the genetic causes of human disease. Within the project, ~3.9 million distinct single-nucleotide polymorphisms (SNPs) have been genotyped in 270 individuals from four worldwide populations. The project data are available for unrestricted public use at the HapMap website. This site, which is the primary portal to genotype data produced by the project, offers bulk downloads of the data set, as well as interactive data browsing and analysis tools that are not available elsewhere. In many cases, a researcher will be interested in downloading HapMap data from a region of interest for local analysis. This protocol describes the direct download of genotype, frequency, tag-SNPs, and other reports from the project website, using the genome browser.
Language	English
Publishing date	2008-07-01
Publishing country	United States
Document type	Journal Article
DOI	10.1101/pdb.prot5024
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Article: Retrieving HapMap Data Using HapMart.

Smith, Albert Vernon

CSH protocols

2008 Volume 2008, Page(s) pdb.prot5026

Abstract	INTRODUCTIONThe primary goal of the International Haplotype Map Project has been to develop a haplotype map of the human genome that describes the common patterns of genetic variation, in order to accelerate the search for the genetic causes of human disease. Within the project, ~3.9 million distinct single-nucleotide polymorphisms (SNPs) have been genotyped in 270 individuals from four worldwide populations. The project data are available for unrestricted public use at the HapMap Web site. This site, which is the primary portal to genotype data produced by the project, offers bulk downloads of the data set, as well as interactive data browsing and analysis tools that are not available elsewhere. Because of performance considerations, interactive access to HapMap data via the genome browser on the HapMap Web site is limited to regions no more than 5 Mb wide. Researchers who wish to obtain data for chromosome- or genome-wide data have two choices: Bulk download or HapMart access. HapMart, described in this protocol, allows researchers to select SNPs using diverse criteria and to display just those aspects of the data set that they are interested in.
Language	English
Publishing date	2008-07-01
Publishing country	United States
Document type	Journal Article
DOI	10.1101/pdb.prot5026
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Article ; Online: Associations between Ambient Air Pollutants and Clonal Hematopoiesis of Indeterminate Potential.

Leiser, Claire L / Whitsel, Eric A / Reiner, Alexander / Rich, Stephen S / Rotter, Jerome I / Taylor, Kent D / Tracy, Russel P / Kooperberg, Charles / Smith, Albert Vernon / Manson, JoAnn E / Mychaleckyj, Josyf C / Bick, Alexander G / Szpiro, Adam A / Kaufman, Joel D

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

2023 Volume 32, Issue 10, Page(s) 1470–1473

Abstract: Background: Clonal hematopoiesis of indeterminate potential (CHIP) is an age-related somatic mutation associated with incident hematologic cancer. Environmental stressors which, like air pollution, generate oxidative stress at the cellular level, may ... ...

Abstract	Background: Clonal hematopoiesis of indeterminate potential (CHIP) is an age-related somatic mutation associated with incident hematologic cancer. Environmental stressors which, like air pollution, generate oxidative stress at the cellular level, may induce somatic mutations and some mutations may provide a selection advantage for persistence and expansion of specific clones. Methods: We used data from the Multi-Ethnic Study of Atherosclerosis (MESA) N = 4,379 and the Women's Health Initiative (WHI) N = 7,701 to estimate cross-sectional associations between annual average air pollution concentrations at participant address the year before blood draw using validated spatiotemporal models. We used covariate-adjusted logistic regression to estimate risk of CHIP per interquartile range increases in particulate matter (PM2.5; 4 μg/m3) and nitrogen dioxide (NO2; 10 ppb) as ORs (95% confidence intervals). Results: Prevalence of CHIP at blood draw (variant allele fraction > 2%) was 4.4% and 8.7% in MESA and WHI, respectively. The most common CHIP driver mutation was in DNMT3A. Neither pollutant was associated with CHIP: ORMESA PM2.5 = 1.00 (0.68-1.45), ORMESA NO2 = 1.05 (0.69-1.61), ORWHI PM2.5 = 0.97 (0.86-1.09), ORWHI NO2 = 0.98 (0.88-1.10); or with DNMT3A-driven CHIP. Conclusions: We did not find evidence that air pollution contributes to CHIP prevalence in two large observational cohorts. Impact: This is the first study to estimate associations between air pollution and CHIP.
MeSH term(s)	Humans ; Female ; Air Pollutants/adverse effects ; Environmental Pollutants ; Nitrogen Dioxide/adverse effects ; Clonal Hematopoiesis ; Cross-Sectional Studies ; Environmental Exposure/adverse effects ; Environmental Exposure/analysis ; Air Pollution/adverse effects ; Particulate Matter/adverse effects ; Atherosclerosis
Chemical Substances	Air Pollutants ; Environmental Pollutants ; Nitrogen Dioxide (S7G510RUBH) ; Particulate Matter
Language	English
Publishing date	2023-07-18
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1153420-5
ISSN	1538-7755 ; 1055-9965
ISSN (online)	1538-7755
ISSN	1055-9965
DOI	10.1158/1055-9965.EPI-23-0305
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Article ; Online: Meta-imputation: An efficient method to combine genotype data after imputation with multiple reference panels.

Yu, Ketian / Das, Sayantan / LeFaive, Jonathon / Kwong, Alan / Pleiness, Jacob / Forer, Lukas / Schönherr, Sebastian / Fuchsberger, Christian / Smith, Albert Vernon / Abecasis, Gonçalo Rocha

American journal of human genetics

2022 Volume 109, Issue 6, Page(s) 1007–1015

Abstract: Genotype imputation is an integral tool in genome-wide association studies, in which it facilitates meta-analysis, increases power, and enables fine-mapping. With the increasing availability of whole-genome-sequence datasets, investigators have access to ...

Abstract	Genotype imputation is an integral tool in genome-wide association studies, in which it facilitates meta-analysis, increases power, and enables fine-mapping. With the increasing availability of whole-genome-sequence datasets, investigators have access to a multitude of reference-panel choices for genotype imputation. In principle, combining all sequenced whole genomes into a single large panel would provide the best imputation performance, but this is often cumbersome or impossible due to privacy restrictions. Here, we describe meta-imputation, a method that allows imputation results generated using different reference panels to be combined into a consensus imputed dataset. Our meta-imputation method requires small changes to the output of existing imputation tools to produce necessary inputs, which are then combined using dynamically estimated weights that are tailored to each individual and genome segment. In the scenarios we examined, the method consistently outperforms imputation using a single reference panel and achieves accuracy comparable to imputation using a combined reference panel.
MeSH term(s)	Genome ; Genome-Wide Association Study/methods ; Genotype ; Humans ; Polymorphism, Single Nucleotide/genetics ; Research Design
Language	English
Publishing date	2022-05-03
Publishing country	United States
Document type	Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural
ZDB-ID	219384-x
ISSN	1537-6605 ; 0002-9297
ISSN (online)	1537-6605
ISSN	0002-9297
DOI	10.1016/j.ajhg.2022.04.002
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Article ; Online: Genetic overlap between vascular pathologies and Alzheimer's dementia and potential causal mechanisms.

Lin, Yen-Feng / Smith, Albert Vernon / Aspelund, Thor / Betensky, Rebecca A / Smoller, Jordan W / Gudnason, Vilmundur / Launer, Lenore J / Blacker, Deborah

Alzheimer's & dementia : the journal of the Alzheimer's Association

2018 Volume 15, Issue 1, Page(s) 65–75

Abstract: Introduction: We sought to examine the genetic overlap between vascular pathologies and Alzheimer's disease (AD) dementia, and the potential mediating role of vascular pathologies between AD-related genetic variants and late-life cognition.: Methods: ...

Abstract	Introduction: We sought to examine the genetic overlap between vascular pathologies and Alzheimer's disease (AD) dementia, and the potential mediating role of vascular pathologies between AD-related genetic variants and late-life cognition. Methods: For 2907 stroke-free older individuals, we examined the association of polygenic risk scores for AD dementia (ADPRSs) with vascular pathologies and with cognition. Mediation analyses addressed whether association between ADPRSs and cognition was mediated by a vascular pathology. Results: ADPRSs were associated with lobar cerebral microbleeds, white matter lesion load, and coronary artery calcification, mostly explained by single nucleotide polymorphisms in the 19q13 region. The effect of ADPRSs on cognition was partially but significantly mediated by cerebral microbleeds, white matter lesions, and coronary artery calcification. Discussion: Our findings provide evidence for genetic overlap, mostly due to apolipoprotein E (APOE) gene, between vascular pathologies and AD dementia. The association between AD polygenic risk and late-life cognition is mediated in part via effects on vascular pathologies.
MeSH term(s)	Aged ; Alzheimer Disease/genetics ; Alzheimer Disease/pathology ; Alzheimer Disease/physiopathology ; Apolipoproteins E/genetics ; Brain/pathology ; Cognitive Dysfunction/genetics ; Cognitive Dysfunction/pathology ; Female ; Humans ; Male ; Microvessels/pathology ; Neuropsychological Tests ; Peptide Fragments/genetics ; Polymorphism, Single Nucleotide ; Risk Factors ; White Matter/pathology
Chemical Substances	Apolipoproteins E ; Peptide Fragments ; apolipoprotein E (133-149)
Language	English
Publishing date	2018-09-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	2211627-8
ISSN	1552-5279 ; 1552-5260
ISSN (online)	1552-5279
ISSN	1552-5260
DOI	10.1016/j.jalz.2018.08.002
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Article: Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants.

Einson, Jonah / Glinos, Dafni / Boerwinkle, Eric / Castaldi, Peter / Darbar, Dawood / de Andrade, Mariza / Ellinor, Patrick / Fornage, Myriam / Gabriel, Stacey / Germer, Soren / Gibbs, Richard / Hersh, Craig P / Johnsen, Jill / Kaplan, Robert / Konkle, Barbara A / Kooperberg, Charles / Nassir, Rami / Loos, Ruth J F / Meyers, Deborah A /

Mitchell, Braxton D / Psaty, Bruce / Vasan, Ramachandran S / Rich, Stephen S / Rienstra, Michael / Rotter, Jerome I / Saferali, Aabida / Shoemaker, M Benjamin / Silverman, Edwin / Smith, Albert Vernon / Mohammadi, Pejman / Castel, Stephane E / Iossifov, Ivan / Lappalainen, Tuuli

bioRxiv : the preprint server for biology

2023

Abstract: Exonic variants present some of the strongest links between genotype and phenotype. However, these variants can have significant inter-individual pathogenicity differences, known as variable penetrance. In this study, we propose a model where genetically ...

Abstract	Exonic variants present some of the strongest links between genotype and phenotype. However, these variants can have significant inter-individual pathogenicity differences, known as variable penetrance. In this study, we propose a model where genetically controlled mRNA splicing modulates the pathogenicity of exonic variants. By first cataloging exonic inclusion from RNA-seq data in GTEx v8, we find that pathogenic alleles are depleted on highly included exons. Using a large-scale phased WGS data from the TOPMed consortium, we observe that this effect may be driven by common splice-regulatory genetic variants, and that natural selection acts on haplotype configurations that reduce the transcript inclusion of putatively pathogenic variants, especially when limiting to haploinsufficient genes. Finally, we test if this effect may be relevant for autism risk using families from the Simons Simplex Collection, but find that splicing of pathogenic alleles has a penetrance reducing effect here as well. Overall, our results indicate that common splice-regulatory variants may play a role in reducing the damaging effects of rare exonic variants.
Language	English
Publishing date	2023-01-31
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.01.31.526505
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