LIVIVO - Search results -

Search results

Result 1 - 10 of total 364

Search options

Article: Population genetic tools: application to cancer.

Gabriel, Stacey

2007 Volume 34, Issue 2 Suppl 1, Page(s) S21–4

Abstract: The availability of a reference human genome sequence, an increasingly dense catalog, knowledge of common genetic variation, and new developments in technology present an unprecedented opportunity to systematically explore the genetic basis of complex ... ...

Abstract	The availability of a reference human genome sequence, an increasingly dense catalog, knowledge of common genetic variation, and new developments in technology present an unprecedented opportunity to systematically explore the genetic basis of complex human diseases such as cancer. An understanding of the common mutations that can cause distinct human cancers will be critical for identifying new targets for drug discovery, patient stratification for clinical trials, and analysis of drug response data to delineate classes of patients that respond to therapy. The genome structure of cancer can be examined in several ways: (1) large-scale case-control or family studies can investigate germline mutations; and (2) state-of-the-art genomic technologies (eg, high-density oligonucleotide arrays and targeted re-sequencing), can identify somatic alterations. Combined, these approaches will lead to a better understanding of the cancer genome.
MeSH term(s)	Case-Control Studies ; Genetic Variation/genetics ; Genetics, Population ; Genome, Human/genetics ; Germ-Line Mutation/genetics ; Haplotypes/genetics ; Humans ; Mutation/genetics ; Neoplasms/genetics ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide/genetics ; Targeted Gene Repair
Language	English
Publishing date	2007-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	189220-4
ISSN	1532-8708 ; 0093-7754
ISSN (online)	1532-8708
ISSN	0093-7754
DOI	10.1053/j.seminoncol.2007.01.008
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1348: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾
- See ZB MED holdings
- Order with fees

Article: Variation in the human genome and the inherited basis of common disease.

Gabriel, Stacey

Seminars in oncology

2006 Volume 33, Issue 6 Suppl 11, Page(s) S46–9

Abstract: The availability of a reference human genome sequence-an increasingly dense catalog-knowledge of common genetic variation, and new developments in technology present an unprecedented opportunity to systematically explore the genetic basis of complex ... ...

Abstract	The availability of a reference human genome sequence-an increasingly dense catalog-knowledge of common genetic variation, and new developments in technology present an unprecedented opportunity to systematically explore the genetic basis of complex human diseases such as cancer. An understanding of the common mutations that can cause distinct human cancers will be critical for identifying new targets for drug discovery, patient stratification for clinical trials, and analysis of drug response data to delineate classes of patients that respond to therapy. The genome structure of cancer can be investigated in several ways. Germline mutations can be investigated in large-scale, case-control, or family studies. Somatic alternations can be identified using state-of-the-art genomic technologies such as high-density oligonucleotide arrays and targeted resequencing. Combined, these approaches will lead to a better understanding of the cancer genome.
MeSH term(s)	Gene Expression Profiling ; Genetic Predisposition to Disease ; Genetic Variation ; Genome, Human ; Haplotypes/genetics ; Humans ; Mutation/genetics ; Neoplasms/genetics ; Polymorphism, Genetic
Language	English
Publishing date	2006-12
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	189220-4
ISSN	1532-8708 ; 0093-7754
ISSN (online)	1532-8708
ISSN	0093-7754
DOI	10.1053/j.seminoncol.2006.11.001
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1348: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: Estimating epidemiologic dynamics from cross-sectional viral load distributions.

Hay, James A / Kennedy-Shaffer, Lee / Kanjilal, Sanjat / Lennon, Niall J / Gabriel, Stacey B / Lipsitch, Marc / Mina, Michael J

medRxiv : the preprint server for health sciences

2021

Abstract: Estimating an epidemic's trajectory is crucial for developing public health responses to infectious diseases, but incidence data used for such estimation are confounded by variable testing practices. We show instead that the population distribution of ... ...

Abstract	Estimating an epidemic's trajectory is crucial for developing public health responses to infectious diseases, but incidence data used for such estimation are confounded by variable testing practices. We show instead that the population distribution of viral loads observed under random or symptom-based surveillance, in the form of cycle threshold (Ct) values, changes during an epidemic and that Ct values from even limited numbers of random samples can provide improved estimates of an epidemic's trajectory. Combining multiple such samples and the fraction positive improves the precision and robustness of such estimation. We apply our methods to Ct values from surveillance conducted during the SARS-CoV-2 pandemic in a variety of settings and demonstrate new approaches for real-time estimates of epidemic trajectories for outbreak management and response.
Language	English
Publishing date	2021-02-13
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.10.08.20204222
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Evaluation of a Training Toolkit to Improve Clinicians' Skills for Dementia Advance Care Planning.

Kistler, Christine E / Beeber, Anna S / Winzelberg, Gary S / Gabriel, Stacey L / Wretman, Christopher J / Hanson, Laura C

Journal of palliative medicine

2021 Volume 24, Issue 8, Page(s) 1183–1190

Abstract: Background: ...

Abstract	Background:
MeSH term(s)	Advance Care Planning ; Advance Directives ; Communication ; Dementia/therapy ; Female ; Humans ; Male ; Patient Care Planning
Language	English
Publishing date	2021-01-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
ZDB-ID	1427361-5
ISSN	1557-7740 ; 1096-6218
ISSN (online)	1557-7740
ISSN	1096-6218
DOI	10.1089/jpm.2020.0638
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 5440: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Estimating epidemiologic dynamics from cross-sectional viral load distributions.

Hay, James A / Kennedy-Shaffer, Lee / Kanjilal, Sanjat / Lennon, Niall J / Gabriel, Stacey B / Lipsitch, Marc / Mina, Michael J

Science (New York, N.Y.)

2021 Volume 373, Issue 6552

Abstract: Estimating an epidemic's trajectory is crucial for developing public health responses to infectious diseases, but case data used for such estimation are confounded by variable testing practices. We show that the population distribution of viral loads ... ...

Abstract	Estimating an epidemic's trajectory is crucial for developing public health responses to infectious diseases, but case data used for such estimation are confounded by variable testing practices. We show that the population distribution of viral loads observed under random or symptom-based surveillance-in the form of cycle threshold (Ct) values obtained from reverse transcription quantitative polymerase chain reaction testing-changes during an epidemic. Thus, Ct values from even limited numbers of random samples can provide improved estimates of an epidemic's trajectory. Combining data from multiple such samples improves the precision and robustness of this estimation. We apply our methods to Ct values from surveillance conducted during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in a variety of settings and offer alternative approaches for real-time estimates of epidemic trajectories for outbreak management and response.
MeSH term(s)	COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/virology ; COVID-19 Nucleic Acid Testing ; Cross-Sectional Studies ; Epidemiological Monitoring ; Humans ; Incidence ; Models, Theoretical ; Pandemics ; SARS-CoV-2/physiology ; Viral Load
Language	English
Publishing date	2021-06-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abh0635
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 27: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 77: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Technological considerations for genome-guided diagnosis and management of cancer.

Lennon, Niall J / Adalsteinsson, Viktor A / Gabriel, Stacey B

Genome medicine

2016 Volume 8, Issue 1, Page(s) 112

Abstract: Technological, methodological, and analytical advances continue to improve the resolution of our view into the cancer genome, even as we discover ways to carry out analyses at greater distances from the primary tumor sites. These advances are finally ... ...

Abstract	Technological, methodological, and analytical advances continue to improve the resolution of our view into the cancer genome, even as we discover ways to carry out analyses at greater distances from the primary tumor sites. These advances are finally making the integration of cancer genomic profiling into clinical practice feasible. Formalin fixation and paraffin embedding, which has long been the default pathological biopsy medium, is now being supplemented with liquid biopsy as a means to profile the cancer genomes of patients. At each stage of the genomic data generation process-sample collection, preservation, storage, extraction, library construction, sequencing, and variant calling-there are variables that impact the sensitivity and specificity of the analytical result and the clinical utility of the test. These variables include sample degradation, low yields of nucleic acid, and low variant allele fractions (proportions of assayed molecules carrying variant allele(s)). We review here the most common pre-analytical and analytical factors relating to routine cancer patient genome profiling, some solutions to common challenges, and the major sample preparation and sequencing technology choices available today.
MeSH term(s)	Cytological Techniques/methods ; Gene Expression Profiling/methods ; Genome, Human/genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Neoplasms/diagnosis ; Neoplasms/genetics ; Neoplasms/therapy ; Reproducibility of Results ; Sensitivity and Specificity ; Systems Integration
Language	English
Publishing date	2016-10-26
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2484394-5
ISSN	1756-994X ; 1756-994X
ISSN (online)	1756-994X
ISSN	1756-994X
DOI	10.1186/s13073-016-0370-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Gene- and tissue-level interactions in normal gastrointestinal development and Hirschsprung disease.

Chatterjee, Sumantra / Nandakumar, Priyanka / Auer, Dallas R / Gabriel, Stacey B / Chakravarti, Aravinda

Proceedings of the National Academy of Sciences of the United States of America

2019 Volume 116, Issue 52, Page(s) 26697–26708

Abstract: The development of the gut from endodermal tissue to an organ with multiple distinct structures and functions occurs over a prolonged time during embryonic days E10.5-E14.5 in the mouse. During this process, one major event is innervation of the gut by ... ...

Abstract	The development of the gut from endodermal tissue to an organ with multiple distinct structures and functions occurs over a prolonged time during embryonic days E10.5-E14.5 in the mouse. During this process, one major event is innervation of the gut by enteric neural crest cells (ENCCs) to establish the enteric nervous system (ENS). To understand the molecular processes underpinning gut and ENS development, we generated RNA-sequencing profiles from wild-type mouse guts at E10.5, E12.5, and E14.5 from both sexes. We also generated these profiles from homozygous
Language	English
Publishing date	2019-12-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1908756116
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1148: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects.

American journal of human genetics

2024 Volume 111, Issue 1, Page(s) 133–149

Abstract: Bulk-tissue molecular quantitative trait loci (QTLs) have been the starting point for interpreting disease-associated variants, and context-specific QTLs show particular relevance for disease. Here, we present the results of mapping interaction QTLs ( ... ...

Abstract	Bulk-tissue molecular quantitative trait loci (QTLs) have been the starting point for interpreting disease-associated variants, and context-specific QTLs show particular relevance for disease. Here, we present the results of mapping interaction QTLs (iQTLs) for cell type, age, and other phenotypic variables in multi-omic, longitudinal data from the blood of individuals of diverse ancestries. By modeling the interaction between genotype and estimated cell-type proportions, we demonstrate that cell-type iQTLs could be considered as proxies for cell-type-specific QTL effects, particularly for the most abundant cell type in the tissue. The interpretation of age iQTLs, however, warrants caution because the moderation effect of age on the genotype and molecular phenotype association could be mediated by changes in cell-type composition. Finally, we show that cell-type iQTLs contribute to cell-type-specific enrichment of diseases that, in combination with additional functional data, could guide future functional studies. Overall, this study highlights the use of iQTLs to gain insights into the context specificity of regulatory effects.
MeSH term(s)	Humans ; Quantitative Trait Loci/genetics ; Gene Expression Regulation ; Genotype ; Phenotype
Language	English
Publishing date	2024-01-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	219384-x
ISSN	1537-6605 ; 0002-9297
ISSN (online)	1537-6605
ISSN	0002-9297
DOI	10.1016/j.ajhg.2023.11.013
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 107: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Diet Quality Scores Are Positively Associated with Whole Blood-Derived Mitochondrial DNA Copy Number in the Framingham Heart Study.

Ma, Jiantao / Liu, Xue / Zhang, Yuankai / Cheng, Hanning / Gao, Wencheng / Lai, Chao-Qiang / Gabriel, Stacey / Gupta, Namrata / Vasan, Ramachandran S / Levy, Daniel / Liu, Chunyu

The Journal of nutrition

2022 Volume 152, Issue 3, Page(s) 690–697

Abstract: Background: The association between diet quality and mitochondrial DNA copy number (mtDNA-CN) remains to be examined.: Objectives: We aimed to study the relation between diet quality and mtDNA-CN.: Methods: We analyzed data from 2931 Framingham ... ...

Abstract	Background: The association between diet quality and mitochondrial DNA copy number (mtDNA-CN) remains to be examined. Objectives: We aimed to study the relation between diet quality and mtDNA-CN. Methods: We analyzed data from 2931 Framingham Heart Study (FHS) participants (mean age of 57 y, 55% females). Whole-genome sequencing was used to calculate mtDNA-CN from whole-blood samples. We examined the cross-sectional associations between 3 diet quality scores, the Dietary Approaches to Stop Hypertension (DASH) score, the Alternative Healthy Eating Index (AHEI), and the Mediterranean diet score (MDS), and mtDNA-CN. Linear mixed models were used to account for maternal lineage. Results: We observed that a higher DASH score was positively associated with mtDNA-CN after adjusting for sex, age, energy intake, smoking status, alcohol intake, and physical activity level. A 1-SD increase in the DASH score was associated with a 0.042-SD greater mtDNA-CN (95% CI: 0.007, 0.077; P = 0.02). Similarly, for each SD increase in AHEI and MDS, the mtDNA-CN SD increased by 0.056 (95% CI: 0.019, 0.092; P = 0.003) and 0.047 (95% CI: 0.01, 0.083; P = 0.01), respectively. Diet quality scores were associated with neutrophil and lymphocyte counts but not platelet counts, e.g., for a 1-SD increase in the DASH, neutrophils decreased by 0.8% (95% CI: 0.5%, 1.1%; P = 4.1 × 10-6), lymphocytes increased by 0.7% (95% CI: 0.4%, 1%, P = 1.2 × 10-5), and there was no significant change in platelet number (0.1 × 1000/μL; 95% CI: -1.6, 1.9; P = 0.89). Further adjustment for neutrophil, lymphocyte, and platelet counts and the associations between diet quality scores and mtDNA-CN were completely attenuated to nonsignificant (P = 0.95, 0.54, and 0.91, respectively). Conclusions: We observed that higher diet quality is associated with a greater whole-blood derived mtDNA-CN in middle-aged to older adult FHS participants, and that blood cell composition, particularly neutrophil counts, attenuated the association between diet quality and mtDNA-CN.
MeSH term(s)	Aged ; Cross-Sectional Studies ; DNA Copy Number Variations ; DNA, Mitochondrial/genetics ; Diet, Mediterranean ; Female ; Humans ; Longitudinal Studies ; Male ; Middle Aged
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2022-05-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	218373-0
ISSN	1541-6100 ; 0022-3166
ISSN (online)	1541-6100
ISSN	0022-3166
DOI	10.1093/jn/nxab418
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Uc I Zs.205: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: Efficient prevalence estimation and infected sample identification with group testing for SARS-CoV-2

Cleary, Brian / Hay, James A / Blumenstiel, Brendan / Gabriel, Stacey / Regev, Aviv / Mina, Michael J

medRxiv

Abstract: The ongoing pandemic of SARS-CoV-2, a novel coronavirus, caused over 3 million reported cases of coronavirus disease 2019 (COVID-19) and 200,000 reported deaths between December 2019 and April 2020. Cases and deaths will increase as the virus continues ... ...

Abstract	The ongoing pandemic of SARS-CoV-2, a novel coronavirus, caused over 3 million reported cases of coronavirus disease 2019 (COVID-19) and 200,000 reported deaths between December 2019 and April 2020. Cases and deaths will increase as the virus continues its global march outward. In the absence of effective pharmaceutical interventions or a vaccine, wide-spread virological screening is required to inform where restrictive isolation measures should be targeted and when they can be lifted. However, limitations on testing capacity have restricted the ability of governments and institutions to identify individual clinical cases, appropriately measure community prevalence, and mitigate transmission. Group testing offers a way to increase efficiency, by combining samples and testing a small number of pools. Here, we evaluate the effectiveness of group testing designs for individual identification or prevalence estimation of SARS-CoV-2 infection when testing capacity is limited. To do this, we developed mathematical models for epidemic spread, incorporating empirically measured individual-level viral kinetics to simulate changing viral loads in a large population over the course of an epidemic. We used these to construct representative populations and assess pooling strategies for community screening, accounting for variability in viral load samples, dilution effects, changing prevalence and resource constraints. We confirmed our group testing framework through pooled tests on de-identified human nasopharyngeal specimens with viral loads representative of the larger population. We show that group testing designs can both accurately estimate overall prevalence using a small number of measurements and substantially increase the identification rate of infected individuals in resource-limited settings.
Keywords	covid19
Language	English
Publishing date	2020-05-06
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.05.01.20086801
Database	COVID19

Full text online

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

Kategorien

Inter-library loan at ZB MED