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Open AccessJournal ArticleDOI

Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens

Yohann Nédélec, +22 more
- 20 Oct 2016 - 
- Vol. 167, Iss: 3, pp 657-669
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TLDR
It is shown that genetic effects on the immune response are strongly enriched for recent, population-specific signatures of adaptation, including for traits that are key to controlling infection.
About: 
This article is published in Cell.The article was published on 2016-10-20 and is currently open access. It has received 405 citations till now. The article focuses on the topics: Genetic variation & Natural selection.

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Hospitalization and Mortality among Black Patients and White Patients with Covid-19.

Eboni G. Price-Haywood, +3 more
- 27 May 2020 - 
TL;DR: Black race was not associated with higher in-hospital mortality than white race, after adjustment for differences in sociodemographic and clinical characteristics on admission, and black patients had higher prevalences of obesity, diabetes, hypertension, and chronic kidney disease than white patients.
Journal ArticleDOI

New insights into the genetic etiology of Alzheimer’s disease and related dementias

Céline Bellenguez, +401 more
- 01 Apr 2022 - 
TL;DR: This paper performed a two-stage genome-wide association study with 111,326 clinically diagnosed/proxy AD cases and 677,663 controls and found 75 risk loci, of which 42 were new at the time of analysis.
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A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer's disease.

Douglas P Wightman, +89 more
- 01 Sep 2021 - 
TL;DR: This paper identified microglia, immune cells and protein catabolism as relevant genes for late-onset Alzheimer's disease, while identifying and prioritizing previously unidentified genes of potential interest.
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Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response.

Kaur Alasoo, +9 more
- 29 Jan 2018 - 
TL;DR: Analysis of chromatin accessibility and expression quantitative trait loci in stimulated or naïve macrophages identifies loci that constitutively alter chromatin but affect expression only after stimulation, thus indicating an effect on enhancer priming.
Journal ArticleDOI

Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes

Jeremy Schwartzentruber, +13 more
- 15 Feb 2021 - 
TL;DR: In this paper, the authors performed an updated genome-wide AD meta-analysis, which identified 37 risk loci, including new associations near CCDC6, TSPAN14, NCK2 and SPRED2.
References
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Journal ArticleDOI

The Sequence Alignment/Map format and SAMtools

Heng Li, +8 more
- 01 Aug 2009 - 
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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Fast gapped-read alignment with Bowtie 2

Ben Langmead, +3 more
- 01 Apr 2012 - 
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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STAR: ultrafast universal RNA-seq aligner

Alexander Dobin, +8 more
- 01 Jan 2013 - 
TL;DR: The Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure outperforms other aligners by a factor of >50 in mapping speed.
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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

Mark D. Robinson, +2 more
- 01 Jan 2010 - 
TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
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limma powers differential expression analyses for RNA-sequencing and microarray studies

Matthew E. Ritchie, +7 more
- 20 Apr 2015 - 
TL;DR: The philosophy and design of the limma package is reviewed, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
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