PopHuman: the human population genomics browser.

Nucleic Acids Res

Institut de Biotecnologia i de Biomedicina and Department de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.

Published: January 2018

The 1000 Genomes Project (1000GP) represents the most comprehensive world-wide nucleotide variation data set so far in humans, providing the sequencing and analysis of 2504 genomes from 26 populations and reporting >84 million variants. The availability of this sequence data provides the human lineage with an invaluable resource for population genomics studies, allowing the testing of molecular population genetics hypotheses and eventually the understanding of the evolutionary dynamics of genetic variation in human populations. Here we present PopHuman, a new population genomics-oriented genome browser based on JBrowse that allows the interactive visualization and retrieval of an extensive inventory of population genetics metrics. Efficient and reliable parameter estimates have been computed using a novel pipeline that faces the unique features and limitations of the 1000GP data, and include a battery of nucleotide variation measures, divergence and linkage disequilibrium parameters, as well as different tests of neutrality, estimated in non-overlapping windows along the chromosomes and in annotated genes for all 26 populations of the 1000GP. PopHuman is open and freely available at http://pophuman.uab.cat.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753332PMC
http://dx.doi.org/10.1093/nar/gkx943DOI Listing

Publication Analysis

Top Keywords

population genomics
8
nucleotide variation
8
population genetics
8
population
5
pophuman human
4
human population
4
genomics browser
4
browser 1000
4
1000 genomes
4
genomes project
4

Similar Publications

Current state and future prospects of spatial biology in colorectal cancer.

Front Oncol

December 2024

Department of Integrative Translational Sciences, City of Hope, Beckman Research Institute, Duarte, CA, United States.

Over the past century, colorectal cancer (CRC) has become one of the most devastating cancers impacting the human population. To gain a deeper understanding of the molecular mechanisms driving this solid tumor, researchers have increasingly turned their attention to the tumor microenvironment (TME). Spatial transcriptomics and proteomics have emerged as a particularly powerful technology for deciphering the complexity of CRC tumors, given that the TME and its spatial organization are critical determinants of disease progression and treatment response.

View Article and Find Full Text PDF

Since its inception in 2003, the African Society of Human Genetics (AfSHG) has been central to the promotion of genetics research on the continent, and facilitated the networking of African researchers within Africa and abroad, thereby significantly contributing to the career development of African geneticists. The continuation of these accomplishments was stimulated by the 12 international conference of AfSHG held jointly with the 1 Congress of the Malian Society of Human Genetics (MSHG) in Bamako, Mali from September 18 to 21 2019. The main theme of the conference was "Human Genetics and Genomics as a Unifying Factor for Harmony and Progress in Africa".

View Article and Find Full Text PDF

Extracellular Vesicles Are Prevalent and Effective Carriers of Environmental Allergens in Indoor Dust.

Environ Sci Technol

December 2024

Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.

The global incidence of allergic diseases is rising and poses a substantial threat to human health. Allergenic proteins released by various allergenic species play a critical role in the pathogenesis of allergic diseases and have been widely detected in the environmental matrix. However, the release, presence and interaction of environmental allergens with human body remain to be elucidated.

View Article and Find Full Text PDF

Introduction: Recently, the O-6-methylguanine-DNA methyltransferase (MGMT) locus was proposed as influencing the risk of Alzheimer's disease (AD) in women who did not carry the apolipoprotein E ε4 allele. We examined an Amish founder population for any influence of genetic variation in and around the MGMT locus on the risk for dementia.

Methods: Genetic association was performed for single nucleotide polymorphisms (SNPs) surrounding the MGMT locus.

View Article and Find Full Text PDF

Metagenomic sequencing deepened our knowledge about the role of the intestinal microbiota in human health, and several studies with various methodologies explored its dynamics during antibiotic treatments. We compared the impact of four widely used antibiotics on the gut bacterial diversity. We used plasma and fecal samples collected during and after treatment from healthy volunteers assigned to a 5-day treatment either by ceftriaxone (1 g every 24 h through IV route), ceftazidime/avibactam (2 g/500 mg every 8 h through IV route), piperacillin/tazobactam (1 g/500 mg every 8 h through IV route) or moxifloxacin (400 mg every 24 h through oral route).

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!