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The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data

Laura Clarke, Susan Fairley, Xiangqun Zheng-Bradley, Ian Streeter, Emily Perry, Ernesto Lowy, Anne-Marie Tassé, Paul Flicek
2016 Nucleic Acids Research  
The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project.  ...  IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource  ...  ACKNOWLEDGEMENT The authors thank the members of the 1000 Genomes Project for supporting the establishment of the International Genome Sample Resource and Richard Durbin and Bartha Knoppers for support  ... 
doi:10.1093/nar/gkw829 pmid:27638885 pmcid:PMC5210610 fatcat:v3n4pxwbzzbpjmnwbns2uskqhu

Applications of the 1000 Genomes Project resources

Xiangqun Zheng-Bradley, Paul Flicek
2016 Briefings in Functional Genomics  
The 1000 Genomes Project created a valuable, worldwide reference for human genetic variation.  ...  In this article, we will highlight some of the multiple ways that the 1000 Genomes data can be and has been utilized for genetic studies.  ...  Acknowledgements We thank Sophie Janacek for a critical reading of the manuscript and the members of the 1000 Genomes Project Consortium.  ... 
doi:10.1093/bfgp/elw027 pmid:27436001 pmcid:PMC5439288 fatcat:3klaiyxvzngxpjrqzj2i3rrbj4

General resources in Genetics and/or Oncology

Etienne De Braekeleer, Jean Loup Huret, Hossain Mossafa, Katriina Hautaviita, Philippe Dessen
2017 Atlas of Genetics and Cytogenetics in Oncology and Haematology  
This "Deep Insight" is a detailed subchapter of a general review article and summary on Internet databases for cytogeneticists: Internet databases and resources for cytogenetics and cytogenomics.  ...  The International Genome Sample Resource (IGSR) is maintaining and extending the 1000 Genomes Project data.  ...  In continuation of the 1000 Genome project (sequencing 1000 human genome as exomes or whole genomes), the International Genome Sample Resource (IGSR) aims to expand information to new populations, a better  ... 
doi:10.4267/2042/62946 fatcat:ogpkbnstcnbrnm6pawmf32npua

General resources in Genetics and/or Oncology

Etienne De Braekeleer, Jean Loup Huret, Hossain Mossafa, Katriina Hautaviita, Philippe Dessen
2017 Atlas of Genetics and Cytogenetics in Oncology and Haematology  
This "Deep Insight" is a detailed subchapter of a general review article and summary on Internet databases for cytogeneticists: Internet databases and resources for cytogenetics and cytogenomics.  ...  The International Genome Sample Resource (IGSR) is maintaining and extending the 1000 Genomes Project data.  ...  In continuation of the 1000 Genome project (sequencing 1000 human genome as exomes or whole genomes), the International Genome Sample Resource (IGSR) aims to expand information to new populations, a better  ... 
doi:10.4267/2042/62779 fatcat:j3jbmjapd5b3ndhz2xsf7mgaki

Unlocking Big Data for better health

Steven Munevar
2017 Nature Biotechnology  
The IGSR will maintain the data collections from the 1000 Genomes Project, and enable the addition of new samples and data types.  ...  Other resources include the International Genome Sample Resource, which incorporates the data of the 1000 Genomes Project, and the curated GWAS catalog.  ... 
doi:10.1038/nbt.3918 pmid:28700551 fatcat:oqiurm5cgzec7lfenvjvlemxoy

Estimating prevalence of human traits among populations from polygenic risk scores

Britney E. Graham, Brian Plotkin, Louis Muglia, Jason H. Moore, Scott M. Williams
2021 Human Genomics  
We applied a population-specific PRS (psPRS) to 26 populations from the 1000 Genomes to four phenotypes: lactase persistence (LP), melanoma, multiple sclerosis (MS) and height.  ...  AbstractThe genetic basis of phenotypic variation across populations has not been well explained for most traits.  ...  Genomes To assess the role of PRSs in predicting population phenotype distributions, we chose to use only the populations included in The International Genome Sample Resource (IGSR) from the 1000 Genomes  ... 
doi:10.1186/s40246-021-00370-z pmid:34903281 pmcid:PMC8670062 fatcat:6puhfq4vmnhgfjfwu5qyuk24ay

The Human Cell Atlas White Paper [article]

Aviv Regev, Sarah Teichmann, Orit Rozenblatt-Rosen, Michael Stubbington, Kristin Ardlie, Ido Amit, Paola Arlotta, Gary Bader, Christophe Benoist, Moshe Biton, Bernd Bodenmiller, Benoit Bruneau (+64 others)
2018 arXiv   pre-print
We will therefore pursue Phase 1 as a suite of flagship projects in key tissues, systems, and organs.  ...  the resulting resource is truly global.  ...  With somewhat similar goals in mind, the International Genome Sample Resource (IGSR) was established at the EMBL in 2015 to ensure the ongoing utility and relevance of the 1000 Genomes Project, while further  ... 
arXiv:1810.05192v1 fatcat:4ilghu22pvcr7dfmq354z3pdya

Identification and characterization of two functional variants in the human longevity gene FOXO3

Friederike Flachsbart, Janina Dose, Liljana Gentschew, Claudia Geismann, Amke Caliebe, Carolin Knecht, Marianne Nygaard, Nandini Badarinarayan, Abdou ElSharawy, Sandra May, Anne Luzius, Guillermo G. Torres (+22 others)
2017 Nature Communications  
We experimentally validate the in silico predicted allele-dependent binding of transcription factors (CTCF, SRF) to the SNVs.  ...  FOXO3 is consistently annotated as a human longevity gene. However, functional variants and underlying mechanisms for the association remain unknown.  ...  The genotyping of French samples was supported by the Commissariat à l'Energie Atomique-Centre National de Génotypage.  ... 
doi:10.1038/s41467-017-02183-y pmid:29234056 pmcid:PMC5727304 fatcat:xdqocw7xdbfxnmyrhqmqsk6dm4

Steroid-induced ocular hypertension/glaucoma: Focus on pharmacogenomics and implications for precision medicine

M. Elizabeth Fini, Stephen G. Schwartz, Xiaoyi Gao, Shinwu Jeong, Nitin Patel, Tatsuo Itakura, Marianne O. Price, Francis W. Price, Rohit Varma, W. Daniel Stamer
2017 Progress in retinal and eye research  
As the genomics age emerged, it appeared the time was right to renew investigation into genetics.  ...  Results of the first genome-wide association study to identify polymorphisms associated with SIOH, and follow-up on two novel genes linked to the disorder, GPR158 and HCG22, is discussed in the second  ...  The International Genome Sample Resource (IGSR) (http://www.1000genomes.org/) tells us that the frequency of some of the genetic variants associated with IOP response to glucocorticoids identified in our  ... 
doi:10.1016/j.preteyeres.2016.09.003 pmid:27666015 pmcid:PMC5237612 fatcat:6mhhg65aurbrjl63b2lay2r5ci

Genome-wide investigation of selection patents in the Greek population [article]

Nikolaos Avramidis, Democritus University Of Thrace
2021
project.  ...  In the present study we are examining the genetic variation of the Greek population in comparison with other European ones.  ...  As a result of each success of the 1000 Genome Project, The International Genome Sample Resource (IGSR) was set up to ensure the continuous future access and the use of data generated, incorporate additional  ... 
doi:10.26257/heal.duth.11604 fatcat:af6igdbg2vhttf2arc3bjn75uu

Copy number variation of the bacteria-binding mucosal glycoprotein DMBT1: mutation rate, balancing selection and transcript length

Adel F. Alharbi
2022
Genome scans using genetic variation data have identified regions of balancing selection, yet in almost all cases the genetic and functional basis is unknown.  ...  Population genetics analysis was used as an indirect method to estimate the recombination rate based on the historic patterns of genetic variations among DNA sequences of natural populations.  ...  Acknowledgments I gratefully acknowledge my PhD sponsor in Saudi Arabia, the Ministry of Health (MOH), for giving me this opportunity to do my PhD and for their financial support. Thanks also to the  ... 
doi:10.25392/leicester.data.19336496.v1 fatcat:syiuhx74hnbgpofpg5dmzw66qe

Identification and characterization of causative variants of periodontitis in the gene ST8SIA1 [article]

Avneesh Chopra, Technische Universität Berlin, Roland Lauster
2021
The putative effect T-allele of rs2012722 decreased BACH1 binding by 40%. ST8SIA1 was pinpointed as a target gene of the association.  ...  This system was used to identify putative causal variants of a genetic association at the gene ST8SIA1 that increased the risk of periodontitis in smokers.  ...  A typical genome differs from the reference human genome at up to 5.0 million sites according to the 1000 Genomes Project Consortium (1000g) (influence on the pathogenesis of a genetic disease (direct  ... 
doi:10.14279/depositonce-12449 fatcat:cwltfvrwqbcudivobdkyev2y3u