scholarly journals The 1000 Genomes Project: data management and community access

2012 ◽  
Vol 9 (5) ◽  
pp. 459-462 ◽  
Author(s):  
Laura Clarke ◽  
◽  
Xiangqun Zheng-Bradley ◽  
Richard Smith ◽  
Eugene Kulesha ◽  
...  
Keyword(s):  
Data Management ◽  
1000 Genomes Project ◽  
1000 Genomes ◽  
Project Data ◽  
Community Access

scholarly journals Inference of recent admixture using genotype data

2020 ◽  
Author(s):  
Peter Pfaffelhuber ◽  
Elisabeth Sester-Huss ◽  
Franz Baumdicker ◽  
Jana Naue ◽  
Sabine Lutz-Bonengel ◽  
...  
Keyword(s):  
State Of The Art ◽  
Forensic Genetics ◽  
Statistical Test ◽  
Genotype Data ◽  
1000 Genomes Project ◽  
Additional Information ◽  
1000 Genomes ◽  
Project Data ◽  
Ancestry Proportions ◽  
Individual Ancestry

AbstractThe inference of biogeographic ancestry (BGA) has become a focus of forensic genetics. Mis-inference of BGA can have profound unwanted consequences for investigations and society. We show that recent admixture can lead to misclassification and erroneous inference of ancestry proportions, using state of the art analysis tools with (i) simulations, (ii) 1000 genomes project data, and (iii) two individuals analyzed using the ForenSeq DNA Signature Prep Kit. Subsequently, we extend existing tools for estimation of individual ancestry (IA) by allowing for different IA in both parents, leading to estimates of parental individual ancestry (PIA), and a statistical test for recent admixture. Estimation of PIA outperforms IA in most scenarios of recent admixture. Furthermore, additional information about parental ancestry can be acquired with PIA that may guide casework.

scholarly journals Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project

2019 ◽  
Vol 4 ◽  
pp. 50 ◽  
Author(s):  
Ernesto Lowy-Gallego ◽  
Susan Fairley ◽  
Xiangqun Zheng-Bradley ◽  
Magali Ruffier ◽  
Laura Clarke ◽  
...  
Keyword(s):  
De Novo ◽  
Variant Calling ◽  
Final Phase ◽  
1000 Genomes Project ◽  
Data Set ◽  
1000 Genomes ◽  
Project Data

We present a set of biallelic SNVs and INDELs, from 2,548 samples spanning 26 populations from the 1000 Genomes Project, called de novo on GRCh38. We believe this will be a useful reference resource for those using GRCh38. It represents an improvement over the “lift-overs” of the 1000 Genomes Project data that have been available to date by encompassing all of the GRCh38 primary assembly autosomes and pseudo-autosomal regions, including novel, medically relevant loci. Here, we describe how the data set was created and benchmark our call set against that produced by the final phase of the 1000 Genomes Project on GRCh37 and the lift-over of that data to GRCh38.

scholarly journals Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project

2019 ◽  
Vol 4 ◽  
pp. 50 ◽  
Author(s):  
Ernesto Lowy-Gallego ◽  
Susan Fairley ◽  
Xiangqun Zheng-Bradley ◽  
Magali Ruffier ◽  
Laura Clarke ◽  
...  
Keyword(s):  
Variant Calling ◽  
Final Phase ◽  
1000 Genomes Project ◽  
1000 Genomes ◽  
Project Data

We present biallelic SNVs called from 2,548 samples across 26 populations from the 1000 Genomes Project, called directly on GRCh38. We believe this will be a useful reference resource for those using GRCh38, representing an improvement over the “lift-overs” of the 1000 Genomes Project data that have been available to date and providing a resource necessary for the full adoption of GRCh38 by the community. Here, we describe how the call set was created and provide benchmarking data describing how our call set compares to that produced by the final phase of the 1000 Genomes Project on GRCh37.

scholarly journals Comparative Analysis of rs12979860 SNP of the IFNL3 Gene in Children with Hepatitis C and Ethnic Matched Controls Using 1000 Genomes Project Data

PLoS ONE ◽  
2014 ◽  
Vol 9 (1) ◽  
pp. e85899 ◽  
Author(s):  
Giuseppe Indolfi ◽  
Giusi Mangone ◽  
Elisa Bartolini ◽  
Gabriella Nebbia ◽  
Pier Luigi Calvo ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Hepatitis C ◽  
1000 Genomes Project ◽  
1000 Genomes ◽  
Project Data

scholarly journals The International Genome Sample Resource (IGSR) collection of open human genomic variation resources

2019 ◽  
Vol 48 (D1) ◽  
pp. D941-D947 ◽  
Author(s):  
Susan Fairley ◽  
Ernesto Lowy-Gallego ◽  
Emily Perry ◽  
Paul Flicek
Keyword(s):  
Sequence Data ◽  
Genomic Variation ◽  
1000 Genomes Project ◽  
High Coverage ◽  
Web Based ◽  
1000 Genomes ◽  
Open Consent ◽  
Unified View ◽  
Human Genomic ◽  
Project Data

Abstract To sustain and develop the largest fully open human genomic resources the International Genome Sample Resource (IGSR) (https://www.internationalgenome.org) was established. It is built on the foundation of the 1000 Genomes Project, which created the largest openly accessible catalogue of human genomic variation developed from samples spanning five continents. IGSR (i) maintains access to 1000 Genomes Project resources, (ii) updates 1000 Genomes Project resources to the GRCh38 human reference assembly, (iii) adds new data generated on 1000 Genomes Project cell lines, (iv) shares data from samples with a similarly open consent to increase the number of samples and populations represented in the resources and (v) provides support to users of these resources. Among recent updates are the release of variation calls from 1000 Genomes Project data calculated directly on GRCh38 and the addition of high coverage sequence data for the 2504 samples in the 1000 Genomes Project phase three panel. The data portal, which facilitates web-based exploration of the IGSR resources, has been updated to include samples which were not part of the 1000 Genomes Project and now presents a unified view of data and samples across almost 5000 samples from multiple studies. All data is fully open and publicly accessible.

scholarly journals Evaluating the quality of the 1000 genomes project data

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Saurabh Belsare ◽  
Michal Levy-Sakin ◽  
Yulia Mostovoy ◽  
Steffen Durinck ◽  
Subhra Chaudhuri ◽  
...  
Keyword(s):  
1000 Genomes Project ◽  
1000 Genomes ◽  
Project Data

scholarly journals Discovery of Western European R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e41634 ◽  
Author(s):  
Richard A. Rocca ◽  
Gregory Magoon ◽  
David F. Reynolds ◽  
Thomas Krahn ◽  
Vincent O. Tilroe ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Online Community ◽  
1000 Genomes Project ◽  
1000 Genomes ◽  
Community Approach ◽  
Western European ◽  
Project Data

scholarly journals BCFtools/csq: Haplotype-aware variant consequences

2016 ◽  
Author(s):  
Petr Danecek ◽  
Shane A. McCarthy
Keyword(s):  
Genetic Variants ◽  
1000 Genomes Project ◽  
Commercial Use ◽  
1000 Genomes ◽  
Functional Variant ◽  
Order Of Magnitude ◽  
Localized Mode ◽  
Project Data ◽  
Haplotype Information

AbstractMotivation:Prediction of functional variant consequences is an important part of sequencing pipelines, allowing the categorization and prioritization of genetic variants for follow up analysis. However, current predictors analyze variants as isolated events, which can lead to incorrect predictions when adjacent variants alter the same codon, or when a frame-shifting indel is followed by a frame-restoring indel. Exploiting known haplotype information when making consequence predictions can resolve these issues.Results:BCFtools/csq is a fast program for haplotype-aware consequence calling which can take into account known phase. Consequence predictions are changed for 501 of 5019 compound variants found in the 81.7M variants in the 1000 Genomes Project data, with an average of 139 compound variants per haplotype. Predictions match existing tools when run in localized mode, but the program is an order of magnitude faster and requires an order of magnitude less memory.Availability:The program is freely available for commercial and non-commercial use in the BCFtools package which is available for download from http://samtools.github.io/bcftoolsContact:[email protected]

Sign in / Sign up

Export Citation Format

Share Document