scholarly journals Sequencing of GJB2 in Cameroonians and Black South Africans and comparison to 1000 Genomes Project Data Support Need to Revise Strategy for Discovery of Nonsyndromic Deafness Genes in Africans

2014 ◽  
Vol 18 (11) ◽  
pp. 705-710 ◽  
Author(s):  
Jason Bosch ◽  
Jean Jacques N. Noubiap ◽  
Collet Dandara ◽  
Nomlindo Makubalo ◽  
Galen Wright ◽  
...  
Keyword(s):  
1000 Genomes Project ◽  
Nonsyndromic Deafness ◽  
South Africans ◽  
1000 Genomes ◽  
Data Support ◽  
Black South Africans ◽  
Project Data

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 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 In Search of Genetic Markers for Nonsyndromic Deafness in Africa: A Study in Cameroonians and Black South Africans with the GJB6 and GJA1 Candidate Genes

2014 ◽  
Vol 18 (7) ◽  
pp. 481-485 ◽  
Author(s):  
Jason Bosch ◽  
Kamogelo Lebeko ◽  
Jean Jacques Noubiap Nziale ◽  
Collet Dandara ◽  
Nomlindo Makubalo ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genetic Markers ◽  
Nonsyndromic Deafness ◽  
South Africans ◽  
Black South Africans

scholarly journals A comparison of cataloged variation between International HapMap Consortium and 1000 Genomes Project data

2012 ◽  
Vol 19 (2) ◽  
pp. 289-294 ◽  
Author(s):  
Carrie C Buchanan ◽  
Eric S Torstenson ◽  
William S Bush ◽  
Marylyn D Ritchie
Keyword(s):  
1000 Genomes Project ◽  
1000 Genomes ◽  
International Hapmap Consortium ◽  
Project Data

scholarly journals Population-specific diversity of the immunoglobulin constant heavy G chain (IGHG) genes

2021 ◽  
Author(s):  
Arman A. Bashirova ◽  
Wanjing Zheng ◽  
Marjan Akdag ◽  
Danillo G. Augusto ◽  
Nicolas Vince ◽  
...  
Keyword(s):  
Sequence Variation ◽  
Genome Project ◽  
Allelic Polymorphism ◽  
South Africans ◽  
1000 Genomes ◽  
Amino Acid Sequence Variation ◽  
European Americans ◽  
Black South Africans ◽  
Definition Of ◽  
Antibody Function

AbstractHuman immunoglobulin G (IgG) molecules, IgG1, IgG2 and IgG3, exhibit substantial inter-individual variation in their constant heavy chain regions, as discovered by serological methods. This polymorphism is encoded by the IGHG1, IGHG2, and IGHG3 genes and may influence antibody function. We sequenced the coding fragments of these genes in 95 European Americans, 94 African Americans, and 94 Black South Africans. Striking differences were observed between the population groups, including extremely low amino acid sequence variation in IGHG1 among South Africans, and higher IGHG2 and IGHG3 diversity in individuals of African descent compared to individuals of European descent. Molecular definition of the loci illustrates a greater level of allelic polymorphism than previously described, including the presence of common IGHG2 and IGHG3 variants that were indistinguishable serologically. Comparison of our data with the 1000 Genome Project sequences indicates overall agreement between the datasets, although some inaccuracies in the 1000 Genomes Project are likely. These data represent the most comprehensive analysis of IGHG polymorphisms across major populations, which can now be applied to deciphering their functional impact.

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
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