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A database and API for variation, dense genotyping and resequencing data

Daniel Rios, William M McLaren, Yuan Chen, Ewan Birney, Arne Stabenau, Paul Flicek, Fiona Cunningham
2010 BMC Bioinformatics  
Advances in sequencing and genotyping technologies are leading to the widespread availability of multi-species variation data, dense genotype data and large-scale resequencing projects.  ...  Conclusions: Ensembl's powerful, flexible and open source infrastructure for the management of variation, genotyping and resequencing data is freely available at  ...  Acknowledgements The authors acknowledge the following individuals and organisations: Graham McVicker for his early work on the variation database design and schema; Solexa for access to resequencing data  ... 
doi:10.1186/1471-2105-11-238 pmid:20459810 pmcid:PMC2882931 fatcat:2yosg4clebgefb3oql3iqbfr2i

The development and application of genomic selection as a new breeding paradigm

André Eggen
2012 Animal Frontiers  
low heritability, or cannot be quickly, inexpensively, and correctly measured in a large number of animals.  ...  Selection for these traits must be achieved through genomic means.  ...  freely accessible database, the Chicken Variation Database (ChickVD; http://chicken.genomics.org.cn/).  ... 
doi:10.2527/af.2011-0027 fatcat:ujdiz3uvyzdqro67jdhzrxspf4

FORGE: multivariate calculation of gene-wide p-values from Genome-Wide Association Studies Authors and Affiliations [article]

Inti Inal Pedroso, Michael R Barnes, Anbarasu Lourdusamy, Ammar Al-Chalabi, Gerome Breen
2015 bioRxiv   pre-print
We have designed and implemented FORGE, a software suite which implements a range of methods for the combination of p-values for the individual genetic variants within a gene or genomic region.  ...  Multivariate region or gene-wide association are an alternative, allowing for identification of disease genes in a manner more robust to allelic heterogeneity.  ...  A database and API for variation, dense genotyping and resequencing data. BMC Bioinformatics 11, 238 (2010). 36. Devlin, B. & Roeder, K. Genomic control for association studies.  ... 
doi:10.1101/023648 fatcat:77kcly7qvfdjtdbt4lg3xwinuq

Graphical Pangenomics

Erik Garrison, Richard Durbin
2018 Zenodo  
As this model combines both sequence and variation information in one structure it serves as a natural basis for resequencing.  ...  I validate that the variation graph model can be applied to align RNA sequencing data to a splicing graph.  ...  These data models thus provide a sufficient informational basis for resequencing against variation graphs.  ... 
doi:10.5281/zenodo.1463032 fatcat:e65awps6hbav5gczb3ubrf65oi

Sequencing and analysis of an Irish human genome

Pin Tong, James GD Prendergast, Amanda J Lohan, Susan M Farrington, Simon Cronin, Nial Friel, Dan G Bradley, Orla Hardiman, Alex Evans, James F Wilson, Brendan Loftus
2010 Genome Biology  
This analysis has implications for future re-sequencing studies and validates the imputation of Irish haplotypes using data from the current Human Genome Diversity Cell Line Panel (HGDP-CEPH).  ...  Recent studies generating complete human sequences from Asian, African and European subgroups have revealed population-specific variation and disease susceptibility loci.  ...  Acknowledgements We thank members of our research groups for technical assistance and discussions.  ... 
doi:10.1186/gb-2010-11-9-r91 pmid:20822512 pmcid:PMC2965383 fatcat:ck7mmgs2bnh7jpfn2grofngy6u

BRIDGE – A Visual Analytics Web Tool for Barley Genebank Genomics

Patrick König, Sebastian Beier, Martin Basterrechea, Danuta Schüler, Daniel Arend, Martin Mascher, Nils Stein, Uwe Scholz, Matthias Lange
2020 Frontiers in Plant Science  
genotypic and phenotypic data.  ...  A search module to find and select germplasm by passport and phenotypic attributes is included as well as modules to export genotypic data in gzip-compressed variant call format (VCF) files and phenotypic  ...  MB, MM, and ML designed and MB implemented the SNP browser. DS, PK, SB, ML, and DA curated, analyzed, and imported data. ML developed the data storage concept. DA implemented the ISA-Tab export API.  ... 
doi:10.3389/fpls.2020.00701 pmid:32595658 pmcid:PMC7300248 fatcat:kxp5l46dufgbxgra3o3h53erta

Graphical pangenomics

Erik Garrison, Richard Durbin
2018 Zenodo  
As this model combines both sequence and variation information in one structure it serves as a natural basis for resequencing.  ...  I validate that the variation graph model can be applied to align RNA sequencing data to a splicing graph.  ...  These data models thus provide a sufficient informational basis for resequencing against variation graphs.  ... 
doi:10.5281/zenodo.3269840 fatcat:glracsk2jvgb3lehvepq2jl5l4

Genomics-Assisted Breeding in the CGIAR Research Program on Roots, Tubers and Bananas (RTB)

Michael Friedmann, Asrat Asfaw, Noelle Anglin, Luis Becerra, Ranjana Bhattacharjee, Allan Brown, Edward Carey, Morag Ferguson, Dorcus Gemenet, Hanele Lindqvist-Kreuze, Ismail Rabbi, Mathieu Rouard (+2 others)
2018 Agriculture  
Achieving breeding targets and increasing the rate of genetic gains for these vegetatively propagated crops, with long breeding cycles, and genomes with high heterozygosity and different ploidy levels,  ...  For some crops, marker-assisted selection (MAS) is being implemented, and GS has passed the proof-of-concept stage.  ...  Acknowledgments: This review covers the work of many RTB scientists and partners, whose contribution to the advancement of breeding programs, including development of genomic resources is greatly acknowledged  ... 
doi:10.3390/agriculture8070089 fatcat:lkmgtwkayndp3drglicgbdnjtu

A GWAS platform built on iPlant cyber-infrastructure [article]

Liya Wang, Doreen Ware, Carol Lushbough, Nirav Merchant, Lincoln Stein
2014 bioRxiv   pre-print
The platform supports big data management, sharing, and large scale study of both genotype and phenotype data on clusters.  ...  We demonstrated a flexible Genome-Wide Association Study (GWAS) platform built upon the iPlant Collaborative Cyber-infrastructure.  ...  Qi Sun for helping on integrating GBS workflow and analyzing sorghum data, Dr. Kang for helping on EMMAX integration, Dr. Geoffrey Morris for assisting with extracting the sorghum data, Dr.  ... 
doi:10.1101/002881 fatcat:k74kn67mgvfevadbchashlp3ea

The UCSC genome browser database: update 2007

R. M. Kuhn, D. Karolchik, A. S. Zweig, H. Trumbower, D. J. Thomas, A. Thakkapallayil, C. W. Sugnet, M. Stanke, K. E. Smith, A. Siepel, K. R. Rosenbloom, B. Rhead (+13 others)
2007 Nucleic Acids Research  
The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms.  ...  The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data.  ...  We would also like to thank the many collaborators who have contributed annotation data to our project, as well as our users for their feedback and support.  ... 
doi:10.1093/nar/gkl928 pmid:17142222 pmcid:PMC1669757 fatcat:5h65fma2trhvpcjy4glloar4ha

The UCSC Genome Browser Database: update 2006

A. S. Hinrichs
2006 Nucleic Acids Research  
The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms.  ...  The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data.  ...  We would also like to thank the many collaborators who have contributed annotation data to our project, as well as our users for their feedback and support.  ... 
doi:10.1093/nar/gkj144 pmid:16381938 pmcid:PMC1347506 fatcat:fdhl3rwlpnclnox2lrd3k7e7se

Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection

Etienne Paux, Stéphane Lafarge, François Balfourier, Jérémy Derory, Gilles Charmet, Michael Alaux, Geoffrey Perchet, Marion Bondoux, Frédéric Baret, Romain Barillot, Catherine Ravel, Pierre Sourdille (+2 others)
2022 Biology  
There is currently a strong societal demand for sustainability, quality, and safety in bread wheat production.  ...  in a sustainable and fluctuating agricultural context.  ...  Genotyping, Phenotyping, and GWAS Data Integration GnpIS core-DB is a hybrid database composed by a relational database (PostgreSQL) that allows for a high level of data integration though well curated  ... 
doi:10.3390/biology11010149 pmid:35053148 pmcid:PMC8773325 fatcat:ttdipej4mnd4lbflakfcy5pc3i

Gene reuse facilitates rapid radiation and independent adaptation to diverse habitats in the Asian honeybee

Yongkun Ji, Xingan Li, Ting Ji, Junbo Tang, Lifei Qiu, Jiahui Hu, Jiangxing Dong, Shiqi Luo, Shanlin Liu, Paul B. Frandsen, Xuguo Zhou, Sajad H. Parey (+3 others)
2020 Science Advances  
By analyzing 343 genomes of the widespread Asian honeybee, Apis cerana, we showed that multiple peripheral subspecies radiated from a central ancestral population and adapted independently to diverse habitats  ...  Differential expression and RNA interference knockdown revealed the role of Lkr in influencing foraging labor division, suggesting that Lkr facilitates collective tendency for pollen/nectar collection  ...  Public data We downloaded public sequence data of 10 A. cerana workers from Japan and 10 A. mellifera workers from the NCBI SRA database (data S2).  ... 
doi:10.1126/sciadv.abd3590 pmid:33355133 fatcat:expubozbvfer3jn2vy2cdoi4zi

Science, society and biosafety of a field trial with transgenic biofuel poplars

Rebecca Van Acker, Véronique Storme, Geert Goeminne, Bart Ivens, René Custers, Dirk Aerts, Wim Soetaert, John Ralph, Nicholas Santoro, Jean-Charles Leplé, Gilles Pilate, Wout Boerjan
2011 BMC Proceedings  
Recent applications of high-throughput sequencing and genotyping technologies to natural populations of forest Figure 1 (abstract I2) The distribution of Douglas-fir and loblolly pine in North America.  ...  A long history of quantitative genetic experimentation has established the genetic basis for many traits, which are likely adaptive since many of them are also correlated with environmental heterogeneity  ...  The availability of the QMI to rapidly assess the potential risk generated by transgenic plants in characterized ecosystems, is a useful tool to assess the releasing or not of the permission of cultivation  ... 
doi:10.1186/1753-6561-5-s7-i23 fatcat:ulkxqgdupfdktkhsx2kba7pcn4

Construction of a Single Nucleotide Polymorphism Linkage Map for the Silkworm, Bombyx mori, Based on Bacterial Artificial Chromosome End Sequences

K. Yamamoto
2006 Genetics  
Since each of the SNP markers is directly linked to a specific genomic BAC clone and to whole-genome sequence data, and some of them are also linked to EST data, the SNP linkage map will be a powerful  ...  tool for investigating silkworm genome properties, mutation mapping, and map-based cloning of genes of industrial and agricultural interest.  ...  We are also grateful to Hiroshi Minami and Michihiko Shimomura for data analysis and to two anonymous reviewers and the editor for helpful comments.  ... 
doi:10.1534/genetics.105.053801 pmid:16547112 pmcid:PMC1461436 fatcat:iq2pzeeuonh23ciagqltz7npzm
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