9 research outputs found
CSVS, a crowdsourcing database of the Spanish population genetic variability
The knowledge of the genetic variability of the local
population is of utmost importance in personalized
medicine and has been revealed as a critical
factor for the discovery of new disease variants.
Here, we present the Collaborative Spanish
Variability Server (CSVS), which currently contains
more than 2000 genomes and exomes of unrelated Spanish individuals. This database has been generated
in a collaborative crowdsourcing effort collecting
sequencing data produced by local genomic
projects and for other purposes. Sequences have
been grouped by ICD10 upper categories. A web interface
allows querying the database removing one
or more ICD10 categories. In this way, aggregated
counts of allele frequencies of the pseudo-control
Spanish population can be obtained for diseases belonging
to the category removed. Interestingly, in addition
to pseudo-control studies, some population
studies can be made, as, for example, prevalence of
pharmacogenomic variants, etc. In addition, this genomic
data has been used to define the first Spanish
Genome Reference Panel (SGRP1.0) for imputation.
This is the first local repository of variability entirely
produced by a crowdsourcing effort and constitutes
an example for future initiatives to characterize local
variabilityworldwide. CSVS is also part of the GA4GH
Beacon network.Spanish Ministry of Economy and Competitiveness
SAF2017-88908-R
PT17/0009/0006
PI19/00321
CIBERER ACCI-06/07/0036
PI14-948
PI171659Regional Government of Madrid, RAREGenomicsCM
B2017/BMD3721
B2017/BMD-3721European Union (EU)European Union (EU)
676559University Chair UAM-IIS-FJD of Genomic MedicineRamon Areces Foundatio
A crowdsourcing database for the copy-number variation of the spanish population
Background: Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants. Results: Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/. Conclusion: SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database.This work is supported by Grants PID2020-117979RB-I00 from the Spanish Ministry of Science and Innovation; by the Institute of Health Carlos III (project IMPaCT-Data, exp. IMP/00019, IMP/00009 and PI20/01305), co-funded by the European Union, European Regional Development Fund (ERDF, “A way to make Europe”)
A crowdsourcing database for the copy-number variation of the Spanish population
Background: Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants. Results: Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/. Conclusion: SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database
Spontaneous Coronary Artery Dissection: A Disease-Specific, Social Networking Community–Initiated Study
OBJECTIVE: To develop and assess the feasibility of a novel method for identification, recruitment, and retrospective and prospective evaluation of patients with rare conditions
The multi-objective Spanish National Forest Inventory
Aim of study: To present the evolution of the current multi-objective Spanish National Forest Inventory (SNFI) through the assessment of different key indicators on challenging areas of the forestry sector.Area of study: Using information from the Second, Third and Fourth SNFI, this work provides case studies in Navarra, La Rioja, Galicia and Balearic Island regions and at national Spanish scale.Material and methods: These case studies present an estimation of reference values for dead wood by forest types, diameter-age modeling for Populus alba and Populus nigra in riparian forest, the invasiveness of alien species and the invasibility of forest types, herbivore preferences and effects on trees and shrub species, the methodology for estimating cork production , and the combination of SNFI4 information and Airborne Laser Scanning datasets with the aim of updating forest-fire behavior assessment information with a high degree of accuracy.Main results: The results show the suitability and feasibility of the proposed methodologies to estimate the indicators using SNFI data with the exception of the estimation of cork production. In this case, additional field variables were suggested in order to obtain robust estimates.Research highlights: By broadening the variables recorded, the SNFI has become an even more important source of forest information for the development of support tools for decision-making and assessment in diverse strategic fields such as those analyzed in this study
CSVS, a crowdsourcing database of the Spanish population genetic variability
The knowledge of the genetic variability of the local population is of utmost importance in personalized medicine and has been revealed as a critical factor for the discovery of new disease variants. Here, we present the Collaborative Spanish Variability Server (CSVS), which currently contains more than 2000 genomes and exomes of unrelated Spanish individuals. This database has been generated in a collaborative crowdsourcing effort collecting sequencing data produced by local genomic projects and for other purposes. Sequences have been grouped by ICD10 upper categories. A web interface allows querying the database removing one or more ICD10 categories. In this way, aggregated counts of allele frequencies of the pseudo-control Spanish population can be obtained for diseases belonging to the category removed. Interestingly, in addition to pseudo-control studies, some population studies can be made, as, for example, prevalence of pharmacogenomic variants, etc. In addition, this genomic data has been used to define the first Spanish Genome Reference Panel (SGRP1.0) for imputation. This is the first local repository of variability entirely produced by a crowdsourcing effort and constitutes an example for future initiatives to characterize local variability worldwide. CSVS is also part of the GA4GH Beacon network. CSVS can be accessed at: http://csvs.babelomics.org/