About: Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders

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About: Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders
Creator	Valdar, William Cai, Yanwei Oreper, Daniel Pardo-Manuel De Villena, Fernando Tarantino, Lisa
source	Medline; PMC
abstract	The Collaborative Cross (CC) is a panel of recently established multiparental recombinant inbred mouse strains. For the CC, as for any multiparental population (MPP), effective experimental design and analysis benefit from detailed knowledge of the genetic differences between strains. Such differences can be directly determined by sequencing, but until now whole-genome sequencing was not publicly available for individual CC strains. An alternative and complementary approach is to infer genetic differences by combining two pieces of information: probabilistic estimates of the CC haplotype mosaic from a custom genotyping array, and probabilistic variant calls from sequencing of the CC founders. The computation for this inference, especially when performed genome-wide, can be intricate and time-consuming, requiring the researcher to generate nontrivial and potentially error-prone scripts. To provide standardized, easy-to-access CC sequence information, we have developed the Inbred Strain Variant Database (ISVdb). The ISVdb provides, for all the exonic variants from the Sanger Institute mouse sequencing dataset, direct sequence information for CC founders and, critically, the imputed sequence information for CC strains. Notably, the ISVdb also: (1) provides predicted variant consequence metadata; (2) allows rapid simulation of F1 populations; and (3) preserves imputation uncertainty, which will allow imputed data to be refined in the future as additional sequencing and genotyping data are collected. The ISVdb information is housed in an SQL database and is easily accessible through a custom online interface (http://isvdb.unc.edu), reducing the analytic burden on any researcher using the CC.
has issue date	2017-06-05(xsd:dateTime)
bibo:doi	10.1534/g3.117.041491
bibo:pmid	28592645
has license	cc-by
sha1sum (hex)	942326084a2892419bebfb4508ed7158c158fac9
schema:url	https://doi.org/10.1534/g3.117.041491
resource representing a document's title	Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders
has PubMed Central identifier	PMC5473744
has PubMed identifier	28592645
schema:publication	G3 (Bethesda)
resource representing a document's body	covid:942326084a2892419bebfb4508ed7158c158fac9#body_text
is schema:about of	named entity 'Cross' named entity 'COLLABORATIVE' named entity 'SEQUENCE' named entity 'DATABASE' named entity 'FOUNDERS' named entity 'CROSS' named entity 'VARIANT' named entity 'STRAINS' named entity 'THEIR' named entity 'REPOSITORY' named entity 'INBRED STRAIN' named entity 'INFORMED' named entity 'v1.1' named entity 'haplotypes' named entity 'fine-mapping' named entity 'unphased' named entity 'genotypes' named entity 'missense' named entity 'MariaDB' named entity 'probability' named entity 'haplotypes' named entity 'loci' named entity 'genotype' named entity 'homozygous' named entity 'GUI' named entity 'genotype' named entity 'probability' named entity 'allelic' named entity 'sequencing data' named entity 'genotype' named entity 'genetics' named entity 'mice' named entity 'identity-by-descent' named entity 'homozygous' named entity 'chromosome' named entity 'chromosomes' named entity 'chromosome' named entity 'unphased' named entity 'database' named entity 'allelic' named entity 'GUI' named entity 'genome' named entity 'loci' named entity 'genomes' named entity 'haplotypes' named entity 'genome' named entity 'SNPs' named entity 'indels' named entity 'exons' named entity 'unphased' named entity 'outcrossing' named entity 'genetic background' named entity 'SNPs' named entity 'inbred strain' named entity 'follow-up' named entity 'genotype' named entity 'Python' named entity 'CSV' named entity 'common ancestors' named entity 'reproducibility' named entity 'exonic' named entity 'chromosome' named entity 'unphased' named entity 'exon' named entity 'haplotype' named entity 'genotype' named entity 'haplotype' named entity 'alleles' named entity 'GUI' named entity 'structural variants' named entity 'genotype' named entity 'unphased' named entity 'chromosome' named entity 'whole-genome sequencing' named entity 'probability' named entity 'genotypes' named entity 'genotype'

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