About: Whole Genome Sequencing and Progress Toward Full Inbreeding of the Mouse Collaborative Cross Population

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Whole Genome Sequencing and Progress Toward Full Inbreeding of the Mouse Collaborative Cross Population
Creator	Blanchard, Matthew Hock, Pablo Kashfeen, Anwica Ferris, Martin Bell, Timothy Kirchoff, Kathryn Linnertz, Colton Mcmillan, Leonard Miller, Darla Najarian, Maya Pardo-Manuel De Villena, Fernando Shorter, John Sigmon, J
Source	Medline; PMC
abstract	Two key features of recombinant inbred panels are well-characterized genomes and reproducibility. Here we report on the sequenced genomes of six additional Collaborative Cross (CC) strains and on inbreeding progress of 72 CC strains. We have previously reported on the sequences of 69 CC strains that were publicly available, bringing the total of CC strains with whole genome sequence up to 75. The sequencing of these six CC strains updates the efforts toward inbreeding undertaken by the UNC Systems Genetics Core. The timing reflects our competing mandates to release to the public as many CC strains as possible while achieving an acceptable level of inbreeding. The new six strains have a higher than average founder contribution from non-domesticus strains than the previously released CC strains. Five of the six strains also have high residual heterozygosity (>14%), which may be related to non-domesticus founder contributions. Finally, we report on updated estimates on residual heterozygosity across the entire CC population using a novel, simple and cost effective genotyping platform on three mice from each strain. We observe a reduction in residual heterozygosity across all previously released CC strains. We discuss the optimal use of different genetic resources available for the CC population.
has issue date	2019-03-11(xsd:dateTime)
bibo:doi	10.1534/g3.119.400039
bibo:pmid	30858237
has license	cc-by
sha1sum (hex)	3060dac173270e62020e18ce6fcdcb4b8bf4fd8d
schema:url	https://doi.org/10.1534/g3.119.400039
resource representing a document's title	Whole Genome Sequencing and Progress Toward Full Inbreeding of the Mouse Collaborative Cross Population
has PubMed Central identifier	PMC6505143
has PubMed identifier	30858237
schema:publication	G3 (Bethesda)
resource representing a document's body	covid:3060dac173270e62020e18ce6fcdcb4b8bf4fd8d#body_text
is schema:about of	named entity 'strains' named entity 'heterozygosity' named entity 'updated' named entity 'simple' named entity 'panels' named entity 'strains' named entity 'optimal' named entity 'observe' named entity 'residual' named entity 'genotyping' named entity 'Whole Genome Sequencing' named entity 'CROSS' named entity 'OUR' named entity 'POSSIBLE' named entity 'DISCUSS' named entity 'PREVIOUSLY' named entity 'REPORTED' named entity 'PANELS' named entity 'HIGHER' named entity 'SIMPLE' named entity 'SYSTEMS' named entity 'SEQUENCES' named entity 'NEW' named entity 'KEY' named entity 'RELEASED' named entity 'HAVE' named entity 'RECOMBINANT' named entity 'STRAIN' named entity 'INBRED' named entity 'FOUNDER' named entity 'HERE' named entity 'COLLABORATIVE' named entity 'NON-' named entity 'PUBLIC' named entity 'UPDATED' named entity 'CHARACTERIZED' named entity 'FEATURES' named entity 'ESTIMATES' named entity 'STRAINS' named entity 'RESIDUAL' named entity 'PROGRESS' named entity 'MICE' named entity 'EFFECTIVE' named entity 'WHOLE GENOME' named entity 'CORE' named entity 'ADDITIONAL' named entity 'GENOTYPING' named entity 'CROSS' named entity 'POPULATION' named entity 'WHOLE GENOME SEQUENCING' named entity 'INBREEDING' named entity 'COLLABORATIVE' named entity 'UNC' named entity 'RESOURCES' named entity 'HETEROZYGOSITY' named entity 'OBSERVE' named entity 'USE OF' named entity 'REFLECTS' named entity 'ENTIRE' named entity 'TIMING' named entity 'GENOME SEQUENCE' named entity 'REDUCTION' named entity 'GENOMES' named entity 'DIFFERENT' named entity 'THESE' named entity 'RELATED' named entity 'ACCEPTABLE LEVEL' named entity 'AVERAGE' named entity 'GENETIC'

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