A Snapshot of CNVs in the Pig Genome
Publication Date
December 16, 2008
Journal
PLOS ONE
Authors
João Fadista, Marianne Nygaard, Lars Erik Holm, Bo Thomsen, et al
Volume
3
Issue
12
Pages
e3916
DOI
https://dx.plos.org/10.1371/journal.pone.0003916
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0003916
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/19079605
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596487
Europe PMC
http://europepmc.org/abstract/MED/19079605
Web of Science
000265458400002
Scopus
58049191440
Mendeley
http://www.mendeley.com/research/snapshot-cnvs-pig-genome
Events
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Mendeley | Further Information

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CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/914146"], "description"=>"<p>CNVR 28 is shown (zoomed out on bottom left; zoomed in on bottom right) with log2ratio along with the probes (blue bars) covered in this region. Images from Nimblegen SignalMap™ and Ensembl <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003916#pone.0003916-Hubbard1\" target=\"_blank\">[39]</a>.</p>", "links"=>[], "tags"=>["genetics and genomics/animal genetics", "genetics and genomics/bioinformatics", "genetics and genomics/comparative genomics"], "article_id"=>584603, "categories"=>["Genetics"], "users"=>["João Fadista", "Marianne Nygaard", "Lars-Erik Holm", "Bo Thomsen", "Christian Bendixen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003916.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_of_a_CNVR_/584603", "title"=>"Example of a CNVR.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-16 01:16:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/451570"], "description"=>"<div><p>Recent studies of mammalian genomes have uncovered the extent of copy number variation (CNV) that contributes to phenotypic diversity, including health and disease status. Here we report a first account of CNVs in the pig genome covering part of the chromosomes 4, 7, 14, and 17 already sequenced and assembled. A custom tiling oligonucleotide array was used with a median probe spacing of 409 bp for screening 12 unrelated Duroc boars that are founders of a large family material. After a strict CNV calling pipeline, 37 copy number variable regions (CNVRs) across all four chromosomes were identified, with five CNVRs overlapping segmental duplications, three overlapping pig unigenes and one overlapping a RefSeq pig mRNA. This CNV snapshot analysis is the first of its kind in the porcine genome and constitutes the basis for a better understanding of porcine phenotypes and genotypes with the prospect of identifying important economic traits.</p></div>", "links"=>[], "tags"=>["snapshot", "cnvs", "genome"], "article_id"=>149001, "categories"=>["Genetics"], "users"=>["João Fadista", "Marianne Nygaard", "Lars-Erik Holm", "Bo Thomsen", "Christian Bendixen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003916", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Snapshot_of_CNVs_in_the_Pig_Genome/149001", "title"=>"A Snapshot of CNVs in the Pig Genome", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-12-16 02:30:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/914307"], "description"=>"<p>Summary of the CNVR content (in bp) and sequence covered (including gaps) by the oligo array CGH probes.</p>", "links"=>[], "tags"=>["cnvr", "covered", "oligo", "cgh"], "article_id"=>584762, "categories"=>["Genetics"], "users"=>["João Fadista", "Marianne Nygaard", "Lars-Erik Holm", "Bo Thomsen", "Christian Bendixen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003916.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_the_CNVR_content_in_bp_and_sequence_covered_including_gaps_by_the_oligo_array_CGH_probes_/584762", "title"=>"Summary of the CNVR content (in bp) and sequence covered (including gaps) by the oligo array CGH probes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-12-16 01:19:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/914348"], "description"=>"<p>CNVRs indicated in bold overlap segmental duplications.</p><p>The genomic coordinates are relative to the Sus scrofa May 2008 assembly.</p>", "links"=>[], "tags"=>["37", "cnvrs"], "article_id"=>584806, "categories"=>["Genetics"], "users"=>["João Fadista", "Marianne Nygaard", "Lars-Erik Holm", "Bo Thomsen", "Christian Bendixen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003916.t001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_length_bp_status_and_frequency_of_the_37_CNVRs_detected_by_array_CGH_/584806", "title"=>"Distribution, length(bp), status and frequency of the 37 CNVRs detected by array CGH.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-12-16 01:20:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/914249"], "description"=>"<p>A gain is shown in 6 of the test animals relative to the reference (R), as predicted by the pipeline.</p>", "links"=>[], "tags"=>["cnvr", "id"], "article_id"=>584706, "categories"=>["Genetics"], "users"=>["João Fadista", "Marianne Nygaard", "Lars-Erik Holm", "Bo Thomsen", "Christian Bendixen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003916.g004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RT_PCR_for_the_CNVR_ID_28_/584706", "title"=>"RT-PCR for the CNVR ID 28.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-16 01:18:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/914033"], "description"=>"<p>Losses are depicted in red while gains are in green. Not all the 37 CNVRs are visible since some are very close to each other.</p>", "links"=>[], "tags"=>["2008", "cnvrs"], "article_id"=>584494, "categories"=>["Genetics"], "users"=>["João Fadista", "Marianne Nygaard", "Lars-Erik Holm", "Bo Thomsen", "Christian Bendixen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003916.g002", "stats"=>{"downloads"=>4, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ideogram_from_the_Sus_scrofa_May_2008_assembly_representing_the_CNVRs_detected_in_our_study_/584494", "title"=>"Ideogram from the <i>Sus scrofa</i> (May 2008 assembly) representing the CNVRs detected in our study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-16 01:14:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/913964"], "description"=>"<p>See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003916#s4\" target=\"_blank\"><i>Methods</i></a> section for detailed description.</p>", "links"=>[], "tags"=>["pipeline", "assessing"], "article_id"=>584418, "categories"=>["Genetics"], "users"=>["João Fadista", "Marianne Nygaard", "Lars-Erik Holm", "Bo Thomsen", "Christian Bendixen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003916.g001", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Methodological_pipeline_for_assessing_copy_number_variation_in_this_study_/584418", "title"=>"Methodological pipeline for assessing copy number variation in this study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-16 01:13:38"}

PMC Usage Stats | Further Information

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