Use of a Dense Single Nucleotide Polymorphism Map for In Silico Mapping in the Mouse
Publication Date
November 09, 2004
Journal
PLOS Biology
Authors
Mathew T Pletcher, Philip Mc Clurg, Serge Batalov, Andrew I Su, et al
Volume
2
Issue
12
Pages
e393
DOI
https://dx.plos.org/10.1371/journal.pbio.0020393
Publisher URL
http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.0020393
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/15534693
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC526179
Europe PMC
http://europepmc.org/abstract/MED/15534693
Web of Science
000226099600017
Scopus
20044394908
Mendeley
http://www.mendeley.com/research/dense-single-nucleotide-polymorphism-map-silico-mapping-mouse
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/963708"], "description"=>"<p>When the distribution of the SNPs is plotted out genome-wide, the expected irregular clustering of SNPs mark regions where heterozygosity was continuing to segregate during the inbreeding of the C57 family. Likewise, there are regions that were successfully homozygosed before the split of C58/J from the rest of the family members. In all five strain comparisons, no SNPs were found in the distal 25 Mb of MMU19.</p>", "links"=>[], "tags"=>["snp", "sets", "allows", "crosses"], "article_id"=>633639, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Mathew T Pletcher", "Philip McClurg", "Serge Batalov", "Andrew I Su", "S. Whitney Barnes", "Erica Lagler", "Ron Korstanje", "Xiaosong Wang", "Deborah Nusskern", "Molly A Bogue", "Richard J Mural", "Beverly Paigen", "Tim Wiltshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0020393.g001", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Visualization_of_the_SNP_Sets_Allows_for_Mapping_in_Crosses_That_Minimize_the_Number_of_Potential_Modifiers_/633639", "title"=>"Visualization of the SNP Sets Allows for Mapping in Crosses That Minimize the Number of Potential Modifiers", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 09:13:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/963793"], "description"=>"<div><p>(A) A tree, adapted from <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020393#pbio-0020393-Beck1\" target=\"_blank\">Beck et al. (2000)</a>, tracing the lineage of the C57 family of mice (upper tree) shows almost perfect correlation with a phylogenic tree based solely on SNP data (lower tree). The only difference in the two trees is the location of C57BLKS/J, which splits from C57BL/6J sooner in the phylogenic tree because of the genomic contributions of the non-C57 strain, DBA/2J. The maximum parsimony phylogenic tree of the strain relatedness was built using the pseudoalignment of the 10,990 SNP alleles for 48 strains with the Phylip package, version 3.6b.</p>\n <p>(B) The DBA/2J contribution to C57BLKS/J can be visualized in its allelic patterns. The region from 104 Mb to 109 Mb on MMU9 shows the same SNP alleles for both C57BLKS/J and its other parental strain, C57BL/6J (a period represents identity with the C57BLKS/J allele). At 110 Mb, the pattern switches and every C57BLKS/J allele matches the DBA/2J content through 120 Mb. SNP marker names are positioned above the alleles with the first number representing the chromosome the marker is located on, the second number being the Mb position on the chromosome, and the third number being an approximate location within the Mb.</p></div>", "links"=>[], "tags"=>["snp", "ancestries", "genotyped"], "article_id"=>633723, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Mathew T Pletcher", "Philip McClurg", "Serge Batalov", "Andrew I Su", "S. Whitney Barnes", "Erica Lagler", "Ron Korstanje", "Xiaosong Wang", "Deborah Nusskern", "Molly A Bogue", "Richard J Mural", "Beverly Paigen", "Tim Wiltshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0020393.g002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_Wide_SNP_Data_Accurately_Represent_the_Known_Ancestries_of_the_Genotyped_Strains_/633723", "title"=>"Genome-Wide SNP Data Accurately Represent the Known Ancestries of the Genotyped Strains", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 09:13:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/964055"], "description"=>"<div><p>(A) Sequencing of <i>Adcy7</i> in multiple strains revealed 28 SNPs distinguishing three distinct haplotype patterns. All strains were typed with markers selected to represent the three haplotypes. The strain distribution pattern predicted by the SNP data and the sample sequencing for this region was confirmed with NZB/BlNJ and BTBR T+ tf/J, I/LnJ and MA/MyJ, and C3H/HeJ, C57BL6/J, and C57L/J, each separating into unique haplotypes.</p>\n <p>(B) The SNP represented by marker 08.089.597 resulted in a change from a cysteine to a tyrosine in the resulting protein (asterisk). This cysteine is conserved in orthologs of the gene in human, rat, and cow. It is also found at the beginning of a stretch of ten amino acids (indicated by black line) predicted to be one of the protein's ten transmembrane domains. Identical amino acids are black and conserved amino acid changes are gray.</p></div>", "links"=>[], "tags"=>["haplotypes", "reveals", "amino", "hdl"], "article_id"=>633987, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Mathew T Pletcher", "Philip McClurg", "Serge Batalov", "Andrew I Su", "S. Whitney Barnes", "Erica Lagler", "Ron Korstanje", "Xiaosong Wang", "Deborah Nusskern", "Molly A Bogue", "Richard J Mural", "Beverly Paigen", "Tim Wiltshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0020393.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_Adcy7_Haplotypes_Reveals_Amino_Acid_Change_Associated_with_HDL_Phenotype_/633987", "title"=>"Analysis of <i>Adcy7</i> Haplotypes Reveals Amino Acid Change Associated with HDL Phenotype", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 09:15:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/963936"], "description"=>"<div><p>(A) Presence or absence of the retinal degeneration, albino, or agouti phenotypes was given a numerical value of 1 or 0 for use in the mapping algorithm. In each case, the most significant <i>p</i>-value (indicated by an arrow) was obtained for the region that contains the gene known to produce these phenotypes. A closer inspection of the retinal degeneration mapping shows that the maximum linkage region indicated by the algorithm covered a 0.4-Mb region from 102.4 Mb to 102.8 Mb on MMU5.</p>\n <p>(B) <i>Tas1r3</i> is known to be a major control gene for the complex trait of preference for sweet tastes. Values for the sweet preference of 23 strains of mice produced a highly significant association with the one Mb region of MMU4 that contains <i>Tas1r3.</i></p></div>", "links"=>[], "tags"=>["silico", "identifies", "retinal", "loci", "snp"], "article_id"=>633862, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Mathew T Pletcher", "Philip McClurg", "Serge Batalov", "Andrew I Su", "S. Whitney Barnes", "Erica Lagler", "Ron Korstanje", "Xiaosong Wang", "Deborah Nusskern", "Molly A Bogue", "Richard J Mural", "Beverly Paigen", "Tim Wiltshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0020393.g003", "stats"=>{"downloads"=>3, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_Silico_Mapping_Method_Correctly_Identifies_Coat_Color_Retinal_Degeneration_and_Sweet_Preference_Loci_from_SNP_Data_/633862", "title"=>"In Silico Mapping Method Correctly Identifies Coat Color, Retinal Degeneration, and Sweet Preference Loci from SNP Data", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 09:14:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/473595", "https://ndownloader.figshare.com/files/473618", "https://ndownloader.figshare.com/files/473693", "https://ndownloader.figshare.com/files/473774", "https://ndownloader.figshare.com/files/473842", "https://ndownloader.figshare.com/files/473848"], "description"=>"<div><p>Rapid expansion of available data, both phenotypic and genotypic, for multiple strains of mice has enabled the development of new methods to interrogate the mouse genome for functional genetic perturbations. In silico mapping provides an expedient way to associate the natural diversity of phenotypic traits with ancestrally inherited polymorphisms for the purpose of dissecting genetic traits. In mouse, the current single nucleotide polymorphism (SNP) data have lacked the density across the genome and coverage of enough strains to properly achieve this goal. To remedy this, 470,407 allele calls were produced for 10,990 evenly spaced SNP loci across 48 inbred mouse strains. Use of the SNP set with statistical models that considered unique patterns within blocks of three SNPs as an inferred haplotype could successfully map known single gene traits and a cloned quantitative trait gene. Application of this method to high-density lipoprotein and gallstone phenotypes reproduced previously characterized quantitative trait loci (QTL). The inferred haplotype data also facilitates the refinement of QTL regions such that candidate genes can be more easily identified and characterized as shown for <em>adenylate cyclase 7.</em></p> </div>", "links"=>[], "tags"=>["nucleotide", "polymorphism", "silico"], "article_id"=>153327, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Mathew T Pletcher", "Philip McClurg", "Serge Batalov", "Andrew I Su", "S. Whitney Barnes", "Erica Lagler", "Ron Korstanje", "Xiaosong Wang", "Deborah Nusskern", "Molly A Bogue", "Richard J Mural", "Beverly Paigen", "Tim Wiltshire"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.0020393.sd001", "https://dx.doi.org/10.1371/journal.pbio.0020393.sg001", "https://dx.doi.org/10.1371/journal.pbio.0020393.sg002", "https://dx.doi.org/10.1371/journal.pbio.0020393.sg003", "https://dx.doi.org/10.1371/journal.pbio.0020393.st001", "https://dx.doi.org/10.1371/journal.pbio.0020393.st002"], "stats"=>{"downloads"=>19, "page_views"=>29, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Use_of_a_Dense_Single_Nucleotide_Polymorphism_Map_for_In_Silico_Mapping_in_the_Mouse/153327", "title"=>"Use of a Dense Single Nucleotide Polymorphism Map for In Silico Mapping in the Mouse", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-01-20 11:37:37"}

PMC Usage Stats | Further Information

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Relative Metric

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