Imputation of single-nucleotide polymorphisms in inbred mice using local phylogeny.

Genetics
Jeremy R WangLeonard McMillan

Abstract

We present full-genome genotype imputations for 100 classical laboratory mouse strains, using a novel method. Using genotypes at 549,683 SNP loci obtained with the Mouse Diversity Array, we partitioned the genome of 100 mouse strains into 40,647 intervals that exhibit no evidence of historical recombination. For each of these intervals we inferred a local phylogenetic tree. We combined these data with 12 million loci with sequence variations recently discovered by whole-genome sequencing in a common subset of 12 classical laboratory strains. For each phylogenetic tree we identified strains sharing a leaf node with one or more of the sequenced strains. We then imputed high- and medium-confidence genotypes for each of 88 nonsequenced genomes. Among inbred strains, we imputed 92% of SNPs genome-wide, with 71% in high-confidence regions. Our method produced 977 million new genotypes with an estimated per-SNP error rate of 0.083% in high-confidence regions and 0.37% genome-wide. Our analysis identified which of the 88 nonsequenced strains would be the most informative for improving full-genome imputation, as well as which additional strain sequences will reveal more new genetic variants. Imputed sequences and quality scores can be d...Continue Reading

References

Dec 30, 1999·Nature Genetics·J A BeckE M Fisher
Jan 11, 2000·Nucleic Acids Research·S T SherryK Sirotkin
Dec 6, 2002·Nature·UNKNOWN Mouse Genome Sequencing ConsortiumEric S Lander
Jul 31, 2007·Nature Genetics·Hyuna YangFernando Pardo-Manuel de Villena
Feb 28, 2008·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Jin P SzatkiewiczGary A Churchill
May 27, 2009·PLoS Biology·Deanna M ChurchUNKNOWN Mouse Genome Sequencing Consortium
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Aug 7, 2009·The New England Journal of Medicine·Elaine R MardisTimothy J Ley
Aug 12, 2009·Nature Methods·Hyuna YangGary A Churchill
Apr 10, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hyun Min KangEleazar Eskin
May 31, 2011·Nature Genetics·Hyuna YangFernando Pardo-Manuel de Villena
Sep 17, 2011·Nature·Thomas M KeaneDavid J Adams
Feb 22, 2012·Genetics·UNKNOWN Collaborative Cross Consortium
Aug 1, 2010·The 2010 ACM International Conference on Bioinformatics and Computational Biology : ACM-BCB 2010 : Niagara Falls, New York, U.S.A., August 2-4, 2010·Jeremy WangLeonard McMillan

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Citations

Aug 16, 2012·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Gary A ChurchillKaren L Svenson
Sep 11, 2012·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Joseph H NadeauToshihiko Shiroishi
Jul 13, 2013·Current Osteoporosis Reports·Cheryl L Ackert-Bicknell, David Karasik
Oct 10, 2012·Nature Reviews. Genetics·Jonathan Flint, Eleazar Eskin
Apr 18, 2013·American Journal of Respiratory Cell and Molecular Biology·George D LeikaufJames P Fabisiak
Oct 8, 2013·PLoS Genetics·John D CalawayFernando Pardo-Manuel de Villena
Oct 24, 2012·EMBO Molecular Medicine·Annerose BerndtSteven D Shapiro
Dec 12, 2012·Mammalian Genome : Official Journal of the International Mammalian Genome Society·John P Didion, Fernando Pardo-Manuel de Villena
Jun 8, 2014·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Natalia M Gonzales, Abraham A Palmer
Feb 4, 2014·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Allison R RogalaFernando Pardo-Manuel de Villena
May 23, 2014·Toxicological Sciences : an Official Journal of the Society of Toxicology·Rachel J ChurchAlison H Harrill
Aug 1, 2012·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Catherine E WelshFernando Pardo-Manuel de Villena
Jul 3, 2015·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Andrew P Morgan, Catherine E Welsh
Feb 6, 2015·BMC Genomics·Christina L ZhengRobert Hitzemann
Apr 10, 2015·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·B Emma HuangColin R Cavanagh
Aug 19, 2016·Scientific Reports·Rok KoširDamjana Rozman
May 4, 2018·Genome Biology and Evolution·Matthew JobinBrenna M Henn
Oct 22, 2016·G3 : Genes - Genomes - Genetics·Andrew P MorganFernando Pardo-Manuel de Villena
Feb 22, 2012·Genetics·David W Threadgill, Gary A Churchill
Feb 22, 2012·Genetics·UNKNOWN Collaborative Cross Consortium
Jul 6, 2014·Genetics·Megan Phifer-RixeyMichael W Nachman
Mar 3, 2012·G3 : Genes - Genomes - Genetics·David W Threadgill, Gary A Churchill
Oct 15, 2020·American Journal of Physiology. Lung Cellular and Molecular Physiology·Kiflai BeinGeorge D Leikauf

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