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Review: Contrasting genetic architectures in different mouse reference populations used for studying complex traits
- David A. Buchner and
- Joseph H. Nadeau
Genome Res. June 2015 25: 775-791; Published in Advance May 7, 2015, doi:10.1101/gr.187450.114
...specialized resources have been developed to study complex traits in many model organisms. In the mouse, remarkably different pictures of genetic architectures are emerging. Chromosome Substitution Strains (CSSs) reveal many QTLs, large phenotypic effects, pervasive epistasis, and readily identified genetic...
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Resource: Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
- Alistair Miles,
- Zamin Iqbal,
- Paul Vauterin,
- Richard Pearson,
- Susana Campino,
- Michel Theron,
- Kelda Gould,
- Daniel Mead,
- Eleanor Drury,
- John O'Brien,
- Valentin Ruano Rubio,
- Bronwyn MacInnis,
- Jonathan Mwangi,
- Upeka Samarakoon,
- Lisa Ranford-Cartwright,
- Michael Ferdig,
- Karen Hayton,
- Xin-zhuan Su,
- Thomas Wellems,
- Julian Rayner,
- Gil McVean,
- and Dominic Kwiatkowski
Genome Res. September 2016 26: 1288-1299; Published in Advance August 16, 2016, doi:10.1101/gr.203711.115
...clones were Deep sequencing of P. falciparum crosses Genome Research 1289 www..org inconsistent with Mendelian segregation (Mendelian errors) were used to calibrate variant filtering for both calling methods (Methods; Supplemental Figs. S4–S7). After variants were filtered, bothmethods achieved near...
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Research: Genetic analysis in the Collaborative Cross breeding population
- Vivek M. Philip,
- Greta Sokoloff,
- Cheryl L. Ackert-Bicknell,
- Martin Striz,
- Lisa Branstetter,
- Melissa A. Beckmann,
- Jason S. Spence,
- Barbara L. Jackson,
- Leslie D. Galloway,
- Paul Barker,
- Ann M. Wymore,
- Patricia R. Hunsicker,
- David C. Durtschi,
- Ginger S. Shaw,
- Sarah Shinpock,
- Kenneth F. Manly,
- Darla R. Miller,
- Kevin D. Donohue,
- Cymbeline T. Culiat,
- Gary A. Churchill,
- William R. Lariviere,
- Abraham A. Palmer,
- Bruce F. O'Hara,
- Brynn H. Voy,
- and Elissa J. Chesler
Genome Res. August 2011 21: 1223-1238; Published in Advance July 6, 2011, doi:10.1101/gr.113886.110
...scores >1 in the CC lines, fewer extreme high scores were observed, suggesting a restoration of continuous variation of this phenotype. Breeding effects in the Collaborative Cross Genome Research 1227 www..org increase in frequency while other alleles decrease in frequency through the process...
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Research: Deep congenic analysis identifies many strong, context-dependent QTLs, one of which, Slc35b4, regulates obesity and glucose homeostasis
- Soha N. Yazbek,
- David A. Buchner,
- Jonathan M. Geisinger,
- Lindsay C. Burrage,
- Sabrina H. Spiezio,
- Gabriel E. Zentner,
- Chang-Wen Hsieh,
- Peter C. Scacheri,
- Colleen M. Croniger,
- and Joseph H. Nadeau
Genome Res. July 2011 21: 1065-1073; Published in Advance April 19, 2011, doi:10.1101/gr.120741.111
.... 2011. Genetic analysis of complext traits in the emerging collaborative cross. Genome Res (in press). doi: 10.1101/gr.111310.110. Brown KM, MacGregor S, Montgomery GW, Craig DW, Zhao ZZ, Iyadurai KK, Henders A, Homer N, Campbel, MJ, Stark M, et al. 2008. Common sequence variants on 20q11.22 confer...
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Method: Joint genotyping on the fly: Identifying variation among a sequenced panel of inbred lines
- Eric A. Stone
Genome Res. May 2012 22: 966-974; Published in Advance February 23, 2012, doi:10.1101/gr.129122.111
..., Frieman MB Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M, Frieman MB, et al. 2011. Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res 21: 1213–1222. ↵ Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, Fitz J...
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Method: Single-cell genomics for dissection of complex malaria infections
- Shalini Nair,
- Standwell C. Nkhoma,
- David Serre,
- Peter A. Zimmerman,
- Karla Gorena,
- Benjamin J. Daniel,
- François Nosten,
- Timothy J.C. Anderson,
- and Ian H. Cheeseman
Genome Res. June 2014 24: 1028-1038; Published in Advance May 8, 2014, doi:10.1101/gr.168286.113
...through conventional sequencing of infections. [Supplemental material is available for this article.] Infections with micro-organisms almost uniformly show withinhost genetic diversity. This impacts disease pathology and influences a wide range of life-history traits (Frank 1996). In malaria, multiple...

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