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RESOURCE: Utilization of a whole genome SNP panel for efficient genetic mapping in the mouse
- Jennifer L. Moran,
- Andrew D. Bolton,
- Pamela V. Tran,
- Alison Brown,
- Noelle D. Dwyer,
- Danielle K. Manning,
- Bryan C. Bjork,
- Cheng Li,
- Kate Montgomery,
- Sandra M. Siepka,
- Martha Hotz Vitaterna,
- Joseph S. Takahashi,
- Tim Wiltshire,
- David J. Kwiatkowski,
- Raju Kucherlapati,
- and David R. Beier
Genome Res. March 2006 16: 436-440; Published in Advance February 3, 2006, doi:10.1101/gr.4563306
....M., Ding, Y., Cassell, M.A., Zhang, W., Wagner, G., Sargent, E.E., Asquith, S., Crew, V., Johnson, K.A., Robinson, P., et al. 2004 . An efficient SNP system for mouse scanning and elucidating strain relationships. Genome Res. 14 : 1806 –1811. ↵ Pletcher, M.T., McClurg, P., Batalov, S., Su, A.I., Barnes, S...
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PERSPECTIVE: The mouse genome
- Jean Louis Guénet
Genome Res. December 2005 15: 1729-1740; doi:10.1101/gr.3728305
...to be composed of long regions (≥1 Mb) containing high single nucleotide polymorphism (SNP) rates, while the rest of it exhibited low SNP rates ( Fig. 2 ). View larger version: In this window In a new window Figure 2. The SNP density between any two inbred strains of mice varies according to the chromosomal...
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Methods: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
- Bastien Chevreux,
- Thomas Pfisterer,
- Bernd Drescher,
- Albert J. Driesel,
- Werner E.G. Müller,
- Thomas Wetter,
- and Sándor Suhai
Genome Res. June 2004 14: 1147-1159; Published in Advance May 12, 2004, doi:10.1101/gr.1917404
...the ongoing assembly process is used, as well as possibly supplied additional information for each sequence-like known SNPs, known motifs, or strain (or cell or organism) types. The importance of detecting SNPs in an assembly process can be seen by comparing Figure 1 with Figure 2 , in which we show how...
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Research: After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection
- Amine Namouchi,
- Xavier Didelot,
- Ulrike Schöck,
- Brigitte Gicquel,
- and Eduardo P.C. Rocha
Genome Res. April 2012 22: 721-734; Published in Advance February 29, 2012, doi:10.1101/gr.129544.111
...; they are reliable; they can be precisely assessed; and they have a low reverse mutation rate and homoplasy index (Comas et al. 2009). They are thus ideal to investigate the genomic imprint of natural selection and genetic recombination. Results Whole- SNP discovery and phylogeny of MTBC strains The s of three M...
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Research: Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance
- Tim Downing,
- Hideo Imamura,
- Saskia Decuypere,
- Taane G. Clark,
- Graham H. Coombs,
- James A. Cotton,
- James D. Hilley,
- Simonne de Doncker,
- Ilse Maes,
- Jeremy C. Mottram,
- Mike A. Quail,
- Suman Rijal,
- Mandy Sanders,
- Gabriele Schönian,
- Olivia Stark,
- Shyam Sundar,
- Manu Vanaerschot,
- Christiane Hertz-Fowler,
- Jean-Claude Dujardin,
- and Matthew Berriman
Genome Res. December 2011 21: 2143-2156; Published in Advance October 28, 2011, doi:10.1101/gr.123430.111
...homozygous at sequence level. This was not the case, as an average of 293 heterozygous SNPs were detected per strain on the nine chromosomes showing s = 1. Accordingly, we concluded that the latter chromosomes were disomic. Fluorescent in situ hybridization (FISH) has been used to characterize variable...
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Research: Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages
- Tracy Jiaye Lee,
- Yu-Ching Liu,
- Wei-An Liu,
- Yu-Fei Lin,
- Hsin-Han Lee,
- Huei-Mien Ke,
- Jen-Pan Huang,
- Mei-Yeh Jade Lu,
- Chia-Lun Hsieh,
- Kuo-Fang Chung,
- Gianni Liti,
- and Isheng Jason Tsai
Genome Res. May 2022 32: 864-877; Published in Advance March 31, 2022, doi:10.1101/gr.276286.121
..., reproduce, and persist in nature (Liti 2015).Most S. cerevisiae biology has been based on experiments on a handful of laboratory domesticated strains, but comprehensive analyses of the ecology and evolutionary biology of S. cerevisiae in the wild are still unavailable. In nature, S. cerevisiae have been...
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Method: Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors
- Nitan Shalon,
- David A. Relman,
- and Eitan Yaffe
Genome Res. May 2022 32: 986-1003; Published in Advance April 12, 2022, doi:10.1101/gr.275894.121
...reference genomic dataWe tested the empirical prevalence of dominant-phantom cycles using simulated data derived from bacterial chromosomal s. DomCycle was applied to simulated shotgun data derived from an in silico mixture of 155 linearized s, including several conspecific strains (total assembly size 450...
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Resource: High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues
- Guo-Jen Huang,
- Sagiv Shifman,
- William Valdar,
- Martina Johannesson,
- Binnaz Yalcin,
- Martin S. Taylor,
- Jennifer M. Taylor,
- Richard Mott,
- and Jonathan Flint
Genome Res. June 2009 19: 1133-1140; Published in Advance April 17, 2009, doi:10.1101/gr.088120.108
...resolution inherent in crosses between inbred strains. We provide a megabase resolution map of thousands of eQTLs in hippocampus, lung, and liver samples from heterogeneous stock (HS) mice in which 843 QTLs have also been mapped at megabase resolution. We exploit dense mouse SNP data to show that artifacts...
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Research: Pedigree-based estimation of human mobile element retrotransposition rates
- Julie Feusier,
- W. Scott Watkins,
- Jainy Thomas,
- Andrew Farrell,
- David J. Witherspoon,
- Lisa Baird,
- Hongseok Ha,
- Jinchuan Xing,
- and Lynn B. Jorde
Genome Res. October 2019 29: 1567-1577; doi:10.1101/gr.247965.118
...at its 5′ flanking region, which may have occurred during the insertion event, and thus does not have a TSD. Alu #4 is de novo in individual 8327 (NA07355) but is also present at low levels by IGV and PCR in sibling 8439 (NA07351) (Supplemental Fig. S1). Amplification of a nearby SNP indicates...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...studies may overlook. On the other hand, analyses of genomic variation frequently reveal a complex interplay among sequence changes, including single-nucleotide polymorphisms (SNPs) and structural variations (SVs), which are associated with altered gene expression and phenotypic traits (Collins et al...

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