TY  - JOUR
A1  - Atanur, Santosh S.
A1  - Birol, İnanç
A1  - Guryev, Victor
A1  - Hirst, Martin
A1  - Hummel, Oliver
A1  - Morrissey, Catherine
A1  - Behmoaras, Jacques
A1  - Fernandez-Suarez, Xose M.
A1  - Johnson, Michelle D.
A1  - McLaren, William M.
A1  - Patone, Giannino
A1  - Petretto, Enrico
A1  - Plessy, Charles
A1  - Rockland, Kathleen S.
A1  - Rockland, Charles
A1  - Saar, Kathrin
A1  - Zhao, Yongjun
A1  - Carninci, Piero
A1  - Flicek, Paul
A1  - Kurtz, Ted
A1  - Cuppen, Edwin
A1  - Pravenec, Michal
A1  - Hubner, Norbert
A1  - Jones, Steven J.M.
A1  - Birney, Ewan
A1  - Aitman, Timothy J.
T1  - The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
Y1  - 2010/06/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 791 
EP  - 803 
DO  - 10.1101/gr.103499.109 
VL  - 20 
IS  - 6 
UR  - http://genome.cshlp.org/content/20/6/791.abstract 
N2  - The spontaneously hypertensive rat (SHR) is the most widely studied animal model of hypertension. Scores of SHR quantitative loci (QTLs) have been mapped for hypertension and other phenotypes. We have sequenced the SHR/OlaIpcv genome at 10.7-fold coverage by paired-end sequencing on the Illumina platform. We identified 3.6 million high-quality single nucleotide polymorphisms (SNPs) between the SHR/OlaIpcv and Brown Norway (BN) reference genome, with a high rate of validation (sensitivity 96.3%–98.0% and specificity 99%–100%). We also identified 343,243 short indels between the SHR/OlaIpcv and reference genomes. These SNPs and indels resulted in 161 gain or loss of stop codons and 629 frameshifts compared with the BN reference sequence. We also identified 13,438 larger deletions that result in complete or partial absence of 107 genes in the SHR/OlaIpcv genome compared with the BN reference and 588 copy number variants (CNVs) that overlap with the gene regions of 688 genes. Genomic regions containing genes whose expression had been previously mapped as cis-regulated expression quantitative trait loci (eQTLs) were significantly enriched with SNPs, short indels, and larger deletions, suggesting that some of these variants have functional effects on gene expression. Genes that were affected by major alterations in their coding sequence were highly enriched for genes related to ion transport, transport, and plasma membrane localization, providing insights into the likely molecular and cellular basis of hypertension and other phenotypes specific to the SHR strain. This near complete catalog of genomic differences between two extensively studied rat strains provides the starting point for complete elucidation, at the molecular level, of the physiological and pathophysiological phenotypic differences between individuals from these strains. 
ER  -