Physiol. Genomics Genetics/Genomics of Vascular Disease Workshop
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

Physiol. Genomics 32: 273-282, 2008. First published November 20, 2007; doi:10.1152/physiolgenomics.00208.2007
1094-8341/08 $8.00
This Article
Right arrow Abstract Freely available
Right arrow Full Text (PDF)
Right arrow Supplemental Table
Right arrow All Versions of this Article:
32/3/273    most recent
00208.2007v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Worley, K. C.
Right arrow Articles by Gibbs, R. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Worley, K. C.
Right arrow Articles by Gibbs, R. A.
Received 10 September 2007; accepted in final form 15 November 2007.
Physiological Genomics 32:273-282 (2008)
1094-8341/08 $8.00 © 2008 American Physiological Society

Perspective

Rats in the genomic era

K. C. Worley, G. M. Weinstock and R. A. Gibbs

Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas


   ABSTRACT
TOP
 ABSTRACT
INTRODUCTION
 RESULTS
 GRANTS
 REFERENCES
 
The rat genome project and the resources that it has generated are transforming the translation of rat biology to human medicine. The rat genome was sequenced to a high quality "draft," the structure and location of the genes were predicted, and a global assessment was published (Gibbs RA et al., Nature 428: 493–521, 2004). Since that time, researchers have made use of the genome sequence and annotations and related resources. We take this opportunity to review the currently available rat genome resources and to discuss the progress and future plans for the rat genome.

Rattus norvegicus; genome sequence; single nucleotide polymorphisms; haplotype map; finished sequence


   INTRODUCTION
TOP
 ABSTRACT
 INTRODUCTION
RESULTS
 GRANTS
 REFERENCES
 
THE LABORATORY RAT IS IMPORTANT for biomedical research, with more than 28,000 publications annually since 1966 and almost 37,000 annually since 1996 (3). The rat genome project has generated numerous resources (Table 1), including the draft genome sequence, genetic maps, cDNA sequences, consomic rat lines, and additional bacterial artificial chromosome (BAC) libraries. Over 700 strains (53), including transgenic, congenic, intercross, and recombinant inbred lines of rats are being used to understand human biology. The rat has traditionally been thought of as a model for physiological systems, but with the genome sequence and related resources genetic studies are becoming more common.


View this table:
[in this window]
[in a new window]

  		Table 1. Resources from the Genome Project

 
Although a researcher may think of genome sequences as standardized and defined entities, genome sequences are not all of the same quality and consistency. Understanding the limitations of the data is important to make the best use of them. Fig. 1 shows the steps used to subclone, sequence, and assemble genome sequences; presents some of the limitations of the assembly process; and describes the difference between a "draft" genome sequence and a "finished" genome sequence.


Figure 1
Figure 1
View larger version (60K):
[in this window]
[in a new window]

  		Fig. 1. Genome sequencing and assembly. Sequencing large genomes is accomplished by subcloning random small pieces of the genome into cloning vectors, sequencing the ends of the clone inserts, and reassembling the pieces. A: chromosomes of the rat, as normally visualized and laid end to end in a virtual linear sequence. B: exploded view of a small region of the genome (expanded ~3 orders of magnitude). Below are shown whole genome shotgun libraries prepared in a variety of sizes including bacterial artificial chromosomes (BACs, 150–250 kb, orange), fosmids (35–50 kb, green), and plasmids (2–10 kb, dark blue). C: subclones are sequenced from each end, maintaining the information about the pairing of end sequences and the expected distance between the end sequences based on the insert size of the library. D: the 2 types of information available for sequence assembly; overlaps of reads based on sequence similarity and space of mate-pairs based on subclone library insert size. E: increasing sequence coverage improves the consensus sequence assembly by increasing redundancy, raising the quality of consensus bases, and by adding scaffolding information to order and orient assembled sequences. F: contiguous consensus sequences are called contigs. Contigs that are placed relative to each other based on end-pair information make up sequence scaffolds. G: sequencing is not perfect. Sequence failure causes loss of both the sequence and the clone insert distance information. In some cases, the insert size standard deviation for a sequencing subclone library is too great, and the distance information cannot be used reliably to constrain the assembly. Genomic features can cause cloning bias so that regions (lighter color) are not represented. And there can be a mismatch between the sizes of genomic features and the clone sizes used to sequence the genome such that repeats cannot be spanned. H: draft sequence showing the types of remaining errors. Draft sequences have high-quality sequence in the bulk of the contigs, with remaining errors and low-quality sequence primarily located near the ends of contigs next to remaining sequence gaps. I: finished genome sequence in purple is of high quality, with <1 error in 10,000 bp. The process of finishing adds sequence coverage (shown in light blue), including directed sequencing reads to a draft sequence to improve automatic assemblies and allow manual breaking and merging of contigs and scaffolds to create a finished sequence. Features such as the transcript sequence of a typical gene shown in black at the bottom can be missing parts (the exon in the region of the light blue sequence reads) or have rearrangements in the draft genome sequence that are corrected in the finished sequence.

 
The initial publication of the draft human genome sequence in 2001 (32) was followed by additional draft genome publications (7–9, 30, 34, 35, 35a, 41a, 41b, 42, 48), along with the publication of the finished human reference genome (10, 12–15, 20, 21, 23, 25, 26, 28, 36–39, 43, 45, 46, 51, 56, 57). At the time of publication, the rat was only the second draft mammalian genome beyond human, and the triangulation possible with the three genomes (human, mouse, and rat) was powerful for informing the genome analysis of the three species.


   RESULTS
TOP
 ABSTRACT
 INTRODUCTION
 RESULTS
GRANTS
 REFERENCES
 
The Brown Norway rat (Rattus norvegicus) genome was sequenced in a project supported by the National Human Genome Research Institute (NHGRI) and the National Heart, Lung, and Blood Institute (NHLBI) (41a) where the intended product was a draft sequence. This project produced a genome assembly using a variety of sequence and map resources [BAC skim sequence, whole genome shotgun (WGS) sequence, BAC end sequences, BAC fpc map (31)] and a new BAC skim-WGS combined strategy and a new genome assembly program, Atlas (24), that combined the two types of data. Care was taken to increase the quality of the draft since there would not be an opportunity to correct errors during a finishing phase.

The genome assembly was examined in great detail by an analysis group formed by experts in computational biology and rat genetics. Overall, the data were found to be of adequate quality to support the desired analyses and the resulting annotations (41a). Table 2 lists the number of gene predictions reported in the draft rat, mouse, and human genomes and the finished human genome. In addition to the quality of the genome sequence, the statistics depend upon the gene prediction method, the alignment criteria, and the amount of expressed sequence evidence, which is much more abundant for human and mouse than for rat (expressed sequence tags in GenBank in millions: 8.13 human, 4.85 mouse, and only 0.83 rat). Most of the human orthologs are represented, with ~90% of the rat genes possessing a single ortholog in the human genome, and careful analysis of rat proteases showed that 93% have 1:1 orthologs in mouse (41a). Reciprocal best hits between proteins from the three gene predictions sets identified 12,440 1:1:1 orthologs with a mean amino acid identity of 88.0% and mean nucleotide identity is 85.1% (41a). Although the number of exons per gene and average exon length are similar in the three species (mouse, human, rat), the intron lengths vary with the longest average intron in human, followed by rat and then mouse (41a).


View this table:
[in this window]
[in a new window]

  		Table 2. Published gene predictions in human, mouse, and rat genomes

 
The genome sequence has been upgraded once since the initial publication by replacing the draft with the available finished sequence from BACs (~55 Mb, e.g., from the ENCODE regions, marked in blue in Supplementary Table S1).1 The lack of support for producing finished regions in the initial genome project limited these resources.

Since the initial genome project, the Mammalian Gene Collection (MGC) project (34a, 34b, 50) has targeted the sequencing of 6,200 rat cDNAs [5,349 are available in GenBank (15a)], and the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) has produced ~3 million WGS sequence reads for an additional eight strains to discover sequence variation. In addition, Applied Biosystems has released ~1x coverage of the genome in reads from the Sprague-Dawley (SD) strain. The description of the strains that have additional sequence data and the number of quantitative trait loci (QTLs) that have been described in each are given in Table 3, along with the number of sequence reads available and the number of single nucleotide polymorphisms (SNPs) derived from the sequence.


View this table:
[in this window]
[in a new window]

  		Table 3. Strains data summary

 
The rat research community has made extensive use of the genome sequence. In addition to its significance as an experimental model for human disease, the rat genome has had a major impact in the analysis of mammalian evolution (22, 33, 40, 41). The draft genome has received high marks for correcting existing sequences in addition to adding previously unknown sequences (11). A number of improvements were proposed and funded by the NHGRI to provide an even more complete genome with improved accuracy. This upgrade, the phase 2 genome, includes reassembly of the genome with the latest version of the Atlas assembler, targeted finishing of problematic regions, and a draft sequence of the Y chromosome, which was not represented in the original draft genome.

The current rat assembly (RNOR 3.4) comprises 419 ultrabactigs (regions defined by a path of BACs) comprising 137,000 sequence contigs. The sequence contigs represent 92% of the regions spanned by the ultrabactigs. About 96% of this sequence is mapped on chromosomes; 2/3 of the remainder is unmapped, while 1/3 is mapped to a chromosome but unplaced.

The quality of the sequence is reflected in a number of measures. The assembly includes segmental duplications (defined as >5 kb and >90% identity) for 2.9% of its bases (41a, 52). Compared with finished sequence, individual contigs are by and large of finished quality (41a). Thus, the areas that remain to be addressed are regions that pose special problems to genome assembly. These include regions with unusual repeat structures, polymorphisms, possible BAC rearrangements, low sequence coverage (perhaps due to cloning bias), etc. A few specific cases have been pointed out by the rat research community and are being used to define the methods required to upgrade the assembly.

For example, Dr. Tim Aitman presented evidence of a duplication in the Fcgr3 locus implicated in autoimmune nephritis that was not represented in the rat genome assembly. The duplication appears in rat but not in the mouse genome. Fcgr3 has undergone at least two duplications since the divergence of the mouse and rat lineages, and the rat has at least three expressed genes. The syntenic region in humans has also undergone copy number variation associated with disease, and the region is not well resolved in the human genome assembly. Resolving the differences between human, mouse, and rat is important for understanding both disease studies and mammalian evolution.

A second example region of a recent duplication in rats is the Cd36 region that is involved in fatty acid transport and linked to a number of cardiovascular and diabetes disease phenotypes (4). Comparison of finished sequence for human, mouse, and rat would be important for understanding complex diseases and their models. The genomic events of duplication and emergence of pseudogenes are paradigms for the effects of genome plasticity on evolution of complex phenotypes.

A third region of concern is the rat titan locus. Titin is the largest protein known to date, spanning >2 MB in the genome and showing elaborate alternative splicing.

A final example is a 5 MB region on chromosome 1 that is of interest for phenotypes of stroke (44), hypertension (16), and metabolic syndrome (27), with a number of candidate genes (P2ry2, P2Y, P2ry6, Pde2a, and Slco2b1). This region has repeat sequences that need to be resolved.

There were also anecdotal reports of regions in the assembly that were not merged due to apparent polymorphism. There were also a few possible regions of misassembly identified by comparison with the genetic maps (31, 54). Validation of the assembly in these regions would improve the quality and utility of both the sequence and the genetic map.

The later versions of the Atlas software have improved methods to deal with repeats and new modules for heterozygosity in highly polymorphic genomes (48) and more efficient handling of BAC sequences from clone pools. These methods are anticipated to improve the assembly of problematic regions.

Since the release of the v. 3.4 genome assembly, an additional 266 BACs spanning 100 Mb have been finished to human quality standards (47), and 598 BACs have been brought to a ENCODE ordered and oriented status (6) by the BCM-HGSC. A summary of the available finished sequence is given in Table 4, and details about each finished clone are given in Supplemental Table S1. These finished sequences are available for incorporation in an upgraded genome assembly.


View this table:
[in this window]
[in a new window]

  		Table 4. Finished BAC clones§

 
The current assembly has additional room for improvement in regions that are not captured by the BAC tiling path. Versions of the Atlas assembly software have been developed and used for WGS-only assemblies of honey bee (8), sea urchin (48), bovine, and macaque (41b). The macaque genome comparisons of multiple assemblies demonstrated the value of combining assemblies to gain benefits from different methods (41b). The phase 2 genome will combine unique sequence data from a WGS-only assembly with the data from the combined WGS-plus-BAC assembly for a more complete representation of the genome.

During the initial genome project, the Y chromosome was sequenced to about twofold WGS coverage. One of the reasons for the low coverage was the unusually large size of the BN Y chromosome. The phase 2 genome upgrade includes higher level of sequencing on the Y chromosome using a rat strain with a more representatively sized Y chromosome. The sequencing strategy will combine WGS sequence and low coverage sequence skims from male BAC library clones.

Traditional finishing strategies use a BAC subclone as the substrate and layer additional Sanger sequencing reads from subclones or directed PCR products to increase coverage. Newer sequencing technologies (see review Ref. 5), such as those from Roche's 454 Life Sciences, Illumina's Solexa, and Applied Biosystems' Solid, are available that produce large volumes of sequence data in a short period of time. Combining these high-volume sequence production methods with other methods for finishing such as those that use pooled BAC substrates or regions selected by array hybridization will make it possible to finish many more regions of the rat genome for the same price. These developments will make it possible to address many more of the remaining challenging regions and perhaps to finish the entire rat genome.

There are a large number of rat strains, most of which were developed as models for common complex human diseases (3). A dense radiation hybrid map with ~25,000 elements and the detailed comparative maps for rat, mouse, and human link the rat physiology and QTLs to mouse and human genetics. Current limits on QTL mapping in the rat are 2–10 cM; additional SNPs and haplotype maps will be required to reduce the size of these regions.

Although the rat does not yet have as many well-characterized phenotypes associated with single genes as does the mouse, it leads the way in known quantitative genetic traits. A number of rat QTLs have been mapped (e.g., copper metabolism, pituitary tumor growth, aerobic capacity, blood pressure and hypertension, ethanol tolerance, behavioral conditioning, anxiety, fat accumulation, chemical carcinogenesis, arthritis, diabetes, and cardiovascular disease), and in some cases (e.g., the last three listed) the genes have been cloned by position.

Current SNP resources.
There are 43,798 rat RefSNPs in dbSNP (37a), with 1,605 validated using functional assays. Dr. Norbert Hübner, funded through the EU STAR program, has generated 2,707,538 SNPs from cDNAs from four strains (SHR, WKY, GK, and SS). These SNPs, as well as the SNPS from the US NHGRI-funded SNP discovery effort (3), will be genotyped in an additional 50 strains through the EU STAR program funding. This genotyping will enable the development of a haplotype map. The previous rat SNP map based on cDNA from four strains (SHRSP, BN, WKY, and SD) has 12,395 interstrain polymorphic sites (55). The US NHGRI-funded SNP discovery effort (3) has sequenced eight strains (PVG, F344, SS, LEW, BB, FHH, DA, and SHR). The available sequence data is summarized in Table 3. The estimated yield for these strains is 1 SNP per 500–600 bp.

Conclusions
The phase 2 upgrade to the genomic sequence will provide a more complete and accurate genome sequence that will, in combination with the additional markers from the SNP discovery project, improve gene hunting via improved correlations between phenotypic data and ancestral sequence origin across many inbred strains and the identification of shared segments in rat strains used for intercross/backcross experiments. In additional to these rat-specific resources, general improvement in genomic tools through the advanced resequencing technologies will allow rapid gene targeted analyses. All of these developments will continue to push the translation of rat models of disease to better understand human health.


   GRANTS
TOP
 ABSTRACT
 INTRODUCTION
 RESULTS
 GRANTS
REFERENCES
 
The phase 2 genome project and the SNP discovery project are funded by NHGRI Grant 2 U54 HG-003273.


   FOOTNOTES
 
Address for reprint requests and other correspondence: K. C. Worley, Human Genome Sequencing Center, Dept. of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, MS BCM226, Rm. 1419.01, Houston, TX 77030 (e-mail: kworley{at}bcm.edu)

Article published online before print. See web site for date of publication (http://physiolgenomics.physiology.org).

1 The online version of this article contains supplemental material. Back


   REFERENCES
TOP
 ABSTRACT
 INTRODUCTION
 RESULTS
 GRANTS
 REFERENCES
 

  1. Aitman TJ, Gibbs RA, Weinstock GM, Hubner N, Jensen-Seaman MI, Maloney D, Jacob HJ. Proposal for discovering SNPs from eight commonly used inbred rat strains (http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/RatSNPSeq.pdf).
  2. Aitman TJ, Glazier AM, Wallace CA, Cooper LD, Norsworthy PJ, Wahid FN, Al-Majali KM, Trembling PM, Mann CJ, Shoulders CC, Graf D, St Lezin E, Kurtz TW, Kren V, Pravenec M, Ibrahimi A, Abumrad NA, Stanton LW, Scott J. Identification of Cd36 (Fat) as an insulin-resistance gene causing defective fatty acid and glucose metabolism in hypertensive rats. Nat Genet 21: 76-83, 1999.[CrossRef][Web of Science][Medline]
  3. Bentley DR. Whole-genome re-sequencing. Curr Opin Genet Dev 16: 545–552, 2006.[CrossRef][Web of Science][Medline]
  4. Blakesley RW, Hansen NF, Mullikin JC, Thomas PJ, McDowell JC, Maskeri B, Young AC, Benjamin B, Brooks SY, Coleman BI, Gupta J, Ho SL, Karlins EM, Maduro QL, Stantripop S, Tsurgeon C, Vogt JL, Walker MA, Masiello CA, Guan X, Bouffard GG, Green ED. An intermediate grade of finished genomic sequence suitable for comparative analyses. Genome Res 14: 2235–2244, 2004.[Abstract/Free Full Text]
  5. Consortium Chimpanzee Sequencing and Analysis. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69–87, 2005.[CrossRef][Medline]
  6. Consortium Honeybee Genome Sequencing. Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443: 931–949, 2006.[CrossRef][Medline]
  7. Consortium International Chicken Genome Sequencing. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695–716, 2004.[CrossRef][Medline]
  8. Consortium International Human Genome Sequencing. Finishing the euchromatic sequence of the human genome. Nature 431: 931–945, 2004.[CrossRef][Medline]
  9. Daniels D, Suzuki A, Shapiro E, Luo L, Yee DK, Fluharty SJ. Rattus norvegicus melanocortin 3 receptor: a corrected sequence. Peptides 26: 1835–1841, 2005.[CrossRef][Web of Science][Medline]
  10. Deloukas P, Earthrowl ME, Grafham DV, Rubenfield M, French L, Steward CA, Sims SK, Jones MC, Searle S, Scott C, Howe K, Hunt SE, Andrews TD, Gilbert JG, Swarbreck D, Ashurst JL, Taylor A, Battles J, Bird CP, Ainscough R, Almeida JP, Ashwell RI, Ambrose KD, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Bates K, Beasley H, Bray-Allen S, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Cahill P, Camire D, Carter NP, Chapman JC, Clark SY, Clarke G, Clee CM, Clegg S, Corby N, Coulson A, Dhami P, Dutta I, Dunn M, Faulkner L, Frankish A, Frankland JA, Garner P, Garnett J, Gribble S, Griffiths C, Grocock R, Gustafson E, Hammond S, Harley JL, Hart E, Heath PD, Ho TP, Hopkins B, Horne J, Howden PJ, Huckle E, Hynds C, Johnson C, Johnson D, Kana A, Kay M, Kimberley AM, Kershaw JK, Kokkinaki M, Laird GK, Lawlor S, Lee HM, Leongamornlert DA, Laird G, Lloyd C, Lloyd DM, Loveland J, Lovell J, McLaren S, McLay KE, McMurray A, Mashreghi-Mohammadi M, Matthews L, Milne S, Nickerson T, Nguyen M, Overton-Larty E, Palmer SA, Pearce AV, Peck AI, Pelan S, Phillimore B, Porter K, Rice CM, Rogosin A, Ross MT, Sarafidou T, Sehra HK, Shownkeen R, Skuce CD, Smith M, Standring L, Sycamore N, Tester J, Thorpe A, Torcasso W, Tracey A, Tromans A, Tsolas J, Wall M, Walsh J, Wang H, Weinstock K, West AP, Willey DL, Whitehead SL, Wilming L, Wray PW, Young L, Chen Y, Lovering RC, Moschonas NK, Siebert R, Fechtel K, Bentley D, Durbin R, Hubbard T, Doucette-Stamm L, Beck S, Smith DR, Rogers J. The DNA sequence and comparative analysis of human chromosome 10. Nature 429: 375–381, 2004.[CrossRef][Medline]
  11. Deloukas P, Matthews LH, Ashurst J, Burton J, Gilbert JG, Jones M, Stavrides G, Almeida JP, Babbage AK, Bagguley CL, Bailey J, Barlow KF, Bates KN, Beard LM, Beare DM, Beasley OP, Bird CP, Blakey SE, Bridgeman AM, Brown AJ, Buck D, Burrill W, Butler AP, Carder C, Carter NP, Chapman JC, Clamp M, Clark G, Clark LN, Clark SY, Clee CM, Clegg S, Cobley VE, Collier RE, Connor R, Corby NR, Coulson A, Coville GJ, Deadman R, Dhami P, Dunn M, Ellington AG, Frankland JA, Fraser A, French L, Garner P, Grafham DV, Griffiths C, Griffiths MN, Gwilliam R, Hall RE, Hammond S, Harley JL, Heath PD, Ho S, Holden JL, Howden PJ, Huckle E, Hunt AR, Hunt SE, Jekosch K, Johnson CM, Johnson D, Kay MP, Kimberley AM, King A, Knights A, Laird GK, Lawlor S, Lehvaslaiho MH, Leversha M, Lloyd C, Lloyd DM, Lovell JD, Marsh VL, Martin SL, McConnachie LJ, McLay K, McMurray AA, Milne S, Mistry D, Moore MJ, Mullikin JC, Nickerson T, Oliver K, Parker A, Patel R, Pearce TA, Peck AI, Phillimore BJ, Prathalingam SR, Plumb RW, Ramsay H, Rice CM, Ross MT, Scott CE, Sehra HK, Shownkeen R, Sims S, Skuce CD, Smith ML, Soderlund C, Steward CA, Sulston JE, Swann M, Sycamore N, Taylor R, Tee L, Thomas DW, Thorpe A, Tracey A, Tromans AC, Vaudin M, Wall M, Wallis JM, Whitehead SL, Whittaker P, Willey DL, Williams L, Williams SA, Wilming L, Wray PW, Hubbard T, Durbin RM, Bentley DR, Beck S, Rogers J. The DNA sequence and comparative analysis of human chromosome 20. Nature 414: 865–871, 2001.[CrossRef][Medline]
  12. Dunham A, Matthews LH, Burton J, Ashurst JL, Howe KL, Ashcroft KJ, Beare DM, Burford DC, Hunt SE, Griffiths-Jones S, Jones MC, Keenan SJ, Oliver K, Scott CE, Ainscough R, Almeida JP, Ambrose KD, Andrews DT, Ashwell RI, Babbage AK, Bagguley CL, Bailey J, Bannerjee R, Barlow KF, Bates K, Beasley H, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burrill W, Carder C, Carter NP, Chapman JC, Clamp ME, Clark SY, Clarke G, Clee CM, Clegg SC, Cobley V, Collins JE, Corby N, Coville GJ, Deloukas P, Dhami P, Dunham I, Dunn M, Earthrowl ME, Ellington AG, Faulkner L, Frankish AG, Frankland J, French L, Garner P, Garnett J, Gilbert JG, Gilson CJ, Ghori J, Grafham DV, Gribble SM, Griffiths C, Hall RE, Hammond S, Harley JL, Hart EA, Heath PD, Howden PJ, Huckle EJ, Hunt PJ, Hunt AR, Johnson C, Johnson D, Kay M, Kimberley AM, King A, Laird GK, Langford CJ, Lawlor S, Leongamornlert DA, Lloyd DM, Lloyd C, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, McLaren SJ, McMurray A, Milne S, Moore MJ, Nickerson T, Palmer SA, Pearce AV, Peck AI, Pelan S, Phillimore B, Porter KM, Rice CM, Searle S, Sehra HK, Shownkeen R, Skuce CD, Smith M, Steward CA, Sycamore N, Tester J, Thomas DW, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Wilming L, Wray PW, Wright MW, Young L, Coulson A, Durbin R, Hubbard T, Sulston JE, Beck S, Bentley DR, Rogers J, Ross MT. The DNA sequence and analysis of human chromosome 13. Nature 428: 522–528, 2004.[CrossRef][Medline]
  13. Dunham I, Hunt AR, Collins JE, Bruskiewich R, Beare DM, Clamp M, Smink LJ, Ainscough R, Almeida JP, Babbage A, Bagguley C, Bailey J, Barlow K, Bates KN, Beasley O, Bird CP, Blakey S, Bridgeman AM, Buck D, Burgess J, Burrill WD, Burton J, Carder C, Carter NP, Chen Y, Clark G, Clegg SM, Cobley V, Cole CG, Collier RE, Connor RE, Conroy D, Corby N, Coville GJ, Cox AV, Davis J, Dawson E, Dhami PD, Dockree C, Dodsworth SJ, Durbin RM, Ellington A, Evans KL, Fey JM, Fleming K, French L, Garner AA, Gilbert JGR, Goward ME, Grafham D, Griffiths MN, Hall C, Hall R, Hall-Tamlyn G, Heathcott RW, Ho S, Holmes S, Hunt SE, Jones MC, Kershaw J, Kimberley A, King A, Laird GK, Langford CF, Leversha MA, Lloyd C, Lloyd DM, Martyn ID, Mashreghi-Mohammadi M, Matthews L, McCann OT, McClay J, McLaren S, McMurray AA, Milne SA, Mortimore BJ, Odell CN, Pavitt R, Pearce AV, Pearson D, Phillimore BJ, Phillips SH, Plumb RW, Ramsay H, Ramsey Y, Rogers L, Ross MT, Scott CE, Sehra HK, Skuce CD, Smalley S, Smith ML, Soderlund C, Spragon L, Steward CA, Sulston JE, Swann RM, Vaudin M, Wall M, Wallis JM, Whiteley MN, Willey D, Williams L, Williams S, Williamson H, Wilmer TE, Wilming L, Wright CL, Hubbard T, Bentley DR, Beck S, Rogers J, Shimizu N, Minoshima S, Kawasaki K, Sasaki T, Asakawa S, Kudoh J, Shintani A, Shibuya K, Yoshizaki Y, Aoki N, Mitsuyama S, Roe BA, Chen F, Chu L, Crabtree J, Deschamps S, Do A, Do T, Dorman A, Fang F, Fu Y, Hu P, Hua A, Kenton S, Lai H, Lao HI, Lewis J, Lewis S, Lin S-P, Loh P, Malaj E, Nguyen T, Pan H, Phan S, Qi S, Qian Y, Ray L, Ren Q, Shaull S, Sloan D, Song L, Wang Q, Wang Y, Wang Z, White J, Willingham D, Wu H, Yao Z, Zhan M, Zhang G, Chissoe S, Murray J, Miller N, Minx P, Fulton R, Johnson D, Bemis G, Bentley D, Bradshaw H, Bourne S, Cordes M, Du Z, Fulton L, Goela D, Graves T, Hawkins J, Hinds K, Kemp K, Latreille P, Layman D, Ozersky P, Rohlfing T, Scheet P, Walker C, Wamsley A, Wohldmann P, Pepin K, Nelson J, Korf I, Bedell JA, Hillier L, Mardis E, Waterston R, Wilson R, Emanuel BS, Shaikh T, Kurahashi H, Saitta S, Budarf ML, McDermid HE, Johnson A, Wong ACC, Morrow BE, Edelmann L, Kim UJ, Shizuya H, Simon MI, Dumanski JP, Peyrard M, Kedra D, Seroussi E, Fransson I, Tapia I, Bruder CE, O'Brien KP. The DNA sequence of human chromosome 22. Nature 402: 489–495, 1999.[CrossRef][Medline]
  14. Entrez. CoreNucleotide (http://www.ncbi.nlm.nih.gov/Database/index.html).
  15. Frantz S, Clemitson JR, Bihoreau MT, Gauguier D, Samani NJ. Genetic dissection of region around the Sa gene on rat chromosome 1: evidence for multiple loci affecting blood pressure. Hypertension 38: 216–221, 2001.[Abstract/Free Full Text]
  16. Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck D, Dunham A, Scott CE, Howe KL, Woodfine K, Spencer CC, Jones MC, Gillson C, Searle S, Zhou Y, Kokocinski F, McDonald L, Evans R, Phillips K, Atkinson A, Cooper R, Jones C, Hall RE, Andrews TD, Lloyd C, Ainscough R, Almeida JP, Ambrose KD, Anderson F, Andrew RW, Ashwell RI, Aubin K, Babbage AK, Bagguley CL, Bailey J, Beasley H, Bethel G, Bird CP, Bray-Allen S, Brown JY, Brown AJ, Buckley D, Burton J, Bye J, Carder C, Chapman JC, Clark SY, Clarke G, Clee C, Cobley V, Collier RE, Corby N, Coville GJ, Davies J, Deadman R, Dunn M, Earthrowl M, Ellington AG, Errington H, Frankish A, Frankland J, French L, Garner P, Garnett J, Gay L, Ghori MR, Gibson R, Gilby LM, Gillett W, Glithero RJ, Grafham DV, Griffiths C, Griffiths-Jones S, Grocock R, Hammond S, Harrison ES, Hart E, Haugen E, Heath PD, Holmes S, Holt K, Howden PJ, Hunt AR, Hunt SE, Hunter G, Isherwood J, James R, Johnson C, Johnson D, Joy A, Kay M, Kershaw JK, Kibukawa M, Kimberley AM, King A, Knights AJ, Lad H, Laird G, Lawlor S, Leongamornlert DA, Lloyd DM, Loveland J, Lovell J, Lush MJ, Lyne R, Martin S, Mashreghi-Mohammadi M, Matthews L, Matthews NS, McLaren S, Milne S, Mistry S, Moore MJ, Nickerson T, O'Dell CN, Oliver K, Palmeiri A, Palmer SA, Parker A, Patel D, Pearce AV, Peck AI, Pelan S, Phelps K, Phillimore BJ, Plumb R, Rajan J, Raymond C, Rouse G, Saenphimmachak C, Sehra HK, Sheridan E, Shownkeen R, Sims S, Skuce CD, Smith M, Steward C, Subramanian S, Sycamore N, Tracey A, Tromans A, Van Helmond Z, Wall M, Wallis JM, White S, Whitehead SL, Wilkinson JE, Willey DL, Williams H, Wilming L, Wray PW, Wu Z, Coulson A, Vaudin M, Sulston JE, Durbin R, Hubbard T, Wooster R, Dunham I, Carter NP, McVean G, Ross MT, Harrow J, Olson MV, Beck S, Rogers J, Bentley DR, Banerjee R, Bryant SP, Burford DC, Burrill WD, Clegg SM, Dhami P, Dovey O, Faulkner LM, Gribble SM, Langford CF, Pandian RD, Porter KM, Prigmore E. The DNA sequence and biological annotation of human chromosome 1. Nature 441: 315–321, 2006.[CrossRef][Medline]
  17. Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, Aerts A, Altherr M, Ashworth L, Bajorek E, Black S, Branscomb E, Caenepeel S, Carrano A, Caoile C, Chan YM, Christensen M, Cleland CA, Copeland A, Dalin E, Dehal P, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Garcia C, Georgescu AM, Glavina T, Gomez M, Gonzales E, Groza M, Hammon N, Hawkins T, Haydu L, Ho I, Huang W, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Larionov V, Leem SH, Lopez F, Lou Y, Lowry S, Malfatti S, Martinez D, McCready P, Medina C, Morgan J, Nelson K, Nolan M, Ovcharenko I, Pitluck S, Pollard M, Popkie AP, Predki P, Quan G, Ramirez L, Rash S, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, She X, Smith D, Slezak T, Solovyev V, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wagner M, Wheeler J, Wu K, Xie G, Yang J, Dubchak I, Furey TS, DeJong P, Dickson M, Gordon D, Eichler EE, Pennacchio LA, Richardson P, Stubbs L, Rokhsar DS, Myers RM, Rubin EM, Lucas SM. The DNA sequence and biology of human chromosome 19. Nature 428: 529–535, 2004.[CrossRef][Medline]
  18. Hancock JM. A bigger mouse? The rat genome unveiled. Bioessays 26: 1039–1042, 2004.[CrossRef][Web of Science][Medline]
  19. Hattori M, Fujiyama A, Taylor TD, Watanabe H, Yada T, Park HS, Toyoda A, Ishii K, Totoki Y, Choi DK, Groner Y, Soeda E, Ohki M, Takagi T, Sakaki Y, Taudien S, Blechschmidt K, Polley A, Menzel U, Delabar J, Kumpf K, Lehmann R, Patterson D, Reichwald K, Rump A, Schillhabel M, Schudy A, Zimmermann W, Rosenthal A, Kudoh J, Schibuya K, Kawasaki K, Asakawa S, Shintani A, Sasaki T, Nagamine K, Mitsuyama S, Antonarakis SE, Minoshima S, Shimizu N, Nordsiek G, Hornischer K, Brant P, Scharfe M, Schon O, Desario A, Reichelt J, Kauer G, Blocker H, Ramser J, Beck A, Klages S, Hennig S, Riesselmann L, Dagand E, Haaf T, Wehrmeyer S, Borzym K, Gardiner K, Nizetic D, Francis F, Lehrach H, Reinhardt R, Yaspo ML. The DNA sequence of human chromosome 21. Nature 405: 311–319, 2000.[CrossRef][Medline]
  20. Havlak P, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Weinstock GM, Gibbs RA. The Atlas genome assembly system. Genome Res 14: 721–732, 2004.[Abstract/Free Full Text]
  21. Heilig R, Eckenberg R, Petit JL, Fonknechten N, Da Silva C, Cattolico L, Levy M, Barbe V, de Berardinis V, Ureta-Vidal A, Pelletier E, Vico V, Anthouard V, Rowen L, Madan A, Qin S, Sun H, Du H, Pepin K, Artiguenave F, Robert C, Cruaud C, Bruls T, Jaillon O, Friedlander L, Samson G, Brottier P, Cure S, Segurens B, Aniere F, Samain S, Crespeau H, Abbasi N, Aiach N, Boscus D, Dickhoff R, Dors M, Dubois I, Friedman C, Gouyvenoux M, James R, Madan A, Mairey-Estrada B, Mangenot S, Martins N, Menard M, Oztas S, Ratcliffe A, Shaffer T, Trask B, Vacherie B, Bellemere C, Belser C, Besnard-Gonnet M, Bartol-Mavel D, Boutard M, Briez-Silla S, Combette S, Dufosse-Laurent V, Ferron C, Lechaplais C, Louesse C, Muselet D, Magdelenat G, Pateau E, Petit E, Sirvain-Trukniewicz P, Trybou A, Vega-Czarny N, Bataille E, Bluet E, Bordelais I, Dubois M, Dumont C, Guerin T, Haffray S, Hammadi R, Muanga J, Pellouin V, Robert D, Wunderle E, Gauguet G, Roy A, Sainte-Marthe L, Verdier J, Verdier-Discala C, Hillier L, Fulton L, McPherson J, Matsuda F, Wilson R, Scarpelli C, Gyapay G, Wincker P, Saurin W, Quetier F, Waterston R, Hood L, Weissenbach J. The DNA sequence and analysis of human chromosome 14. Nature 421: 601–607, 2003.[CrossRef][Medline]
  22. Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK. The DNA sequence of human chromosome 7. Nature 424: 157–164, 2003.[CrossRef][Medline]
  23. Hubner N, Wallace CA, Zimdahl H, Petretto E, Schulz H, Maciver F, Mueller M, Hummel O, Monti J, Zidek V, Musilova A, Kren V, Causton H, Game L, Born G, Schmidt S, Muller A, Cook SA, Kurtz TW, Whittaker J, Pravenec M, Aitman TJ. Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat Genet 37: 243–253, 2005.[CrossRef][Web of Science][Medline]
  24. Humphray SJ, Oliver K, Hunt AR, Plumb RW, Loveland JE, Howe KL, Andrews TD, Searle S, Hunt SE, Scott CE, Jones MC, Ainscough R, Almeida JP, Ambrose KD, Ashwell RI, Babbage AK, Babbage S, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beasley H, Beasley O, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burford D, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Chen Y, Clarke G, Clark SY, Clee CM, Clegg S, Collier RE, Corby N, Crosier M, Cummings AT, Davies J, Dhami P, Dunn M, Dutta I, Dyer LW, Earthrowl ME, Faulkner L, Fleming CJ, Frankish A, Frankland JA, French L, Fricker DG, Garner P, Garnett J, Ghori J, Gilbert JG, Glison C, Grafham DV, Gribble S, Griffiths C, Griffiths-Jones S, Grocock R, Guy J, Hall RE, Hammond S, Harley JL, Harrison ES, Hart EA, Heath PD, Henderson CD, Hopkins BL, Howard PJ, Howden PJ, Huckle E, Johnson C, Johnson D, Joy AA, Kay M, Keenan S, Kershaw JK, Kimberley AM, King A, Knights A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd C, Lloyd DM, Lovell J, Martin S, Mashreghi-Mohammadi M, Matthews L, McLaren S, McLay KE, McMurray A, Milne S, Nickerson T, Nisbett J, Nordsiek G, Pearce AV, Peck AI, Porter KM, Pandian R, Pelan S, Phillimore B, Povey S, Ramsey Y, Rand V, Scharfe M, Sehra HK, Shownkeen R, Sims SK, Skuce CD, Smith M, Steward CA, Swarbreck D, Sycamore N, Tester J, Thorpe A, Tracey A, Tromans A, Thomas DW, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Williams SA, Wilming L, Wray PW, Young L, Ashurst JL, Coulson A, Blöcker H, Durbin R, Sulston JE, Hubbard T, Jackson MJ, Bentley DR, Beck S, Rogers J, Dunham I. DNA sequence and analysis of human chromosome 9. Nature 429: 369–374, 2004.[CrossRef][Medline]
  25. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409: 860–921, 2001.[CrossRef][Medline]
  26. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biemont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431: 946–957, 2004.[CrossRef][Medline]
  27. Krzywinski M, Wallis J, Gosele C, Bosdet I, Chiu R, Graves T, Hummel O, Layman D, Mathewson C, Wye N, Zhu B, Albracht D, Asano J, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Davito J, Fjell C, Gaige T, Ganten D, Girn N, Guggenheimer K, Himmelbauer H, Kreitler T, Leach S, Lee D, Lehrach H, Mayo M, Mead K, Olson T, Pandoh P, Prabhu AL, Shin H, Tanzer S, Thompson J, Tsai M, Walker J, Yang G, Sekhon M, Hillier L, Zimdahl H, Marziali A, Osoegawa K, Zhao S, Siddiqui A, de Jong PJ, Warren W, Mardis E, McPherson JD, Wilson R, Hubner N, Jones S, Marra M, Schein J. Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. Genome Res 14: 766–779, 2004.[Abstract/Free Full Text]
  28. Lindblad-Toh K. Genome sequencing: three's company. Nature 428: 475–476, 2004.[CrossRef][Medline]
  29. Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ 3rd, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, Grabherr M, Kellis M, Kleber M, Bardeleben C, Goodstadt L, Heger A, Hitte C, Kim L, Koepfli KP, Parker HG, Pollinger JP, Searle SM, Sutter NB, Thomas R, Webber C, Broad Institute Genome Sequencing Platform, Lander ES. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438: 803–819, 2005.[CrossRef][Medline]
  30. Mammalian Gene Collection Project Team. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res 14: 2121–2127, 2004.[Abstract/Free Full Text]
  31. Mammalian Gene Collection Project Team. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci USA 99: 16899–16903, 2002.[Abstract/Free Full Text]
  32. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K. Genome of the marsupial Monodelphis domesticareveals innovation in non-coding sequences. Nature 447: 167–177, 2007.[CrossRef][Medline]
  33. Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520–562, 2002.[CrossRef][Medline]
  34. Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, Jones MC, Horton R, Hunt SE, Scott CE, Gilbert JG, Clamp ME, Bethel G, Milne S, Ainscough R, Almeida JP, Ambrose KD, Andrews TD, Ashwell RI, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beare DM, Beasley H, Beasley O, Bird CP, Blakey S, Bray-Allen S, Brook J, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Clark SY, Clark G, Clee CM, Clegg S, Cobley V, Collier RE, Collins JE, Colman LK, Corby NR, Coville GJ, Culley KM, Dhami P, Davies J, Dunn M, Earthrowl ME, Ellington AE, Evans KA, Faulkner L, Francis MD, Frankish A, Frankland J, French L, Garner P, Garnett J, Ghori MJ, Gilby LM, Gillson CJ, Glithero RJ, Grafham DV, Grant M, Gribble S, Griffiths C, Griffiths M, Hall R, Halls KS, Hammond S, Harley JL, Hart EA, Heath PD, Heathcott R, Holmes SJ, Howden PJ, Howe KL, Howell GR, Huckle E, Humphray SJ, Humphries MD, Hunt AR, Johnson CM, Joy AA, Kay M, Keenan SJ, Kimberley AM, King A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd CR, Lloyd DM, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, Maslen GL, Matthews L, McCann OT, McLaren SJ, McLay K, McMurray A, Moore MJ, Mullikin JC, Niblett D, Nickerson T, Novik KL, Oliver K, Overton-Larty EK, Parker A, Patel R, Pearce AV, Peck AI, Phillimore B, Phillips S, Plumb RW, Porter KM, Ramsey Y, Ranby SA, Rice CM, Ross MT, Searle SM, Sehra HK, Sheridan E, Skuce CD, Smith S, Smith M, Spraggon L, Squares SL, Steward CA, Sycamore N, Tamlyn-Hall G, Tester J, Theaker AJ, Thomas DW, Thorpe A, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, White SS, Whitehead SL, Whittaker H, Wild A, Willey DJ, Wilmer TE, Wood JM, Wray PW, Wyatt JC, Young L, Younger RM, Bentley DR, Coulson A, Durbin R, Hubbard T, Sulston JE, Dunham I, Rogers J, Beck S. The DNA sequence and analysis of human chromosome 6. Nature 425: 805–811, 2003.[CrossRef][Medline]
  35. Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Wei S, Wheeler DA, Wright MW, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clendenning J, Clerc-Blankenburg KP, Chen R, Chen Z, Davis C, Delgado O, Dinh HH, Dong W, Draper H, Ernst S, Fu G, Gonzalez-Garay ML, Garcia DK, Gillett W, Gu J, Hao B, Haugen E, Havlak P, He X, Hennig S, Hu S, Huang W, Jackson LR, Jacob LS, Kelly SH, Kube M, Levy R, Li Z, Liu B, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Palmeiri A, Pasternak S, Perez LM, Phelps KA, Plopper FJ, Qiang B, Raymond C, Rodriguez R, Saenphimmachak C, Santibanez J, Shen H, Shen Y, Subramanian S, Tabor PE, Verduzco D, Waldron L, Wang J, Wang J, Wang Q, Williams GA, Wong GK, Yao Z, Zhang J, Zhang X, Zhao G, Zhou J, Zhou Y, Nelson D, Lehrach H, Reinhardt R, Naylor SL, Yang H, Olson M, Weinstock G, Gibbs RA. The DNA sequence, annotation and analysis of human chromosome 3. Nature 440: 1194–1198, 2006.[CrossRef][Medline]
  36. National Center for Biotechnology Information. dbSNP. Bethesda, MD: National Center for Biotechnology Information, build 126.
  37. Nusbaum C, Mikkelsen TS, Zody MC, Asakawa S, Taudien S, Garber M, Kodira CD, Schueler MG, Shimizu A, Whittaker CA, Chang JL, Cuomo CA, Dewar K, FitzGerald MG, Yang X, Allen NR, Anderson S, Asakawa T, Blechschmidt K, Bloom T, Borowsky ML, Butler J, Cook A, Corum B, DeArellano K, DeCaprio D, Dooley KT, Dorris L 3rd, Engels R, Glockner G, Hafez N, Hagopian DS, Hall JL, Ishikawa SK, Jaffe DB, Kamat A, Kudoh J, Lehmann R, Lokitsang T, Macdonald P, Major JE, Matthews CD, Mauceli E, Menzel U, Mihalev AH, Minoshima S, Murayama Y, Naylor JW, Nicol R, Nguyen C, O'Leary SB, O'Neill K, Parker SC, Polley A, Raymond CK, Reichwald K, Rodriguez J, Sasaki T, Schilhabel M, Siddiqui R, Smith CL, Sneddon TP, Talamas JA, Tenzin P, Topham K, Venkataraman V, Wen G, Yamazaki S, Young SK, Zeng Q, Zimmer AR, Rosenthal A, Birren BW, Platzer M, Shimizu N, Lander ES. DNA sequence and analysis of human chromosome 8. Nature 439: 331–335, 2006.[CrossRef][Medline]
  38. Nusbaum C, Zody MC, Borowsky ML, Kamal M, Kodira CD, Taylor TD, Whittaker CA, Chang JL, Cuomo CA, Dewar K, FitzGerald MG, Yang X, Abouelleil A, Allen NR, Anderson S, Bloom T, Bugalter B, Butler J, Cook A, DeCaprio D, Engels R, Garber M, Gnirke A, Hafez N, Hall JL, Norman CH, Itoh T, Jaffe DB, Kuroki Y, Lehoczky J, Lui A, Macdonald P, Mauceli E, Mikkelsen TS, Naylor JW, Nicol R, Nguyen C, Noguchi H, O'Leary SB, O'Neill K, Piqani B, Smith CL, Talamas JA, Topham K, Totoki Y, Toyoda A, Wain HM, Young SK, Zeng Q, Zimmer AR, Fujiyama A, Hattori M, Birren BW, Sakaki Y, Lander ES. DNA sequence and analysis of human chromosome 18. Nature 437: 551–555, 2005.[CrossRef][Medline]
  39. Pennisi E. Genomics. New sequence boosts rats' research appeal. Science 303: 455–458, 2004.[Abstract/Free Full Text]
  40. Petit-Zeman S. Rat genome sequence reignites preclinical model debate. Nat Rev Drug Discov 3: 287–288, 2004.[CrossRef][Web of Science][Medline]
  41. Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493–521, 2004.[CrossRef][Medline]
  42. Rhesus Macaque Genome Sequencing and Analysis Consortium. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222–234, 2007.[Abstract/Free Full Text]
  43. Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, Durbin KJ, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MA, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res 15: 1–18, 2005.[Abstract/Free Full Text]
  44. Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, Platzer M, Howell GR, Burrows C, Bird CP, Frankish A, Lovell FL, Howe KL, Ashurst JL, Fulton RS, Sudbrak R, Wen G, Jones MC, Hurles ME, Andrews TD, Scott CE, Searle S, Ramser J, Whittaker A, Deadman R, Carter NP, Hunt SE, Chen R, Cree A, Gunaratne P, Havlak P, Hodgson A, Metzker ML, Richards S, Scott G, Steffen D, Sodergren E, Wheeler DA, Worley KC, Ainscough R, Ambrose KD, Ansari-Lari MA, Aradhya S, Ashwell RI, Babbage AK, Bagguley CL, Ballabio A, Banerjee R, Barker GE, Barlow KF, Barrett IP, Bates KN, Beare DM, Beasley H, Beasley O, Beck A, Bethel G, Blechschmidt K, Brady N, Bray-Allen S, Bridgeman AM, Brown AJ, Brown MJ, Bonnin D, Bruford EA, Buhay C, Burch P, Burford D, Burgess J, Burrill W, Burton J, Bye JM, Carder C, Carrel L, Chako J, Chapman JC, Chavez D, Chen E, Chen G, Chen Y, Chen Z, Chinault C, Ciccodicola A, Clark SY, Clarke G, Clee CM, Clegg S, Clerc-Blankenburg K, Clifford K, Cobley V, Cole CG, Conquer JS, Corby N, Connor RE, David R, Davies J, Davis C, Davis J, Delgado O, Deshazo D, Dhami P, Ding Y, Dinh H, Dodsworth S, Draper H, Dugan-Rocha S, Dunham A, Dunn M, Durbin KJ, Dutta I, Eades T, Ellwood M, Emery-Cohen A, Errington H, Evans KL, Faulkner L, Francis F, Frankland J, Fraser AE, Galgoczy P, Gilbert J, Gill R, Glöckner G, Gregory SG, Gribble S, Griffiths C, Grocock R, Gu Y, Gwilliam R, Hamilton C, Hart EA, Hawes A, Heath PD, Heitmann K, Hennig S, Hernandez J, Hinzmann B, Ho S, Hoffs M, Howden PJ, Huckle EJ, Hume J, Hunt PJ, Hunt AR, Isherwood J, Jacob L, Johnson D, Jones S, de Jong PJ, Joseph SS, Keenan S, Kelly S, Kershaw JK, Khan Z, Kioschis P, Klages S, Knights AJ, Kosiura A, Kovar-Smith C, Laird GK, Langford C, Lawlor S, Leversha M, Lewis L, Liu W, Lloyd C, Lloyd DM, Loulseged H, Loveland JE, Lovell JD, Lozado R, Lu J, Lyne R, Ma J, Maheshwari M, Matthews LH, McDowall J, McLaren S, McMurray A, Meidl P, Meitinger T, Milne S, Miner G, Mistry SL, Morgan M, Morris S, Müller I, Mullikin JC, Nguyen N, Nordsiek G, Nyakatura G, O'Dell CN, Okwuonu G, Palmer S, Pandian R, Parker D, Parrish J, Pasternak S, Patel D, Pearce AV, Pearson DM, Pelan SE, Perez L, Porter KM, Ramsey Y, Reichwald K, Rhodes S, Ridler KA, Schlessinger D, Schueler MG, Sehra HK, Shaw-Smith C, Shen H, Sheridan EM, Shownkeen R, Skuce CD, Smith ML, Sotheran EC, Steingruber HE, Steward CA, Storey R, Swann RM, Swarbreck D, Tabor PE, Taudien S, Taylor T, Teague B, Thomas K, Thorpe A, Timms K, Tracey A, Trevanion S, Tromans AC, d'Urso M, Verduzco D, Villasana D, Waldron L, Wall M, Wang Q, Warren J, Warry GL, Wei X, West A, Whitehead SL, Whiteley MN, Wilkinson JE, Willey DL, Williams G, Williams L, Williamson A, Williamson H, Wilming L, Woodmansey RL, Wray PW, Yen J, Zhang J, Zhou J, Zoghbi H, Zorilla S, Buck D, Reinhardt R, Poustka A, Rosenthal A, Lehrach H, Meindl A, Minx PJ, Hillier LW, Willard HF, Wilson RK, Waterston RH, Rice CM, Vaudin M, Coulson A, Nelson DL, Weinstock G, Sulston JE, Durbin R, Hubbard T, Gibbs RA, Beck S, Rogers J, Bentley DR. The DNA sequence of the human X chromosome. Nature 434: 325–337, 2005.[CrossRef][Medline]
  45. Rubattu S, Volpe M, Kreutz R, Ganten U, Ganten D, Lindpaintner K. Chromosomal mapping of quantitative trait loci contributing to stroke in a rat model of complex human disease. Nat Genet 13: 429–434, 1996.[CrossRef][Web of Science][Medline]
  46. Scherer SE, Muzny DM, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Montgomery KT, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Lovering RC, Wheeler DA, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clerc-Blankenburg KP, Davis C, Delgado O, Dinh HH, Draper H, Gonzalez-Garay ML, Havlak P, Jackson LR, Jacob LS, Kelly SH, Li L, Li Z, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Pasternak S, Perez LM, Plopper FJ, Santibanez J, Shen H, Tabor PE, Verduzco D, Waldron L, Wang Q, Williams GA, Zhang J, Zhou J, Allen CC, Amin AG, Anyalebechi V, Bailey M, Barbaria JA, Bimage KE, Bryant NP, Burch PE, Burkett CE, Burrell KL, Calderon E, Cardenas V, Carter K, Casias K, Cavazos I, Cavazos SR, Ceasar H, Chacko J, Chan SN, Chavez D, Christopoulos C, Chu J, Cockrell R, Cox CD, Dang M, Dathorne SR, David R, Davis CM, Davy-Carroll L, Deshazo DR, Donlin JE, D'Souza L, Eaves KA, Egan A, Emery-Cohen AJ, Escotto M, Flagg N, Forbes LD, Gabisi AM, Garza M, Hamilton C, Henderson N, Hernandez O, Hines S, Hogues ME, Huang M, Idlebird DG, Johnson R, Jolivet A, Jones S, Kagan R, King LM, Leal B, Lebow H, Lee S, LeVan JM, Lewis LC, London P, Lorensuhewa LM, Loulseged H, Lovett DA, Lucier A, Lucier RL, Ma J, Madu RC, Mapua P, Martindale AD, Martinez E, Massey E, Mawhiney S, Meador MG, Mendez S, Mercado C, Mercado IC, Merritt CE, Miner ZL, Minja E, Mitchell T, Mohabbat F, Mohabbat K, Montgomery B, Moore N, Morris S, Munidasa M, Ngo RN, Nguyen NB, Nickerson E, Nwaokelemeh OO, Nwokenkwo S, Obregon M, Oguh M, Oragunye N, Oviedo RJ, Parish BJ, Parker DN, Parrish J, Parks KL, Paul HA, Payton BA, Perez A, Perrin W, Pickens A, Primus EL, Pu LL, Puazo M, Quiles MM, Quiroz JB, Rabata D, Reeves K, Ruiz SJ, Shao H, Sisson I, Sonaike T, Sorelle RP, Sutton AE, Svatek AF, Svetz LA, Tamerisa KS, Taylor TR, Teague B, Thomas N, Thorn RD, Trejos ZY, Trevino BK, Ukegbu ON, Urban JB, Vasquez LI, Vera VA, Villasana DM, Wang L, Ward-Moore S, Warren JT, Wei X, White F, Williamson AL, Wleczyk R, Wooden HS, Wooden SH, Yen J, Yoon L, Yoon V, Zorrilla SE, Nelson D, Kucherlapati R, Weinstock G, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequence Production Team. The finished DNA sequence of human chromosome 12. Nature 440: 346–351, 2006.[CrossRef][Medline]
  47. Schmutz J, Martin J, Terry A, Couronne O, Grimwood J, Lowry S, Gordon LA, Scott D, Xie G, Huang W, Hellsten U, Tran-Gyamfi M, She X, Prabhakar S, Aerts A, Altherr M, Bajorek E, Black S, Branscomb E, Caoile C, Challacombe JF, Chan YM, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Lopez F, Lou Y, Martinez D, Medina C, Morgan J, Nandkeshwar R, Noonan JP, Pitluck S, Pollard M, Predki P, Priest J, Ramirez L, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wheeler J, Wu K, Yang J, Dickson M, Cheng JF, Eichler EE, Olsen A, Pennacchio LA, Rokhsar DS, Richardson P, Lucas SM, Myers RM, Rubin EM. The DNA sequence and comparative analysis of human chromosome 5. Nature 431: 268–274, 2004.[CrossRef][Medline]
  48. Schmutz J, Wheeler J, Grimwood J, Dickson M, Yang J, Caoile C, Bajorek E, Black S, Chan YM, Denys M, Escobar J, Flowers D, Fotopulos D, Garcia C, Gomez M, Gonzales E, Haydu L, Lopez F, Ramirez L, Retterer J, Rodriguez A, Rogers S, Salazar A, Tsai M, Myers RM. Quality assessment of the human genome sequence. Nature 429: 365–368, 2004.[CrossRef][Medline]
  49. Sea Urchin Genome Sequencing Consortium. The genome of the sea urchin Strongylocentrotus purpuratus. Science 314: 941–952, 2006.[Abstract/Free Full Text]
  50. Strausberg RL, Feingold EA, Klausner RD, Collins FS. The mammalian gene collection. Science 286: 455–457, 1999.[Abstract/Free Full Text]
  51. Taylor TD, Noguchi H, Totoki Y, Toyoda A, Kuroki Y, Dewar K, Lloyd C, Itoh T, Takeda T, Kim DW, She X, Barlow KF, Bloom T, Bruford E, Chang JL, Cuomo CA, Eichler E, FitzGerald MG, Jaffe DB, LaButti K, Nicol R, Park HS, Seaman C, Sougnez C, Yang X, Zimmer AR, Zody MC, Birren BW, Nusbaum C, Fujiyama A, Hattori M, Rogers J, Lander ES, Sakaki Y. Human chromosome 11 DNA sequence and analysis including novel gene identification. Nature 440: 497–500, 2006.[CrossRef][Medline]
  52. Tuzun E, Bailey JA, Eichler EE. Recent segmental duplications in the working draft assembly of the brown Norway rat. Genome Res 14: 493–506, 2004.[Abstract/Free Full Text]
  53. Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ; RGD Team. The Rat Genome Database, update 2007—easing the path from disease to data and back again. Nucl Acids Res 35: D658–D662, 2007.[Abstract/Free Full Text]
  54. Wilder SP, Bihoreau MT, Argoud K, Watanabe TK, Lathrop M, Gauguier D. Integration of the rat recombination and EST maps in the rat genomic sequence and comparative mapping analysis with the mouse genome. Genome Res 14: 758–765, 2004.[Abstract/Free Full Text]
  55. Zimdahl H, Nyakatura G, Brandt P, Schulz H, Hummel O, Fartmann B, Brett D, Droege M, Monti J, Lee YA, Sun Y, Zhao S, Winter EE, Ponting CP, Chen Y, Kasprzyk A, Birney E, Ganten D, Hubner N. A SNP map of the rat genome generated from cDNA sequences. Science 303: 807, 2004.[Free Full Text]
  56. Zody MC, Garber M, Adams DJ, Sharpe T, Harrow J, Lupski JR, Nicholson C, Searle SM, Wilming L, Young SK, Abouelleil A, Allen NR, Bi W, Bloom T, Borowsky ML, Bugalter BE, Butler J, Chang JL, Chen CK, Cook A, Corum B, Cuomo CA, de Jong PJ, DeCaprio D, Dewar K, FitzGerald M, Gilbert J, Gibson R, Gnerre S, Goldstein S, Grafham DV, Grocock R, Hafez N, Hagopian DS, Hart E, Norman CH, Humphray S, Jaffe DB, Jones M, Kamal M, Khodiyar VK, LaButti K, Laird G, Lehoczky J, Liu X, Lokyitsang T, Loveland J, Lui A, Macdonald P, Major JE, Matthews L, Mauceli E, McCarroll SA, Mihalev AH, Mudge J, Nguyen C, Nicol R, O'Leary SB, Osoegawa K, Schwartz DC, Shaw-Smith C, Stankiewicz P, Steward C, Swarbreck D, Venkataraman V, Whittaker CA, Yang X, Zimmer AR, Bradley A, Hubbard T, Birren BW, Rogers J, Lander ES, Nusbaum C. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. Nature 440: 1045–1049, 2006.[CrossRef][Medline]
  57. Zody MC, Garber M, Sharpe T, Young SK, Rowen L, O'Neill K, Whittaker CA, Kamal M, Chang JL, Cuomo CA, Dewar K, FitzGerald MG, Kodira CD, Madan A, Qin S, Yang X, Abbasi N, Abouelleil A, Arachchi HM, Baradarani L, Birditt B, Bloom S, Bloom T, Borowsky ML, Burke J, Butler J, Cook A, DeArellano K, DeCaprio D, Dorris L 3rd, Dors M, Eichler EE, Engels R, Fahey J, Fleetwood P, Friedman C, Gearin G, Hall JL, Hensley G, Johnson E, Jones C, Kamat A, Kaur A, Locke DP, Madan A, Munson G, Jaffe DB, Lui A, Macdonald P, Mauceli E, Naylor JW, Nesbitt R, Nicol R, O'Leary SB, Ratcliffe A, Rounsley S, She X, Sneddon KM, Stewart S, Sougnez C, Stone SM, Topham K, Vincent D, Wang S, Zimmer AR, Birren BW, Hood L, Lander ES, Nusbaum C. Analysis of the DNA sequence and duplication history of human chromosome 15. Nature 440: 671–675, 2006.[CrossRef][Medline]



This article has been cited by other articles:


Home page
 Physiol. GenomicsHome page
D. H. T. IJpelaar, A. Schulz, J. Aben, A. van der Wal, J. A. Bruijn, R. Kreutz, and E. de Heer
Genetic predisposition for glomerulonephritis-induced glomerulosclerosis in rats is linked to chromosome 1
Physiol Genomics, October 8, 2008; 35(2): 173 - 181.
[Abstract] [Full Text] [PDF]

This Article
Right arrow Abstract Freely available
Right arrow Full Text (PDF)
Right arrow Supplemental Table
Right arrow All Versions of this Article:
32/3/273    most recent
00208.2007v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Worley, K. C.
Right arrow Articles by Gibbs, R. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Worley, K. C.
Right arrow Articles by Gibbs, R. A.

HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Visit Other APS Journals Online
Copyright © 2008 by the American Physiological Society.