Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping

Hitte, Christophe; Madeoy, Jennifer; Kirkness, Ewen F.; Priat, Catherine; Lorentzen, Travis D.; Senger, Fabrice; Thomas, D. M.; Derrien, Thomas; Ramirez, Christina M.; Scott, Carol; Evanno, Gwénaëlle; Pullar, Barbara; Cadieu, Édouard; Oza, Vinay; Lourgant, Kristelle; Jaffe, David B.; Tacher, Sandrine; Dreano, Stéphane; Berkova, Nadejda; André, Catherine; Deloukas, Panos; Fraser, Claire M.; Lindblad‐Toh, Kerstin; Ostrander, Elaine A.; Galibert, Francis

doi:10.1038/nrg1658

Cited by 63 publications

(41 citation statements)

References 29 publications

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“…The sequence assembly validated much of what was already hypothesized from comparative genome map studies. The genome is approximately 2.4 billion bases and is comprised of approximately 250 conserved segments when compared to the human genome 16,17,21,[65][66][67] . The assembled sequence is estimated to cover 98% of the dog genome with the majority of genes containing no sequence gaps.…”

Section: Canine Genome Maps and The Canine Genome Sequencementioning

confidence: 99%

“…Recent studies have brought advances in understanding the genetics of breed development 15 and the availability of ever higher resolution maps [16][17][18][19][20][21] . These have led to the mapping of disease loci for a variety of diseases including metabolic disorders 22,23 , blindness [24][25][26][27][28] , cancer 29,30 neurologic disorders 31,32 , hip dysplasia 33 epilepsy 34 , as well as several morphologic traits 35,36 .…”

Section: Introductionmentioning

confidence: 99%

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Finding cardiovascular disease genes in the dog

Parker

Meurs

Ostrander

2006

Journal of Veterinary Cardiology

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Recent advances in canine genomics are changing the landscape of veterinary biology, and by default, veterinary medicine. No longer are clinicians locked into traditional methods of diagnoses and therapy. Rather major advances in canine genetics and genomics from the past five years are now changing the way the veterinarian of the 21 st century practices medicine.First, the availability of a dense genome map gives canine genetics a much needed foothold in comparative medicine, allowing advances made in human and mouse genetics to be applied to companion animals. Second, the recently released 7.5x whole genome sequence of the dog is facilitating the identification of hereditary disease genes. Finally, development of genetic tools for rapid screening of families and populations at risk for inherited disease means that the cost of identifying and testing for disease loci will significantly decrease in coming years.Out of these advances will come major changes in companion animal diagnostics and therapy. Clinicians will be able to offer their clients genetic testing and counseling for a myriad of disorders. Such advances are certain to generate healthier and more long lived dogs, improving quality of life for owner and pet alike. The clinician of the 21 st century, therefore, faces incredible opportunities as well as challenges in the management of genetic disease. In this review we summarize recent findings in canine genomics and discuss their application to the study of canine cardiac health.

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Section: Canine Genome Maps and The Canine Genome Sequencementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Finding cardiovascular disease genes in the dog

Parker

Meurs

Ostrander

2006

Journal of Veterinary Cardiology

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“…The assembly was anchored to the canine chromosomes using data from both radiation hybrid and cytogenetic maps 11,13,14 . Roughly 97% of the assembled sequence was ordered and oriented on the chromosomes, showing an excellent agreement with the two maps.…”

Section: Generating a Draft Genome Sequencementioning

confidence: 99%

“…With the exception of human, dog is the most intensely studied animal in medical practice, with detailed family history and pathology data often available 8 . Using genetic resources developed over the past 15 years [11][12][13][14][15][16] , researchers have already identified mutations in genes underlying ,25 mendelian diseases 17,18 . There are also growing efforts to understand the genetic basis of phenotypic variation such as skeletal morphology 10,19 .…”

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confidence: 99%

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Lindblad‐Toh¹,

Wade²,

Mikkelsen³

et al. 2005

Nature

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Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

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“…At least 100 continuous bases from a minimum of one exon were present for nearly 85% of individual canine genes. In the end, a total of 10,348 gene-based markers were mapped, creating a comparative map of uniformly spaced genes across all canine chromosomes except the Y (Hitte et al 2005). The map provides a tremendous resource for the fox genomics community.…”

mentioning

confidence: 99%