The Genom of Homo sapiens.pdf

Building Comparative Maps Using 1.5x Sequence Coverage:Human Chromosome 1p and the Canine GenomeR. GUYON,* E.F. KIRKNESS, † T.D. LORENTZEN, ‡ C. HITTE,* K.E. COMSTOCK, ‡ P. QUIGNON,*T. DERRIEN,* C. ANDRÉ,* C.M. FRASER, † F. GALIBERT,* AND E.A. OSTRANDER ‡*UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, 35043 Rennes Cédex, France;† The Institute for Genomic Research, Rockville, Maryland 20850; ‡ Clinical and Human Biology Divisions,Fred Hutchinson Cancer Research Center, D4-100, Seattle, Washington 98109-1024The ability to test the association between phenotypeand genotype within biological systems of interest is limitedby the degree to which the genome map of any modelsystem can be rigorously aligned with the reference humanand mouse maps. Although extensive reciprocalchromosome paint studies have outlined the general evolutionaryrelationships between the chromosomes of dogand other mammals, details of the conserved synteny thatexist between the human and dog genomes are still lacking.Similarly, there is a paucity of information regardingthe relationship between model genomes.In the case of the canine genome, reciprocal chromosomepainting has enabled investigators to broadly establishthe evolutionary relationship between canine chromosomesand cytogenetic bands defining humanchromosome arms (Breen et al. 1999b; Yang et al. 1999).These data suggest the existence of 68–73 conserved regions(Breen et al. 1999b; Yang et al. 1999; Sargan et al.2000), and radiation hybrid data suggest a total of 76 conservedsegments between human and dog (Guyon et al.2003). Radiation hybrid data demonstrate that several caninechromosomes, such as Canis familiaris chromosomes(CFA) 8, 12, 22–24, and most of the smaller caninechromosomes are apparently composed of a single continuoussection of the human genome; others, such asCFA1 through CFA7, retain two to four portions of severaldistinct human chromosomes, and still others, suchas CFA15, correspond to as many as five HSA fragments(Guyon et al. 2003). This fact, combined with the nearly1600 microsatellite markers now ordered on the canineradiation hybrid (RH) map (Parker et al. 2001; Guyon etal. 2003), ensures that genome-wide scans on informativecanine families can be carried out with relative ease, andthe corresponding chromosome arm in the humangenome can be quickly and correctly identified.However, within the large syntenic regions that defineeach canine chromosome, there is a paucity of mappedgenes that severely limits the ability to move from a generalregion of interest to selection of specific candidategenes. Indeed, only 900 canine-specific genes have beenplaced on the most recent version of the canine RH map(Guyon et al. 2003), and still fewer on the meiotic linkagemap (Parker et al. 2001). Overall, the distribution ofgene-based markers averages only one per 3 Mb. Althoughthese data support the hypothesis that blocks ofseveral megabases are well conserved throughout the caninegenome, the number of mapped genes within anysingle block is insufficient for assigning breakpoints ofconserved synteny. This limits the degree to which initialfindings of linkage in canine families can be followed bysuccessful positional cloning efforts, and reduces the utilityof the human genome sequence for tackling problemsof interest in other mammalian systems. Thus, it remainsa priority of the canine genome-mapping community toadd more gene-based markers to the canine map.In this study, we have tested the hypothesis that 1x sequencecoverage of the canine genome is sufficient topermit identification and mapping of the canine orthologsof most human genes. Toward this aim, we focused on thehuman chromosome 1p arm (HSA1p), which is known tocontain several disease-associated genes of interest. The1x sequence was used to identify canine orthologs of 158genes from HSA1p, and RH mapping of 120 of them allowedproduction of a dense comparative map betweenhuman and dog in this region of interest. Human HSA1pcorresponds to seven conserved segments within fivechromosomal regions (CFA 2, 5, 6, 15, and 17) with geneorders and limits well defined. The study presented here,therefore, illustrates the power of combining 1.5x shotgunsequence data and a one megabase resolution RHmap for building a comparative map with the human sequence.The net result is a unified resource suitable forstudies aimed at positional cloning of mapped loci, candidategene assessment, and evolutionary analyses. Wesuggest that, for many additional genomes, this will be apowerful and economical approach for characterizinggenome structure and evolutionary relationships.RESULTSStarting from a set of 187 HSA1p genes, fragments of158 putative orthologs were retrieved from the canine genomicsequence data. For 144 genes, canine-specificprimers were designed and 126 were successfully typedon the RHDF5000-2 canine RH panel (Vignaux et al.1999). RH data from the markers were computed with thelatest 3270-marker RH map (Guyon et al. 2003) using theMultiMap and Traveling Salesman (TSP)/CONCORDEsoftwares (Matise et al.1994; Agarwala et al. 2000). Ofthese 126 gene markers, 120 could be incorporated in 5 ofCold Spring Harbor Symposia on Quantitative Biology, Volume LXVIII. © 2003 Cold Spring Harbor Laboratory Press 0-87969-709-1/04. 171