A human genome map of comparative anchor tagged sequences

Abstract

Effective comparative mapping inference utilizing developing gene maps of animal species requires the inclusion of anchored reference loci that are homologous to genes mapped in the more "gene-dense" mouse and human maps. Nominated anchor loci, termed comparative anchor tagged sequences (CATS), have been ordered in the mouse linkage map, but due to the dearth of common polymorphisms among human coding genes have not been well represented in human linkage maps. We present here an ordered framework map of 314 comparative anchor markers in humans based on mapping analysis in the Genebridge 4 panel of radiation hybrid cell lines, plus empirically optimized CATS PCR primers which detect these markers. The ordering of these homologous gene markers in human and mouse maps provides a framework for comparative gene mapping of representative mammalian species.

A Radiation Hybrid Map of the Cat Genome: Implications for Comparative Mapping

“…The 424 coding loci placed on the final map ( Fig.1) were comprised of the following markers: 228 feline-specific ESTs, 70 feline genes deposited in GenBank, 70 comparative anchor locus-derived STSs (Venta et al 1996;Lyons et al 1997;Jiang et al 1998), 40 newly developed or published (Murphy et al 1999a,b) locus-specific STSs developed in our laboratory, seven human ESTs (Chen et al 1999), and nine STSs for feline-specific endogenous retroelement insertions (RD-114). A detailed list of primers, sources, and locus information is available from the following website (http://lgd.nci.nih.gov).…”

“…When data were only available for the Stanford G3-based map, these were converted to a Genebridge-4-estimated range on the basis of the corresponding map interval (www.ncbi.nlm.nih.gov/genemap). Fourteen human loci had been assayed previously in our laboratory (Chen et al 1999;Murphy et al 1999b) using the human Genebridge-4 panel (Research Genetics) and positioned onto the current Sanger Center framework (www.sanger.ac.uk/RHserver). In most cases, primers were designed within 3' UTRs of sequences acquired from GenBank.…”

Extensive Conservation of Sex Chromosome Organization Between Cat and Human Revealed by Parallel Radiation Hybrid Mapping

“…Human X chromosome loci were localized by typing markers specific for each gene (Table 1) on the GeneBridge4 (GB4) panel (Research Genetics, Inc.) and submitting scored vectors to the Sanger Centre RH server. Protocols for the human RH genotyping are as described previously (Chen et al 1999). …”

Development and Characterization of CATS Markers for Genetic Linkage Mapping in the House Musk Shrew, Suncus murinus

“…This is the first report of the detection of length polymorphism in the 5 co-dominant markers in this species in the elucidation of CATS markers. In other works, CATS polymorphism detection was mainly by restriction fragment length polymorphism (RFLP) and/or by single strand conformation polymorphism (SSCP) analysis [3,14,15]. Greater polymorphism discrimination would likely have resulted if RFLP screening or SSCP analysis were applied to the musk shrew [15].…”

“…These gene specific PCR primers, named Comparative Anchor Tagged Sequences (CATS), were designed to span introns for polymorphism ascertainment, and to include sufficient exonic sequences (25-400 bp) for gene identification. Markers developed in this manner have been used to generate comparative genome maps in the human, cat, dog, horse and other domesticated species [2,3,14,15]. Expanding gene mapping studies to other eutherian species will add enormously to the knowledge of eutherian genome evolution, especially if the same set of comparative anchor loci are examined, because the relationships of many of the orders of eutherian mammals are difficult to deduce [18].…”