"KARIBIN," an information resource for obtaining genomic information in a cytogenetic band

Abstract

KARIBIN () is a karyotypic region-based integrated information resource that provides a comprehensive view of the integrated mapping and sequencing data for the human genome. A cytogenetic band is linked to a genetic or physical location using fluorescence in situ hybridization (FISH) mapping data. The genetic, physical mapping data and the sequencing data are integrated using STS markers positioned on multiple maps. For each cytogenetic band, the user can obtain the most up-to-date information that includes genetic and physical maps, human transcript gene map, YAC and PAC/BAC clone coverage, disease gene phenotype, and high throughput genomic sequences from the major human genome sequencing centers. This information provides a framework for future experiments and may accelerate the process of disease gene hunting. It is envisioned that other cytogenetic-based information such as chromosome aberrations can be linked to this framework.

Figure 1

Linking a cytogenetic band to the rest of the genome data using an STS-mediated approach. The input data are shown in light rectangles, which include the cytogenetic band and the FISH-anchored STS markers. The output data are displayed in dark rectangles, which include the OMIM gene map, the sequencing status, the genetic, physical, and transcript maps and YAC and BAC/PAC coverage.

Figure 2

Graphic overview of the integrated genetic, physical, and cytogenetic maps for chromosome 7. Seven maps are displayed from top to bottom in the following order: the RH map from SHGC, the integrated RH and YAC contig map from WI/MIT, the map with consistent markers, the YAC contig map from NHGRI, the genetic map from Généthon, the genetic map from CHLC, and the cytogenetic map. Green lines link the consistent STS markers mapped by at least three groups, and their relative orders are preserved on the consistent map. The black lines linking a cytogenetic band to STS markers on the genetic and physical maps represent the whole-genome FISH mapping data (Green et al. 1994). Red lines indicate the inconsistent STS markers. The yellow polygon highlights the regions on various maps that correspond to 7p21. The graphic view is a screen dump of the Chromoscope program (J. Zhang and J. Ostell, unpubl.).

Figure 3

Mapping a cytogenetic band by interpolation. 1q12 is a band with no FISH mapping data. The yellow polygon highlights the regions that corresponds to 1q12, which were interpolated from the flanking FISH-mapped bands 1p13 and 1q22–q23.

Figure 4

WWW user interface for KARIBIN.

Figure 5

Summary of the genome information related to band 7q31. The chromosomal locations of the YAC contigs from WI/MIT are based on their RH mapping coordinates.

Figure 6

Graphic view of the CFTR region on YAC contig Ctg[sWSS26].

Figure 7

Tabular view of physical mapping data related to a band.