Integration of the Cytogenetic Map with the Draft Human Genome Sequence

Abstract

Chemically staining metaphase chromosomes resulting in an alternating dark and light banding pattern provides a tool by which abnormalities in chromosomes from diseased cells can be identified. The localization of these aberrations to a chromosomal region provides clues as to which gene or genes may contribute to a particular disease. With the sequencing of the human genome, it became critical to determine the positions of these cytogenetic bands within the sequence in order to take advantage of vast amount of information now anchored to the sequence, especially the locations of genes. The molecular basis of cytogenetic bands is not well understood, therefore their positions cannot be determined solely based on sequence information. We developed a dynamic programming algorithm that employs results from approximately 9,500 fluorescence in situ hybridization (FISH) experiments to approximate the locations of the 850 high-resolution bands in the June 2002 version of the draft human genome sequence. These band predictions support previously identified correlations between band stain intensity and certain structural characteristics of chromosomes, namely GC content, repeat structure content, CpG island density, gene density, and degree of condensation.

Ideogram Comparisons

Chromosome 1 Chromosome 2 Chromosome 3 Chromosome 4
Chromosome 5 Chromosome 6 Chromosome 7 Chromosome 8
Chromosome 9 Chromosome 10 Chromosome 11 Chromosome 12
Chromosome 13 Chromosome 14 Chromosome 15 Chromosome 16
Chromosome 17 Chromosome 18 Chromosome 19 Chromosome 20
Chromosome 21 Chromosome 22 Chromosome X Chromosome Y

BANDER Software

Available for Linux/Unix platforms only. Source code and sample input files included. Please see README for an explanation of the files.

bander.tgz - tar and zipped file of all source and sample input and output files.

Bander - directory of all files.


Terrence Furey
Last modified: Wed Apr 23 07:51:27 PDT 2003