Integration of the Cytogenetic Map with the Draft Human Genome Sequence
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.