Journal Article

Integration of the cytogenetic map with the draft human genome sequence

Terrence S. Furey and David Haussler

in Human Molecular Genetics

Volume 12, issue 9, pages 1037-1044
Published in print May 2003 | ISSN: 0964-6906
Published online May 2003 | e-ISSN: 1460-2083 | DOI: http://dx.doi.org/10.1093/hmg/ddg113
Integration of the cytogenetic map with the draft human genome sequence

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Chemically staining metaphase chromosomes resulting in an alternating dark and light banding pattern provide 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 ∼9500 fluorescence in situ hybridization 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.

Journal Article.  6511 words.  Illustrated.

Subjects: Genetics and Genomics

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