Integration of the cytogenetic map with the draft human genome sequence.

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 approximately 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.

[1]  J. Zeuthen,et al.  Chromosome banding and compaction , 2004, Human Genetics.

[2]  J. Melo,et al.  The molecular biology of chronic myeloid leukemia. , 2000, Blood.

[3]  T. Sharma,et al.  Characterization of G-banded chromosomes of the Indian muntjac and progression of banding patterns through different stages of condensation. , 1985, Cytogenetics and Cell Genetics.

[4]  U. Francke.  Digitized and differentially shaded human chromosome ideograms for genomic applications. , 1994, Cytogenetics and cell genetics.

[5]  J. Rowley.  A New Consistent Chromosomal Abnormality in Chronic Myelogenous Leukaemia identified by Quinacrine Fluorescence and Giemsa Staining , 1973, Nature.

[6]  Alex E. Lash,et al.  A systematic, high-resolution linkage of the cytogenetic and physical maps of the human genome , 2000, Nature Genetics.

[7]  D. Ledbetter,et al.  Multicolor Spectral Karyotyping of Human Chromosomes , 1996, Science.

[8]  Wendy A. Bickmore,et al.  The distribution of CpG islands in mammalian chromosomes , 1994, Nature Genetics.

[9]  R. Pazdur,et al.  Approval summary for imatinib mesylate capsules in the treatment of chronic myelogenous leukemia. , 2002, Clinical cancer research : an official journal of the American Association for Cancer Research.

[10]  F. Mitelman.  ISCN 1991 : guidelines for cancer cytogenetics : supplement to An international system for human cytogenetic nomenclature : recommendations of the Standing Committee on Human Cytogenetic Nomenclature, Subcommittee on Cancer Cytogenetics , 1992 .

[11]  U. K. Laemmli,et al.  Metaphase chromosome structure: Bands arise from a differential folding path of the highly AT-rich scaffold , 1994, Cell.

[12]  B. Druker,et al.  Lessons learned from the development of an abl tyrosine kinase inhibitor for chronic myelogenous leukemia. , 2000, The Journal of clinical investigation.

[13]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[14]  B. Trask,et al.  Fluorescence in situ hybridization: applications in cytogenetics and gene mapping. , 1991, Trends in genetics : TIG.

[15]  Collins Fs.  Identifying human disease genes by positional cloning. , 1990 .

[16]  M. A. Goldman,et al.  Replication timing of genes and middle repetitive sequences. , 1984, Science.

[17]  Takashi Gojobori,et al.  In silico chromosome staining: Reconstruction of Giemsa bands from the whole human genome sequence , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[19]  G. Bernardi,et al.  The isochore organization of the human genome. , 1989, Annual review of genetics.

[20]  D. Pinkel,et al.  Comparative Genomic Hybridization for Molecular Cytogenetic Analysis of Solid Tumors , 2022 .

[21]  D. Comings.  Mechanisms of chromosome banding and implications for chromosome structure. , 1978, Annual review of genetics.

[22]  T. Caspersson,et al.  The 24 fluorescence patterns of the human metaphase chromosomes - distinguishing characters and variability. , 2009, Hereditas.

[23]  D. Ward,et al.  Chromosomal and nuclear distribution of the HindIII 1.9-kb human DNA repeat segment , 2004, Chromosoma.

[24]  P. Nowell,et al.  A minute chromosome in human chronic granulocytic leukemia , 1960 .

[25]  David Haussler,et al.  A Generalized Hidden Markov Model for the Recognition of Human Genes in DNA , 1996, ISMB.

[26]  Lawrence R. Rabiner,et al.  A tutorial on hidden Markov models and selected applications in speech recognition , 1989, Proc. IEEE.

[27]  J. Korenberg,et al.  Base ratio, DNA content, and quinacrine-brightness of human chromosomes. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[28]  D. Haussler,et al.  Genie--gene finding in Drosophila melanogaster. , 2000, Genome research.

[29]  Van Nostrand,et al.  Error Bounds for Convolutional Codes and an Asymptotically Optimum Decoding Algorithm , 1967 .

[30]  Barbara J. Trask,et al.  Human genetics and disease: Human cytogenetics: 46 chromosomes, 46 years and counting , 2002, Nature Reviews Genetics.

[31]  C Sander,et al.  Predicting protein structure using hidden Markov models , 1997, Proteins.

[32]  G. Bernardi,et al.  The human genome: organization and evolutionary history. , 1995, Annual review of genetics.

[33]  Richard Hughey,et al.  Hidden Markov models for detecting remote protein homologies , 1998, Bioinform..

[34]  T. Caspersson,et al.  Chemical differentiation along metaphase chromosomes. , 1968, Experimental cell research.

[35]  F. Mitelman.  ISCN 1995 : an international system for human cytogenetic nomenclature (1995) : recommendations of the International Standing Committee on Human Cytogenetic Nomenclature : Memphis, Tennessee, USA, October 9-13, 1994 , 1995 .

[36]  D. Haussler,et al.  Integration of cytogenetic landmarks into the draft sequence of the human genome , 2001, Nature.

[37]  R. Durbin,et al.  Biological sequence analysis: Background on probability , 1998 .

[38]  Jr. G. Forney,et al.  The viterbi algorithm , 1973 .

[39]  L. Manuelidis,et al.  SINEs and LINEs cluster in distinct DNA fragments of Giemsa band size , 1989, Chromosoma.

[40]  F. Collins.  Identifying human disease genes by positional cloning. , 1990, Harvey lectures.

[41]  Mary C. Rykowski,et al.  Human genome organization: Alu, LINES, and the molecular structure of metaphase chromosome bands , 1988, Cell.

[42]  V. Solovyev,et al.  Ab initio gene finding in Drosophila genomic DNA. , 2000, Genome research.

[43]  Donna R. Maglott,et al.  RefSeq and LocusLink: NCBI gene-centered resources , 2001, Nucleic Acids Res..

[44]  G. Holmquist,et al.  Characterization of Giemsa dark- and light-band DNA , 1982, Cell.

[45]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[46]  Philip Lijnzaad,et al.  The Ensembl genome database project , 2002, Nucleic Acids Res..