Grant Number:	5R03CA101515-02 Interpret this number
Primary Investigator:	Liang, Ping
Organization:	Roswell Park Cancer Institute Corp
Project Title:	Computational Analysis of Cancer Cytogenetic Data
Fiscal Year:	2004

DESCRIPTION (provided by applicant): Characterization of non-random recurrent chromosomal aberrations have proven to be a useful instrument for identification of genes related to cancers and other genetic diseases and for improving diagnosis and prognosis of certain types of cancer. Current studies on characterization of cytogenetic signatures have been limited to the use of data available as individual clinical cases or as small-scale epidemiologic surveys with a primary focus on individual abnormalities and breakpoints using manual approaches. Due to the limitation on data size and the simplicity of methods, more complex patterns and critical breakpoints have not been revealed. Comprehensive cytogenetic data analyzed with new strategies and methodologies are needed to identify novel cytogenetic signatures for human cancer. The proposed project involves analysis of the unprecedented comprehensive cancer etiologic/cytogenetic data deposited in the Mitelman Database of Chromosomal Aberrations in Cancers using computational approaches. By first establishing a computational algorithm with the capability to decode karyotype data to reveal all cytogenetic changes implied by the simplified cytogenetics nomenclature, and by taking advantage of the first digitally compiled comprehensive data of cancer chromosomal aberrations, the project aims: 1) to attempt to establish cytogenetic signatures for cancers without previously known cytogenetic characteristics; 2) to identify new cytogenetic signatures for cancers with established patterns; and 3) to study relationships among different cancers and general patterns for all human chromosomal aberrations. The data resulting from this project should shed light on the molecular basis of poorly understood cancers, the multistage process of tumorigenesis, and relationships among different cancers, and it may provide a global picture of all cancers at the cytogenetic level.




Alu recombination-mediated structural deletions in the chimpanzee genome.
Authors: Han K. , Lee J. , Meyer T.J. , Wang J. , Sen S.K. , Srikanta D. , Liang P. , Batzer M.A. .
Source: PLoS genetics, 2007 Oct; 3(10), p. 1939-49.
EPub date: 2007-09-10.
PMID: 17953488
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Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons.
Authors: Lee J. , Cordaux R. , Han K. , Wang J. , Hedges D.J. , Liang P. , Batzer M.A. .
Source: Gene, 2007-04-01; 390(1-2), p. 18-27.
EPub date: 2006-09-16.
PMID: 17055192
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Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies.
Authors: Konkel M.K. , Wang J. , Liang P. , Batzer M.A. .
Source: Gene, 2007-04-01; 390(1-2), p. 28-38.
EPub date: 2006-08-30.
PMID: 17034961
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Human genomic deletions mediated by recombination between Alu elements.
Authors: Sen S.K. , Han K. , Wang J. , Lee J. , Wang H. , Callinan P.A. , Dyer M. , Cordaux R. , Liang P. , Batzer M.A. .
Source: American journal of human genetics, 2006 Jul; 79(1), p. 41-53.
EPub date: 2006-05-03.
PMID: 16773564
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Mutational data integration in gene-oriented files of the Hermansky-Pudlak Syndrome database.
Authors: Li W. , He M. , Zhou H. , Bourne J.W. , Liang P. .
Source: Human mutation, 2006 May; 27(5), p. 402-7.
PMID: 16550546
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dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans.
Authors: Wang J. , Song L. , Grover D. , Azrak S. , Batzer M.A. , Liang P. .
Source: Human mutation, 2006 Apr; 27(4), p. 323-9.
PMID: 16511833
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Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms.
Authors: Wang J. , Song L. , Gonder M.K. , Azrak S. , Ray D.A. , Batzer M.A. , Tishkoff S.A. , Liang P. .
Source: Gene, 2006-01-03; 365, p. 11-20.
EPub date: 2006-01-10.
PMID: 16376498
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aCGHViewer: a generic visualization tool for aCGH data.
Authors: Shankar G. , Rossi M.R. , McQuaid D.E. , Conroy J.M. , Gaile D.G. , Cowell J.K. , Nowak N.J. , Liang P. .
Source: Cancer informatics, 2006; 2, p. 36-43.
PMID: 17404607
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Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.
Authors: Liang P. , Nair J.R. , Song L. , McGuire J.J. , Dolnick B.J. .
Source: BMC genomics, 2005-09-14; 6, p. 125.
EPub date: 2005-09-14.
PMID: 16162288
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Molecular mechanism of inhibition of survivin transcription by the GC-rich sequence-selective DNA binding antitumor agent, hedamycin: evidence of survivin down-regulation associated with drug sensitivity.
Authors: Wu J. , Ling X. , Pan D. , Apontes P. , Song L. , Liang P. , Altieri D.C. , Beerman T. , Li F. .
Source: The Journal of biological chemistry, 2005-03-11; 280(10), p. 9745-51.
EPub date: 2005-01-05.
PMID: 15637054
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Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages.
Authors: Han K. , Sen S.K. , Wang J. , Callinan P.A. , Lee J. , Cordaux R. , Liang P. , Batzer M.A. .
Source: Nucleic acids research, 2005; 33(13), p. 4040-52.
EPub date: 2005-07-20.
PMID: 16034026
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