Will the new cytogenetics replace the old cytogenetics?

With the advent of array‐based comparative genomic hybridization technology, the analog cytogenetic analysis that has been used for the past 100 years could be replaced by the quantitative, microarray‐based molecular analysis. Major advantages of the new array‐based cytogenetic technologies are the high resolution and the high throughput. This technology is the first to offer an autonomous whole‐chromosome analysis in one hybridization reaction for the detection of submicroscopic gains/losses. However, as with any new technology, it needs to be validated with regard to its performance in various applications (e.g. clinical genetic testing and cancer applications), comparative cost, and the data interpretation.

[1]  Alfred Pingoud,et al.  Real‐Time Polymerase Chain Reaction , 2003, Chembiochem : a European journal of chemical biology.

[2]  A. Syvänen,et al.  Assessing hematopoietic chimerism after allogeneic stem cell transplantation by multiplexed SNP genotyping using microarrays and quantitative analysis of SNP alleles , 2004, Leukemia.

[3]  G. Węgrzyn,et al.  An introduction to DNA chips: principles, technology, applications and analysis. , 2001, Acta biochimica Polonica.

[4]  C. Lundsteen,et al.  High resolution comparative genomic hybridisation analysis reveals imbalances in dyschromosomal patients with normal or apparently balanced conventional karyotypes , 2000, European Journal of Human Genetics.

[5]  T. Lai,et al.  Receptor mediated effect of serotonergic transmission in patients with bipolar affective disorder , 2003, Journal of medical genetics.

[6]  H. Kohlhammer,et al.  Hidden gene amplifications in aggressive B-cell non-Hodgkin lymphomas detected by microarray-based comparative genomic hybridization , 2003, Oncogene.

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

[8]  Ash A. Alizadeh,et al.  Genome-wide analysis of DNA copy number variation in breast cancer using DNA microarrays , 1999, Nature Genetics.

[9]  P. N. Rao,et al.  Unexpected retention and concomitant loss of subtelomeric regions in balanced chromosome anomalies by FISH. , 2002, American journal of medical genetics.

[10]  Patrick G Buckley,et al.  Genomic microarrays in the spotlight. , 2004, Trends in genetics : TIG.

[11]  J. Lupski,et al.  Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease. , 2004, Human molecular genetics.

[12]  D. Pinkel,et al.  Molecular cytogenetics: diagnosis and prognostic assessment. , 1992, Current opinion in biotechnology.

[13]  R. Veitia,et al.  Deletions of distal 9p associated with 46,XY male to female sex reversal: definition of the breakpoints at 9p23.3-p24.1. , 1997, Genomics.

[14]  Allan Bradley,et al.  Genome-wide detection of chromosomal imbalances in tumors using BAC microarrays , 2002, Nature Biotechnology.

[15]  C. Lundsteen,et al.  High resolution comparative genomic hybridisation in clinical cytogenetics , 2001, Journal of medical genetics.

[16]  E. Schröck,et al.  Molecular cytogenetic analysis of formalin-fixed, paraffin-embedded solid tumors by comparative genomic hybridization after universal DNA-amplification. , 1993, Human molecular genetics.

[17]  T. Ried,et al.  Novel molecular cytogenetic techniques for identifying complex chromosomal rearrangements: technology and applications in molecular medicine. , 2000, Expert reviews in molecular medicine.

[18]  P. D. de Jong,et al.  Chromosomal breakpoint mapping by arrayCGH using flow-sorted chromosomes. , 2003, BioTechniques.

[19]  J. Veltman,et al.  Definition of a critical region on chromosome 18 for congenital aural atresia by arrayCGH. , 2003, American journal of human genetics.

[20]  M. Shapero,et al.  High-resolution analysis of DNA copy number using oligonucleotide microarrays. , 2004, Genome research.

[21]  D Rutovitz,et al.  Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors. , 1993, Seminars in cancer biology.

[22]  Bradley P. Coe,et al.  A tiling resolution DNA microarray with complete coverage of the human genome , 2004, Nature Genetics.

[23]  Ajay N. Jain,et al.  Assembly of microarrays for genome-wide measurement of DNA copy number , 2001, Nature Genetics.

[24]  R. Gibbs,et al.  A clone-array pooled shotgun strategy for sequencing large genomes. , 2001, Genome research.

[25]  S. P. Fodor,et al.  High density synthetic oligonucleotide arrays , 1999, Nature Genetics.

[26]  F. Molinari,et al.  Fluorescence genotyping for screening cryptic telomeric rearrangements. , 2002, Methods in molecular biology.

[27]  M R Speicher,et al.  Multiplex-FISH for pre- and postnatal diagnostic applications. , 1999, American journal of human genetics.

[28]  Han G Brunner,et al.  High-throughput analysis of subtelomeric chromosome rearrangements by use of array-based comparative genomic hybridization. , 2002, American journal of human genetics.

[29]  G. Houge,et al.  Usefulness of high-resolution comparative genomic hybridization (CGH) for detecting and characterizing constitutional chromosome abnormalities. , 2002, American journal of medical genetics.

[30]  K. Hirschhorn,et al.  Proposed guidelines for diagnosis of chromosome mosaicism in amniocytes based on data derived from chromosome mosaicism and pseudomosaicism studies , 1992, Prenatal diagnosis.

[31]  Michael R. Speicher,et al.  The coloring of cytogenetics , 1996, Nature Medicine.

[32]  D. Pinkel,et al.  A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications. , 2002, Human molecular genetics.

[33]  Ton Feuth,et al.  Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. , 2003, American journal of human genetics.

[34]  Wen-Lin Kuo,et al.  Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors. , 2003, Cancer research.

[35]  Chad A Shaw,et al.  Development of a comparative genomic hybridization microarray and demonstration of its utility with 25 well-characterized 1p36 deletions. , 2003, Human molecular genetics.

[36]  R. Eils,et al.  New concepts to improve resolution and sensitivity of molecular cytogenetic diagnostics by multicolor fluorescence in situ hybridization. , 2001, Cytometry.

[37]  N. Lindor,et al.  Application of multicolor fluorescent in situ hybridization for enhanced characterization of chromosomal abnormalities in congenital disorders. , 2001, Mayo Clinic proceedings.

[38]  Ash A. Alizadeh,et al.  Genome-wide analysis of DNA copy-number changes using cDNA microarrays , 1999, Nature Genetics.

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

[40]  H. Kreipe,et al.  Multiplex RT-PCR for the Detection of Common BCR-ABL Fusion Transcripts in Paraffin-Embedded Tissues From Patients With Chronic Myeloid Leukemia and Acute Lymphoblastic Leukemia , 2003, Diagnostic molecular pathology : the American journal of surgical pathology, part B.

[41]  S. Mundle,et al.  Clinical implications of advanced molecular cytogenetics in cancer , 2004, Expert review of molecular diagnostics.

[42]  D J Lockhart,et al.  Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. , 2000, Genome research.

[43]  Daniel Pinkel,et al.  Genomic microarrays in human genetic disease and cancer. , 2003, Human molecular genetics.

[44]  N. Carpenter,et al.  Molecular cytogenetics , 2001, Seminars in pediatric neurology.

[45]  S. P. Fodor,et al.  Light-directed, spatially addressable parallel chemical synthesis. , 1991, Science.

[46]  Molecular cytogenetics in childhood leukemia. , 2004, Methods in molecular medicine.

[47]  J. Flint,et al.  Perfect endings: a review of subtelomeric probes and their use in clinical diagnosis , 2000, Journal of medical genetics.

[48]  D. Kupfer,et al.  Linkage and association between serotonin 2A receptor gene polymorphisms and bipolar I disorder , 2003, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

[49]  Yao-Shan Fan,et al.  Comprehensive cytogenetic analysis including multicolor spectral karyotyping and interphase fluorescence in situ hybridization in lymphoma diagnosis. a summary of 154 cases. , 2003, Cancer genetics and cytogenetics.

[50]  D. Ward,et al.  Karyotyping human chromosomes by combinatorial multi-fluor FISH , 1996, Nature Genetics.

[51]  C. Nusbaum,et al.  Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. , 1998, Science.

[52]  T. Ried,et al.  The role of cytokines in immunological tolerance: potential for therapy , 2000, Expert Reviews in Molecular Medicine.

[53]  R. deLeeuw,et al.  Methods for high throughput validation of amplified fragment pools of BAC DNA for constructing high resolution CGH arrays , 2004, BMC Genomics.

[54]  D. Albertson.  Profiling Breast Cancer by Array CGH , 2003, Breast Cancer Research and Treatment.

[55]  V. Siu,et al.  Detection of submicroscopic aberrations in patients with unexplained mental retardation by fluorescence in situ hybridization using multiple subtelomeric probes , 2001, Genetics in Medicine.

[56]  P. Jacobs,et al.  Estimates of the frequency of chromosome abnormalities detectable in unselected newborns using moderate levels of banding. , 1992, Journal of medical genetics.

[57]  J. Flint,et al.  The detection of subtelomeric chromosomal rearrangements in idiopathic mental retardation , 1995, Nature Genetics.