Comparative genomic hybridization to detect variation in the copy number of large DNA segments.

Array comparative genomic hybridization (CGH) is an excellent tool to scan the genome for copy number variations (CNVs) when used conscientiously. This article is intended to provide an understanding of the basic principles of array CGH and the different options available to the user to design their array CGH experiments. Specifically, the six subsections discuss the different array platforms available, test and reference DNA preparation, reference DNA choice, the basics of hybridization, data processing, and our current understanding of CNVs in the human genome.

[1]  J. Lupski.  Structural variation in the human genome. , 2007, The New England journal of medicine.

[2]  D. Conrad,et al.  Global variation in copy number in the human genome , 2006, Nature.

[3]  A. Piotrowski,et al.  Analysis of copy number variation in the normal human population within a region containing complex segmental duplications on 22q11 using high-resolution array-CGH. , 2006, Genomics.

[4]  Xavier Estivill,et al.  Complex patterns of copy number variation at sites of segmental duplications: an important category of structural variation in the human genome , 2006, Human Genetics.

[5]  A. Ashworth,et al.  Array CGH using whole genome amplification of fresh-frozen and formalin-fixed, paraffin-embedded tumor DNA. , 2006, Genomics.

[6]  Sang Cheol Kim,et al.  Systematic analysis of cDNA microarray-based CGH. , 2006, International journal of molecular medicine.

[7]  Evan E Eichler,et al.  Widening the spectrum of human genetic variation , 2006, Nature Genetics.

[8]  Peter J. Park,et al.  Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data , 2005, Bioinform..

[9]  J. Dumanski,et al.  Localization of a putative low‐penetrance ependymoma susceptibility locus to 22q11 using a chromosome 22 tiling‐path genomic microarray , 2005, Genes, chromosomes & cancer.

[10]  E. Eichler,et al.  Segmental duplications and copy-number variation in the human genome. , 2005, American journal of human genetics.

[11]  Alain Bernheim,et al.  Detecting single DNA copy number variations in complex genomes using one nanogram of starting DNA and BAC-array CGH. , 2005, Nucleic acids research.

[12]  Robert Kincaid,et al.  Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Qing-Rong Chen,et al.  cDNA array-CGH profiling identifies genomic alterations specific to stage and MYCN-amplification in neuroblastoma , 2004, BMC Genomics.

[14]  L. Feuk,et al.  Detection of large-scale variation in the human genome , 2004, Nature Genetics.

[15]  R. Gibbs,et al.  Genomic segmental polymorphisms in inbred mouse strains , 2004, Nature Genetics.

[16]  Kenny Q. Ye,et al.  Large-Scale Copy Number Polymorphism in the Human Genome , 2004, Science.

[17]  B. Ylstra,et al.  High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides , 2004, Journal of Clinical Pathology.

[18]  Rameen Beroukhim,et al.  Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. , 2004, Nucleic acids research.

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

[20]  Owen T McCann,et al.  Replication timing of the human genome. , 2004, Human molecular genetics.

[21]  N. Carter,et al.  A Molecular Cytogenetic Clone Resource for Chromosome 22 , 2004, Chromosome Research.

[22]  Sarah Barber,et al.  A set of BAC clones spanning the human genome. , 2004, Nucleic acids research.

[23]  J. Sebat,et al.  Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. , 2003, Genome research.

[24]  John Quackenbush.  Microarray data normalization and transformation , 2002, Nature Genetics.

[25]  M. Adams,et al.  Recent Segmental Duplications in the Human Genome , 2002, Science.

[26]  Ajay N. Jain,et al.  Fully automatic quantification of microarray image data. , 2002, Genome research.

[27]  Kylie L. Gorringe,et al.  Degenerate oligonucleotide primed-polymerase chain reaction-based array comparative genomic hybridization for extensive amplicon profiling of breast cancers : a new approach for the molecular analysis of paraffin-embedded cancer tissue. , 2001, The American journal of pathology.

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

[29]  The International HapMap Consortium,et al.  A physical map of the human genome , 2001 .

[30]  T. Ried,et al.  Integration of cytogenetic data with genome maps and available probes: present status and future promise. , 2000, Seminars in hematology.

[31]  W. Kuo,et al.  Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene , 2000, Nature Genetics.

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

[33]  B. Birren,et al.  Human genome anatomy: BACs integrating the genetic and cytogenetic maps for bridging genome and biomedicine. , 1999, Genome research.

[34]  M. Morley,et al.  A resource of mapped human bacterial artificial chromosome clones. , 1999, Genome Research.

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

[36]  W. Kuo,et al.  High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays , 1998, Nature Genetics.

[37]  H. Döhner,et al.  Matrix‐based comparative genomic hybridization: Biochips to screen for genomic imbalances , 1997, Genes, chromosomes & cancer.

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

[39]  N. Carter,et al.  Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. , 1992, Genomics.