Home LiteratureArticle Details
PMID: 17597776 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Review

Methods and strategies for analyzing copy number variation using DNA microarrays.

Nature genetics ·Vol. 39 ·No. 7 Suppl ·2007-07-00 ·Pages S16-21

Carter NP

Abstract

The association of DNA copy-number variation (CNV) with specific gene function and human disease has been long known, but the wide scope and prevalence of this form of variation has only recently been fully appreciated. The latest studies using microarray technology have demonstrated that as much as 12% of the human genome and thousands of genes are variable in copy number, and this diversity is likely to be responsible for a significant proportion of normal phenotypic variation. Current challenges involve developing methods not only for detecting and cataloging CNVs in human populations at increasingly higher resolution but also for determining the association of CNVs with biological function, recent human evolution, and common and complex human disease.

MeSH Terms
Chromosomes, Artificial, Bacterial/genetics Chromosomes, Human, Pair 18/genetics Cloning, Molecular DNA, Complementary/genetics Gene Dosage Genetic Variation Genome, Human Genotype Humans Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis/methods Phenotype Polymerase Chain Reaction Polymorphism, Single Nucleotide
Chemicals
DNA, Complementary
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Carter Nigel P
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. [email protected]
References (52)
52 references, click to expand
  1. Development of NF2 gene specific, strictly sequence defined diagnostic microarray for deletion detection.
    J Mol Med (Berl). 2003 Jul;81(7):443-51 PMID: 12830322
  2. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays.
    Nat Genet. 1998 Oct;20(2):207-11 PMID: 9771718
  3. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances.
    Genes Chromosomes Cancer. 1997 Dec;20(4):399-407 PMID: 9408757
  4. Integration of cytogenetic landmarks into the draft sequence of the human genome.
    Nature. 2001 Feb 15;409(6822):953-8 PMID: 11237021
  5. Neurological disorders in patients with chromosomal anomalies.
    Neuropediatrics. 1980 Aug;11(3):203-49 PMID: 6999382
  6. High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides.
    J Clin Pathol. 2004 Jun;57(6):644-6 PMID: 15166273
  7. A haplotype map of the human genome.
    Nature. 2005 Oct 27;437(7063):1299-320 PMID: 16255080
  8. Quinacrine mustard and nucleolar organizer region heteromorphisms in twins.
    Acta Genet Med Gemellol (Roma). 1981;30(1):39-49 PMID: 7199799
  9. Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome.
    Am J Hum Genet. 2006 Aug;79(2):275-90 PMID: 16826518
  10. Accurate and reliable high-throughput detection of copy number variation in the human genome.
    Genome Res. 2006 Dec;16(12):1566-74 PMID: 17122085
  11. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays.
    Genome Res. 2006 Dec;16(12):1575-84 PMID: 17122084
  12. Copy number variation: new insights in genome diversity.
    Genome Res. 2006 Aug;16(8):949-61 PMID: 16809666
  13. Genome assembly comparison identifies structural variants in the human genome.
    Nat Genet. 2006 Dec;38(12):1413-8 PMID: 17115057
  14. Fine-scale structural variation of the human genome.
    Nat Genet. 2005 Jul;37(7):727-32 PMID: 15895083
  15. The somatic chromosomes in mongolism.
    Lancet. 1959 Apr 4;1(7075):710 PMID: 13642857
  16. A high-resolution survey of deletion polymorphism in the human genome.
    Nat Genet. 2006 Jan;38(1):75-81 PMID: 16327808
  17. Large-scale copy number polymorphism in the human genome.
    Science. 2004 Jul 23;305(5683):525-8 PMID: 15273396
  18. New amplified and highly expressed genes discovered in the ERBB2 amplicon in breast cancer by cDNA microarrays.
    Cancer Res. 2001 Nov 15;61(22):8235-40 PMID: 11719455
  19. Size variation polymorphisms of the short arm of human acrocentric chrosomes determined by R-banding by fluorescence using acridine orange (RFA).
    Hum Genet. 1977 Sep 22;38(2):231-4 PMID: 908571
  20. Sequence variation in genes and genomic DNA: methods for large-scale analysis.
    Annu Rev Genomics Hum Genet. 2000;1:329-60 PMID: 11701633
  21. Segmental duplications and copy-number variation in the human genome.
    Am J Hum Genet. 2005 Jul;77(1):78-88 PMID: 15918152
  22. Global variation in copy number in the human genome.
    Nature. 2006 Nov 23;444(7118):444-54 PMID: 17122850
  23. Advanced sequencing technologies: methods and goals.
    Nat Rev Genet. 2004 May;5(5):335-44 PMID: 15143316
  24. SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.
    Nucleic Acids Res. 2005;33(11):3455-64 PMID: 15961730
  25. Increasing the information content of STS-based genome maps: identifying polymorphisms in mapped STSs.
    Genomics. 1996 Jan 1;31(1):123-6 PMID: 8808290
  26. Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors.
    Semin Cancer Biol. 1993 Feb;4(1):41-6 PMID: 8448377
  27. Detection of large-scale variation in the human genome.
    Nat Genet. 2004 Sep;36(9):949-51 PMID: 15286789
  28. The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X.
    Nature. 2001 Feb 15;409(6822):942-3 PMID: 11237015
  29. BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH).
    Nucleic Acids Res. 2006;34(2):445-50 PMID: 16439806
  30. B group short-arm deletion syndrome.
    Birth Defects Orig Artic Ser. 1971 Jun;7(7):89-97 PMID: 4950926
  31. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome.
    Science. 1998 May 15;280(5366):1077-82 PMID: 9582121
  32. A comprehensive analysis of common copy-number variations in the human genome.
    Am J Hum Genet. 2007 Jan;80(1):91-104 PMID: 17160897
  33. Structural variation of the human genome.
    Annu Rev Genomics Hum Genet. 2006;7:407-42 PMID: 16780417
  34. Gene sequencing. The race for the $1000 genome.
    Science. 2006 Mar 17;311(5767):1544-6 PMID: 16543431
  35. A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays.
    Cancer Res. 2005 Jul 15;65(14):6071-9 PMID: 16024607
  36. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats.
    Am J Hum Genet. 1991 Oct;49(4):746-56 PMID: 1897522
  37. Common deletion polymorphisms in the human genome.
    Nat Genet. 2006 Jan;38(1):86-92 PMID: 16468122
  38. Circular binary segmentation for the analysis of array-based DNA copy number data.
    Biostatistics. 2004 Oct;5(4):557-72 PMID: 15475419
  39. Molecular karyotyping: array CGH quality criteria for constitutional genetic diagnosis.
    J Histochem Cytochem. 2005 Mar;53(3):413-22 PMID: 15750031
  40. Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer.
    Proc Natl Acad Sci U S A. 2001 May 8;98(10):5711-6 PMID: 11331760
  41. A tiling resolution DNA microarray with complete coverage of the human genome.
    Nat Genet. 2004 Mar;36(3):299-303 PMID: 14981516
  42. High-resolution mapping of amplifications and deletions in pediatric osteosarcoma by use of CGH analysis of cDNA microarrays.
    Genes Chromosomes Cancer. 2003 Nov;38(3):215-25 PMID: 14506695
  43. Ultra-high resolution array painting facilitates breakpoint sequencing.
    J Med Genet. 2007 Jan;44(1):51-8 PMID: 16971479
  44. Amplification and overexpression of Elongin C gene discovered in prostate cancer by cDNA microarrays.
    Lab Invest. 2002 May;82(5):629-37 PMID: 12004003
  45. Challenges and standards in integrating surveys of structural variation.
    Nat Genet. 2007 Jul;39(7 Suppl):S7-15 PMID: 17597783
  46. Hotspots for copy number variation in chimpanzees and humans.
    Proc Natl Acad Sci U S A. 2006 May 23;103(21):8006-11 PMID: 16702545
  47. Gene Copy Number Analysis by Fluorescence in Situ Hybridization and Comparative Genomic Hybridization
    Methods. 1996 Feb;9(1):113-21 PMID: 9245350
  48. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation.
    Genome Res. 2003 Oct;13(10):2291-305 PMID: 12975311
  49. Genome-wide analysis of DNA copy-number changes using cDNA microarrays.
    Nat Genet. 1999 Sep;23(1):41-6 PMID: 10471496
  50. Exon array CGH: detection of copy-number changes at the resolution of individual exons in the human genome.
    Am J Hum Genet. 2005 May;76(5):750-62 PMID: 15756638
  51. Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms.
    Genome Res. 1998 Jul;8(7):748-54 PMID: 9685323
  52. [The crying cat syndrome and its reciprocal].
    Ann Genet. 1965;8(1):11-5 PMID: 5294630
Article Info
Journal
Nature genetics
Abbr.
Nat Genet
ISSN
1061-4036
Published
2007-07-00
Pages
S16-21
Language
English
Region
United States
NLM ID
9216904
PMCID
PMC2697494
Subset
IM
Grants
Wellcome Trust · 077008 · United Kingdom
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]