Advertisement

Array Comparative Genomic Hybridization: An Overview of Protocols, Applications, and Technology Trends

  • Diponkar Banerjee
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 973)

Abstract

From the earliest observations of human chromosomes in the late 1800s to modern day next generation sequencing technologies, much has been learned about human cancers by the vigorous application of the techniques of the day. In general, resolution has improved tremendously, and correspondingly the size of the datasets generated has grown exponentially such that computational methods required to handle massive datasets have had to be devised. This chapter provides a brief synopsis of the evolution of such techniques as an introduction to the subsequent chapters that provide methods and applications, relevant to research, and clinical diagnostics.

Key words

Karyotyping Comparative genomic hybridization BAC arrays Submegabase resolution tiling BAC array-CGH cDNA and oligonucleotide microarrays Single nucleotide polymorphism (SNP) arrays Next generation sequencing (NGS) Copy number variation (CNV) Structural variants (SV) 

References

  1. 1.
    Arnold J (1879) Beobachtungen über Kerntheilungen in den Zellen der Geschwülste. Virchows Arch 78:279–301CrossRefGoogle Scholar
  2. 2.
    Flemming W (1882) Beitrige zur Kenntniss der Zelle und ihrer Lebenserscheinungen. Part III. Arch mikr Anat 20:1–86CrossRefGoogle Scholar
  3. 3.
    Tjio JH, Levan A (1956) The chromosome number of man. Hereditas 42:1–6CrossRefGoogle Scholar
  4. 4.
    Caspersson T, Farber S, Foley GE, Kudynowski J, Modest EJ, Simonsson E, Wagh U, Zech L (1968) Chemical differentiation along metaphase chromosomes. Exp Cell Res 49(1):219–222. doi: 10.1016/0014-4827(68)90538-7 PubMedCrossRefGoogle Scholar
  5. 5.
    Kallioniemi OP, Kallioniemi A, Piper J, Isola J, Waldman FM, Gray JW, Pinkel D (1994) Optimizing comparative genomic hybridization for analysis of DNA sequence copy number changes in solid tumors. Genes Chromosomes Cancer 10(4):231–243PubMedCrossRefGoogle Scholar
  6. 6.
    Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258(5083):818–821PubMedCrossRefGoogle Scholar
  7. 7.
    Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, Cremer T, Lichter P (1997) Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20(4):399–407. doi:10.1002/(SICI)1098-2264(199712)20:4<399::AID-GCC12>3.0.CO;2-I[pii]PubMedCrossRefGoogle Scholar
  8. 8.
    Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20(2):207–211. doi: 10.1038/2524 PubMedCrossRefGoogle Scholar
  9. 9.
    Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23(1):41–46. doi: 10.1038/12640 PubMedCrossRefGoogle Scholar
  10. 10.
    Le Scouarnec S, Gribble SM (2012) Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics. Heredity (Edinb) 108(1):75–85. doi:hdy2011100[pii]10.1038/hdy.2011.100 CrossRefGoogle Scholar
  11. 11.
    Church DM, Lappalainen I, Sneddon TP, Hinton J, Maguire M, Lopez J, Garner J, Paschall J, DiCuccio M, Yaschenko E, Scherer SW, Feuk L, Flicek P (2010) Public data archives for genomic structural variation. Nat Genet 42(10):813–814. doi:ng1010-813[pii]10.1038/ng1010-813 PubMedCrossRefGoogle Scholar
  12. 12.
    Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AW, Robson S, Stirrups K, Valsesia A, Walter K, Wei J, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME (2010) Origins and functional impact of copy number variation in the human genome. Nature 464(7289):704–712. doi:nature08516[pii]10.1038/nature08516 PubMedCrossRefGoogle Scholar
  13. 13.
    Feuk L, Carson AR, Scherer SW (2006) Structural variation in the human genome. Nat Rev Genet 7(2):85–97. doi:nrg1767[pii]10.1038/nrg1767 PubMedCrossRefGoogle Scholar
  14. 14.
    Feuk L, Marshall CR, Wintle RF, Scherer SW (2006) Structural variants: changing the landscape of chromosomes and design of disease studies. Hum Mol Genet 15 Spec No 1:R57–66 doi: 15/suppl_1/R57[pii]10.1093/hmg/ddl057Google Scholar
  15. 15.
    Khaja R, Zhang J, MacDonald JR, He Y, Joseph-George AM, Wei J, Rafiq MA, Qian C, Shago M, Pantano L, Aburatani H, Jones K, Redon R, Hurles M, Armengol L, Estivill X, Mural RJ, Lee C, Scherer SW, Feuk L (2006) Genome assembly comparison identifies structural variants in the human genome. Nat Genet 38(12):1413–1418. doi:ng1921[pii]10.1038/ng1921 PubMedCrossRefGoogle Scholar
  16. 16.
    Komura D, Shen F, Ishikawa S, Fitch KR, Chen W, Zhang J, Liu G, Ihara S, Nakamura H, Hurles ME, Lee C, Scherer SW, Jones KW, Shapero MH, Huang J, Aburatani H (2006) Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res 16(12):1575–1584. doi:gr.5629106[pii]10.1101/gr.5629106 PubMedCrossRefGoogle Scholar
  17. 17.
    Pang AW, MacDonald JR, Pinto D, Wei J, Rafiq MA, Conrad DF, Park H, Hurles ME, Lee C, Venter JC, Kirkness EF, Levy S, Feuk L, Scherer SW (2010) Towards a comprehensive structural variation map of an individual human genome. Genome Biol 11(5):R52. doi:gb-2010-11-5-r52[pii]10.1186/gb-2010-11-5-r52 PubMedCrossRefGoogle Scholar
  18. 18.
    Pinto D, Marshall C, Feuk L, Scherer SW (2007) Copy-number variation in control population cohorts. Hum Mol Genet 16 Spec No. 2:R168–173. doi:16/R2/R168[pii]10.1093/hmg/ddm241Google Scholar
  19. 19.
    Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L (2007) Challenges and standards in integrating surveys of structural variation. Nat Genet 39(7 Suppl):S7–S15. doi:ng2093[pii]10.1038/ng2093PubMedCrossRefGoogle Scholar
  20. 20.
    Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavare S, Deloukas P, Hurles ME, Dermitzakis ET (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315(5813):848–853. doi:315/5813/848[pii]10.1126/science.1136678 PubMedCrossRefGoogle Scholar
  21. 21.
    Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW (2006) Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet Genome Res 115(3–4):205–214. doi:95916[pii]10.1159/000095916 PubMedCrossRefGoogle Scholar
  22. 22.
    Solomon E, Borrow J, Goddard AD (1991) Chromosome aberrations and cancer. Science 254(5035):1153–1160PubMedCrossRefGoogle Scholar
  23. 23.
    Houldsworth J, Chaganti RS (1994) Comparative genomic hybridization: an overview. Am J Pathol 145(6):1253–1260PubMedGoogle Scholar
  24. 24.
    Cremer T, Tesin D, Hopman AH, Manuelidis L (1988) Rapid interphase and metaphase assessment of specific chromosomal changes in neuroectodermal tumor cells by in situ hybridization with chemically modified DNA probes. Exp Cell Res 176(2):199–220PubMedCrossRefGoogle Scholar
  25. 25.
    de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD (2011) Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet 7(12):e1002384. doi:10.1371/journal.pgen.1002384PGENETICS-D-11-01686[pii] PubMedCrossRefGoogle Scholar
  26. 26.
    Newkirk HL, Knoll JH, Rogan PK (2005) Distortion of quantitative genomic and expression hybridization by Cot-1 DNA: mitigation of this effect. Nucleic Acids Res 33(22):e191. doi:33/22/e191[pii]10.1093/nar/gni190[doi] PubMedCrossRefGoogle Scholar
  27. 27.
    Chen X, Knauf JA, Gonsky R, Wang M, Lai EH, Chissoe S, Fagin JA, Korenberg JR (1998) From amplification to gene in thyroid cancer: a high-resolution mapped ­bacterial-artificial-chromosome resource for cancer chromosome aberrations guides gene discovery after comparative genome hybridization. Am J Hum Genet 63(2):625–637. doi: S0002-9297(07)61506-7[pii] PubMedCrossRefGoogle Scholar
  28. 28.
    Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, Conroy J, Hamilton G, Hindle AK, Huey B, Kimura K, Law S, Myambo K, Palmer J, Ylstra B, Yue JP, Gray JW, Jain AN, Pinkel D, Albertson DG (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 29(3):263–264. doi:10.1038/ng754ng754[pii] PubMedCrossRefGoogle Scholar
  29. 29.
    Fiegler H, Carr P, Douglas EJ, Burford DC, Hunt S, Scott CE, Smith J, Vetrie D, Gorman P, Tomlinson IP, Carter NP (2003) DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones. Genes Chromosomes Cancer 36(4):361–374. doi: 10.1002/gcc.10155 PubMedCrossRefGoogle Scholar
  30. 30.
    Ishkanian AS, Malloff CA, Watson SK, DeLeeuw RJ, Chi B, Coe BP, Snijders A, Albertson DG, Pinkel D, Marra MA, Ling V, MacAulay C, Lam WL (2004) A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 36(3):299–303. doi:10.1038/ng1307ng1307[pii] PubMedCrossRefGoogle Scholar
  31. 31.
    Aarts M, Dannenberg H, deLeeuw RJ, van Nederveen FH, Verhofstad AA, Lenders JW, Dinjens WN, Speel EJ, Lam WL, de Krijger RR (2006) Microarray-based CGH of sporadic and syndrome-related pheochromocytomas using a 0.1–0.2 Mb bacterial artificial chromosome array spanning chromosome arm 1p. Genes Chromosomes Cancer 45(1):83–93. doi: 10.1002/gcc.20268 PubMedCrossRefGoogle Scholar
  32. 32.
    Aviel-Ronen S, Coe BP, Lau SK, da Cunha SG, Zhu CQ, Strumpf D, Jurisica I, Lam WL, Tsao MS (2008) Genomic markers for malignant progression in pulmonary adenocarcinoma with bronchioloalveolar features. Proc Natl Acad Sci USA 105(29):10155–10160. doi:0709618105[pii]10.1073/pnas.0709618105 PubMedCrossRefGoogle Scholar
  33. 33.
    Baldwin C, Garnis C, Zhang L, Rosin MP, Lam WL (2005) Multiple microalterations detected at high frequency in oral cancer. Cancer Res 65(17):7561–7567. doi:65/17/7561[pii]10.1158/0008-5472.CAN-05-1513 PubMedGoogle Scholar
  34. 34.
    Buys TP, Chari R, Lee EH, Zhang M, MacAulay C, Lam S, Lam WL, Ling V (2007) Genetic changes in the evolution of multidrug resistance for cultured human ovarian cancer cells. Genes Chromosomes Cancer 46(12):1069–1079. doi: 10.1002/gcc.20492 PubMedCrossRefGoogle Scholar
  35. 35.
    Callagy G, Pharoah P, Chin SF, Sangan T, Daigo Y, Jackson L, Caldas C (2005) Identification and validation of prognostic markers in breast cancer with the complementary use of array-CGH and tissue microarrays. J Pathol 205(3):388–396. doi: 10.1002/path.1694 PubMedCrossRefGoogle Scholar
  36. 36.
    Coe BP, Henderson LJ, Garnis C, Tsao MS, Gazdar AF, Minna J, Lam S, Macaulay C, Lam WL (2005) High-resolution chromosome arm 5p array CGH analysis of small cell lung carcinoma cell lines. Genes Chromosomes Cancer 42(3):308–313. doi: 10.1002/gcc.20137 PubMedCrossRefGoogle Scholar
  37. 37.
    Coe BP, Lee EH, Chi B, Girard L, Minna JD, Gazdar AF, Lam S, MacAulay C, Lam WL (2006) Gain of a region on 7p22.3, containing MAD1L1, is the most frequent event in small-cell lung cancer cell lines. Genes Chromosomes Cancer 45(1):11–19. doi: 10.1002/gcc.20260 PubMedCrossRefGoogle Scholar
  38. 38.
    de Leeuw RJ, Davies JJ, Rosenwald A, Bebb G, Gascoyne RD, Dyer MJ, Staudt LM, Martinez-Climent JA, Lam WL (2004) Comprehensive whole genome array CGH profiling of mantle cell lymphoma model genomes. Hum Mol Genet 13(17):1827–1837. doi:10.1093/hmg/ddh195ddh195[pii] PubMedCrossRefGoogle Scholar
  39. 39.
    Espinosa AB, Mackintosh C, Maillo A, Gutierrez L, Sousa P, Merino M, Ortiz J, de Alava E, Orfao A, Tabernero MD (2008) Array-based comparative genomic hybridization of mapped BAC DNA clones to screen for chromosome 14 copy number abnormalities in meningiomas. Eur J Hum Genet 16(12):1450–1458. doi:ejhg2008128[pii]10.1038/ejhg.2008.128 PubMedCrossRefGoogle Scholar
  40. 40.
    Gao K, Lockwood WW, Li J, Lam W, Li G (2008) Genomic analyses identify gene candidates for acquired irinotecan resistance in melanoma cells. Int J Oncol 32(6):1343–1349PubMedGoogle Scholar
  41. 41.
    Garnis C, Lockwood WW, Vucic E, Ge Y, Girard L, Minna JD, Gazdar AF, Lam S, MacAulay C, Lam WL (2006) High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH. Int J Cancer 118(6):1556–1564. doi: 10.1002/ijc.21491 PubMedCrossRefGoogle Scholar
  42. 42.
    Goldstein M, Meller I, Issakov J, Orr-Urtreger A (2006) Novel genes implicated in embryonal, alveolar, and pleomorphic rhabdomyosarcoma: a cytogenetic and molecular analysis of primary tumors. Neoplasia 8(5):332–343. doi: 10.1593/neo.05829 PubMedCrossRefGoogle Scholar
  43. 43.
    Ishkanian AS, Mallof CA, Ho J, Meng A, Albert M, Syed A, van der Kwast T, Milosevic M, Yoshimoto M, Squire JA, Lam WL, Bristow RG (2009) High-resolution array CGH identifies novel regions of genomic alteration in intermediate-risk prostate cancer. Prostate 69(10):1091–1100. doi: 10.1002/pros.20959 PubMedCrossRefGoogle Scholar
  44. 44.
    Lockwood WW, Coe BP, Williams AC, MacAulay C, Lam WL (2007) Whole genome tiling path array CGH analysis of segmental copy number alterations in cervical cancer cell lines. Int J Cancer 120(2):436–443. doi: 10.1002/ijc.22335 PubMedCrossRefGoogle Scholar
  45. 45.
    O’Toole SA, Dunn E, Sheppard BL, Klocker H, Bektic J, Smyth P, Martin C, Sheils O, O’Leary JJ (2006) Genome-wide analysis of deoxyribonucleic acid in endometrial cancer using comparative genomic hybridization microarrays. Int J Gynecol Cancer 16(2): 834–842. doi:IJG530[pii]10.1111/ j.1525-1438.2006.00530.x PubMedCrossRefGoogle Scholar
  46. 46.
    Savola S, Klami A, Tripathi A, Niini T, Serra M, Picci P, Kaski S, Zambelli D, Scotlandi K, Knuutila S (2009) Combined use of expression and CGH arrays pinpoints novel candidate genes in Ewing sarcoma family of tumors. BMC Cancer 9:17. doi:1471-2407-9-17[pii]10.1186/1471-2407-9-17 PubMedCrossRefGoogle Scholar
  47. 47.
    Murphy D, Parker J, Zhou M, Fadlelmola FM, Steidl C, Karsan A, Gascoyne RD, Chen H, Banerjee D (2010) Constitutively overexpressed 21 kDa protein in Hodgkin lymphoma and aggressive non-Hodgkin lymphomas identified as cytochrome B5b (CYB5B). Mol Cancer 9:14. doi:1476-4598-9-14[pii]10.1186/1476-4598-9-14 PubMedCrossRefGoogle Scholar
  48. 48.
    Fadlelmola FM, Zhou M, de Leeuw RJ, Dosanjh NS, Harmer K, Huntsman D, Lam WL, Banerjee D (2008) Sub-megabase resolution tiling (SMRT) array-based comparative genomic hybridization profiling reveals novel gains and losses of chromosomal regions in Hodgkin Lymphoma and Anaplastic Large Cell Lymphoma cell lines. Mol Cancer 7:2. doi:1476-4598-7-2[pii]10.1186/1476-4598-7-2 PubMedCrossRefGoogle Scholar
  49. 49.
    Heiskanen M, Kononen J, Barlund M, Torhorst J, Sauter G, Kallioniemi A, Kallioniemi O (2001) CGH, cDNA and tissue microarray analyses implicate FGFR2 amplification in a small subset of breast tumors. Anal Cell Pathol 22(4):229–234PubMedGoogle Scholar
  50. 50.
    Heiskanen MA, Bittner ML, Chen Y, Khan J, Adler KE, Trent JM, Meltzer PS (2000) Detection of gene amplification by genomic hybridization to cDNA microarrays. Cancer Res 60(4):799–802PubMedGoogle Scholar
  51. 51.
    Brennan C, Zhang Y, Leo C, Feng B, Cauwels C, Aguirre AJ, Kim M, Protopopov A, Chin L (2004) High-resolution global profiling of genomic alterations with long oligonucleotide microarray. Cancer Res 64(14):4744–4748. doi:10.1158/0008-5472.CAN-04-1241 64/14/4744[pii] PubMedCrossRefGoogle Scholar
  52. 52.
    Carvalho B, Ouwerkerk E, Meijer GA, Ylstra B (2004) High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides. J Clin Pathol 57(6): 644–646PubMedCrossRefGoogle Scholar
  53. 53.
    Smetana J, Frohlich J, Vranova V, Mikulasova A, Kuglik P, Hajek R (2011) Oligonucleotide-based array CGH as a diagnostic tool in multiple myeloma patients. Klin Onkol 24(Suppl):S43–S48PubMedGoogle Scholar
  54. 54.
    Waddell N, Arnold J, Cocciardi S, da Silva L, Marsh A, Riley J, Johnstone CN, Orloff M, Assie G, Eng C, Reid L, Keith P, Yan M, Fox S, Devilee P, Godwin AK, Hogervorst FB, Couch F, Grimmond S, Flanagan JM, Khanna K, Simpson PT, Lakhani SR, Chenevix-Trench G (2010) Subtypes of familial breast tumours revealed by expression and copy number profiling. Breast Cancer Res Treat 123(3):661–677. doi: 10.1007/s10549-009-0653-1 PubMedCrossRefGoogle Scholar
  55. 55.
    Toujani S, Dessen P, Ithzar N, Danglot G, Richon C, Vassetzky Y, Robert T, Lazar V, Bosq J, Da Costa L, Perot C, Ribrag V, Patte C, Wiels J, Bernheim A (2009) High resolution genome-wide analysis of chromosomal alterations in Burkitt’s lymphoma. PLoS One 4(9):e7089. doi: 10.1371/journal.pone. 0007089 PubMedCrossRefGoogle Scholar
  56. 56.
    Tefferi A, Sirhan S, Sun Y, Lasho T, Finke CM, Weisberger J, Bale S, Compton J, LeDuc CA, Pardanani A, Thorland EC, Shevchenko Y, Grodman M, Chung WK (2009) Oligonucleotide array CGH studies in myeloproliferative neoplasms: comparison with JAK2V617F mutational status and conventional chromosome analysis. Leuk Res 33(5):662–664. doi:S0145-2126(08)00416-5[pii]10.1016/j.leukres.2008.09.009 PubMedCrossRefGoogle Scholar
  57. 57.
    Maciejewski JP, Tiu RV, O’Keefe C (2009) Application of array-based whole genome scanning technologies as a cytogenetic tool in haematological malignancies. Br J Haematol 146(5):479–488. doi:BJH7757[pii]10.1111/j.1365-2141.2009.07757.xPubMedCrossRefGoogle Scholar
  58. 58.
    Legoffic A, Calvo EL, Barthet M, Delpero JR, Dagorn JC, Iovanna JL (2009) Identification of genomic alterations associated with the aggressiveness of pancreatic cancer using an ultra-high-resolution CGH array. Pancreatology 9(3):267–272. doi:000212092[pii]10.1159/000212092 PubMedCrossRefGoogle Scholar
  59. 59.
    Cooke SL, Pole JC, Chin SF, Ellis IO, Caldas C, Edwards PA (2008) High-resolution array CGH clarifies events occurring on 8p in carcinogenesis. BMC Cancer 8:288. doi:1471-2407-8-288[pii]10.1186/1471-2407-8-288 PubMedCrossRefGoogle Scholar
  60. 60.
    Lee JJ, Au AY, Foukakis T, Barbaro M, Kiss N, Clifton-Bligh R, Staaf J, Borg A, Delbridge L, Robinson BG, Wallin G, Hoog A, Larsson C (2008) Array-CGH identifies cyclin D1 and UBCH10 amplicons in anaplastic thyroid carcinoma. Endocr Relat Cancer 15(3):801–815. doi:15/3/801[pii]10.1677/ERC-08-0018 PubMedCrossRefGoogle Scholar
  61. 61.
    Giefing M, Arnemann J, Martin-Subero JI, Nielander I, Bug S, Hartmann S, Arnold N, Tiacci E, Frank M, Hansmann ML, Kuppers R, Siebert R (2008) Identification of candidate tumour suppressor gene loci for Hodgkin and Reed-Sternberg cells by characterisation of homozygous deletions in classical Hodgkin lymphoma cell lines. Br J Haematol 142(6): 916–924. doi:BJH7262[pii]10.1111/ j.1365-2141.2008.07262.x PubMedCrossRefGoogle Scholar
  62. 62.
    Chen HI, Hsu FH, Jiang Y, Tsai MH, Yang PC, Meltzer PS, Chuang EY, Chen Y (2008) A probe-density-based analysis method for array CGH data: simulation, normalization and centralization. Bioinformatics 24(16): 1749–1756. doi:btn321[pii]10.1093/bioinformatics/btn321 PubMedCrossRefGoogle Scholar
  63. 63.
    Fuhrmann C, Schmidt-Kittler O, Stoecklein NH, Petat-Dutter K, Vay C, Bockler K, Reinhardt R, Ragg T, Klein CA (2008) High-resolution array comparative genomic hybridization of single micrometastatic tumor cells. Nucleic Acids Res 36(7):e39. doi:gkn101[pii]10.1093/nar/gkn101 PubMedCrossRefGoogle Scholar
  64. 64.
    Bernheim A, Toujani S, Saulnier P, Robert T, Casiraghi O, Validire P, Temam S, Menard P, Dessen P, Fouret P (2008) High-resolution array comparative genomic hybridization analysis of human bronchial and salivary adenoid cystic carcinoma. Lab Invest 88(5):464–473. doi:labinvest200818[pii]10.1038/labinvest.2008.18 PubMedCrossRefGoogle Scholar
  65. 65.
    Costa JL, Meijer G, Ylstra B, Caldas C (2008) Array comparative genomic hybridization copy number profiling: a new tool for translational research in solid malignancies. Semin Radiat Oncol 18(2):98–104. doi:S1053-4296(07)00096-3[pii]10.1016/j.semradonc.2007.10.005 PubMedCrossRefGoogle Scholar
  66. 66.
    Steinemann D, Cario G, Stanulla M, Karawajew L, Tauscher M, Weigmann A, Gohring G, Ludwig WD, Harbott J, Radlwimmer B, Bartram C, Lichter P, Schrappe M, Schlegelberger B (2008) Copy number alterations in childhood acute lymphoblastic leukemia and their association with minimal residual disease. Genes Chromosomes Cancer 47(6):471–480. doi: 10.1002/gcc.20557 PubMedCrossRefGoogle Scholar
  67. 67.
    Zafrakas M, Tarlatzis BC, Streichert T, Pournaropoulos F, Wolfle U, Smeets SJ, Wittek B, Grimbizis G, Brakenhoff RH, Pantel K, Bontis J, Gunes C (2008) Genome-wide microarray gene expression, array-CGH analysis, and telomerase activity in advanced ovarian endometriosis: a high degree of differentiation rather than malignant potential. Int J Mol Med 21(3):335–344PubMedGoogle Scholar
  68. 68.
    Mantripragada KK, Spurlock G, Kluwe L, Chuzhanova N, Ferner RE, Frayling IM, Dumanski JP, Guha A, Mautner V, Upadhyaya M (2008) High-resolution DNA copy number profiling of malignant peripheral nerve sheath tumors using targeted microarray-based comparative genomic hybridization. Clin Cancer Res 14(4):1015–1024. doi:14/4/1015[pii]10.1158/1078-0432.CCR-07-1305 PubMedCrossRefGoogle Scholar
  69. 69.
    Patel A, Kang SH, Lennon PA, Li YF, Rao PN, Abruzzo L, Shaw C, Chinault AC, Cheung SW (2008) Validation of a targeted DNA microarray for the clinical evaluation of recurrent abnormalities in chronic lymphocytic leukemia. Am J Hematol 83(7):540–546. doi: 10.1002/ajh.21145 PubMedCrossRefGoogle Scholar
  70. 70.
    Persson F, Winnes M, Andren Y, Wedell B, Dahlenfors R, Asp J, Mark J, Enlund F, Stenman G (2008) High-resolution array CGH analysis of salivary gland tumors reveals fusion and amplification of the FGFR1 and PLAG1 genes in ring chromosomes. Oncogene 27(21):3072–3080. doi:1210961[pii]10.1038/sj.onc.1210961 PubMedCrossRefGoogle Scholar
  71. 71.
    Ferreira BI, Alonso J, Carrillo J, Acquadro F, Largo C, Suela J, Teixeira MR, Cerveira N, Molares A, Gomez-Lopez G, Pestana A, Sastre A, Garcia-Miguel P, Cigudosa JC (2008) Array CGH and gene-expression profiling reveals distinct genomic instability patterns associated with DNA repair and cell-cycle checkpoint pathways in Ewing’s sarcoma. Oncogene 27(14):2084–2090. doi:1210845[pii]10.1038/sj.onc.1210845 PubMedCrossRefGoogle Scholar
  72. 72.
    Flibotte S, Moerman DG (2008) Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization. BMC Genomics 9:497. doi:1471-2164-9-497[pii]10.1186/ 1471-2164-9-497 PubMedCrossRefGoogle Scholar
  73. 73.
    Lepretre F, Villenet C, Quief S, Nibourel O, Jacquemin C, Troussard X, Jardin F, Gibson F, Kerckaert JP, Roumier C, Figeac M (2010) Waved aCGH: to smooth or not to smooth. Nucleic Acids Res 38(7):e94. doi:gkp1215[pii]10.1093/nar/gkp1215 PubMedCrossRefGoogle Scholar
  74. 74.
    van de Wiel MA, Brosens R, Eilers PH, Kumps C, Meijer GA, Menten B, Sistermans E, Speleman F, Timmerman ME, Ylstra B (2009) Smoothing waves in array CGH tumor profiles. Bioinformatics 25(9):1099–1104. doi:btp132[pii]10.1093/bioinformatics/btp132 PubMedCrossRefGoogle Scholar
  75. 75.
    Marioni JC, Thorne NP, Valsesia A, Fitzgerald T, Redon R, Fiegler H, Andrews TD, Stranger BE, Lynch AG, Dermitzakis ET, Carter NP, Tavare S, Hurles ME (2007) Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. Genome Biol 8(10):R228. doi:gb-2007-8-10-r228[pii]10.1186/gb-2007-8-10-r228 PubMedCrossRefGoogle Scholar
  76. 76.
    Raiford DW, Krane DE, Doom TE, Raymer ML (2010) Automated isolation of translational efficiency bias that resists the confounding effect of GC(AT)-content. IEEE/ACM Trans Comput Biol Bioinform 7(2):238–250. doi: 10.1109/TCBB.2008.65 PubMedCrossRefGoogle Scholar
  77. 77.
    Knijnenburg J, van der Burg M, Tanke HJ, Szuhai K (2007) Optimized amplification and fluorescent labeling of small cellsamples for genomic array-CGH. Cytometry A 71(8):585–591. doi: 10.1002/cyto.a. 20412 PubMedGoogle Scholar
  78. 78.
    Khojasteh M, Lam WL, Ward RK, MacAulay C (2005) A stepwise framework for the normalization of array CGH data. BMC Bioinformatics 6:274. doi:1471-2105-6-274[pii]10.1186/1471-2105-6-274 PubMedCrossRefGoogle Scholar
  79. 79.
    Kelley R, Feizi H, Ideker T (2008) Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. Bioinformatics 24(1):71–77. doi:btm347[pii]10.1093/bioinformatics/btm347 PubMedCrossRefGoogle Scholar
  80. 80.
    Dobbin KK, Kawasaki ES, Petersen DW, Simon RM (2005) Characterizing dye bias in microarray experiments. Bioinformatics 21(10): 2430–2437. doi:bti378[pii]10.1093/bioinformatics/bti378 PubMedCrossRefGoogle Scholar
  81. 81.
    Martin-Magniette ML, Aubert J, Cabannes E, Daudin JJ (2005) Evaluation of the gene-specific dye bias in cDNA microarray experiments. Bioinformatics 21(9):1995–2000. doi:bti302[pii]10.1093/bioinformatics/bti302 PubMedCrossRefGoogle Scholar
  82. 82.
    Rosenzweig BA, Pine PS, Domon OE, Morris SM, Chen JJ, Sistare FD (2004) Dye bias correction in dual-labeled cDNA microarray gene expression measurements. Environ Health Perspect 112(4):480–487PubMedCrossRefGoogle Scholar
  83. 83.
    Dombkowski AA, Thibodeau BJ, Starcevic SL, Novak RF (2004) Gene-specific dye bias in microarray reference designs. FEBS Lett 560(1–3):120–124. doi:10.1016/S0014-5793(04) 00083-3S0014579304000833[pii] PubMedCrossRefGoogle Scholar
  84. 84.
    Lindblad-Toh K, Tanenbaum DM, Daly MJ, Winchester E, Lui WO, Villapakkam A, Stanton SE, Larsson C, Hudson TJ, Johnson BE, Lander ES, Meyerson M (2000) Loss-of-heterozygosity analysis of small-cell lung ­carcinomas using single-nucleotide polymorphism arrays. Nat Biotechnol 18(9):1001–1005. doi: 10.1038/79269 PubMedCrossRefGoogle Scholar
  85. 85.
    Janne PA, Li C, Zhao X, Girard L, Chen TH, Minna J, Christiani DC, Johnson BE, Meyerson M (2004) High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines. Oncogene 23(15):2716–2726. doi:10.1038/sj.onc.1207329 1207329[pii] PubMedCrossRefGoogle Scholar
  86. 86.
    Kawamata N, Ogawa S, Gueller S, Ross SH, Huynh T, Chen J, Chang A, Nabavi-Nouis S, Megrabian N, Siebert R, Martinez-Climent JA, Koeffler HP (2009) Identified hidden genomic changes in mantle cell lymphoma using high-resolution single nucleotide polymorphism genomic array. Exp Hematol 37(8):937–946. doi:S0301-472X(09)00175-1[pii]10.1016/j.exphem.2009.04.012 PubMedCrossRefGoogle Scholar
  87. 87.
    Shlien A, Malkin D (2009) Copy number variations and cancer. Genome Med 1(6):62. doi:gm62[pii]10.1186/gm62 PubMedCrossRefGoogle Scholar
  88. 88.
    Walter MJ, Payton JE, Ries RE, Shannon WD, Deshmukh H, Zhao Y, Baty J, Heath S, Westervelt P, Watson MA, Tomasson MH, Nagarajan R, O’Gara BP, Bloomfield CD, Mrozek K, Selzer RR, Richmond TA, Kitzman J, Geoghegan J, Eis PS, Maupin R, Fulton RS, McLellan M, Wilson RK, Mardis ER, Link DC, Graubert TA, DiPersio JF, Ley TJ (2009) Acquired copy number alterations in adult acute myeloid leukemia genomes. Proc Natl Acad Sci USA 106(31):12950–12955. doi:0903091106[pii]10.1073/pnas.0903091106 PubMedCrossRefGoogle Scholar
  89. 89.
    Barresi V, Romano A, Musso N, Capizzi C, Consoli C, Martelli MP, Palumbo G, Di Raimondo F, Condorelli DF (2010) Broad copy neutral-loss of heterozygosity regions and rare recurring copy number abnormalities in normal karyotype-acute myeloid leukemia genomes. Genes Chromosomes Cancer 49(11):1014–1023. doi: 10.1002/gcc.20810 PubMedCrossRefGoogle Scholar
  90. 90.
    Cheung KJ, Delaney A, Ben-Neriah S, Schein J, Lee T, Shah SP, Cheung D, Johnson NA, Mungall AJ, Telenius A, Lai B, Boyle M, Connors JM, Gascoyne RD, Marra MA, Horsman DE (2010) High resolution analysis of follicular lymphoma genomes reveals somatic recurrent sites of copy-neutral loss of heterozygosity and copy number alterations that target single genes. Genes Chromosomes Cancer 49(8):669–681. doi: 10.1002/gcc.20780 PubMedCrossRefGoogle Scholar
  91. 91.
    Hagenkord JM, Monzon FA, Kash SF, Lilleberg S, Xie Q, Kant JA (2010) Array-based karyotyping for prognostic assessment in chronic lymphocytic leukemia: performance comparison of Affymetrix 10 K2.0, 250 K Nsp, and SNP6.0 arrays. J Mol Diagn: JMD 12(2):184–196. doi:S1525-1578(10)60047-5[pii]10.2353/jmoldx.2010.090118 PubMedCrossRefGoogle Scholar
  92. 92.
    Hartmann S, Gesk S, Scholtysik R, Kreuz M, Bug S, Vater I, Doring C, Cogliatti S, Parrens M, Merlio JP, Kwiecinska A, Porwit A, Piccaluga PP, Pileri S, Hoefler G, Kuppers R, Siebert R, Hansmann ML (2010) High resolution SNP array genomic profiling of peripheral T cell lymphomas, not otherwise specified, identifies a subgroup with chromosomal ­aberrations affecting the REL locus. Br J Haematol 148(3):402–412. doi:BJH7956[pii]10.1111/j.1365-2141.2009.07956.x PubMedCrossRefGoogle Scholar
  93. 93.
    Zarghooni M, Bartels U, Lee E, Buczkowicz P, Morrison A, Huang A, Bouffet E, Hawkins C (2010) Whole-genome profiling of pediatric diffuse intrinsic pontine gliomas highlights platelet-derived growth factor receptor alpha and poly (ADP-ribose) polymerase as potential therapeutic targets. J Clin Oncol 28(8):1337–1344. doi:JCO.2009.25.5463[pii]10.1200/JCO.2009.25.5463 PubMedCrossRefGoogle Scholar
  94. 94.
    Tiu RV, Gondek LP, O’Keefe CL, Elson P, Huh J, Mohamedali A, Kulasekararaj A, Advani AS, Paquette R, List AF, Sekeres MA, McDevitt MA, Mufti GJ, Maciejewski JP (2011) Prognostic impact of SNP array karyotyping in myelodysplastic syndromes and related myeloid malignancies. Blood 117(17):4552–4560. doi:blood-2010-07-295857[pii]10.1182/blood-2010-07-295857 PubMedCrossRefGoogle Scholar
  95. 95.
    Heinrichs S, Li C, Look AT (2010) SNP array analysis in hematologic malignancies: avoiding false discoveries. Blood 115(21):4157–4161. doi:blood-2009-11-203182[pii]10.1182/blood-2009-11-203182 PubMedCrossRefGoogle Scholar
  96. 96.
    Curtis C, Lynch AG, Dunning MJ, Spiteri I, Marioni JC, Hadfield J, Chin SF, Brenton JD, Tavare S, Caldas C (2009) The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 10:588. doi:1471-2164-10-588[pii]10.1186/1471-2164-10-588 PubMedCrossRefGoogle Scholar
  97. 97.
    Alkan C, Coe BP, Eichler EE (2011) Genome structural variation discovery and genotyping. Nat Rev Genet 12(5):363–376. doi:nrg2958[pii]10.1038/nrg2958[doi] PubMedCrossRefGoogle Scholar
  98. 98.
    Cooper GM, Zerr T, Kidd JM, Eichler EE, Nickerson DA (2008) Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nat Genet 40(10):1199–1203. doi:ng.236[pii]10.1038/ng.236 PubMedCrossRefGoogle Scholar
  99. 99.
    Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald T, Lionel AC, Thiruvahindrapuram B, Macdonald JR, Mills R, Prasad A, Noonan K, Gribble S, Prigmore E, Donahoe PK, Smith RS, Park JH, Hurles ME, Carter NP, Lee C, Scherer SW, Feuk L (2011) Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol 29(6):512–520. doi:nbt.1852[pii]10.1038/nbt.1852 PubMedCrossRefGoogle Scholar
  100. 100.
    Halper-Stromberg E, Frelin L, Ruczinski I, Scharpf R, Jie C, Carvalho B, Hao H, Hetrick K, Jedlicka A, Dziedzic A, Doheny K, Scott AF, Baylin S, Pevsner J, Spencer F, Irizarry RA (2011) Performance assessment of copy number microarray platforms using a spike-in experiment. Bioinformatics 27(8):1052–1060. doi: 10.1093/bioinformatics/btr106 PubMedCrossRefGoogle Scholar
  101. 101.
    Krijgsman O, Israeli D, Haan JC, van Essen HF, Smeets SJ, Eijk PP, Steenbergen RD, Kok K, Tejpar S, Meijer GA, Ylstra B (2012) CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material. Genes Chromosomes Cancer 51(4):344–352. doi: 10.1002/gcc.21920 PubMedCrossRefGoogle Scholar
  102. 102.
    Przybytkowski E, Ferrario C, Basik M (2011) The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome. BMC Med Genomics 4:16. doi:1755-8794-4-16[pii]10.1186/1755-8794-4-16PubMedCrossRefGoogle Scholar
  103. 103.
    Keller A, Backes C, Leidinger P, Kefer N, Boisguerin V, Barbacioru C, Vogel B, Matzas M, Huwer H, Katus HA, Stahler C, Meder B, Meese E (2011) Next-generation sequencing identifies novel microRNAs in peripheral blood of lung cancer patients. Mol Biosyst 7(12):3187–3199. doi: 10.1039/c1mb05353a PubMedCrossRefGoogle Scholar
  104. 104.
    Watahiki A, Wang Y, Morris J, Dennis K, O’Dwyer HM, Gleave M, Gout PW (2011) MicroRNAs associated with metastatic prostate cancer. PLoS One 6(9):e24950. doi:10.1371/journal.pone.0024950 PONE-D-11-04350[pii] PubMedCrossRefGoogle Scholar
  105. 105.
    Edgren H, Murumagi A, Kangaspeska S, Nicorici D, Hongisto V, Kleivi K, Rye IH, Nyberg S, Wolf M, Borresen-Dale AL, Kallioniemi O (2011) Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol 12(1):R6. doi:gb-2011-12-1-r6[pii]10.1186/gb-2011-12-1-r6 PubMedCrossRefGoogle Scholar
  106. 106.
    Robbins CM, Tembe WA, Baker A, Sinari S, Moses TY, Beckstrom-Sternberg S, Beckstrom-Sternberg J, Barrett M, Long J, Chinnaiyan A, Lowey J, Suh E, Pearson JV, Craig DW, Agus DB, Pienta KJ, Carpten JD (2011) Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors. Genome Res 21(1):47–55. doi:gr.107961.110[pii]10.1101/gr.107961.110 PubMedCrossRefGoogle Scholar
  107. 107.
    Walsh T, Lee MK, Casadei S, Thornton AM, Stray SM, Pennil C, Nord AS, Mandell JB, Swisher EM, King MC (2010) Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci USA 107(28):12629–12633. doi:1007983107[pii]10.1073/pnas.1007983107 PubMedCrossRefGoogle Scholar
  108. 108.
    Wood HM, Belvedere O, Conway C, Daly C, Chalkley R, Bickerdike M, McKinley C, Egan P, Ross L, Hayward B, Morgan J, Davidson L, MacLennan K, Ong TK, Papagiannopoulos K, Cook I, Adams DJ, Taylor GR, Rabbitts P (2010) Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. Nucleic Acids Res 38(14):e151. doi:gkq510[pii]10.1093/nar/gkq510PubMedCrossRefGoogle Scholar
  109. 109.
    Walter MJ, Graubert TA, Dipersio JF, Mardis ER, Wilson RK, Ley TJ (2009) Next-generation sequencing of cancer genomes: back to the future. Per Med 6(6):653. doi: 10.2217/pme.09.52 PubMedCrossRefGoogle Scholar
  110. 110.
    Aparicio SA, Huntsman DG (2010) Does massively parallel DNA resequencing signify the end of histopathology as we know it? J Pathol 220(2):307–315. doi: 10.1002/path.2636 PubMedGoogle Scholar
  111. 111.
    Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, Burleigh A, Delaney A, Gelmon K, Guliany R, Senz J, Steidl C, Holt RA, Jones S, Sun M, Leung G, Moore R, Severson T, Taylor GA, Teschendorff AE, Tse K, Turashvili G, Varhol R, Warren RL, Watson P, Zhao Y, Caldas C, Huntsman D, Hirst M, Marra MA, Aparicio S (2009) Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 461(7265):809–813. doi:nature08489[pii]10.1038/nature08489 PubMedCrossRefGoogle Scholar
  112. 112.
    Rothberg JM (2012) Life Technologies Introduces the Benchtop Ion Proton™ Sequencer; Designed to Decode a Human Genome in One Day for $1,000. http://www.lifetechnologies.com/us/en/home/about-us/news-gallery/press-releases/2012/life-techologies-itroduces-the-bechtop-io-proto.html.
  113. 113.
    Przeworski M, Hudson RR, Di Rienzo A (2000) Adjusting the focus on human variation. Trends Genet: TIG 16(7):296–302. doi:S0168-9525(00)02030-8[pii] PubMedCrossRefGoogle Scholar
  114. 114.
    Reich DE, Schaffner SF, Daly MJ, McVean G, Mullikin JC, Higgins JM, Richter DJ, Lander ES, Altshuler D (2002) Human genome sequence variation and the influence of gene history, mutation and recombination. Nat Genet 32(1):135–142. doi:10.1038/ng947ng947[pii] PubMedCrossRefGoogle Scholar
  115. 115.
    Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stutz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO (2011) Mapping copy number variation by population-scale genome sequencing. Nature 470(7332):59–65. doi:nature09708[pii]10.1038/nature09708 PubMedCrossRefGoogle Scholar
  116. 116.
    Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, Eichler EE (2010) Diversity of human copy number variation and multicopy genes. Science 330(6004):641–646. doi:330/6004/641[pii]10.1126/science.1197005 PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Department of Pathology and Laboratory MedicineThe Ottawa HospitalOttawaCanada

Personalised recommendations