CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Huang, Jing ^a   Wei, Wen ^a   Chen, Joyce ^a   Zhang, Jane ^a   Liu, Guoying ^a   Di, Xiaojun ^a   Mei, Rui ^a   Ishikawa, Shumpei ^b   Aburatani, Hiroyuki ^b   Jones, Keith W ^a   Shapero, Michael H ^a  

^a Thermo Fisher Scientific   (United States)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX PHENOTYPE; COPY NUMBER VARIATIONS; HUMAN BREAST CANCER CELLS; INTENSITY INFORMATION; OLIGONUCLEOTIDE ARRAYS; SENSITIVITY AND SPECIFICITY; TUMOR SUPPRESSOR GENES; VERIFICATION METHOD;

ALGORITHMS; CELL CULTURE; CELLS; DNA; GENES; OLIGONUCLEOTIDES; ONCOGENIC VIRUSES;

POLYMERASE CHAIN REACTION;

DNA; EPIDERMAL GROWTH FACTOR RECEPTOR 2;

ACCURACY; ARTICLE; AUTOMATION; BREAST CANCER; CANCER CELL CULTURE; CANCER GENETICS; COMPUTER PROGRAM; CONTROLLED STUDY; COPY NUMBER ANALYSIS WITH REGRESSION AND TREE; DNA MICROARRAY; GC RICH SEQUENCE; GENE STRUCTURE; GENETIC ALGORITHM; GENETIC VARIABILITY; GENOTYPE; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; KARYOTYPE; MATHEMATICAL COMPUTING; ONCOGENE; PHENOTYPE; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; RECEIVER OPERATING CHARACTERISTIC; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR SUPPRESSOR GENE; X CHROMOSOME; ALGORITHM; ALLELE; CHROMOSOME MAP; DNA SEQUENCE; GENE DOSAGE; GENE FREQUENCY; GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; REPRODUCIBILITY;

ALGORITHMS; ALLELES; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, X; DNA MUTATIONAL ANALYSIS; DNA, NEOPLASM; GENE DOSAGE; GENE FREQUENCY; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

EID: 33644942486     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-83     Document Type: Article

References (64)

1. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M: Large-scale copy number polymorphism in the human genome. Science 2004, 305:525-528.
2. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C: Detection of large-scale variation in the human genome. Nat Genet 2004, 36:949-951.
3. Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, Oseroff VV, Albertson DG, Pinkel D, Eichler EE: Segmental duplications and copynumber variation in the human genome. Am J Hum Genet 2005, 77:78-88.
4. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE: Finescale structural variation of the human genome. Nat Genet 2005, 37:727-732.
5. Feuk L, Carson AR, Scherer SW: Structural variation in the human genome. Nat Rev Genet 2006, 7:85-97.
6. Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK: A high-resolution survey of deletion polymorphism in the human genome. Nat Genet 2006, 38:75-81.
7. Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA: Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet 2006, 38:82-85.
8. McCarrol SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee C, Daly MJ, Altshuler DM: Common deletion polymorphisms in the human genome. Nat Genet 2006, 38:86-92.
9. Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Borresen-Dale AL, Brown PO: Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A 2002, 99:12963-12968.
10. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO: Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 1999, 23:41-46.
11. 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: Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 2001, 29:263-264.
12. 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: High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998, 20:207-211.
13. Lucito R, Healy J, Alexander J, Reiner A, Esposito D, Chi M, Rodgers L, Brady A, Sebat J, Troge J, West JA, Rostan S, Nguyen KC, Powers S, Ye KQ, Olshen A, Venkatraman E, Norton L, Wigler M: Representational Oligonucleotide Microarray Analysis: A High-Resolution Method to Detect Genome Copy Number Variation. Genome Res 2003.
14. Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D, Kincaid R, Tsang P, Curry B, Baird K, Meltzer PS, Yakhini Z, Bruhn L, Laderman S: Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A 2004, 101:17765-17770.
15. Brennan C, Zhang Y, Leo C, Feng B, Cauwels C, Aguirre AJ, Kim M, Protopopov A, Chin L: High-resolution global profiling of genomic alterations with long oligonucleotide microarray. Cancer Res 2004, 64:4744-4748.
16. Hayashizaki Y, Hirotsune S, Okazaki Y, Hatada I, Shibata H, Kawai J, Hirose K, Watanabe S, Fushiki S, Wada S, Sugimoto T, Kobayakawa K, Kawara T, Katsuki M, Shibuya T, Mukai T: Restriction landmark genomic scanning method and its various applications. Electrophoresis 1993, 14:251-258.
17. Schrock E, du Manoir S, Veldman T, Schoell B, Wienberg J, Ferguson-Smith MA, Ning Y, Ledbetter DH, Bar-Am I, Soenksen D, Garini Y, Ried T: Multicolor spectral karyotyping of human chromosomes. Science 1996, 273:494-497.
18. Lisitsyn N, Wigler M: Cloning the differences between two complex genomes. Science 1993, 259:946-951.
19. Wang TL, Maierhofer C, Speicher MR, Lengauer C, Vogelstein B, Kinzler KW, Velculescu VE: Digital karyotyping. Proc Natl Acad Sci U S A 2002, 99:16156-16161.
20. Tengs T, LaFramboise T, Den RB, Hayes DN, Zhang J, DebRoy S, Gentleman RC, O'Neill K, Birren B, Meyerson M: Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments. Nucleic Acids Res 2004, 32:e121.
21. Volik S, Zhao S, Chin K, Brebner JH, Herndon DR, Tao Q, Kowbel D, Huang G, Lapuk A, Kuo WL, Magrane G, De Jong P, Gray JW, Collins C: End-sequence profiling: sequence-based analysis of aberrant genomes. Proc Natl Acad Sci U S A 2003, 100:7696-7701.
22. Pinkel D, Landegent J, Collins C, Fuscoe J, Segraves R, Lucas J, Gray J: Fluorescence in situ hybridization with human chromosome-specific libraries: detection of trisomy 21 and translocations of chromosome 4. Proc Natl Acad Sci U S A 1988, 85:9138-9142.
23. Fodor SP, Rava RP, Huang XC, Pease AC, Holmes CP, Adams CL: Multiplexed biochemical assays with biological chips. Nature 1993, 364:555-556.
24. Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D: Light-directed, spatially addressable parallel chemical synthesis. Science 1991, 251:767-773.
25. Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SP: Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A 1994, 91:5022-5026.
26. 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: Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat Biotechnol 2000, 18:1001-1005.
27. Wang ZC, Lin M, Wei LJ, Li C, Miron A, Lodeiro G, Harris L, Ramaswamy S, Tanenbaum DM, Meyerson M, Iglehart JD, Richardson A: Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancers. Cancer Res 2004, 64:64-71.
28. Mei R, Galipeau PC, Prass C, Berno A, Ghandour G, Patil N, Wolff RK, Chee MS, Reid BJ, Lockhart DJ: Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res 2000, 10:1126-1137.
29. Kennedy GC, Matsuzaki H, Dong S, Liu WM, Huang J, Liu G, Su X, Cao M, Chen W, Zhang J, Liu W, Yang G, Di X, Ryder T, He Z, Surti U, Phillips MS, Boyce-Jacino MT, Fodor SP, Jones KW: Large-scale genotyping of complex DNA. Nat Biotechnol 2003, 21:1233-1237.
30. Matsuzaki H, Loi H, Dong S, Tsai YY, Fang J, Law J, Di X, Liu WM, Yang G, Liu G, Huang J, Kennedy GC, Ryder TB, Marcus GA, Walsh PS, Shriver MD, Puck JM, Jones KW, Mei R: Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high density oligonucleotide array. Genome Res 2004, 14:414-425.
31. Janne PA, Li C, Zhao X, Girard L, Chen TH, Minna J, Christiani DC, Johnson BE, Meyerson M: High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines. Oncogene 2004, 23:2716-2726.
32. Irving JA, Bloodworth L, Bown NP, Case MC, Hogarth LA, Hall AG: Loss of heterozygosity in childhood acute lymphoblastic leukemia detected by genome-wide microarray single nucleotide polymorphism analysis. Cancer Res 2005, 65:3053-3058.
33. Hu N, Wang C, Hu Y, Yang HH, Giffen C, Tang ZZ, Han XY, Goldstein AM, Emmert-Buck MR, Buetow KH, Taylor PR, Lee MP: Genome-wide association study in esophageal cancer using GeneChip mapping 10K array. Cancer Res 2005, 65:2542-2546.
34. Bignell GR, Huang J, Greshock J, Watt S, Butler A, West S, Grigorova M, Jones KW, Wei W, Stratton MR, Futreal PA, Weber B, Shapero MH, Wooster R: High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 2004, 14:287-295.
35. Huang J, Wei W, Zhang J, Liu G, Bignell GR, Stratton MR, Futreal PA, Wooster R, Jones KW, Shapero MH: Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics 2004, 1:287-299.
36. Rauch A, Ruschendorf F, Huang J, Trautmann U, Becker C, Thiel C, Jones KW, Reis A, Nurnberg P: Molecular karyotyping using an SNP array for genomewide genotyping. J Med Genet 2004, 41:916-922.
37. Zhou X, Mok SC, Chen Z, Li Y, Wong DT: Concurrent analysis of loss of heterozygosity (LOH) and copy number abnormality (CNA) for oral premalignancy progression using the Affymetrix 10K SNP mapping array. Hum Genet 2004, 115:327-330.
38. Raghavan M, Lillington DM, Skoulakis S, Debernardi S, Chaplin T, Foot NJ, Lister TA, Young BD: Genome-wide single nucleotide polymorphism analysis reveals frequent partial uniparental disomy due to somatic recombination in acute myeloid leukemias. Cancer Res 2005, 65:375-378.
39. Wong KK, Tsang YT, Shen J, Cheng RS, Chang YM, Man TK, Lau CC: Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA. Nucleic Acids Res 2004, 32:e69.
40. Herr A, Grutzmann R, Matthaei A, Artelt J, Schrock E, Rump A, Pilarsky C: High-resolution analysis of chromosomal imbalances using the Affymetrix 10K SNP genotyping chip. Genomics 2005, 85:392-400.
41. Speicher MR, Carter NP: The new cytogenetics: blurring the boundaries with molecular biology. Nat Rev Genet 2005, 6:782-792.
42. Matsuzaki H, Dong S, Loi H, Di X, Liu G, Hubbell E, Law J, Berntsen T, Chadha M, Hui H, Yang G, Kennedy GC, Webster TA, Cawley S, Walsh PS, Jones KW, Fodor SPA, Mei R: Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods 2004, 1:109-111.
43. Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, Sangiovanni JP, Mane SM, Mayne ST, Bracken MB, Ferris FL, Ott J, Barnstable C, Hoh J: Complement factor H polymorphism in age-related macular degeneration. Science 2005, 308:385-389.
44. Slater HR, Bailey DK, Ren H, Cao M, Bell K, Nasioulas S, Henke R, Choo KH, Kennedy GC: High-Resolution Identification of Chromosomal Abnormalities Using Oligonucleotide Arrays Containing 116,204 SNPs. Am J Hum Genet 2005, 77:709-726.
45. Breiman L, Friedman J, Olshen R, Stone C: Classification and Regression Trees., Wardsworth; 1984.
46. Lin M, Wei LJ, Sellers WR, Lieberfarb M, Wong WH, Li C: dChip-SNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics 2004, 20:1233-1240.
47. Nannya Y, Sanada M, Nakazaki K, Hosoya N, Wang L, Hangaishi A, Kurokawa M, Chiba S, Bailey DK, Kennedy GC, Ogawa S: A robust algorithm for copy number detection using high-density oil-gonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res 2005, 65:6071-6079.
48. Slamon DJ, Godolphin W, Jones LA, Holt JA, Wong SG, Keith DE, Levin WJ, Stuart SG, Udove J, Ullrich A, Press MF: Studies of the HER-2/neu proto-oncogene in human breast and ovarian cancer. Science 1989, 244:707-712.
49. Kallioniemi A, Kallioniemi OP, Piper J, Tanner M, Stokke T, Chen L, Smith HS, Pinkel D, Gray JW, Waldman FM: Detection and mapping of amplified DNA sequences in breast cancer by comparative genomic hybridization. Proc Natl Acad Sci U S A 1994, 91:2156-2160.
50. Kallioniemi OP, Kallioniemi A, Kurisu W, Thor A, Chen LC, Smith HS, Waldman FM, Pinkel D, Gray JW: ERBB2 amplification in breast cancer analyzed by fluorescence in situ hybridization. Proc Natl Acad Sci U S A 1992, 89:5321-5325.
51. Hastie T, Tibshirani R, Friedman J: The Elements of Statistical Learning, Data Mining, Inference, and Prediction., Springer; 2001.
52. Lai WR, Johnson MD, Kucherlapati R, Park PJ: Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 2005, 21:3763-3770.
53. Laframboise T, Weir BA, Zhao X, Beroukhim R, Li C, Harrington D, Sellers WR, Meyerson M: Allele-specific amplification in cancer revealed by SNP array analysis. PLoS Comput Biol 2005, 1:e65.
54. Fridlyand J, Snijders AM, Pinkel D, Albertson DG, Jain AN: Hidden Markov models approach to the analysis of array CGH data. Journal of Multivariate Analysis 2004, 90:132-153.
55. Zhao X, Weir BA, LaFramboise T, Lin M, Beroukhim R, Garraway L, Beheshti J, Lee JC, Naoki K, Richards WG, Sugarbaker D, Chen F, Rubin MA, Janne PA, Girard L, Minna J, Christiani D, Li C, Sellers WR, Meyerson M: Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis. Cancer Res 2005, 65:5561-5570.
56. Olshen AB, Venkatraman ES, Lucito R, Wigler M: Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004, 5:557-572.
57. Olshen AB, Venkatraman ES: Change-point analysis of array-based comparative genomic hybridization data. 2002.
58. Daruwala RS, Rudra A, Ostrer H, Lucito R, Wigler M, Mishra B: A versatile statistical analysis algorithm to detect genome copy number variation. Proc Natl Acad Sci U S A 2004, 101:16292-16297.
59. Wang P, Kim Y, Pollack J, Narasimhan B, Tibshirani R: A method for calling gains and losses in array CGH data. Biostatistics 2005, 6:45-58.
60. Di X, Matsuzaki H, Webster TA, Hubbell E, Liu G, Dong S, Bartell D, Huang J, Chiles R, Yang G, Shen MM, Kulp D, Kennedy GC, Mei R, Jones KW, Cawley S: Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays. Bioinformatics 2005, 21:1958-1963.
61. Copy Number Analyzer for GeneChip [http://www.genome.umin.jp]
62. dChip Software: Gene Expression Microarray and SNP Microarray Analysis [http://www.dchip.org]
63. Collins FS, Brooks LD, Chakravarti A: A DNA polymorphism discovery resource for research on human genetic variation. Genome Res 1998, 8:1229-1231.
64. Ishikawa S, Komura D, Tsuji S, Nishimura K, Yamamoto S, Panda B, Huang J, Fukayama M, Jones KW, Aburatani H: Allelic dosage analysis with genotyping microarrays. Biochem Biophys Res Comm 2005, 333:1309-1314.