Statistical methods for detecting genomic alterations through array-based comparative genomic hybridization (CGH)

Frontiers in Bioscience

Volumn 9, Issue , 2004, Pages 540-549

  Wang, Yuedong ^a   Guo, Sun Wei ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b MEDICAL COLLEGE OF WISCONSIN   (United States)

Author keywords

Array based comparative genomic hybridization; Genomic alterations; Hybrid adaptive splines; Microarrays; Review; Statistical methods; t statistic

Indexed keywords

ARTICLE; CARCINOGENESIS; CLINICAL ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; DIAGNOSTIC VALUE; DISEASE SIMULATION; DNA MICROARRAY; ENDOMETRIOSIS; FEMALE; HUMAN; METHODOLOGY; MOLECULAR GENETICS; MUTATION; SAMPLING; STATISTICAL ANALYSIS; CHROMOSOME ABERRATION; COMPUTER SIMULATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; GENOME; NUCLEIC ACID HYBRIDIZATION; STATISTICS;

CHROMOSOME ABERRATIONS; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; ENDOMETRIOSIS; FEMALE; GENOME, HUMAN; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; STATISTICS;

EID: 2542472385     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/1186     Document Type: Article

References (27)

1. Kallioniemi A, O. P. Kallioniemi, D. Sudar, D. Rutovitz, J. W. Gray, F. Waldman, and D. Pinkel: Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258, 818-821 (1992)
2. Bentz M., A. Plesch, S. Stilgenbauer, H. Dohner, P. Lichter: Minimal sizes of deletions detected by comparative genomic hybridization. Genes Chromosomes Cancer 21, 172-175 (1988)
3. Kirchhoff M., T. Gerdes, J. Maahr, H. Rose, M. Bentz, H. Dohner H. & C. Lundsteen: Deletions below 10 megabasepairs are detected in comparative genomic hybridization by standard reference intervals. Genes Chromosomes Cancer 25, 410-413 (1999)
4. Veltman J.A., E. F. Schoenmakers, B. H. Bussen, I. Janssen, G. Merkx, B. van Cleef, C. M. van Ravenswaaij, H. G. Brunner, D. Smeets & A. G. van Kessel: High-throughput analysis of subtelomeric chromosome rearrangements by use of array-based comparative genomic hybridization. Am J Hum Genet. 70, 1269-1276 (2002)
5. Wessendorf S., B. Fritz, G. Wrobel, M. Nessling, S. Lampel, D. Goettel, M. Kuepper, S. Joo, T. Hopman, F. Kokocinski, H. Dohner, M. Bentz, C. Schwaenen & P. Lichter: Automated screening for genomic imbalances using matrix-based comparative genomic hybridization. Lab Invest. 82, 47-60 (2002)
6. Solinas-Toldo S., S. Lampel, S. Stilgenbauer, J. Nickolenko, A. Benner, H. Dohner, T. Cremer & P. Lichter: Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20, 399-407 (1997)
7. Pinkel D., R. Segraves, D. Sudar, S. Clark, I. Poole, D. Kowbel, C. Collins, W. L. Kuo, C. Chen, Y. Zhai, S. H. Dairkee, B. M. Ljung, J. W. Gray & D. G. Albertson: High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 20, 207-211 (1998)
8. Pollack J. R., C. M. Perou, A. A. Alizadeh, M. B. Eisen, A. Pergamenschikov, C. F. Williams, S. S. Jeffrey, D. Botstein, P. O. Brown: Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet. 23, 41-46 (1999)
9. Snijders A. M., N. Nowak, R. Segraves, S. Blackwood, N. Brown, J. Conroy, G. Hamilton, A. K. Hindle, B. Huey, K. Kimura, S. Law, K. Myambo, J. Palmer, B. Ylstra, J. P. Yue, J. W. Gray, A. N. Jain, D. Pinkel & D. G. Albertson: Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet. 29, 263-264 (2001)
10. Schena M., D. Shalon, R. W. Davis & P. O. Brown: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470 (1995)
11. Piper J., D. Rutovitz, D. Sudar, A. Kallioniemi, O. P. Kallioniemi, F. M. Waldman, J. W. Gray & D. Pinkel: Computer image analysis of comparative genomic hybridization. Cytometry 19, 10-26 (1995)
12. Cher M.L., G. S. Bova, D. H. Moore, E. J. Small, P. R. Carroll, S. S. Pin, J. I. Epstein, W. B. Isaacs & R. H. Jensen: Genetic alterations in untreated metastases and androgen-independent prostate cancer detected by comparative genomic hybridization and allelotyping. Cancer Res. 56, 3091-3102 (1996)
13. du Manoir S., O. P. Kallioniemi, P. Lichter, J. Piper, P. A. Benedetti, A. D. Carothers, J. A. Fantes, J. M. Garcia-Sagredo, T. Gerdes & M. Giollant: Hardware and software requirements for quantitative analysis of comparative genomic hybridization. Cytometry 19, 4-9 (1995)
14. Lundsteen C., J. Maahr, B. Christensen, T. Bryndorf, M. Bentz, P. Lichter & T. Gerdes: Image analysis in comparative genomic hybridization. Cytometry 19, 42-50 (1995)
15. Schleger C., N. Arens, H. Zentgraf, U. Bleyl & C. Verbeke: Identification of frequent chromosomal aberrations in ductal adenocarcinoma of the pancreas by comparative genomic hybridization (CGH). J Pathol. 191, 27-32 (2000)
16. Moore D.H., M. Pallavicini, M. L. Cher & J. W. Gray: A t-statistic for objective interpretation of comparative genomic hybridization (CGH) profiles. Cytometry 25, 183-90 (1997)
17. Bruder C.E., C. Hirvela, I. Tapia-Paez, I. Fransson, R. Segraves, G. Hamilton, X. X. Zhang, D. G. Evans, A. J. Wallace, M. E. Baser, J. Zucman-Rossi, M. Hergersberg, E. Boltshauser, L. Papi, G. A. Rouleau, G. Poptodorov, A. Jordanova, H. Rask-Andersen, L. Kluwe, V. Mautner, M. Sainio, G. Hung, T. Mathiesen, C. Moller, S. M. Pulst, H. Harder, A. Heiberg, M. Honda, M. Niimura, S. Sahlen, E. Blennow, D. G. Albertson, D. Pinkel, J. P. Dumanski: High resolution deletion analysis of constitutional DNA from neurofibromatosis type 2 (NF2) patients using microarray-CGH. Hum Mol Genet. 10, 271-282 (2001)
18. Wilhelm M., J. A. Veltman, A. B. Olshen, A. N. Jain, D. H. Moore, J. C. Presti Jr, G. Kovacs & F. M. Waldman: Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer. Cancer Res. 62, 957-960 (2002)
19. Piper J., S. Stegenga, E. Pestova, H. Marble, M. Lucas, K. Wilber & W. King: In Third Euroconference on Quantitative Molecular Cytogenetics, Rosenn, Sweden. July 4-6, 109-114 (2002)
20. Carothers A.D.: A likelihood-based approach to the estimation of relative DNA copy number by comparative genomic hybridization. Biometrics 53, 848-856 (1997)
21. Luo, Z. & G. Wahba: Hybrid Adaptive Splines. J. Am. Stat. Assoc. 92, 107-116 (1997)
22. Telenius H., N. P. Carter, C. E. Bebb, M. Nordenskjold, B. A. Ponder & A. Tunnacliffe: Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 13, 718-725 (1992)
23. Wang X., S. Ghosh & S. W. Guo: Quantitative quality control in microarray image processing and data acquisition. Nucleic Acids Res. , E75-5 (2001)
24. Yang Y. H., S. Dudoit, P. Luu, D. M. Lin, V. Peng, J. Ngai, T. P. Speed: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30, E15 (2002)
25. Wahba, G.: Spline Models for Observational Data. SIAM, Philadelphia (1990)
26. Wang, Y. & G. Wahba: Bootstrap Confidence Intervals for Smoothing Spline Estimates and Their Comparison to Bayesian Confidence Intervals. J. Statist. Comput. Simul. 51, 263-279 (1995)
27. Benjamini, Y.D. & Y. Hochberg: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Royal. Stat. Soc. B 57, 289-300 (1995)