SIRAC: Supervised identification of regions of aberration in aCGH datasets

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Lai, Carmen ^a   Horlings, Hugo M ^b   van de Vijver, Marc J ^b   van Beers, Eric H ^b   Nederlof, Petra M ^b   Wessels, Lodewyk F A ^b   Reinders, Marcel J T ^a  

^a DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^b NETHERLANDS CANCER INSTITUTE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROCESS; BREAST CANCER; DNA AMPLIFICATION; DNA COPY NUMBERS; SUPERVISED ALGORITHM;

ALGORITHMS; DISEASES; GENES; PROBES;

DNA;

DNA; TUMOR PROTEIN;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BREAST CANCER; CHROMOSOME ABERRATION; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA PROBE; GENE AMPLIFICATION; GENE DELETION; GENETIC ALGORITHM; HUMAN; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; MUTATIONAL ANALYSIS; SENSITIVITY AND SPECIFICITY; STRUCTURAL BIOINFORMATICS; ALGORITHM; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; BREAST TUMOR; CHROMOSOME MAP; COMPUTER PROGRAM; DNA SEQUENCE; GENETIC DATABASE; GENETICS; IN SITU HYBRIDIZATION; METHODOLOGY; NUCLEOTIDE SEQUENCE;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; BREAST NEOPLASMS; CHROMOSOME MAPPING; DATABASES, GENETIC; DNA MUTATIONAL ANALYSIS; HUMANS; IN SITU HYBRIDIZATION; NEOPLASM PROTEINS; PATTERN RECOGNITION, AUTOMATED; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 38149124831     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-422     Document Type: Article

References (39)

1. Lengauer C, Kinzler K, Vogelstein B: Genetic instabilities in human cancer. Nature 1998, 396(6712):643-649. 10.1038/25292 9872311
2. Sotiriou C, Piccart M: Taking gene-expression profiling to the clinic: when will molecular signatures become relevant to patient care? Nature Reviews Cancer 2007, 7(7):545-553. 10.1038/nrc2173 17585334
3. Pinkel D, Albertson D: Array comparative genomic hybridization and its applications to cancer. Nature Genetics 2005, 37:s11-s17. 10.1038/ng1569 15920524
4. Bertucci F, Viens P, Hingamp P, Nasser V, Houlgatte R, Birnbaum D: Breast Cancer Revisited Using Dna Array-Based Gene Expression Profiling. Int J Cancer 2003, 103:565-571. 10.1002/ijc.10867 12494462
5. Kallioniemi A Kallioniemi O Sudar D Rutovitz D Gray J Waldman F Pinkel D Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors Science 1992 258 818 821 10.1126/science.1359641 1359641
6. Veltman J, Fridlyand J, Pejavar S, Olshen A, Korkola J, DeVries S, Pand Kuo W, Carroll Pinkel D, Albertson D, Cordon-Cardo C, Jain A, Waldman F: Array-based Comparative Genomic Hybridization for Genome-Wide Screening of DNA Copy Number in Bladder Tumors. Cancer Research 2003, 63:2872-2880. 12782593
7. Callagy G, Pharoah P, Chin S, Sangan T, Daigo Y, Jackson L, Caldas C: Identification and validation of prognostic markers in breast cancer with the complementary use of array-CGH and tissue microarrays. J Pathol 2005, 205(3):388-396. 10.1002/path.1694 15682439
8. Naylor T, Greshock J, Wang Y, Colligon T, Yu Q, Clemmer V, Zaks T, Weber B: High resolution genomic analysis of sporadic breast cancer using array-based comparative genomic hybridization. Breast Cancer Research 2005, 7(6):R1186-R1198, 1410746 16457699 10.1186/bcr1356
9. Schwaenen C, Nessling M, Wessendorf S, Salvi T, Wrobel G, Radlwimmer B, Kestler H, Haslinger C, Stilgenbauer S, Dohner H, Bentz M, Lichter P: Automated array-based genomic profiling in chronic lymphocytic leukemia: Development of a clinical tool and discovery of recurrent genomic alterations. PNAS 2004, 101(4): 039-1044. 327147 14730057 10.1073/ pnas.0304717101
10. Lai W, Johnson M, Kucherlapati R, Park P: Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 2005, 21(19):3763-3770. 10.1093/bioinformatics/ bti611 16081473
11. Picard F, Robin S, Lavielle M, Vaisse C, Daudin J: A statistical approach for array CGH data analysis. BMC Bioinformatics 2005, 6(27):549559-15705208.
12. Jong K, Marchiori E, van der Vaart A, Ylstra B, Weiss M, Meijer G: Chromosomal Breakpoint Detection in Human Cancer Applications of Evolutionary Computing. EvoBIO: Evolutionary Computation and Bioinformatics, LNCS 2611 Springer 2003, 54-65
13. Jong K, Marchiori E, Meijer G, van der Vaart A, Ylstra B: Breakpoint Identification and Smoothing of array Comparative Genomic Hybridization data. Bioinformatics 2004, 20(18):3636-3637. 10.1093/bioinformatics/ bth355 15201182
14. 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. 10.1093/biostatistics/kxh017 15618527
15. Fridlyand J, Snijders A, Ylstra B: Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 2006. 6(96):1459181-16620391.
16. Hyman E, Kauraniemi P, Impact of DNA Amplification on Gene Expression Patterns in Breast Cancer. Cancer Research 2002, 62:6240-6245. 12414653
17. Guo X, Lui Wea: Identifying cancer-related genes in nasopharyngeal carcinoma cell lines using DNA and mRNA expression profiling analyses. International Journal of Oncology 2002, 21:1197-1204. 12429968
18. Diskin T, Eck SJ, Greshock J, Mosse Y, Naylor T, Stoeckert C Jr, Weber BL, Maris J, Grant G: STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Research 2006, 16(9):1149-1158. 1557772 16899652 10.1101/gr.5076506
19. Furge K, Dykema K, Ho C, Chen X: Comparison of array-based comparative genomic hybridization with gene expression-based regional expression biases to identify genetic abnormalities in hepatocellular carcinoma. BMC Genomics 2005, 6-67. 1134655 15882461
20. Levin D, Ghosh AM, Cho K, Kardia S: A model-based scan statistic for identifying extreme chromosomal regions of gene expression in human tumors. Bioinformatics 2005, 21(12):2867-2874. 10.1093/bioinformatics/ bti417 15814559
21. Yi Y, Mirosevich J, Shyr Y, Matusik R, George A: Coupled analysis of gene expression and chromosomal location. Genomics 2005, 85:401-412. 10.1016/j.ygeno.2004.11.011 15718107
22. Dressman M, Baras A, Malinowski R, Alvis L, Kwon I, Walz T, Polymeropoulos M: Gene expression profiling detects gene amplification and differentiates tumor types in breast cancer. Cancer Research 2003, 63:2194-2199. 12727839
23. Melendez B, Martinez-Delgado B, Cuadros M, Fernandez V, Diaz-Uriarte R, Benitez J: Identification of amplified and highly expressed genes in amplicons of the T-cell line huT78 detected by cDNA microarray CGH, Molecular Cancer 2005, 4-5. 546232 15656903
24. Martinez-Climent JA, Alizadeh AA, Segraves R Blesa, D Rubio-Moscardo, F Albertson DG, Garcia-Conde J, Dyer MJ, Levy R, Pinkel D, Lossos IS: Transformation of follicular lymphoma to diffuse large cell lymphoma is associated with a heterogeneous set of DNA copy number and gene expression alterations. Blood 2003, 101(8):3109-3117. 10.1182/ blood-2002-07-2119 12406872
25. Sanchez-Izquierdo D, Buchonnet G, Siebert R, Gascoyne R, Climent J, Karran L, Marin M, Blesa D, Horsman D, Rosenwald A, Staudt L, Albertson D, Du M, Ye H, Marynen P, Garcia-Conde J, Pinkel D, Dyer M, Martinez-Climent J: MALT1 is deregulated by both chromosomal translocation and amplification in B-cell non-Hodgkin lymphoma. Blood 2003, 101:4539-4546. 10.1182/blood-2002-10-3236 12560219
26. Adler A, Lin M, Horlings H, Nuyten D, van de Vijver M, Chang H: Genetic regulators of large-scale transcriptional signatures in cancer. Nature Genetics 2006, 38(4):1435790-16518402.
27. Tusher V, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. PNAS 2001, 98(9):5116-5121. 33173 11309499 10.1073/pnas.091062498
28. van de Vijver M, He Y, van t Veer L, Dai H, Hart A, Voskuil D, Schreiber G, Peterse J, Roberts C, Marton M, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, van der Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R: A Gene-Expression Signature as a Predictor of Survival in Breast Cancer. The New England Journal of Medicine 2002, 347(25):1999-2009. 10.1056/NEJMoa021967 12490681
29. van Beers E, van Welsem T, Wessels L, Li Y, Oldenburg R, Devilee P, Cornelisse C, Verhoef S, Hogervorst F, van't Veer P, Nederlof LJ: Comparative Genomic Hybridization Profiles in Human BRCA1 and BRCA2 Breast Tumors Highlight Differential Sets of Genomic Aberrations. Cancer Research 2005 65(3);822-827. 15705879
30. Perou C, Sorlie T, Eisen M, van de Rijn M, Jeffrey S, Rees C, Pollack J, Ross D, Johnsen H, Akslen L, Fluge O, Pergamenschikov A, Williams C, Zhu S, Lonning P, Borresen-Dale A, Brown P, Botstein D: Molecular portraits of human breast tumours Nature 2000. 406(6797):747-752. 10.1038/35021093 10963602
31. Sorlie T, Perou C, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen M, van de Rijn M, Jeffrey S, Thorsen T, Quist H, Matese J, Brown P, Botstein D, Lonning E, Borresen-Dale A: Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications PNAS 2001, 98(19):10869-10864. 58566 11553815 10.1073/ pnas.191367098
32. Sorlie T, Tibshirani R, Parker J, Hastie T, Marron J, Nobel S, Deng A, Johnsen H, Pesich R, Geisler S, Demeter J, Perou C, Lonning P, Brown P, Borresen-Dale A, Botstein D: Repeated observation of breast tumor subtypes in independent gene expression data sets. PNAS 2003, 100(14):8418-8423. 166244 12829800 10.1073/pnas.0932692100
33. Bergamaschi A, Kim Y, Wang P, Sorlie T, Hernandez-Boussard T, Lonning P, Tibshirani R, Borresen-Dale A, Pollack J: Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer Genes Chromosomes Cancer 2006, 45(11):1033-1040. 10.1002/gcc.20366 16897746
34. Olshen A, Venkatraman E, Lucito R, Wigler M: Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004, 5(4):557-572. 10.1093/biostatistics/kxh008 15475419
35. Kauraniemi P, Barlund M, Monni O, Kallioniemi A: New Amplified and Highly Expressed Genes Discovered in the ERBB2 Amplicon in Breast Cancer by cDNA Microarrays. Cancer Research 2001, 61:8235-8240. 11719455
36. Reyal F, Stransky N, Bernard-Pierrot I, Vincent-Salomon A, de Rycke Y, Elvin P, Cassidy A, Graham A, Spraggon C, Desille Y, Fourquet A, Nos C, Pouillart P, Magdelenat H, Stoppa-Lyonnet D, Couturier J, Sigal-Zafrani B, Asselain B, Sastre-Garau X, Delattre O, Thiery J, Radvanyi F: Visualizing Chromosomes as Transcriptome Correlation Maps: Evidence of Chromosomal Domains Containing Co-expressed Genes. A Study of 130 Invasive Ductal Breast Carcinomas. Cancer Research 2005, 65(4):1376-1383. 10.1158/0008-5472.CAN-04-2706 15735024
37. Saramaki O, Porkka K, Vessella R, Visakorpi T: Genetic aberrations in prostate cancer by microarray analysis. Int J Cancer 2006, 119:1322-1329. 10.1002/ijc.21976 16642477
38. Chin K, DeVries S, Fridlyand J, Spellman P, Roydasgupta R, Kuo W, Lapuk A, Neve R, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng Z, Chew K, Pinkel D, Jain A, Ljung B, Esserman L, Albertson D, Waldman F, Gray J: Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 2006, 10:529-541. 10.1016/j.ccr.2006.10.009 17157792
39. Nymark P, Wikman H, Ruosaari S, Hollmen G, Vanhala E, Karjalainen A, Anttila S, Knuutila S: Identification of Specific Gene Copy Number Changes in Asbestos-Related Lung Cancer. Cancer Research 2006, 66(11):5737-5743. 10.1158/0008-5472.CAN-06-0199 16740712