Detection of local DNA copy number changes in lung cancer population analyses using a multi-scale approach

References

• Benjamini, Y., and Y. Hochberg. 1995. “Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing.” Journal of the Royal Statistical Society B 57:12.
   Google Scholar
• Carter, N. P. 2007. “Methods and Strategies for Analyzing Copy Number Variation Using DNA Microarrays.” Nature Genetics 39(7 Suppl):S16–21.
   PubMed Web of Science ®Google Scholar
• Davies, H., et al. 2006. “High Throughput DNA Sequence Variant Detection by Conformation Sensitive Capillary Electrophoresis and Automated Peak Comparison.” Genomics 87(3):427–32.
   PubMed Web of Science ®Google Scholar
• Hsu, L., et al. 2005. “Denoising Array-Based Comparative Genomic Hybridization Data Using Wavelets.” Biostatistics 6(2):211–26.
   PubMed Web of Science ®Google Scholar
• Huang, Y. T., X. Lin, L. R. Chirieac, et al. 2011. “Impact On Disease Development, Genomic Location and Biological Function of Copy Number Alterations in Non-Small Cell Lung Cancer.” PloS One 6(8):e22961.
   PubMed Web of Science ®Google Scholar
• Huang, Y. T., X. Lin, Y. Liu, et al. 2011. Cigarette Smoking Increases Copy Number Alterations in Nonsmall-Cell Lung Cancer. Proceedings of the National Academy of Sciences of the United States of America.
   Google Scholar
• Kachouie, N. N., X. Lin, and A. Schwartzman. 2014. “FDR Control of Detected Regions by Multi-Scale Matched Filtering.” Communications in Statistics--Simulation and Computation. Advance online publication. doi:10.1080/03610918.2014.957842
   PubMedGoogle Scholar
• Kallioniemi, A., et al. 1992. “Comparative Genomic Hybridization for Molecular Cytogenetic Analysis of Solid Tumors.” Science 258(5083):818–21.
   PubMed Web of Science ®Google Scholar
• Kallioniemi, O. P., et al. 1992. “ERBB2 Amplification in Breast Cancer Analyzed by Fluorescence in Situ Hybridization.” Proceedings of the National Academy of Sciences of the United States of America 89(12):5321–5.
   PubMed Web of Science ®Google Scholar
• Koski, T. A., et al. 2009. “Array Comparative Genomic Hybridization Identifies a Distinct DNA Copy Number Profile in Renal Cell Cancer Associated With Hereditary Leiomyomatosis and Renal Cell Cancer.” Genes, Chromosomes & Cancer 48(7):544–51.
   PubMed Web of Science ®Google Scholar
• Lai, Y., and H. Zhao. 2005. “A Statistical Method to Detect Chromosomal Regions with DNA Copy Number Alterations using SNP-Array-Based CGH Data.” Computational Biology and Chemistry 29(1):47–54.
   PubMed Web of Science ®Google Scholar
• Li, C., and W. H. Wong. 2003. “The Analysis of Gene Expression Data: Methods and Software.” In DNA-Chip Analyzer (dChip), edited by E. G. G Parmigiani, R Irizarry, and S. L Zeger, 12. NY: Springer.
   Google Scholar
• Li, W., A. Lee, and P. K. Gregersen. 2009. “Copy-Number-Variation and Copy-Number-Alteration Region Detection by Cumulative Plots.” BMC Bioinformatics 10 Suppl 1:S67.
   PubMed Web of Science ®Google Scholar
• Liao, P. S., Chen, T. S., Chung, P. C.. 2001. “A Fast Algorithm for Multilevel Thresholding.” Journal. Information. Science Engineering 17(5):713–27.
   Web of Science ®Google Scholar
• Muggeo, V. M., and G. Adelfio. 2011. “Efficient Change Point Detection for Genomic Sequences of Continuous Measurements.” Bioinformatics 27(2):161–6.
   PubMed Web of Science ®Google Scholar
• Oga, A., et al. 2011. “Loss of 6q or 8p23 Is Associated With the Total Number of DNA Copy Number Aberrations in Adenoid Cystic Carcinoma.” Oncology Reports 26:1393–8.
   Google Scholar
• Olshen, A. B., et al. 2004. “Circular Binary Segmentation for the Analysis of Array-Based DNA Copy Number Data.” Biostatistics 5(4):557–72.
   PubMed Web of Science ®Google Scholar
• Pollack, J. R., et al. 1999. “Genome-Wide Analysis of DNA Copy-Number Changes Using cDNA Microarrays.” Nature Genetics 23(1):41–6.
   PubMed Web of Science ®Google Scholar
• Schwartzman, A., A. Jaffe, Y. Gavrilov, and C. A Meyer. 2013. “Multiple Testing of Local Maxima for Detection of Peaks in ChIP-Seq Data.” Annals of Applied Statistics 7(1):471–494.
   PubMed Web of Science ®Google Scholar
• Takeuchi, I., et al. 2009. “The Potential of Copy Number Gains and Losses, Detected by Array-Based Comparative Genomic Hybridization, for Computational Differential Diagnosis of B-cell Lymphomas and Genetic Regions Involved in Lymphomagenesis.” Haematologica 94(1):61–9.
   PubMed Web of Science ®Google Scholar
• Thomas, R., et al. 2011. “Refining Tumor-Associated Aneuploidy Through ‘Genomic Recoding’ of Recurrent DNA Copy Number Aberrations in 150 Canine Non-Hodgkin Lymphomas.” Leukemia & Lymphoma 52(7):1321–35.
   PubMed Web of Science ®Google Scholar
• Wang, Y., et al. 2011. “Non-Parametric Change-Point Method for Differential Gene Expression Detection.” PloS one 6(5):e20060.
   PubMed Web of Science ®Google Scholar
• Weir, B. A., et al. 2007. “Characterizing the Cancer Genome in Lung Adenocarcinoma.” Nature 450(7171):893–8.
   PubMed Web of Science ®Google Scholar