Discriminant Analysis of Lung Cancer Using Nonlinear Clustering of Copy Numbers

References

• Muggeo VM, Adelfio G. Efficient change point detection for genomic sequences of continuous measurements. Bioinformatics. 2011;27(2):161–166. doi:10.1093/bioinformatics/btq647.
   PubMed Web of Science ®Google Scholar
• Wang Y, Wu C, Ji Z, Wang B, Liang Y. Non-parametric change-point method for differential gene expression detection. PLoS One. 2011;6(5):e20060. doi:10.1371/journal.pone.0020060.
   PubMed Web of Science ®Google Scholar
• Lai Y, Zhao H. A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data. Comput Biol Chem. 2005;29(1):47–54. doi:10.1016/j.compbiolchem.2004.12.004.
   PubMed Web of Science ®Google Scholar
• Li W, Lee A, Gregersen PK. Copy-number-variation and copy-number alteration region detection by cumulative plots. BMC Bioinformatics. 2009;10(S1):S67. doi:10.1186/1471-2105-10-S1-S67.
   PubMedGoogle Scholar
• Takeuchi I, Tagawa H, Tsujikawa A, Nakagawa M, Katayama-Suguro M, Guo Y, et al. 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. 2009;94(1):61–69. doi:10.3324/haematol.12986.
   PubMed Web of Science ®Google Scholar
• Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet. 1999;23(1):41–46. doi:10.1038/12640.
   PubMed Web of Science ®Google Scholar
• Carter NP. Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet. 2007;39(S7):S16–S21. doi:10.1038/ng2028.
   PubMedGoogle Scholar
• Li C, Wong WH. DNA-chip analyzer (dChip). In: Parmigiani E.G. G, Irizarry R, Zeger SL, editors. The analysis of gene expression data: methods and software. New York (NY): Springer; 2003. p. 12.
   Google Scholar
• Davies H, Dicks E, Stephens P, Cox C, Teague J, Greenman C, et al. High throughput DNA sequence variant detection by conformation sensitive capillary electrophoresis and automated peak comparison. Genomics. 2006;87(3):427–432. doi:10.1016/j.ygeno.2005.11.008.
   PubMed Web of Science ®Google Scholar
• Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. 2004;5(4):557–572. doi:10.1093/biostatistics/kxh008.
   PubMed Web of Science ®Google Scholar
• Hsu L, Al e. Denoising array-based comparative genomic hybridization data using wavelets. Biostatistics. 2005;6(2):211–226. doi:10.1093/biostatistics/kxi004.
   PubMed Web of Science ®Google Scholar
• Kallioniemi A, Kallioniemi O, Sudar D, Rutovitz D, Gray J, Waldman F, et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science. 1992;258(5083):818–821. doi:10.1126/science.1359641.
   PubMed Web of Science ®Google Scholar
• Kallioniemi OP, Kallioniemi A, Kurisu W, Thor A, Chen LC, Smith HS, et al. ERBB2 amplification in breast cancer analyzed by fluorescence in situ hybridization. Proc Natl Acad Sci. 1992;89(12):5321–5325. doi:10.1073/pnas.89.12.5321.
   PubMed Web of Science ®Google Scholar
• Koski TA, Lehtonen HJ, Jee KJ, Ninomiya S, Joosse SA, Vahteristo P, et al. 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. 2009;48(7):544–551. doi:10.1002/gcc.20663.
   PubMed Web of Science ®Google Scholar
• Oga A. Loss of 6q or 8p23 is associated with the total number of DNA copy number aberrations in adenoid cystic carcinoma. Oncol Rep. 2011;26:1393–1398. doi:10.3892/or.2011.1446.
   PubMed Web of Science ®Google Scholar
• Thomas R, Seiser EL, Motsinger-Reif A, Borst L, Valli VE, Kelley K, et al. Refining tumor-associated aneuploidy through ‘genomic recoding’ of recurrent DNA copy number aberrations in 150 canine non-Hodgkin lymphomas. Leuk Lymphoma. 2011;52(7):1321–1335. doi:10.3109/10428194.2011.559802.
   PubMed Web of Science ®Google Scholar
• Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005;437(7057):376–380. doi:10.1038/nature03959.
   PubMed Web of Science ®Google Scholar
• Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet. 2008;9:387–402. doi:10.1146/annurev.genom.9.081307.164359.
   PubMed Web of Science ®Google Scholar
• Ansorge WJ. Next-generation DNA sequencing techniques. N Biotechnol. 2009;25(4):195–203. doi:10.1016/j.nbt.2008.12.009.
   PubMed Web of Science ®Google Scholar
• Eichler EE, Flint J, Gibson G, Kong A, Leal S, Moore J, et al. Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet. 2010;11(6):446–450. doi:10.1038/nrg2809.
   PubMed Web of Science ®Google Scholar
• Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA. 2009;106(23):9362–9367. doi:10.1073/pnas.0903103106.
   PubMed Web of Science ®Google Scholar
• Li B, Leal S. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet. 2008;83(3):311–321. doi:10.1016/j.ajhg.2008.06.024.
   PubMed Web of Science ®Google Scholar
• Madsen B, Browning S. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet. 2009;5(2):e1000384. doi:10.1371/journal.pgen.1000384.
   PubMed Web of Science ®Google Scholar
• Morgenthaler S, Thilly WG. A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST). Mutat Res. 2007;615(1–2):28–56. doi:10.1016/j.mrfmmm.2006.09.003.
   PubMed Web of Science ®Google Scholar
• Li B, Leal S. Discovery of rare variants via sequencing: implications for the design of complex trait association studies. PLoS Genet. 2009;5(5):e1000481. doi:10.1371/journal.pgen.1000481.
   PubMed Web of Science ®Google Scholar
• Price A, Kryukov G, de Bakker P, Purcell S, Staples J, Wei L, et al. Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet. 2010;86(6):832–838. doi:10.1016/j.ajhg.2010.04.005.
   PubMed Web of Science ®Google Scholar
• Little J, Bradley L, Bray MS, Clyne M, Dorman J, Ellsworth DL, et al. Reporting, appraising, and integrating data on genotype prevalence and gene-disease associations. Am J Epidemiol. 2002;156(4):300–310. doi:10.1093/oxfordjournals.aje.a000179.
   PubMed Web of Science ®Google Scholar
• Takeuchi I, Tagawa H, Tsujikawa A, Nakagawa M, Katayama-Suguro M, Guo Y, et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet. 1999;23(1):41. doi:10.1038/12640.
   PubMed Web of Science ®Google Scholar
• Kim TM, Yim SH, Lee JS, Kwon MS, Ryu JW, Kang HM, et al. Genome-wide screening of genomic alterations and their clinicopathologic implications in non–small cell lung cancers. Clin Cancer Res. 2005;11(23):8235–8242. doi:10.1158/1078-0432.CCR-05-1157.
   PubMed Web of Science ®Google Scholar
• Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, et al. Characterizing the cancer genome in lung adenocarcinoma. Nature. 2007;450(7171):893–898. doi:10.1038/nature06358.
   PubMed Web of Science ®Google Scholar
• Huang YT, Lin X, Liu Y, Chirieac LR, McGovern R, Wain J, et al. Cigarette smoking increases copy number alterations in nonsmall-cell lung cancer. Proc Natl Acad Sci USA. 2011;108:16345–16350. doi:10.1073/pnas.1102769108.
   PubMed Web of Science ®Google Scholar
• Huang YT, Lin X, Chirieac LR, McGovern R, Wain JC, Heist RS, et al. Impact on disease development, genomic location and biological function of copy number alterations in non-small cell lung cancer. PLoS One. 2011;6(8):e22961. doi:10.1371/journal.pone.0022961.
   PubMed Web of Science ®Google Scholar
• Kachouie NN, Lin X, Schwartzman A. FDR control of detected regions by multiscale matched filtering. Commun Stat. 2017;46(1):127–144. doi:10.1080/03610918.2014.957842.
   Google Scholar
• Kachouie NN, Lin X, Christiani DC, Schwartzman A. Detection of local DNA copy number changes in lung cancer population analyses using a multi-scale approach. Commun Stat. 2015;1(4):206–216. doi:10.1080/23737484.2016.1197079.
   Google Scholar
• Kachouie NN, Christiani DC. DNA copy number gain in lung cancer and non-involved tissue. J Bioanal Biostat. 2016;1(1):1–5.
   Google Scholar
• Kachouie NN, Deebani W, Christiani DC. Identifying similarities and disparities between DNA copy number changes in cancer and matched blood samples. Cancer Invest. 2019;37(10):535–545. doi:10.1080/07357907.2019.1667368.
   PubMed Web of Science ®Google Scholar
• Nagi S, Bhattacharyya DK. Cluster analysis of cancer data using semantic similarity, sequence similarity and biological measures. Netw Model Anal Health Inform Bioinformatics. 2014;3(1):67. doi:10.1007/s13721-014-0067-9.
   Google Scholar
• Zhu Y, Li H, Miller DJ, Wang Z, Xuan J, Clarke R, et al. caBIG™ VISDA: modeling, visualization, and discovery for cluster analysis of genomic data. BMC Bioinformatics. 2008;9(1):383. doi:10.1186/1471-2105-9-383.
   PubMedGoogle Scholar
• Gentleman R, Vincent C, Wolfgang H, Rafael I, Sandrine D, editors. Bioinformatics and computational biology solutions using R and Bioconductor. Berlin (Germany): Springer Science & Business Media; 2006.
   Google Scholar
• Campbell C. An introduction to kernel methods. Stud Fuzziness Soft Comput. 2011;66:155–192.
   Google Scholar
• Dhillon IS, Guan Y, Kulis B. Kernel k-means: spectral clustering and normalized cuts. Proceedings of the tenth ACM SIGKDD international conference on Knowledge discovery and data mining. New York, NY: ACM; 2004. p. 551–556.
   Google Scholar
• Baykara O, Bakir B, Buyru N, Kaynak K, Dalay N. Amplification of chromosome 8 genes in lung cancer. J Cancer. 2015;6(3):270–275. doi:10.7150/jca.10638.
   PubMed Web of Science ®Google Scholar
• Björkqvist AM, Tammilehto L, Nordling S, Nurminen M, Anttila S, Mattson K, et al. Comparison of DNA copy number changes in malignant mesothelioma, adenocarcinoma and large-cell anaplastic carcinoma of the lung. Br J Cancer. 1998;77(2):260–269. doi:10.1038/bjc.1998.42.
   PubMed Web of Science ®Google Scholar
• Luk C, Tsao MS, Bayani J, Shepherd F, Squire JA. Molecular cytogenetic analysis of non-small cell lung carcinoma by spectral karyotyping and comparative genomic hybridization. Cancer Genet Cytogenet. 2001;125(2):87–99. doi:10.1016/S0165-4608(00)00363-0.
   PubMedGoogle Scholar
• Pei J, Balsara BR, Li W, Litwin S, Gabrielson E, Feder M, et al. Genomic imbalances in human lung adenocarcinomas and squamous cell carcinomas. Genes Chromosom Cancer. 2001;31(3):282–287. doi:10.1002/gcc.1145.
   PubMed Web of Science ®Google Scholar
• Petersen I, Bujard M, Petersen S, Wolf G, Goeze A, Schwendel A, et al. Patterns of chromosomal imbalances in adenocarcinoma and squamous cell carcinoma of the lung. Cancer Res. 1997;57(12):2331–2335.
   PubMed Web of Science ®Google Scholar
• Balsara BR, Testa JR. Chromosomal imbalances in human lung cancer. Oncogene. 2002;21(45):6877–6883. doi:10.1038/sj.onc.1205836.
   PubMed Web of Science ®Google Scholar