SNP and gene networks construction and analysis from classification of copy number variations data

BMC Bioinformatics

Volumn 12, Issue SUPPL.5, 2011, Pages

  Liu, Yang ^a   Lee, Yiu F ^a   Ng, Michael K ^a  

^a HONG KONG BAPTIST UNIVERSITY   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL ANALYSIS; BIOLOGICAL PROCESS; CLASSIFICATION MODELS; COPY NUMBER VARIATIONS; DNA COPY NUMBERS; FUNCTIONAL RELATIONSHIP; GENOMIC DNA COPY NUMBERS; STATISTICAL SOFTWARE;

COMPLEX NETWORKS; MATHEMATICAL MODELS;

GENES;

ARTICLE; CASE CONTROL STUDY; COMPUTER PROGRAM; COPY NUMBER VARIATION; GENE REGULATORY NETWORK; GENETIC ASSOCIATION; GENETICS; HIRSCHSPRUNG DISEASE; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; SINGLE NUCLEOTIDE POLYMORPHISM;

CASE-CONTROL STUDIES; DIABETES MELLITUS, TYPE 1; DNA COPY NUMBER VARIATIONS; GENE REGULATORY NETWORKS; GENOME-WIDE ASSOCIATION STUDY; HIRSCHSPRUNG DISEASE; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 79960713932     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S5-S4     Document Type: Article

References (42)

1. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nature Reviews Genetics 2006, 7:85-97.
2. Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler-Smith C, Hurles ME, Carter NP, Scherer SW, Lee C. Copy number variation: New insights in genome diversity. Genome Research 2006, 16:949-961. 10.1101/gr.3677206, 16809666.
3. 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. 10.1126/science.1098918, 15273396.
4. Iafrate AJ, Feuk L, Riveral MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. Detection of large-scale variation in the human genome. Nature Genetics 2004, 36:949-951. 10.1038/ng1416, 15286789.
5. Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK. A high-resolution survey of deletion polymorphism in the human genome. Nature Genetics 2006, 38:75-81. 10.1038/ng1697, 16327808.
6. McCarroll 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. Nature Genetics 2006, 38:86-92. 10.1038/ng1696, 16468122.
7. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME. Global variation in copy number in the human genome. Nature 2006, 444:444-454. 10.1038/nature05329, 2669898, 17122850.
8. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992, 258:818-821. 10.1126/science.1359641, 1359641.
9. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung B, Gray JW, Albertson DG. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genetics 1998, 20:207-211. 10.1038/2524, 9771718.
10. 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.
11. Pique-Regi R, Monso-Varona J, Ortega A, Seeger RC, Triche TJ, Asgharzadeh S. Sparse representation and Bayesian detection of genome copy number alterations from microarray data. Bioinformatics 2008, 24(3):309-318. 10.1093/bioinformatics/btm601, 2704547, 18203770.
12. Wu LY, Chipman HA, Bull SB, Briollais L, Wang K. A Bayesian segmentation approach to ascertain copy number variations at the population level. Bioinformatics 2009, 25(13):1669-1679. 10.1093/bioinformatics/btp270, 19389735.
13. Chen J, Wang YP. A Statistical Change Point Model Approach for the Detection of DNA Copy Number Variations in Array CGH Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2009, 6:529-541.
14. Oldridge DA, Banerjee S, Setlur SR, Sboner A, Demichelis F. Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays. Nucleic Acids Research 2010, 38:3275-3286. 10.1093/nar/gkq073, 2879534, 20156996.
15. Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen T, Girard L, Minna J, Christiani D, Leo C, Gray JW, Sellers WR, Meyerson M. An Integrated View of Copy Number and Allelic Alterations in the Cancer Genome Using Single Nucleotide Polymorphism Arrays. Cancer Research 2004, 64:3060-3071. 10.1158/0008-5472.CAN-03-3308, 15126342.
16. 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.
17. Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, Bassett AS, Seller A, Holmes CC, Ragoussis J. QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Research 2007, 35:2013-2025. 10.1093/nar/gkm076, 1874617, 17341461.
18. Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SFA, Hakonarson H, Bucan M. Penn CNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Research 2007, 17:1665-1674. 10.1101/gr.6861907, 2045149, 17921354.
19. Bastian BC, Olshen AB, LeBoit PE, Pinkel D. Classifying Melanocytic Tumors Based on DNA Copy Number Changes. American Journal of Pathology 2003, 163:1765-1770. 10.1016/S0002-9440(10)63536-5, 1892437, 14578177.
20. O'Hagan RC, Brennan CW, Strahs A, Zhang X, Kannan K, Donovan M, Cauwels C, Sharpless NE, Wong WH, Chin L. Array Comparative Genome Hybridization for Tumor Classification and Gene Discovery in Mouse Models of Malignant Melanoma. Cancer Res 2003, 63:5352-5356.
21. Baumbusch LO, Aaroe J, Johansen FE, Hicks J, Sun H, Bruhn L, Gunderson K, Naume B, Kristensen VN, Liestol K, Borresen-Dale AL, Lingjaerde OC. Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors. BMC Genomics 2008, 9:379. 10.1186/1471-2164-9-379, 2547478, 18691401.
22. Myllykangas S, Tikka J, Bohling T, Knuutila S, Hollmen J. Classification of human cancers based on DNA copy number amplification modeling. BMC Medical Genomics 2008, 1:15. 10.1186/1755-8794-1-15, 2397431, 18477412.
23. Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, Cawley S, Hubbell E, Veitch J, Collins PJ, Darvishi K, Lee C, Nizzari MM, Gabriel SB, Purcell S, Daly MJ, Altshuler D. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nature Genetics 2008, 40:1253-1260. 10.1038/ng.237, 2756534, 18776909.
24. 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 Oligonucleotide Single Nucleotide Polymorphism Genotyping Arrays. Cancer Res 2005, 65:6071-6079. 10.1158/0008-5472.CAN-05-0465, 16024607.
25. Li C, Wong WH. DNA-Chip Analyzer (dChip). The analysis of gene expression data: methods and software 2003, 120-141. New York: Springer, Parmigiani G, Garrett ES, Irizarry R, Zeger SL.
26. Lin M, Wei LJ, Sellers WR, Lieberfarb M, Wong WH, Li C. dChipSNP: Significance Curve and Clustering of SNP-Array-Based Loss-of-Heterozygosity Data. Bioinformatics 2004, 20:1233-1240. 10.1093/bioinformatics/bth069, 14871870.
27. Hupe P, Stransky N, Thiery J, Radvanyi F, Barillot E. Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics 2004, 20:3413-3422. 10.1093/bioinformatics/bth418, 15381628.
28. Peiffer DA, Le JM, Steemers FJ, Chang W, Jenniges T, Garcia F, Haden K, Li J, Shaw CA, Belmont J, Cheung SW, Shen RM, Barker DL, Gunderson KL. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res 2006, 16(9):1136-1148. 10.1101/gr.5402306, 1557768, 16899659.
29. Bair E, Tibshirani R. Machine learning method applied to DNA microarray data can improve the diagnosis of cancer. SIGKDD Explorations 2003, 5:48-55.
30. Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A. 2002, 99(10):6567-6572. 10.1073/pnas.082099299, 124443, 12011421.
31. PLINK. , http://pngu.mgh.harvard.edu/purcell/plink
32. Burton P. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007, 447:661-678. 10.1038/nature05911, 2719288, 17554300.
33. Hovind P, Hansen TK, Tarnow L, Thiel S, Steffensen R, Flyvbjerg A, Parving H. Mannose-Binding Lectin as a Predictor of Microalbuminuria in Type 1 Diabetes. Diabetes 2005, 54:1523-1527. 10.2337/diabetes.54.5.1523, 15855341.
34. Maassen A, 't Hart LM, van Essen E, Heine RJ, Nijpels G, Tafrechi RSJ, Raap AK, Janssen GMC, Lemkes HH. Mitochondrial Diabetes: Molecular Mechanisms and Clinical Presentation. Diabetes 2004, 53:S103-S109. 10.2337/diabetes.53.2007.S103, 14749274.
35. Tarsio JF, Reger LA, Furcht LT. Molecular mechanisms in basement membrane complications of diabetes. Alterations in heparin, laminin, and type IV collagen association. Diabetes 1988, 37:532-539. 10.2337/diabetes.37.5.532, 3360214.
36. Bioconductor. , http://www.bioconductor.org
37. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
38. Schlicker A, Domingues FS, Rahnenfuhrer J, Lengauer T. A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 2006, 7:302.1-302.16. 1559652, 16776819.
39. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504. 10.1101/gr.1239303, 403769, 14597658.
40. Zheng Q, Wang XJ. GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res 2008, 36(Web Server issue):W358-363. 2447756, 18487275.
41. Korbel JO, Tirosh-Wagner T, Urban AE, Chen XN, Kasowski M, Dai L, Grubert F, Erdman C, Gao MC, Lange K, Sobel EM, Barlow GM, Aylsworth AS, Carpenter NJ, Clark RD, Cohen MY, Doran E, Falik-Zaccai T, Lewin SO, Lott IT, McGillivray BC, Moeschler JB, Pettenati MJ, Pueschel SM, Rao KW, Shaffer LG, Shohat M, Riper AJV, Warburton D, Weissman S, Gerstein MB, Snyder M, Korenberg JR. The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. PNAS 2009, 106:12031-12036. 10.1073/pnas.0813248106, 2709665, 19597142.
42. Yamakawa K, Huot YK, Haendelt MA, Hubert R, Chen XN, Lyons GE, Korenberg JR. DSCAM: a novel member of the immunoglobulin superfamily maps in a Down syndrome region and is involved in the development of the nervous system. Human Molecular Genetics 1998, 7:227-237. 10.1093/hmg/7.2.227, 9426258.