Çokgen: A software for the identification of rare copy number variation from SNP microarrays

Pacific Symposium on Biocomputing 2010, PSB 2010

Volumn , Issue , 2010, Pages 371-382

  Yavaş, Gökhan ^a   Koyutürk, Mehmet ^a,b   Özsoyoǧlu, Meral ^a   Gould, Meetha P ^b   Laframboise, Thomas ^b  

^a Case Western Reserve University   (United States)

^b CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADJUSTABLE PARAMETERS; ALGORITHMIC PROBLEMS; ALZHEIMER DISEASE; CONFIGURABILITY; COPY NUMBER; CROHN'S DISEASE; EXPERIMENTAL PLATFORM; GENOMICS; HUMAN CELLS; MODEL-BASED METHOD; OBJECTIVE FUNCTIONS; OPTIMIZATION PROBLEMS; SINGLE NUCLEOTIDE POLYMORPHISM ARRAYS; TARGET APPLICATION;

DISEASES; GENES; HEURISTIC METHODS; IDENTIFICATION (CONTROL SYSTEMS); OPTIMIZATION;

C (PROGRAMMING LANGUAGE);

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER PROGRAM; COPY NUMBER VARIATION; DNA MICROARRAY; GENETIC MARKER; GENOMICS; HUMAN; HUMAN GENOME; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICS; VALIDATION STUDY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DNA COPY NUMBER VARIATIONS; GENETIC MARKERS; GENOME, HUMAN; GENOMICS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 77954310602     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (35)

1. International HapMap Consortium. Nature, 437(7063): 1241-2 (2005).
2. Affymetrix. Genome-Wide Human SNP Array 6.0 data sheet. Santa Clara (California) (2007).
3. Illumina. Human1M-duo beadchip data sheet. San Diego (California) (2007).
4. Feuk L, Carson AR, Scherer SW. Nat Rev Genet, 7(2): 85-97 (2006).
5. Iafrate AJ, Feuk L, Rivera MN, et al. Nat Genet, 36(9):949-51 (2004).
6. Tuzun E, Sharp AJ, Bailey JA, et al. Nat Genet, 37(7):727-32 (2005).
7. Redon R, Ishikawa S, Fitch KR, et al. Nature, 444(7118):444-54 (2006).
8. Korbel JO, Urban AE, Affourtit JP, et al. Science, 318(5849):420-6 (2007).
9. Rovelet-Lecrux A, Hannequin D, Raux G, et al. Nat Genet, 38(1):24-6 (2006).
10. Fellermann K, Stange DE, Schaeffeler E, et al. Am J Hum Genet, 79(3):439-48 (2006).
11. Sebat J, Lakshmi B, Malhotra D, et al. Science, 316(5823):445-9 (2007).
12. Xu B, Roos JL, Levy S, et al. Nat Genet, 40(7):880-5 (2008).
13. Zhao X, Li C, Paez JG, et al. Cancer Res, 64(9):3060-71 (2004).
14. Peiffer DA, Le JM, Steemers FJ, et al. Genome Res, 16(9):1136-48 (2006).
15. Gunderson KL, Steemers FJ, Lee G, et al. Nat Genet, 37(5):549-54 (2005).
16. Lindblad-Toh K, Tanenbaum DM, Daly MJ, et al. Nat Biotechnol, 18(9):1001-5 (2000).
17. Bolstad BM, Irizarry RA, Astrand M, et al. Bioinformatics, 19(2):185-93 (2003).
18. Lin M, Wei LJ, Sellers WR, et al. Bioinformatics, 20:1233-40 (2004).
19. Laframboise T, Harrington D, Weir BA. Biostatistics, 8(2):323-36 (2007).
20. Bengtsson H, Irizarry R, Carvalho B, et al. Bioinformatics, 24(6):759-67 (2008).
21. Korn JM, Kuruvilla FG, McCarroll SA, et al. Nat Genet, 40(10):1253-60 (2008).
22. Zhao X, Weir BA, LaFramboise T, et al. Cancer Res, 65(13):5561-70 (2005).
23. Olshen AB, Venkatraman ES, Lucito R, et al. Biostatistics, 5(4):557-72 (2004).
24. Venkatraman ES, Olshen AB. Bioinformatics, 23(6):657-63 (2007).
25. Polzehl J, Spokoiny S. J R Stat Soc, Ser B, 62(2):335-354 (2000).
26. Hupé P, Stransky N, Thiery JP, et al. Bioinformatics, 20(18):3413-22 (2004).
27. Affymetrix File Parsing SDK [http://www.bioconductor.org/packages/2.2/ bioc/html/affxparser.html].
28. McCarroll SA, Kuruvilla FG, Korn JM, et al. Nat Genet, 40(10):1166-74 (2008).
29. Kirkpatrick S, Gelatt CD Jr, Vecchi MP. Science, 220(4598):671-680 (1983).
30. dChip Software Website [http://www.dchip.org].
31. Li C, Wong WH. PNAS, 98:31-6 (2001).
32. Pinto D, Marshall C, Feuk L, et al. Hum Mol Genet, 16 Spec No. 2:R168-73 (2007).
33. Database of Genomic Variants [http://projects.tcag.ca/variation/].
34. Schouten JP, McElgunn CJ, Waaijer R, et al. Nucleic Acids Res, 30(12): e57 (2002).
35. LaFramboise Lab Software Website [http://mendel.gene.cwru.edu/ laframboiselab/software.php].