Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Flibotte, Stephane ^a   Moerman, Donald G ^b,c  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; HELMINTH DNA;

ARTICLE; CAENORHABDITIS ELEGANS; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; CROSS HYBRIDIZATION; DNA DETERMINATION; DNA MICROARRAY; DNA STRUCTURE; FEMALE; GENE DELETION; GENE FREQUENCY; GENETIC ENGINEERING; HUMAN; MALE; MELTING POINT; NONHUMAN; NUCLEOTIDE SEQUENCE; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; ANIMAL; COMPARATIVE STUDY; GENETICS; GENOME; METHODOLOGY; OLIGONUCLEOTIDE PROBE; SENSITIVITY AND SPECIFICITY;

CAENORHABDITIS ELEGANS;

ANIMALS; BASE SEQUENCE; CAENORHABDITIS ELEGANS; DNA, HELMINTH; GENOME, HELMINTH; GENOME, HUMAN; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; RESEARCH DESIGN; SENSITIVITY AND SPECIFICITY; SEQUENCE DELETION;

EID: 55349108569     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-497     Document Type: Article

References (29)

1. 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 Res 2006, 16:949-961. 10.1101/gr.3677206 16809666
2. 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 González JR Gratacòs 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 17122850
3. Sebat J Lakshmi B Malhotra D Troge J Lese-Martin C Walsh T Yamrom B Yoon S Krasnitz A Kendall J Leotta A Pai D Zhang R Lee YH Hicks J Spence SJ Lee AT Puura K Lehtimäki T Ledbetter D Gregersen PK Bregman J Sutcliffe JS Jobanputra V Chung W Warburton D King MC Skuse D Geschwind DH Gilliam TC Ye K Wigler M Strong association of de novo copy number mutations with autism Science 2007, 316:445-449. 10.1126/science.1138659 17363630
4. Walsh T McClellan JM McCarthy SE Addington AM Pierce SB Cooper GM Nord AS Kusenda M Malhotra D Bhandari A Stray SM Rippey CF Roccanova P Makarov V Lakshmi B Findling RL Sikich L Stromberg T Merriman B Gogtay N Butler P Eckstrand K Noory L Gochman P Long R Chen Z Davis S Baker C Eichler EE Meltzer PS Nelson SF Singleton AB Lee MK Rapoport JL King MC Sebat J Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia Science 2008, 320:539-543. 10.1126/science.1155174 18369103
5. Maydan JS Flibotte S Edgley ML Lau J Selzer RR Richmond TA Pofahl NJ Thomas JH Moerman DG Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization Genome Res 2007, 17:337-347. 1800925 17267812 10.1101/gr.5690307
6. Egan CM Sridhar S Wigler M Hall IM Recurrent DNA copy number in the laboratory mouse Nat Genet 2007, 39:1384-1389. 10.1038/ng.2007.19 17965714
7. Kane MD Jatkoe TA Stumpf CR Lu J Thomas JD Madore SJ Assessment of the sensitivity and specificity of oligonucleotide (50 mer) microarrays Nucleic Acids Res 2000, 28:4552-4557. 113865 11071945 10.1093/nar/ 28.22.4552
8. Relógio A Schwager C Richter A Ansorge W Valcárcel J Optimization of oligonucleotide-based DNA microarrays Nucleic Acids Res 2002, 30:e51. 117213 12034852 10.1093/nar/30.11.e51
9. Sharp AJ Itsara A Cheng Z Alkan C Schwartz S Eichler EE Optimal design of oligonucleotide microarrays for measurement of DNA copy-number Hum Mol Genet 2007, 16:2770-2779. 10.1093/hmg/ddm234 17725982
10. Wei H Kuan PF Tian S Yang C Nie J Sengupta S Ruotti V Jonsdottir GA Keles S Thomson JA Stewart R A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets Nucleic Acids Res 2008, 36:2926-2938. 2396435 18385155 10.1093/nar/gkn133
11. Moerman DG Barstead RJ Towards a mutation in every gene in Caenorhabditis elegans Brief Funct Genomic Proteomic 2008, 7:195-204. 10.1093/bfgp/eln016 18417533
12. Baross A Delaney AD Li HI Nayar T Flibotte S Qian H Chan SY Asano J Ally A Cao M Birch P Brown-John M Fernandes N Go A Kennedy G Langlois S Eydoux P Friedman JM Marra MA Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data BMC Bioinformatics 2007, 8:368. 2148068 17910767 10.1186/ 1471-2105-8-368
13. Kennedy GC Matsuzaki H Dong S Liu WM Huang J Liu G Su X Cao M Chen W Zhang J Liu W Yang G Di X Ryder T He Z Surti U Phillips MS Boyce-Jacino MT Fodor SP Jones KW Large-scale genotyping of complex DNA Nat Biotechnol 2003, 21:1233-1237. 10.1038/nbt869 12960966
14. Bignell GR Huang J Greshock J Watt S Butler A West S Grigorova M Jones KW Wei W Stratton MR Futreal PA Weber B Shapero MH Wooster R High-resolution analysis of DNA copy number using oligonucleotide microarrays Genome Res 2004, 14:287-295. 327104 14762065 10.1101/ gr.2012304
15. Mei R Hubbell E Bekiranov S Mittmann M Christians FC Shen MM Lu G Fang J Liu WM Ryder T Kaplan P Kulp D Webster TA Probe selection for high-density oligonucleotide arrays Proc Natl Acad Sci USA 2003, 100:11237-11242. 208741 14500916 10.1073/pnas.1534744100
16. Zhang L Wu C Carta R Zhao H Free energy of DNA duplex formation on short oligonucleotide microarrays Nucleic Acids Res 2007, 35:e18. 1807971 17169993 10.1093/nar/gkl1064
17. Gräf S Nielsen FG Kurtz S Huynen MA Birney E Stunnenberg H Flicek P Optimized design and assessment of whole genome tiling arrays Bioinformatics 2007, 23:i195-204. 10.1093/bioinformatics/btm200 17646297
18. Breslauer KJ Frank R Blöcker H Marky LA Predicting DNA duplex stability from the base sequence Proc Natl Acad Sci USA 1986, 83:3746-3750. 323600 3459152 10.1073/pnas.83.11.3746
19. Sugimoto N Nakano S Yoneyama M Honda K Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes Nucleic Acids Res 1996, 24:4501-4505. 146261 8948641 10.1093/nar/24.22.4501
20. Griffith M Tang MJ Griffith OL Morin RD Chan SY Asano JK Zeng T Flibotte S Ally A Baross A Hirst M Jones SJ Morin GB Tai IT Marra MA ALEXA: A microarray design platform for alternative expression analysis Nat Methods 2008, 5:118. 10.1038/nmeth0208-118 18235430
21. Baldocchi RA Glynne RJ Chin K Kowbel D Collins C Mack DH Gray JW Design considerations for array CGH to oligonucleotide arrays Cytometry A 2005, 67:129-136. 16163695
22. Singh-Gasson S Green RD Yue Y Nelson C Blattner F Sussman MR Cerrina F Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array Nat Biotechnol 1999, 17:974-978. 10.1038/ 13664 10504697
23. Sherry ST Ward MH Kholodov M Baker J Phan L Smigielski EM Sirotkin K dbSNP: The NCBI database of genetic variation Nucleic Acids Res 2001, 29:308-311. 29783 11125122 10.1093/nar/29.1.308
24. Iafrate AJ Feuk L Rivera MN Listewnik ML Donahoe PK Qi Y Scherer SW Lee C Detection of large-scale variation in the human genome Nat Genet 2004, 36(9):949-951. 10.1038/ng1416 15286789
25. Zhang J Feuk L Duggan GE Khaja R Scherer SW Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome Cytogenet Genome Res 2006, 115:205-214. 10.1159/000095916 17124402
26. Edgar R Domrachev M Lash AE Gene expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Res 2002, 30:207-210. 99122 11752295 10.1093/nar/30.1.207
27. NCBI Gene Expression Omnibus, Series GSE12208 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12208
28. Markham NR Hybrid: A software system for nuclei acid folding, hybridizing and melting predictions Masters thesis Rensselaer Polytechnic Institute, Troy, NY 2003
29. Zhang Z Schwartz S Wagner L Miller W A greedy algorithm for aligning DNA sequences J Comput Biol 2000, 7:203-214. 10.1089/10665270050081478 10890397