Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays

Nucleic Acids Research

Volumn 33, Issue 3, 2005, Pages 1-9

  Karaman, Mazen W ^a   Groshen, Susan ^b   Lee, Chi Chiang ^a   Pike, Brian L ^a   Hacia, Joseph G ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATM PROTEIN; DNA; OLIGONUCLEOTIDE; CELL CYCLE PROTEIN; DNA BINDING PROTEIN; PROTEIN SERINE THREONINE KINASE; TUMOR SUPPRESSOR PROTEIN;

ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA MICROARRAY; GENE DELETION; GENE INSERTION; GENE MUTATION; GENE SEQUENCE; HUMAN; MOLECULAR PROBE; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; BASE MISPAIRING; CHEMISTRY; DNA SEQUENCE; EVALUATION; GENE EXPRESSION REGULATION; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; POINT MUTATION; REPRODUCIBILITY;

ATAXIA TELANGIECTASIA;

BASE PAIR MISMATCH; BASE SEQUENCE; CELL CYCLE PROTEINS; DNA MUTATIONAL ANALYSIS; DNA-BINDING PROTEINS; HUMANS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; POINT MUTATION; PROTEIN-SERINE-THREONINE KINASES; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION; TUMOR SUPPRESSOR PROTEINS;

EID: 26444591999     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gni034     Document Type: Article

References (52)

1. Mir,K.U. and Southern,E.M. (2000) Sequence variation in genes and genomic DNA: Methods for large-scale analysis. Annu. Rev. Genomics Hum. Genet., 1, 329-360.
2. Kolchinsky,A. and Mirzabekov,A. (2002) Analysis of SNPs and other genomic variations using gel-based chips. Hum. Mutat., 19, 343-360.
3. Hacia,J.G. and Collins,F.S. (1999) Mutational analysis using oligonucleotide microarrays. J. Med. Genet., 36, 730-736.
4. Hacia,J.G. (1999) Resequencing and mutational analysis using oligonucleotide microarrays. Nature Genet., 21, 42-47.
5. Warrington,J.A., Shah,N.A., Chen,X., Janis,M., Liu,C., Kondapalli,S., Reyes,V., Savage,M.P., Zhang,Z., Watts,R. et al. (2002) New developments in high-throughput resequencing and variation detection using high density microarrays. Hum. Mutat., 19, 402-409.
6. Ahrendt,S.A., Halachmi,S., Chow,J.T., Wu,L., Halachmi,N., Yang,S.C., Wehage,S., Jen,J. and Sidransky,D. (1999) Rapid p53 sequence analysis in primary lung cancer using an oligonucleotide probe array. Proc. Natl Acad. Sci. USA, 96, 7382-7387.
7. Cargill,M., Altshuler,D., Ireland,J., Sklar,P., Ardlie,K., Patil,N., Shaw,N., Lane,C.R., Lim,E.P., Kalyanaraman,N. et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nature Genet., 22, 231-238.
8. Chee,M., Yang,R., Hubbell,E., Berno,A., Huang,X.C., Stern,D., Winkler,J., Lockhart,D.J., Monis,M.S. and Fodor,S.P. (1996) Accessing genetic information with high-density DNA arrays. Science, 274 610-614.
9. Cutler,D.J., Zwick,M.E., Carrasquillo,M.M., Yohn,C.T., Tobin,K.P., Kashuk,C., Mathews,D.J., Shah,N.A., Eichler,E.E., Warrington,J.A. et al. (2001) High-throughput variation detection and genotyping using microarrays. Genome Res., 11, 1913-1925.
10. Dong,S., Wang,E., Hsie,L., Cao,Y., Chen,X. and Gingeras,T.R. (2001) Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation. Genome Res. 11, 1418-1424.
11. Frazer,K.A., Sheehan,J.B., Stokowski,R.P., Chen,X., Hosseini,R., Cheng,J.F., Fodor,S.P., Cox,D.R. and Patil,N. (2001) Evolutionarily conserved sequences on human chromosome 21. Genome Res., 11, 1651-1659.
12. Kozal,M.J., Shah,N., Shen,N., Yang,R., Fucini,R., Merigan,T.C., Richman,D.D., Morris,D., Hubbell,E., Chee,M. et al. (1996) Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nature Med., 2, 753-759.
13. Lindblad-Toh,K., Winchester,E., Daly,M.J., Wang,D.G., Hirschhorn,J.N., Laviolette,J.P., Ardlie,K., Reich,D.E., Robinson,E., Sklar,P. et al. (2000) Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nature Genet., 24, 381-386.
14. Maitra,A., Cohen,Y., Gillespie,S.E., Mambo,E., Fukushima,N., Hoque,M.O., Shah,N., Goggins,M., Califano,J., Sidransky,D. et al. (2004) The Human MitoChip: A high-throughput sequencing microarray for mitochondrial mutation detection. Genome Res., 14, 812-819.
15. Patil,N., Berno,A.J., Hinds,D.A., Barrett,W.A., Doshi,J.M., Hacker,C.R., Kautzer,C.R., Lee,D.H., Marjoribanks,C., McDonough,D.P. et al. (2001) Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science, 294, 1719-1723.
16. Takahashi,Y., Ishii,Y., Nagata,T., Ikarashi,M., Ishikawa,K. and Asai,S. (2003) Clinical application of oligonucleotide probe array for full-length gene sequencing of TP53 in colon cancer. Oncology, 64, 54-60.
17. Wang,D.G., Fan,J.B., Siao,C.J., Berno,A., Young,P., Sapolsky,R., Ghandour,G., Perkins,N., Winchester,E., Spencer,J. et al. (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science, 280, 1077-1082.
18. Wen,W.H. and Press,M.F. (2004) Identification of TP53 mutations in human cancers using oligonucleotide microarrays. Methods Mol. Med., 97, 323-335.
19. Wikman,F.P., Lu,M.L., Thykjaer,T., Olesen,S.H., Andersen,L.D., Cordon-Cardo,C. and Orntoft,T.F. (2000) Evaluation of the performance of a p53 sequencing microarray chip using 140 previously sequenced bladder tumor samples. Clin. Chem., 46, 1555-1561.
20. Yershov,G., Barsky,V., Belgovskiy,A., Kirillov,E., Kreindlin,E., Ivanov,I., Parinov,S., Guschin,D., Drobishev,A., Dubiley,S. et al. (1996) DNA analysis and diagnostics on oligonucleotide microchips. Proc. Natl Acad. Sci. USA, 93, 4913-4918.
21. Wong,C.W., Albert,T.J., Vega,V.B., Norton,J.E., Cutler,D.J., Richmond,T.A., Stanton,L.W., Liu,E.T. and Miller,L.D. (2004) Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays. Genome Res., 14, 398-405.
22. Frazer,K.A., Chen,X., Hinds,D.A., Pant,P.V., Patil,N. and Cox,D.R. (2003) Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Res., 13, 341-346.
23. Frazer,K.A., Wade,C.M., Hinds,D.A., Patil,N., Cox D.R. and Daly,M.J. (2004) Segmental phylogenetic relationships of inbred mouse strains revealed by fine-scale analysis of sequence variation across 4.6 mb of mouse genome. Genome Res., 14, 1493-1500.
24. Cronin,M.T., Fucini,R.V., Kim,S.M., Masino,R.S., Wespi,R.M. and Miyada,C.G. (1996) Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays. Hum. Mutat., 7, 244-255.
25. Hacia,J.G., Brody,L.C., Chee,M.S., Fodor,S.P. and Collins,F.S. (1996) Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis. Nature Genet., 14, 441-447.
26. Hacia,J.G., Woski,S.A., Fidanza,J., Edgemon,K., Hunt,N., McGall,G., Fodor,S.P. and Collins,F.S. (1998) Enhanced high density oligonucleotide array-based sequence analysis using modified nucleoside triphosphates. Nucleic Acids Res., 26, 4975-4982.
27. Hacia,J.G., Sun,B., Hunt,N., Edgemon,K., Mosbrook,D., Robbins,C., Fodor,S.P., Tagle,D.A. and Collins,F.S. (1998) Strategies for mutational analysis of the large multiexon ATM gene using high-density oligonucleotide arrays. Genome Res., 8, 1245-1258.
28. Hacia,J.G., Edgemon,K., Sun,B., Stern,D., Fodor,S.P. and Collins,F.S. (1998) Two color hybridization analysis using high density oligonucleotide arrays and energy transfer dyes. Nucleic Acids Res. 26, 3865-3866.
29. Hacia,J.G., Edgemon,K., Fang,N., Mayer,R.A., Sudano,D., Hunt,N. and Collins,F.S. (2000) Oligonucleotide microarray based detection of repetitive sequence changes. Hum. Mutat., 16, 354-363.
30. Fang,N.Y., Greiner,T.C., Weisenburger,D.D., Chan,W.C., Vose,J.M., Smith,L.M., Armitage,J.O., Mayer,R.A., Pike,B.L., Collins,F.S. et al. (2003) Oligonucleotide microarrays demonstrate the highest frequency of ATM mutations in the mantle cell subtype of lymphoma. Proc. Natl Acad. Sci. USA, 100, 5372-5377.
31. Lipkin,S.M., Rozek,L.S., Rennert,G., Yang,W., Chen,P.C., Hacia,J., Hunt,N., Shin,B., Fodor,S., Kokoris,M. et al. (2004) The MLH1 D132H variant is associated with susceptibility to sporadic colorectal cancer. Nature Genet., 36, 694-699.
32. Shiloh,Y. (2003) ATM and related protein kinases: Safeguarding genome integrity. Nature Rev. Cancer, 3, 155-168.
33. Gumy-Pause,F., Wacker,P. and Sappino,A.P. (2004) ATM gene and lymphoid malignancies. Leukemia, 18, 238-242.
34. Znosko,B.M., Silvestri,S.B., Volkman,H., Boswell,B. and Serra,M.J. (2002) Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges. Biochemistry, 41, 10406-10417.
35. Holland,J.A. and Hoffman,D.W. (1996) Structural features and stability of an RNA triple helix in solution. Nucleic Acids Res., 24, 2841-2848.
36. Gyi,J.I., Lane,A.N., Conn,G.L. and Brown,T. (1998) Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologous DNA and RNA duplexes. Biochemistry, 37, 73-80.
37. Ratmeyer,L., Vinayak,R., Zhong,Y.Y., Zon,G. and Wilson,W.D. (1994) Sequence specific thermodynamic and structural properties for DNA.RNA duplexes. Biochemistry, 33, 5298-5304.
38. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
39. Zhu,J. and Wartell,R.M. (1999) The effect of base sequence on the stability of RNA and DNA single base bulges. Biochemistry, 38 15986-15993.
40. Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
41. Dimitrov,R.A. and Zuker,M. (2004) Prediction of hybridization and melting for double-stranded nucleic acids. Biophys. J., 87, 215-226.
42. Fodor,S.P., Read,J.L., Pirrung,M.C., Stryer,L., Lu,A.T. and Solas,D. (1991) Light-directed, spatially addressable parallel chemical synthesis. Science, 251, 767-773.
43. McGall,G.H. and Christians,F.C. (2002) High-density genechip oligonucleotide probe arrays. Adv. Biochem. Eng. Biotechnol., 77, 21-42.
44. Nagpal,S., Karaman,M.W., Timmerman,M.M., Ho,V.V., Pike,B.L. and Hacia,J.G. (2004) Improving the sensitivity and specificity of gene expression analysis in highly related organisms through the use of electronic masks. Nucleic Acids Res., 32, e51.
45. Luebke,K.J., Balog,R.P. and Garner,H.R. (2003) Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts. Nucleic Acids Res., 31, 750-758.
46. Matveeva,O.V., Shabalina,S.A., Nemtsov,V.A., Tsodikov,A.D., Gesteland,R.F. and Atkins,J.F. (2003) Thermodynamic calculations and statistical correlations for oligo-probes design. Nucleic Acids Res. 31, 4211-4217.
47. Rouillard,J.M., Zuker,M. and Gulari,E. (2003) OligoArray 2.0: Design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res., 31, 3057-3062.
48. Zhang,L., Miles,M.F. and Aldape,K.D. (2003) A model of molecular interactions on short oligonucleotide microarrays. Nat. Biotechnol. 21, 818-821.
49. Mei,R., Hubbell,E., Bekiranov,S., Mittmann,M., Christians,F.C., Shen,M.M., Lu,G., Fang,J., Liu,W.M., Ryder,T. et al. (2003) Probe selection for high-density oligonucleotide arrays. Proc. Natl Acad. Sci. USA, 100, 11237-11242.
50. Held,G.A., Grinstein,G. and Tu,Y. (2003) Modeling of DNA microarray data by using physical properties of hybridization. Proc. Natl Acad. Sci. USA, 100, 7575-7580.
51. Fidanza,J.A. and McGall,G.H. (1999) High-density nucleoside analog probe arrays for enhanced hybridization. Nucleosides Nucleotides, 18 1293-1295.
52. Hoheisel,J.D. (1996) Sequence-independent and linear variation of oligonucleotide DNA binding stabilities. Nucleic Acids Res., 24 430-432.