Resequencing and mutational analysis using oligonucleotide microarrays

Oligonucleotide microarray (DNA chip)–based hybridization analysis is a promising new technology which potentially allows rapid and cost–effective screens for all possible mutations and sequence variations in genomic DNA. Here, I review current strategies and uses for DNA chip–based resequencing and mutational analysis, the underlying principles of experimental designs, and future efforts to improve the sensitivity and specificity of chip–based assays.

[1]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[2]  M. Wapenaar,et al.  The X chromosome shows less genetic variation at restriction sites than the autosomes. , 1986, American journal of human genetics.

[3]  W. Bains,et al.  A novel method for nucleic acid sequence determination. , 1988, Journal of theoretical biology.

[4]  K. Khrapko,et al.  An oligonucleotide hybridization approach to DNA sequencing , 1989, FEBS letters.

[5]  R. Drmanac,et al.  Sequencing of megabase plus DNA by hybridization: theory of the method. , 1989, Genomics.

[6]  H A Erlich,et al.  Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[7]  L. Hood,et al.  Development of an automated procedure for fluorescent DNA sequencing. , 1990, Genomics.

[8]  S. P. Fodor,et al.  Light-directed, spatially addressable parallel chemical synthesis. , 1991, Science.

[9]  E. Southern,et al.  Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. , 1992, Genomics.

[10]  Manish S. Shah,et al.  A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes , 1993, Cell.

[11]  Y. Rogers,et al.  Genetic Bit Analysis: a solid phase method for typing single nucleotide polymorphisms. , 1994, Nucleic acids research.

[12]  C R Cantor,et al.  Enhanced DNA sequencing by hybridization. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[14]  E. Southern,et al.  DNA chips: analysing sequence by hybridization to oligonucleotides on a large scale. , 1996, Trends in genetics : TIG.

[15]  G. Mcgall,et al.  Light-directed synthesis of high-density oligonucleotide arrays using semiconductor photoresists. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[16]  James L. Winkler,et al.  Accessing Genetic Information with High-Density DNA Arrays , 1996, Science.

[17]  A. Metspalu,et al.  Mutation detection by solid phase primer extension , 1996, Human mutation.

[18]  N. Shen,et al.  Extensive polymorphisms observed in HIV–1 clade B protease gene using high–density oligonucleotide arrays , 1996, Nature Medicine.

[19]  D. Lockhart,et al.  Expression monitoring by hybridization to high-density oligonucleotide arrays , 1996, Nature Biotechnology.

[20]  A. Mirzabekov,et al.  DNA analysis and diagnostics on oligonucleotide microchips. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[21]  S. M. Kim,et al.  Cystic fibrosis mutation detection by hybridization to light‐generated DNA probe arrays , 1996, Human mutation.

[22]  A. Mirzabekov,et al.  DNA sequencing by hybridization to microchip octa-and decanucleotides extended by stacked pentanucleotides. , 1996, Nucleic acids research.

[23]  S. P. Fodor,et al.  Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two–colour fluorescence analysis , 1996, Nature Genetics.

[24]  J. Hoheisel Sequence-independent and linear variation of oligonucleotide DNA binding stabilities. , 1996, Nucleic acids research.

[25]  A. Blanchard,et al.  High-density oligonucleotide arrays , 1996 .

[26]  K. Merikangas,et al.  Strategies to identify genes for complex diseases. , 1997, Annals of medicine.

[27]  L Peltonen,et al.  Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays. , 1997, Genome research.

[28]  E. Southern,et al.  Selecting effective antisense reagents on combinatorial oligonucleotide arrays , 1997, Nature Biotechnology.

[29]  A. Mirzabekov,et al.  Fractionation, phosphorylation and ligation on oligonucleotide microchips to enhance sequencing by hybridization. , 1997, Nucleic acids research.

[30]  M. Heller,et al.  Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Y. Rogers,et al.  Nested genetic bit analysis (N-GBA) for mutation detection in the p53 tumor suppressor gene. , 1997, Nucleic acids research.

[32]  M. Heller,et al.  Electric field directed nucleic acid hybridization on microchips. , 1997, Nucleic acids research.

[33]  H. Arlinghaus,et al.  Analysis of biosensor chips for identification of nucleic acids. , 1997, Analytical chemistry.

[34]  Francis S. Collins,et al.  Variations on a Theme: Cataloging Human DNA Sequence Variation , 1997, Science.

[35]  J. Hoheisel,et al.  Hybridisation based DNA screening on peptide nucleic acid (PNA) oligomer arrays. , 1997, Nucleic acids research.

[36]  I. Gottesman,et al.  At issue: genes, experience, and chance in schizophrenia--positioning for the 21st century. , 1997, Schizophrenia bulletin.

[37]  M Schena,et al.  Microarrays: biotechnology's discovery platform for functional genomics. , 1998, Trends in biotechnology.

[38]  S. P. Fodor,et al.  Strategies for mutational analysis of the large multiexon ATM gene using high-density oligonucleotide arrays. , 1998, Genome research.

[39]  S. P. Fodor,et al.  Evolutionary sequence comparisons using high-density oligonucleotide arrays , 1998, Nature Genetics.

[40]  S. P. Fodor,et al.  Enhanced high density oligonucleotide array-based sequence analysis using modified nucleoside triphosphates. , 1998, Nucleic acids research.

[41]  J. Hodgson,et al.  DNA chips: An array of possibilities , 1998, Nature Biotechnology.

[42]  M. Durand,et al.  The stability of duplexes involving AT and/or G4EtC base pairs is not dependent on their AT/G4EtC ratio content. Implication for DNA sequencing by hybridization. , 1998, Nucleic acids research.

[43]  C. Nusbaum,et al.  Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. , 1998, Science.

[44]  S. P. Fodor,et al.  Two color hybridization analysis using high density oligonucleotide arrays and energy transfer dyes. , 1998, Nucleic acids research.

[45]  G. Ramsay DNA chips: State-of-the art , 1998, Nature Biotechnology.

[46]  R. Drmanac,et al.  Accurate sequencing by hybridization for DNA diagnostics and individual genomics , 1998, Nature Biotechnology.

[47]  P. Lizardi,et al.  Mutation detection and single-molecule counting using isothermal rolling-circle amplification , 1998, Nature Genetics.

[48]  E. Boerwinkle,et al.  DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene , 1998, Nature Genetics.

[49]  A. Mirzabekov,et al.  Immobilization of DNA in polyacrylamide gel for the manufacture of DNA and DNA-oligonucleotide microchips. , 1998, Analytical biochemistry.

[50]  L. Liotta,et al.  Laser-capture microdissection: opening the microscopic frontier to molecular analysis. , 1998, Trends in genetics : TIG.

[51]  M. Bittner,et al.  Expression profiling using cDNA microarrays , 1999, Nature Genetics.

[52]  S. P. Fodor,et al.  High density synthetic oligonucleotide arrays , 1999, Nature Genetics.

[53]  E. Southern,et al.  Molecular interactions on microarrays , 1999, Nature Genetics.

[54]  A. Chakravarti Population genetics—making sense out of sequence , 1999, Nature Genetics.