Mutational analysis using oligonucleotide microarrays

The development of inexpensive high throughput methods to identify individual DNA sequence differences is important to the future growth of medical genetics. This has become increasingly apparent as epidemiologists, pathologists, and clinical geneticists focus more attention on the molecular basis of complex multifactorial diseases. Such undertakings will rely upon genetic maps based upon newly discovered, common, single nucleotide polymorphisms. Furthermore, candidate gene approaches used in identifying disease associated genes necessitate screening large sequence blocks for changes tracking with the disease state. Even after such genes are isolated, large scale mutational analyses will often be needed for risk assessment studies to define the likely medical consequences of carrying a mutated gene. This review concentrates on the use of oligonucleotide arrays for hybridisation based comparative sequence analysis. Technological advances within the past decade have made it possible to apply this technology to many different aspects of medical genetics. These applications range from the detection and scoring of single nucleotide polymorphisms to mutational analysis of large genes. Although we discuss published scientific reports, unpublished work from the private sector1 2 could also significantly affect the future of this technology.

[1]  R. Cotton,et al.  Mutation detection , 2020, Nature.

[2]  Kunkel Jm,et al.  Spontaneous subclavain vein thrombosis: a successful combined approach of local thrombolytic therapy followed by first rib resection. , 1989 .

[3]  S. P. Fodor,et al.  Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays , 1999, Nature Genetics.

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

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

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

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

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

[9]  Peter J. Coassin,et al.  Biopolymer synthesis on polypropylene supports: oligonucleotide arrays. , 1995, Analytical biochemistry.

[10]  K. Gunderson,et al.  Mutation detection by ligation to complete n-mer DNA arrays. , 1998, Genome research.

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

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

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

[14]  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.

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

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

[17]  M. Heller,et al.  Preparation and hybridization analysis of DNA/RNA from E. coli on microfabricated bioelectronic chips , 1998, Nature Biotechnology.

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

[19]  J. Hacia.  Resequencing and mutational analysis using oligonucleotide microarrays , 1999, Nature Genetics.

[20]  Leonid Kruglyak,et al.  The use of a genetic map of biallelic markers in linkage studies , 1997, Nature Genetics.

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

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

[23]  Stephen J. Chanock,et al.  Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips , 1999, Nature Biotechnology.

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

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

[26]  D. Bowtell,et al.  Options available—from start to finish—for obtaining expression data by microarray , 1999, Nature Genetics.

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

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

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

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

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

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

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

[34]  A. Syvänen.  From gels to chips: “Minisequencing” primer extension for analysis of point mutations and single nucleotide polymorphisms , 1999, Human mutation.

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

[36]  A. Berno,et al.  Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. , 1998, Genome research.

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

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

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

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

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

[42]  A. Mirzabekov,et al.  Manual manufacturing of oligonucleotide, DNA, and protein microchips. , 1997, Analytical biochemistry.

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

[44]  K. Khrapko,et al.  [Determination of the nucleotide sequence of DNA using hybridization with oligonucleotides. A new method]. , 1988, Doklady Akademii nauk SSSR.

[45]  N. Thuong,et al.  Smoothing of the thermal stability of DNA duplexes by using modified nucleosides and chaotropic agents. , 1999, Nucleic acids research.

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

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

[48]  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.

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

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

[51]  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.

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

[53]  A. Brice.  Unstable mutations and neurodegenerative disorders , 1998, Journal of Neurology.

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

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

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