| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
Minireview |
1 Department of Applied Genomics, Genometrix Inc., The Woodlands, TX 77381, and Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109.
Abstract
Background: Pharmacogenetics is a scientific discipline that examines the genetic basis for individual variations in response to therapeutics. Pharmacogenetics promises to develop individualized medicines tailored to patients’ genotypes. However, identifying and genotyping a vast number of genetic polymorphisms in large populations also pose a great challenge.
Approach: This article reviews the recent technology development in mutation detection and genotyping with a focus on genotyping of single nucleotide polymorphisms (SNPs).
Content: Novel mutations/polymorphisms are commonly identified by conformation-based mutation screening and direct high-throughput heterozygote sequencing. With a large amount of public sequence information available, in silico SNP mapping has also emerged as a cost-efficient way for new polymorphism identification. Gel electrophoresis-based genotyping methods for known polymorphisms include PCR coupled with restriction fragment length polymorphism analysis, multiplex PCR, oligonucleotide ligation assay, and minisequencing. Fluorescent dye-based genotyping technologies are emerging as high-throughput genotyping platforms, including oligonucleotide ligation assay, pyrosequencing, single-base extension with fluorescence detection, homogeneous solution hybridization such as TaqMan®, and molecular beacon genotyping. Rolling circle amplification and InvaderTM assays are able to genotype directly from genomic DNA without PCR amplification. DNA chip-based microarray and mass spectrometry genotyping technologies are the latest development in the genotyping arena.
Summary: Large-scale genotyping is crucial to the identification of the genetic make-ups that underlie the onset of diseases and individual variations in drug responses. Enabling technologies to identify genetic polymorphisms rapidly, accurately, and cost effectively will dramatically impact future drug and development processes.
The following articles in journals at HighWire Press have cited this article:
|
|
 |
|
  J. B. Overdevest, D. Theodorescu, and J. K. Lee Utilizing the Molecular Gateway: The Path to Personalized Cancer Management Clin. Chem., April 1, 2009; 55(4): 684 - 697. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Misra, J.-Y. Hong, and S. Kim Multiplex Genotyping of Cytochrome P450 Single-Nucleotide Polymorphisms by Use of MALDI-TOF Mass Spectrometry Clin. Chem., May 1, 2007; 53(5): 933 - 939. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Se Fum Wong, J. J. Kuei, N. Prasad, E. Agonafer, G. A. Mendoza, T. J. Pemberton, and P. I. Patel A Simple Method for DNA Isolation from Clotted Blood Extricated Rapidly from Serum Separator Tubes Clin. Chem., March 1, 2007; 53(3): 522 - 524. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J Peltonen, J A Welsh, and K H Vahakangas Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Human and Experimental Toxicology, January 1, 2007; 26(1): 9 - 18. [Abstract] [PDF]
|
|
|
|
 |
|
 C. L. Aquilante, I. Zineh, A. L. Beitelshees, and T. Y. Langaee Common laboratory methods in pharmacogenomics studies. Am. J. Health Syst. Pharm., November 1, 2006; 63(21): 2101 - 2110. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Szantai, Z. Ronai, M. Sasvari-Szekely, G. Bonn, and A. Guttman Multicapillary Electrophoresis Analysis of Single-Nucleotide Sequence Variations in the Deoxycytidine Kinase Gene Clin. Chem., September 1, 2006; 52(9): 1756 - 1762. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. P. Price, V. Thiruvenkataswamy, L. Mickan, L. Unicomb, R. E. Rios, F. Huygens, and P. M. Giffard Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing. J. Med. Microbiol., August 1, 2006; 55(Pt 8): 1061 - 1070. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. G. Ehm, M. R. Nelson, and N. K. Spurr Guidelines for conducting and reporting whole genome/large-scale association studies Hum. Mol. Genet., September 1, 2005; 14(17): 2485 - 2488. [Full Text] [PDF]
|
|
|
|
 |
|
 M. Klaften and M. H. de Angelis ARTS: a web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants Nucleic Acids Res., July 1, 2005; 33(suppl_2): W496 - W500. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Kimmel and R. Shamir GERBIL: Genotype resolution and block identification using likelihood PNAS, January 4, 2005; 102(1): 158 - 162. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Yang, T. Yaoi, S. Huang, Q. Yang, S. Hatcher, H. Seet, and J. P. Gregg Detecting the C282Y and H63D Mutations of the HFE Gene by Holliday Junction-Based Allele-Specific Genotyping Methods Clin. Chem., January 1, 2005; 51(1): 210 - 213. [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Jiang, T. Ellis, and A. R. Greenlee Genotyping Parkinson Disease-Associated Mitochondrial Polymorphisms Clin. Med. Res., May 1, 2004; 2(2): 99 - 106. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. P. Johnson, L. M. Haupt, and L. R. Griffiths Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR Nucleic Acids Res., March 26, 2004; 32(6): e55 - e55. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Meyer, A. Fredriksen, and P. M. Ueland High-Level Multiplex Genotyping of Polymorphisms Involved in Folate or Homocysteine Metabolism by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Clin. Chem., February 1, 2004; 50(2): 391 - 402. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. A. Sethi, A. Tybjaerg-Hansen, R. V. Andersen, and B. G. Nordestgaard Nanogen Microelectronic Chip for Large-Scale Genotyping Clin. Chem., February 1, 2004; 50(2): 443 - 446. [Full Text] [PDF]
|
|
|
|
|
|
T. Thiel, R. Kota, I. Grosse, N. Stein, and A. Graner SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development Nucleic Acids Res., January 2, 2004; 32(1): e5 - e5. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Yokoyama, T. Yokoyama, T. Muramatsu, T. Omori, S. Matsushita, S. Higuchi, K. Maruyama, and H. Ishii Macrocytosis, a new predictor for esophageal squamous cell carcinoma in Japanese alcoholic men Carcinogenesis, November 1, 2003; 24(11): 1773 - 1778. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Kinoshita-Kikuta, E. Kinoshita, and T. Koike A novel procedure for simple and efficient genotyping of single nucleotide polymorphisms by using the Zn2+-cyclen complex Nucleic Acids Res., November 15, 2002; 30(22): e126 - e126. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Simeonov and T. T. Nikiforov Single nucleotide polymorphism genotyping using short, fluorescently labeled locked nucleic acid (LNA) probes and fluorescence polarization detection Nucleic Acids Res., September 1, 2002; 30(17): e91 - e91. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. S. Bernard and C. T. Wittwer Real-Time PCR Technology for Cancer Diagnostics Clin. Chem., August 1, 2002; 48(8): 1178 - 1185. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Millward, W. Samowitz, C. T. Wittwer, and P. S. Bernard Homogeneous Amplification and Mutation Scanning of the p53 Gene Using Fluorescent Melting Curves Clin. Chem., August 1, 2002; 48(8): 1321 - 1328. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Pickering, A. Bamford, V. Godbole, J. Briggs, G. Scozzafava, P. Roe, C. Wheeler, F. Ghouze, and S. Cuss Integration of DNA ligation and rolling circle amplification for the homogeneous, end-point detection of single nucleotide polymorphisms Nucleic Acids Res., June 15, 2002; 30(12): e60 - e60. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M.-Z. Xue, O. Bonny, S. Morgenthaler, M. Bochud, V. Mooser, W. G. Thilly, L. Schild, and P.-M. Leong-Morgenthaler Use of Constant Denaturant Capillary Electrophoresis of Pooled Blood Samples to Identify Single-Nucleotide Polymorphisms in the Genes (Scnn1a and Scnn1b) Encoding the {alpha} and {beta} Subunits of the Epithelial Sodium Channel Clin. Chem., May 1, 2002; 48(5): 718 - 728. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Qi, S. Bakht, K. M. Devos, M. D. Gale, and A. Osbourn L-RCA (ligation-rolling circle amplification): a general method for genotyping of single nucleotide polymorphisms (SNPs) Nucleic Acids Res., November 15, 2001; 29(22): e116 - e116. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Ulvik and P. M. Ueland Single Nucleotide Polymorphism (SNP) Genotyping in Unprocessed Whole Blood and Serum by Real-Time PCR: Application to SNPs Affecting Homocysteine and Folate Metabolism Clin. Chem., November 1, 2001; 47(11): 2050 - 2053. [Full Text] [PDF]
|
|
|
|
 |
|
 M. H. Shapero, K. K. Leuther, A. Nguyen, M. Scott, and K. W. Jones SNP Genotyping by Multiplexed Solid-Phase Amplification and Fluorescent Minisequencing Genome Res., November 1, 2001; 11(11): 1926 - 1934. [Abstract] [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
