DOI QR코드

DOI QR Code

Applications of DNA Microarray in Disease Diagnostics

  • Yoo, Seung-Min (Department of Chemical and Biomolecular Engineering (BK21 Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, KAIST) ;
  • Choi, Jong-Hyun (Department of Chemical and Biomolecular Engineering (BK21 Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, KAIST) ;
  • Lee, Sang-Yup (Department of Chemical and Biomolecular Engineering (BK21 Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, KAIST, Department of Bio and Brain Engineering, and Bioinformatics Research Center, KAIST) ;
  • Yoo, Nae-Choon (Department of Internal Medicine, Department of Oncology and Cancer Center, Yonsei University College of Medicine)
  • Published : 2009.07.31

Abstract

Rapid and accurate diagnosis of diseases is very important for appropriate treatment of patients. Recent advances in molecular-level interaction and detection technologies are upgrading the clinical diagnostics by providing new ways of diagnosis, with higher speed and accuracy. In particular, DNA microarrays can be efficiently used in clinical diagnostics which span from discovery of diseaserelevant genes to diagnosis using its biomarkers. Diagnostic DNA microarrays have been used for genotyping and determination of disease-relevant genes or agents causing diseases, mutation analysis, screening of single nucleotide polymorphisms (SNPs), detection of chromosome abnormalities, and global determination of posttranslational modification. The performance of DNA-microarray-based diagnosis is continuously improving by the integration of other tools. Thus, DNA microarrays will play a central role in clinical diagnostics and will become a gold standard method for disease diagnosis. In this paper, various applications of DNA microarrays in disease diagnosis are reviewed. Special effort was made to cover the information disclosed in the patents so that recent trends and missing applications can be revealed.

Keywords

References

  1. Acquila, M., F. Bottini, A. Valetto, D. Caprino, P. G. Mori, and M. P. Bicocchi. 2001. A new strategy for prenatal diagnosis in a sporadic haemophilia B family. Haemophilia 7: 416-418 https://doi.org/10.1046/j.1365-2516.2001.00514.x
  2. Afshari, N., J. Mullaly, M. Afshari, R. F. Steinert, A. P. Adamis, D. Azar, and J. Talamo. 2001. Survey of patients with granular, lattice, Avellino, and Reis-Bucklers corneal dystrophies for mutations in the BIGH3 and gelsolin genes. Arch. Ophthalmol. 119: 16-22
  3. Ampel, N. M., D. G. Mosley, B. England, P. D. Vertz, K. Komatsu, and R. A. Hajjeh. 1998. Coccidioidomycosis in Arizona: Increase in incidence from 1990 to 1995. Clin. Infect. Dis. 27: 1528-1530 https://doi.org/10.1086/515044
  4. Andersen, P. S., C. Jespersgaard, J. Vuust, M. Christiansen, and L. A. Larsen. 2003. Capillary electrophoresis-based single strand DNA conformation analysis in high-throughput mutation screening. Hum. Mutat. 21: 455-465 https://doi.org/10.1002/humu.10169
  5. Anthony, R. M., T. J. Brown, and G. L. French. 2000. Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. J. Clin. Microbiol. 38: 781-788
  6. Athma, P., R. Rappaport, and M. Swift. 1996. Molecular genotyping shows that ataxia telangiectasia heterozygotes are predisposed to breast cancer. Cancer Genet. Cytogenet. 92: 130-134 https://doi.org/10.1016/S0165-4608(96)00328-7
  7. Baelde, H. J., M. Eikmans, P. P. Doran, D. W. Lappin, E. de Heer, and J. A. Bruijn. 2004. Gene expression profiling in glomeruli from human kidneys with diabetic nephropathy. Am. J. Kidney Dis. 43: 636-650 https://doi.org/10.1053/j.ajkd.2003.12.028
  8. Barnes, M. G., B. J. Aronow, L. K. Luyrink, M. B. Moroldo, P. Pavlidis, M. H. Passo, et al. 2004. Gene expression in juvenile arthritis and pondyloarthropathy: Pro-angiogenic ELR+ chemokine genes relate to course of arthritis. Rheumatology 43: 973-979 https://doi.org/10.1093/rheumatology/keh224
  9. Becker, K. G., R. M. Simon, J. E. Bailey-Wilson, B. Freidlin, W. E. Biddison, H. F. McFarland, and J. M. Trent. 1998. Clustering of non-major histocompatibility complex susceptibility candidate loci in human autoimmune diseases. Proc. Natl. Acad. Sci. USA 95: 9979-9984 https://doi.org/10.1073/pnas.95.17.9979
  10. Broeks, A., J. H. Urbanus, A. N. Floore, E. C. Dahler, J. G. Klijn, E. J. Rutgers, et al. 2000. ATM-heterozygous germline mutations contribute to breast cancer-susceptibility. Am. J. Hum. Genet. 66: 494-500 https://doi.org/10.1086/302746
  11. Chen, S. L., C. P. Han, Y. P. Tsao, J. W. Lee, and C. S. Yin. 2006. Identification and typing of human papillomavirus in cervical cancers in Taiwan. Cancer 72: 1939-1945 https://doi.org/10.1002/1097-0142(19930915)72:6<1939::AID-CNCR2820720624>3.0.CO;2-2
  12. Cleven, B. E., M. Palka-Santini, J. Gielen, S. Meembor, M. Krönke, and O. Krut. 2006. Identification and characterization of bacterial pathogens causing bloodstream infections by DNA microarray. J. Clin. Microbiol. 44: 2389-2397 https://doi.org/10.1128/JCM.02291-05
  13. Collas, P. and J. A. Dahl. 2008. Chop it, ChIP it, check it: The current status of chromatin immunoprecipitation. Front. Biosci. 13: 929-943 https://doi.org/10.2741/2733
  14. Concannon, P. and R. A. Gatti. 1997. Diversity of ATM gene mutations detected in patients with ataxia-telangiectasia. Hum. Mutat. 10: 100-107 https://doi.org/10.1002/(SICI)1098-1004(1997)10:2<100::AID-HUMU2>3.0.CO;2-O
  15. Delgado, I. J., D. S. Kim, K. N. Thatcher, J. M. LaSalle, and I. B. Van den Veyver. 2006. Expression profiling of clonal lymphocyte cell cultures from Rett syndrome patients. BMC Med. Genet. 7: 61 https://doi.org/10.1186/1471-2350-7-61
  16. Denning, D. W. 1996. Diagnosis and management of invasive aspergillosis. Curr. Clin. Top. Infect. Dis. 16: 277-299
  17. Dolmetsch, A. M., F. A. Stockl, R. Folberg, I. Gensini, and M. N. Burnier Jr. 1996. Combined granular lattice dystrophy (Avellino) in a patient with no known Italian ancestry. Can. J. Ophthalmol. 31: 29-31
  18. Fridkin, S. K. and W. R. Jarvis. 1996. Epidemiology of nosocomial fungal infections. Clin. Microbiol. Rev. 9: 499- 511
  19. Forbes, J. R. and D. W. Cox. 1998. Functional characterization of missense mutations in ATP7B: Wilson disease mutation or normal variant? Am. J. Hum. Genet. 63: 1663-1674 https://doi.org/10.1086/302163
  20. Gilad, S., A. Bar-Shira, R. Harnik, D. Shkedy, Y. Ziv, R. Khosravi, et al. 1996. Ataxia-telangiectasia: Founder effect among North African Jews. Hum. Mol. Genet. 5: 2033-2037 https://doi.org/10.1093/hmg/5.12.2033
  21. Gladkevich, A., S. A. Nelemans, H. F. Kauffman, and J. Korf. 2005. Microarray profiling of lymphocytes in internal diseases with an altered immune response: Potential and methodology. Mediators Inflamm. 2005: 317-330 https://doi.org/10.1155/MI.2005.317
  22. Hamilton, A. J. 1998. Serodiagnosis of histoplasmosis, paracoccidioidomycosis and penicilliosis marneffei; current status and future trends. Med. Mycol. 36: 351-364 https://doi.org/10.1080/02681219880000571
  23. Hampe, J., S. Schreiber, S. H. Shaw, K. F. Lau, S. Bridger, A. J. Macpherson, et al. 1999. A genomewide analysis provides evidence for novel linkages in inflammatory bowel disease in a large European cohort. Am. J. Hum. Genet. 64: 808-816 https://doi.org/10.1086/302294
  24. Holland, E. J., S. M. Daya, E. M. Stone, R. Folberg, A. A. Dobler, J. D. Cameron, and D. J. Doughman. 1992. Avellino corneal dystrophy: Clinical manifestations and natural history. Ophthalmology 99: 1564-1568 https://doi.org/10.1016/S0161-6420(92)31766-X
  25. Hugot, J. P. and G. Thomas. 1998. Genome-wide scanning in inflammatory bowel diseases. Dig. Dis. 16: 364-369 https://doi.org/10.1159/000016893
  26. Iida, K. and I. Nishimura. 2002. Gene expression profiling by DNA microarray technology. Crit. Rev. Oral Biol. Med. 13: 35-50 https://doi.org/10.1177/154411130201300105
  27. Jun, R. M., H. W. Tchah, T. I. Kim, D. R. Stulting, S. E. Jung, K. Y. Seo, D. H. Lee, and E. K. Kim. 2004. Avellino corneal dystrophy after LASIK. Ophthalmology 111: 463-468 https://doi.org/10.1016/j.ophtha.2003.06.026
  28. Kawaguchi, K., S. Kaneko, M. Honda, F. H. Kawai, S. Yukihiro, and K. Kenichi. 2003. Detection of hepatitis B virus DNA in sera from patients with chronic hepatitis B virus infection by DNA microarray method. J. Clin. Microbiol. 41: 1701-1704 https://doi.org/10.1128/JCM.41.4.1701-1704.2003
  29. Kennedy, S. M., M. McNamara, M. Hillery, C. Hurley, L. M. Collum, and S. Giles. 1996. Combined granular lattice dystrophy (Avellino corneal dystrophy). Br J Ophthalmol. 80: 489-490 https://doi.org/10.1136/bjo.80.5.489
  30. Korkko, J., I. Kaitila, L. Lonnqvist, L. Peltonen, and L. Ala-Kokko. 2002. Sensitivity of conformation sensitive gel electrophoresis in detecting mutations in Marfan syndrome and related conditions. J. Med. Genet. 30: 34-41
  31. Kotilainen, P., J. Jalava, O. Meurman, O. P. Lehtonen, E. Rintala, O. P. Sepp$\ddot{a}$l$\ddot{a}$, E. Eerola, and S. Nikkari. 1998. Diagnosis of meningococcal meningitis by broad-range bacterial PCR with cerebrospinal fluid. J. Clin. Microbiol. 36: 2205-2209
  32. Liu, H. H., X. Cao, Y. Yang, M. G. Liu, and Y. F. Wang. 2006. Array-based nano-amplification technique was applied in detection of hepatitis E virus. J. Biochem. Mol. Biol. 39: 247-252 https://doi.org/10.5483/BMBRep.2006.39.3.247
  33. Ma, J. and C. C. Liew. 2003. Gene profiling identifies secreted protein transcripts from peripheral blood cells in coronary artery disease. J. Mol. Cell. Cardiol. 35: 993-998 https://doi.org/10.1016/S0022-2828(03)00179-2
  34. McNeil, M. M., S. L. Nash, R. A. Hajjeh, M. A. Phelan, L. A. Conn, B. D. Plikaytis, and D. W. Warnock. 2001. Trends in mortality due to invasive mycotic diseases in the United States, 1980-1997. Clin. Infect. Dis. 33: 641-647 https://doi.org/10.1086/322606
  35. Morel, Y. and W. L. Miller. 1991. Clinical and molecular genetics of congenital adrenal hyperplasia due to 21-hydroxylase deficiency. Adv. Hum. Genet. 20: 1-68
  36. Morens, D. M., G. K. Folkers, and A. S. Fauci. 2004. The challenge of emerging and re-emerging infectious diseases. Nature 430: 242-249 https://doi.org/10.1038/nature02759
  37. Mulligan, M. E., L. R. Peterson, R. Y. Kwok, C. R. Clabots, and D. N. Gerding. 1988. Immunoblots and plasmid fingerprints compared with serotyping and polyacrylamide gel electrophoresis for typing Clostridium difficile. J. Clin. Microbiol. 26: 41-46
  38. Payne, A. S., E. J. Kelly, and J. D. Gitlin. 1998. Functional expression of the Wilson disease protein reveals mislocalization and impaired copper-dependent trafficking of the common H1069Q mutation. Proc. Natl. Acad. Sci. USA 95: 10854-10859 https://doi.org/10.1073/pnas.95.18.10854
  39. Petrukhin, K., S. Lutsenko, I. Chernov, B. M. Ross, J. H. Kaplan, and T. C. Gilliam. 1994. Characterization of the Wilson disease gene encoding a P-type copper transporting ATPase: Genomic organization, alternative splicing, and structure/function predictions. Hum. Mol. Genet. 3: 1647-1656 https://doi.org/10.1093/hmg/3.9.1647
  40. Rennie, R. P., C. E. Nord, L. Sjoberg, and I. B. R. Duncan. 1978. Comparison of bacteriophage typing, serotyping, and biotyping as aids in epidemiologic surveillance of Klebsiella infections. J. Clin. Microbiol. 8: 638-642
  41. Speiser, P. W., B. Dupont, P. Rubinstein, A. Piazza, A. Kastelan, and M. I. New. 1985. High frequency of nonclassical steroid 21-hydroxylase deficiency. Am. J. Hum. Genet. 37: 650-667
  42. Stewart, H. S., A. E. Ridgway, M. J. Dixon, R. Bonshek, R. Parveen, and G. Black. 1999. Heterogeneity in granular corneal dystrophy: Identification of three causative mutations in the TGFBI (BIGH3) gene - lessons for corneal amyloidogenesis. Hum. Mutat. 14: 126-132 https://doi.org/10.1002/(SICI)1098-1004(1999)14:2<126::AID-HUMU4>3.0.CO;2-W
  43. Strikas, R. A., L. Anderson, and R. A. Parker. 1986. Temporal and geographic patterns of isolates of nonpolio enteroviruses in the United States, 1970-1983. J. Infect. Dis. 153: 346-351 https://doi.org/10.1093/infdis/153.2.346
  44. Swift, M., D. Morrell, E. Cromartie, A. R. Chamberlin, M. H. Skolnick, and D. T. Bishop. 1986. The incidence and gene frequency of ataxia-telangiectasia in the United States. Am. J. Hum. Genet. 39: 573-583
  45. Swift, M., D. Morrell, R. B. Massey, and C. L. Chase. 1991. Incidence of cancer in 161 families affected by ataxiatelangiectasia. N. Engl. J. Med. 325: 1831-1836 https://doi.org/10.1056/NEJM199112263252602
  46. Thomas, G. R., O. Jensson, G. Gudmundsson, L. Thorsteinsson, and D. W. Cox. 1995. Wilson disease in Iceland: A clinical and genetic study. Am. J. Hum. Genet. 56: 1140-1146
  47. Thomas, G. R., P. C. Bull, E. A. Roberts, J. M. Walshe, and D. W. Cox. 1994. Haplotype studies in Wilson disease. Am. J. Hum. Genet. 54: 71-78
  48. Vanittanakom, N. and T. Sirisanthana. 1997. Penicillium marneffei infection in patients infected with human immunodeficiency virus. Curr. Top. Med. Mycol. 8: 35-42
  49. Waldenstrom, E., A. Lagerkvist, T. Dahlman, K. Westermark, and U. Landegren. 1996. Efficient detection of mutations in Wilson disease by manifold sequencing. Genomics 37: 303-309 https://doi.org/10.1006/geno.1996.0564
  50. Wang, R. F., M. L. Beggs, L. H. Robertson, and C. E. Cerniglia. 2002. Design and evaluation of oligonucleotidemicroarray method for the detection of human intestinal bacteria in fecal samples. FEMS Microbiol. Lett. 213: 175-182 https://doi.org/10.1111/j.1574-6968.2002.tb11302.x
  51. Wang, R. F., S. J. Kim, L. H. Robertson, and C. E. Cerniglia. 2002. Development of a membrane-array method for the detection of human intestinal bacteria in fecal samples. Mol. Cell. Probes. 16: 341-350 https://doi.org/10.1006/mcpr.2002.0432
  52. Warnock, D. W. 1995. Fungal complications of transplantation: Diagnosis, treatment, and prevention. J. Antimicrob. Chemother. 36(Suppl B): 73-90
  53. White, P. C., M. I. New, and B. Dupont. 1987. Congenital adrenal hyperplasia. N. Engl. J. Med. 316: 1519-1524 https://doi.org/10.1056/NEJM198706113162406
  54. Wright, J., S. Teraoka, A. Onengut, S. A. Tolun, R. A. Gatti, H. D. Ochs, and P. Concannon. 1996. A high frequency of distinct ATM gene mutations in ataxia-telangiectasia. Am. J. Hum. Genet. 59: 839-846
  55. Yoo, S. Y., T.-I. Kim, S. Y. Lee, E. K. Kim, K. C. Keum, N. C. Yoo, and W. M. Yoo. 2007. Development of DNA chip for the diagnosis of most common corneal dystrophies caused by mutations in the betaigh3 gene. Br. J. Opththalmol. 91: 722-727 https://doi.org/10.1136/bjo.2006.111070

Cited by

  1. Visual detection of single-stranded target DNA using pyrroloquinoline-quinone-loaded liposomes as a tracer vol.401, pp.2, 2010, https://doi.org/10.1016/j.ab.2010.02.041
  2. Microarray-based enzyme profiling: Recent advances and applications (Review) vol.5, pp.3, 2010, https://doi.org/10.1116/1.3462969
  3. Detection of Single Nucleotide Polymorphisms by a Gold Nanowire‐on‐Film SERS Sensor Coupled with S1 Nuclease Treatment vol.17, pp.31, 2009, https://doi.org/10.1002/chem.201003372
  4. Diagnostic des infections bactériennes par les puces à ADN vol.39, pp.1, 2009, https://doi.org/10.1007/s11834-011-0051-y
  5. Systematic Spatial Bias in DNA Microarray Hybridization Is Caused by Probe Spot Position-Dependent Variability in Lateral Diffusion vol.6, pp.8, 2009, https://doi.org/10.1371/journal.pone.0023727
  6. CNV-WebStore: Online CNV Analysis, Storage and Interpretation vol.12, pp.None, 2009, https://doi.org/10.1186/1471-2105-12-4
  7. Direct labeling rolling circle amplification as a straightforward signal amplification technique for biodetection formats vol.4, pp.5, 2009, https://doi.org/10.1039/c2ay05760c
  8. Ion mobility spectrometry for microbial volatile organic compounds: a new identification tool for human pathogenic bacteria vol.93, pp.6, 2009, https://doi.org/10.1007/s00253-012-3924-4
  9. Unique Reporter-Based Sensor Platforms to Monitor Signalling in Cells vol.7, pp.11, 2009, https://doi.org/10.1371/journal.pone.0050521
  10. Survival transcriptome in the coenzyme Q 10 deficiency syndrome is acquired by epigenetic modifications: a modelling study for human coenzyme Q 10 deficiencies vol.3, pp.3, 2009, https://doi.org/10.1136/bmjopen-2012-002524
  11. Sequence-Selective Detection of Double-Stranded DNA Sequences Using Pyrrole–Imidazole Polyamide Microarrays vol.135, pp.9, 2009, https://doi.org/10.1021/ja309677h
  12. Preparation and Evaluation of a Peptide Nucleic Acid Gene Chip System Associated with Surface Plasmon Resonance vol.18, pp.5, 2013, https://doi.org/10.1007/s12257-012-0844-1
  13. Enhanced Fluorescence Using an Optical Interference Mirror Overlaid with Silver Island Film vol.47, pp.16, 2014, https://doi.org/10.1080/00032719.2014.919507
  14. Molecular Patterns of Neurodevelopmental Preconditioning: A Study of the Effects of Antenatal Steroid Therapy in a Protein-Restriction Mouse Model vol.2014, pp.None, 2009, https://doi.org/10.1155/2014/193816
  15. Eureka-DMA: an easy-to-operate graphical user interface for fast comprehensive investigation and analysis of DNA microarray data vol.15, pp.None, 2009, https://doi.org/10.1186/1471-2105-15-53
  16. The Use of Atomic Force Microscopy for 3D Analysis of Nucleic Acid Hybridization on Microarrays vol.7, pp.2, 2009, https://doi.org/10.32607/20758251-2015-7-2-108-114
  17. Application of Diagnostic Microarray Technique in Subtyping and Pathotyping of Avian Influenza Viruses Isolated in Mongolia vol.46, pp.1, 2009, https://doi.org/10.4167/jbv.2016.46.1.22
  18. Rapid Identification of Pathogenic Variants in Two Cases of Charcot-Marie-Tooth Disease by Gene-Panel Sequencing vol.18, pp.4, 2009, https://doi.org/10.3390/ijms18040770
  19. An automated microfluidic DNA microarray platform for genetic variant detection in inherited arrhythmic diseases vol.143, pp.6, 2018, https://doi.org/10.1039/c7an01648d
  20. Identification of key genes in ruptured atherosclerotic plaques by weighted gene correlation network analysis vol.10, pp.None, 2020, https://doi.org/10.1038/s41598-020-67114-2