Decision criteria for rational selection of homogeneous genotyping platforms for pharmacogenomics testing in clinical diagnostics

Clinical Chemistry and Laboratory Medicine

Volumn 48, Issue 4, 2010, Pages 447-459

  Di Francia, Raffaele ^a   Frigeri, Ferdinando ^a   Berretta, Massimiliano ^b   Cecchin, Erika ^b   Orlando, Claudio ^c   Pinto, Antonio ^a   Pinzani, Pamela ^c  

^a NATIONAL CANCER INSTITUTE   (Italy)

^b CENTRO DI RIFERIMENTO ONCOLOGICO   (Italy)

^c UNIVERSITY OF FLORENCE   (Italy)

Author keywords

Analytical validations criteria; Genotyping methods; Molecular diagnostics

Indexed keywords

ALPHA INTERFERON; FLUORESCENT DYE; LOCKED NUCLEIC ACID; PEPTIDE NUCLEIC ACID;

ANALYTIC METHOD; CLINICAL DECISION MAKING; CLINICAL LABORATORY; DNA DETERMINATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE MUTATION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; HIGH THROUGHPUT SCREENING; HUMAN; IMMUNOASSAY; INTERMETHOD COMPARISON; LIQUID PHASE MICROEXTRACTION; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MULTIPLEX POLYMERASE CHAIN REACTION; PHARMACOGENOMICS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PYROSEQUENCING; REPRODUCIBILITY; REVIEW; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM;

FLUORESCENCE RESONANCE ENERGY TRANSFER; GENOTYPE; HUMANS; INDIVIDUALIZED MEDICINE; OLIGONUCLEOTIDES; PEPTIDE NUCLEIC ACIDS; PHARMACOGENETICS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUALITY CONTROL; SEQUENCE ANALYSIS, DNA;

EID: 77949856139     PISSN: 14346621     EISSN: 14374331     Source Type: Journal    
DOI: 10.1515/CCLM.2010.112     Document Type: Review

References (58)

1. Dai Z, Papp AC, Wang D, Hampel H, Sadee W. Genotyping panel for assessing response to cancer chemotherapy. BMC Med Genomics 2008;1:1-24.
2. Yong WP, Innocenti F, Retain MJ. The role of pharmacogenetics in cancer therapeutics. Br J Clin Pharmacol 2006;62:35-46. (Pubitemid 44195241)
3. Ingelman-Sundberg M. Human drug metabolising cytochrome P450 enzymes: properties and polymorphisms. Naunyn Schmiedebergs Arch Pharmacol 2004;369:89-104.
4. Ekhart C, Rodenhuis S, Smits PH, Beijnen JH, Huitema AD. Relations between polymorphisms in drug-metabolising enzymes and toxicity of chemotherapy with cyclophosphamide, thiotepa and carboplatin. Pharmacogenet Genomics 2008;18:1009-1015
5. Marzolini C, Paus E, Buclin T, Kim RB. Polymorphisms in human MDR1 (P-glycoprotein): recent advances and clinical relevance. Clin Pharmacol Ther 2004;75:13-33.
6. Ikediobi ON. Somatic pharmacogenomics in cancer. Pharmacogenomics J 2008;8:305-314
7. Labussière H, Hayette S, Tigaud I, Michallet M, Nicolini FE. Treatment of chronic myeloid leukemia in 2007. Bull Cancer 2007;94:863-869
8. Kobayashi S, Boggon TJ, Dayaram T, Jänne PA, Kocher O, Meyerson M, et al. EGFR mutation and resistance of nonsmall- cell lung cancer to gefitinib. N Engl J Med 2005;352: 786-792
9. Anderson CA, Pettersson FH, Barrett JC, Zhuang JJ, Ragoussis J, Cardon LR, et al. Evaluating the effects of imputation on the power, coverage, and cost efficiency of genome-wide SNP platforms. Am J Hum Genet 2008;83:112-119
10. Aquilante CL, Zineh I, Beitelshees AL, Langaee TY. Common laboratory methods in pharmacogenomics studies. Am J Health Syst Pharm 2006;63:2101-2110
11. Agarwal RP, Peters SM, Shemirani M, von Ahsen N. Improved real-time multiplex polymerase chain reaction detection of methylenetetrahydrofolate reductase (MTHFR) 677C)T and 1298A)C polymorphisms using nearest neighbor model-based probe design. J Mol Diagn 2007;9:345-350
12. De la Vega FM, Lazaruk KD, Rhodes MD, Wenz MH. Assessment of two flexible and compatible SNP genotyping platforms: TaqMan SNP genotyping assays and the SNPlex genotyping system. Mutat Res 2005;573:111-135
13. Latif S, Bauer-Sardina I, Ranade K, Livak KJ, Kwok PY. Fluorescence polarization in homogeneous nucleic acid analysis II: 59-nuclease assay. Genome Res 2001;11:436-440
14. Tyagi S, Bratu DP, Kramer FR. Multicolor molecular beacons for allele discrimination. Nat Biotechnol 1998;16:49-53.
15. Solinas A, Brown LJ, McKeen C, Mellor JM, Nicol J, Thelwell N, et al. Duplex Scorpion primers in SNP analysis and FRET applications. Nucleic Acids Res 2001;29:E96.
16. Thelwell N, Millington S, Solinas A, Booth J, Brown T. Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Res 2000;28:3752-3761
17. Sun X, Hung K, Wu L, Sidransky D, Guo B. Detection of tumor mutation in the presence of excess amounts of normal DNA. Nat Biotechnol 2002;20:186-189
18. Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA, et al. PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature 1993;365:566-568
19. Fiandaca MJ, Hyldig-Nielsen JJ, Gildea BD, Coull JM. Selfreporting PNA/DNA primers for PCR analysis. Genome Res 2001;11:609-613
20. Taback B, Bilchik AJ, Saha S, Nakayama T, Wiese DA, Turner RR, et al. Peptide nucleic acid clamp PCR: a novel K-ras mutation detection assay for colorectal cancer micrometastases in lymph nodes. Int J Cancer 2004;111:409-414
21. Hancock DK, Schwarz FP, Song F, Wong LJ, Levin BC. Design and use of a peptide nucleic acid for detection of the heteroplasmic low-frequency mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) mutation in human mitochondrial DNA. Clin Chem 2002;48:2155-2163
22. Schatz P, Distler J, Berlin K, Schuster M. Novel method for high throughput DNA methylation marker evaluation using PNA-probe library hybridization and MALDI-TOF detection. Nucleic Acids Res 2006;34:e59.
23. Karadag A, Riminucci M, Bianco P, Cherman N, Kuznetsov SA, Nguyen N, et al. A novel technique based on a PNA hybridization probe and FRET principle for quantification of mutant genotype in fibrous dysplasia/McCune-Albright syndrome. Nucleic Acids Res 2004;32:e63.
24. Luo JD, Chan EC, Shih CL, Chen TL, Liang Y, Hwang TL, et al. Detection of rare mutant K-ras DNA in a single-tube reaction using peptide nucleic acid as both PCR clamp and sensor probe. Nucleic Acids Res 2006;34:e12.
25. Kreuzer KA, Le Coutre P, Landt O, Na IK, Schwarz M, Schultheis K, et al. Preexistence and evolution of imatinib mesylateresistant clones in chronic myelogenous leukemia detected by a PNA-based PCR clamping technique. Ann Hematol 2003; 82:284-289
26. Chen CY, Shiesh SC, Wu SJ. Rapid detection of K-ras mutations in bile by peptide nucleic acid-mediated PCR clamping and melting curve analysis: comparison with restriction fragment length polymorphism analysis. Clin Chem 2004;50:481-489
27. Mouritzen P, Nielsen AT, Pfundheller HM, Choleva Y, Kongsbak L, Møller S. Single nucleotide polymorphism genotyping using locked nucleic acid (LNA). Expert Rev Mol Diagn 2003;3:27-38.
28. Dominguez PL, Kolodney MS. Wild-type blocking polymerase chain reaction for detection of single nucleotide minority mutations from clinical specimens. Oncogene 2005;24:6830-6834
29. Orum H, Jakobsen MH, Koch T, Vuust J, Borre MB. Detection of the factor V Leiden mutation by direct allele-specific hybridization of PCR amplicons to photoimmobilized locked nucleic acids. Clin Chem 1999;45:1898-1905
30. Jacobsen N, Fenger M, Bentzen J, Rasmussen SL, Jakobsen MH, Fenstholt J, et al. Genotyping of the apolipoprotein B R3500Q mutation using immobilized locked nucleic acid capture probes. Clin Chem 2002;48:657-660
31. Jacobsen N, Bentzen J, Meldgaard M, Jakobsen MH, Fenger M, Kauppinen S, et al. LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E. Nucleic Acids Res 2002;30:e100.
32. Guerasimova A, Nyarsik L, Liu JP, Schwartz R, Lange M, Lehrach H, et al. Liquid-based hybridization assay with real-time detection in miniaturized array platforms. Biomol Eng 2006; 23:35-40.
33. Mein CA, Barratt BJ, Dunn MG, Siegmund T, Smith AN, Esposito L, et al. Evaluation of single nucleotide polymorphism typing with invader on PCR amplicons and its automation. Genome Res 2000;10:330-343
34. Kaiser MW, Lyamicheva N, Ma W, Miller C, Neri B, Fors L, et al. A comparison of eubacterial and archaeal structure-specific 59-exonucleases. J Biol Chem 1999;274:21387-21394
35. Ito N, Eto M, Nakamura E, Takahashi A, Tsukamoto T, Toma H, et al. STAT3 polymorphism predicts interferon-alfa response in patients with metastatic renal cell carcinoma. J Clin Oncol 2007;25:2785-2791
36. Imada Y, Fujimoto M, Hirata K, Hirota T, Suzuki Y, Saito H, et al. Large scale genotyping study for asthma in the Japanese population. BMC Res Notes 2009;2:54.
37. Alderborn A, Kristofferson A, Hammerling U. Determination of single-nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res 2000;10:1249-1258
38. Chantepie SP, Vaur D, Grunau C, Salaün V, Briand M, Parienti JJ, et al. ZAP-70 intron1 DNA methylation status: determination by pyrosequencing in B chronic lymphocytic leukemia. Leuk Res 2009 Nov 25. wEpub ahead of printx.
39. Sivertsson A, Platz A, Hansson J, Lundeberg J. Pyrosequencing as an alternative to single-strand conformation polymorphism analysis for detection of N-ras mutations in human melanoma metastases. Clin Chem 2002;48:2164-2170
40. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ. High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem 2003;49(6 Pt 1):853-860
41. Vaughn CP, Elenitoba-Johnson KS. High-resolution melting analysis for detection of internal tandem duplications. J Mol Diagn 2004;6:211-216
42. Willmore-Payne C, Holden JA, Chadwick BE, Layfield LJ. Detection of c-kit-activating mutations in gastrointestinal stromal tumors by high-resolution amplicon melting analysis. Am J Clin Pathol 2004;122:206-216
43. Willmore-Payne C, Holden JA, Layfield LJ. Detection of EGFR and HER2 activating mutations in squamous cell carcinoma involving the head and neck. Modern Pathol 2006;19: 634-640
44. Willmore-Payne C, Holden JA, Tripp S, Layfield LJ. Human malignant melanoma: detection of BRAF- and c-kit-activating mutations by high-resolution amplicon melting analysis. Hum Pathol 2005;36:486-493
45. Willmore-Payne C, Volmar KE, Huening MA, Holden JA, Layfield LJ. Molecular diagnostic testing as an adjunct to morphologic evaluation of pancreatic ductal system brushings: potential augmentation for diagnostic sensitivity. Diagn Cytopathol 2007;35:218-224
46. Simi L, Pratesi N, Vignoli M, Sestini R, Cianchi F, Valanzano R, et al. High-resolution melting analysis for rapid detection of KRAS, BRAF, and PIK3CA gene mutations in colorectal cancer. Am J Clin Pathol 2008;130:247-253
47. Wojdacz TK, Dobrovic A. Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation. Nucleic Acids Res 2007;35:e41.
48. Pang J, Modlin J, Yolken R. Use of modified nucleotides and uracil-DNA glycosylase (UNG) for the control of contamination in the PCR-based amplification of RNA. Mol Cell Probes 1992;6:251-256
49. Dorn-Beineke A, Ahmad-Nejad P, Pfeiffer U, Ramsden S, Pazzagli M, Neumaier M. Improvement of technical and analytical performance in DNA sequencing by external quality assessment- based molecular training. Clin Chem 2006;52:2072-2078
50. Täpp I, Malmberg L, Rennel E, Wik M, Syvänen AC. Homogeneous scoring of single-nucleotide polymorphisms: comparison of the 59-nuclease TaqMan assay and Molecular Beacon probes. Biotechniques 2000;28:732-738
51. Orlando C, Verderio P, Maatman R, Danneberg J, Ramsden S, Neumaier M, et al. EQUAL-qual: a European program for external quality assessment of genomic DNA extraction and PCR amplification. Clin Chem 2007;53:1349-1357
52. Andersson T, Flockhart DA, Goldstein DB, Huang SM, Kroetz DL, Milos PM, et al. Drug-metabolizing enzymes: evidence for clinical utility of pharmacogenomic tests. Clin Pharmacol Ther 2005;78:559-581
53. Cusha WT, Medrano JF. Effect of blood storage time and temperature on DNA yield and quality. Biotechniques 1993;14: 204-207
54. Kreuzer KA, Bohn A, Lass U, Peters UR, Schmidt CA. Influence of DNA polymerases on quantitative PCR results using TaqMan probe format in the LightCycler instrument. Mol Cell Probes 2000;14:57-60.
55. Nauck M, Wieland H, März W. Evaluation of the Roche diagnostics LightCycler-Apo B 3500 mutation detection kit. Clin Chem Lab Med 2000;38:667-671
56. Kyger EM, Krevolin MD, Powell MJ. Detection of the hereditary hemochromatosis gene mutation by real-time fluorescence polymerase chain reaction and peptide nucleic acid clamping. Anal Biochem 1998;260:142-148
57. Innocenti F, Ratain MJ. Update on pharmacogenetics in cancer chemotherapy. Eur J Cancer 2002;38:639-644
58. Little S. Translating single nucleotide polymorphism tests from clinical research to clinical practice. Personalized Medicine 2006;3:95-99