Selection of a Platform for Mutation Detection

Victoria A. Joshi1, Debora Mancini‐DiNardo2, Birgit H. Funke1

1 Department of Pathology, Massachusetts General Hospital, 2 Harvard Medical School‐Partners Healthcare Center for Genetics and Genomics
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 7.15
DOI:  10.1002/0471142905.hg0715s56
Online Posting Date:  January, 2008
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New mutation detection technologies must keep pace by becoming more cost‐effective while offering improved technical sensitivity and higher throughput capacity. In recent years, the number of mutation detection platforms available to the clinical researcher has grown to a point where it is difficult to keep track of all available options as well as their benefits and pitfalls. This unit provides an entry point for a variety of researchers who wish to analyze samples for known or novel mutations and need to determine which platform is most suited for their particular needs. A practical guide is provided in this unit, including a brief overview, information on assay parameters, design and cost considerations, as well as platform flexibility and scalability of the assay. Although the focus here is on applications involving human disease, many of these platforms can be easily adapted to the study of other organisms. Curr. Protoc. Hum. Genet. 56:7.15.1‐7.15.30. © 2008 by John Wiley & Sons, Inc.

Keywords: mutation detection; mutation scanning; genotyping

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Table of Contents

  • Introduction
  • Methods for Direct Mutation Detection
  • Methods for Mutation Scanning
  • Detection of Constitutional Copy Number Variation
  • Methylation Detection
  • Acknowledgements
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

   Ariani, F., Mari, F., Pescucci, C., Longo, I., Bruttini, M., Meloni, I., Hayek, G., Rocchi, R., Zappella, M., and Renieri, A. 2004. Real‐time quantitative PCR as a routine method for screening large rearrangements in Rett syndrome: Report of one case of MECP2 deletion and one case of MECP2 duplication. Hum. Mutat. 24:172‐177.
   Barker, D.L., Hansen, M.S., Faruqi, A.F., Giannola, D., Irsula, O.R., Lasken, R.S., Latterich, M., Makarov, V., Oliphant, A., Pinter, J.H., Shen, R., Sleptsova, I., Ziehler, W., and Lai, E. 2004. Two methods of whole‐genome amplification enable accurate genotyping across a 2320‐SNP linkage panel. Genome Res. 14:901‐907.
   Barrois, M., Bieche, I., Mazoyer, S., Champeme, M.H., Bressac‐de Paillerets, B., and Lidereau, R. 2004. Real‐time PCR‐based gene dosage assay for detecting BRCA1 rearrangements in breast‐ovarian cancer families. Clin. Genet. 65:131‐136.
   Boehm, D., Herold, S., Kuechler, A., Liehr, T., and Laccone, F. 2004. Rapid detection of subtelomeric deletion/duplication by novel real‐time quantitative PCR using SYBR‐green dye. Hum. Mutat. 23:368‐378.
   Boddicker, J.D., Rota, P.A., Kreman, T., Wangeman, A., Lowe, L., Hummel, K.B., Thompson, R., Bellini, W.J., Pentella, M., and Desjardin, L.E. 2007. Real‐time RT‐PCR assay for the detection of mumps virus RNA in clinical specimens. J. Clin. Microbiol. 45:2902‐2908.
   Bodin, L., Beaune, P.H., and Loriot, M.A. 2005. Determination of cytochrome P450 2D6 (CYP2D6) gene copy number by real‐time quantitative PCR. J. Biomed. Biotechnol. 2005:248‐253.
   Cohen, V., Agulnik, J.S., Jarry, J., Batist, G., Small, D., Kreisman, H., Tejada, N.A., Miller, W.H. Jr., and Chong, G. 2006. Evaluation of denaturing high‐performance liquid chromatography as a rapid detection method for identification of epidermal growth factor receptor mutations in nonsmall‐cell lung cancer. Cancer 107:2858‐2865.
   Dalma‐Weiszhausz, D.D., Warrington, J., Tanimoto, E.Y., and Miyada, C.G. 2006. The Affymetrix GeneChip platform: An overview. Methods Enzymol. 410:3‐28.
   Dunbar, S.A. 2006. Applications of Luminex xMAP technology for rapid, high‐throughput multiplexed nucleic acid detection. Clin. Chim. Acta 363:71‐82.
   Fan, J.B., Gunderson, K.L., Bibikova, M., Yeakley, J.M., Chen, J., Wickham Garcia, E., Lebruska, L.L., Laurent, M., Shen, R., and Barker, D. 2006. Illumina universal bead arrays. Methods Enzymol. 410:57‐73.
   Gomez‐Curet, I., Robinson, K.G., Funanage, V.L., Crawford, T.O., Scavina, M., and Wang, W. 2007. Robust quantification of the SMN gene copy number by real‐time TaqMan PCR. Neurogenetics 8:271‐278.
   Grossman, P.D., Bloch, W., Brinson, E., Chang, C.C., Eggerding, F.A., Fung, S., Iovannisci, D.M., Woo, S., and Winn‐Deen, E.S. 1994. High‐density multiplex detection of nucleic acid sequences: Oligonucleotide ligation assay and sequence‐coded separation. Nucleic Acids Res. 22:4527‐4534.
   Hackett, J.L.A., Kellie, J., Gaigalas, A.K., Garrett, C.T., Joseph, L.J., Koch, W.H., Kricka, L.J., McGlennen, R.C., Van Deerlin, V., and Vasquez, G.B. 2006. Diagnostic nucleic acid microarrays; approved guideline. Clinical and Laboratory Standards Institute (formerly NCCLS), Wayne, PA.
   Hoebeeck, J., van der Luijt, R., Poppe, B., De Smet, E., Yigit, N., Claes, K., Zewald, R., de Jong, G.J., De Paepe, A., Speleman, F., and Vandesompele, J. 2005. Rapid detection of VHL exon deletions using real‐time quantitative PCR. Lab. Invest. 85:24‐33.
   Hsu, T.M., Law, S.M., Duan, S., Neri, B.P., and Kwok, P.Y. 2001. Genotyping single‐nucleotide polymorphisms by the invader assay with dual‐color fluorescence polarization detection. Clin. Chem. 47:1373‐1377.
   Janne, P.A., Borras, A.M., Kuang, Y., Rogers, A.M., Joshi, V.A., Liyanage, H., Lindeman, N., Lee, J.C., Halmos, B., Maher, E.A., Distel, R.J., Meyerson, M., and Johnson, B.E. 2006. A rapid and sensitive enzymatic method for epidermal growth factor receptor mutation screening. Clin. Cancer Res. 12:751‐758.
   Kosaki, K., Udaka, T., and Okuyama, T. 2005. DHPLC in clinical molecular diagnostic services. Mol. Genet. Metab. 86:117‐123.
   Kwok, P.Y., Gremaud, M.F., Nickerson, D.A., Hood, L., and Olson, M.V. 1992. Automatable screening of yeast artificial‐chromosome libraries based on the oligonucleotide‐ligation assay. Genomics 13:935‐941.
   Lee, L.G., Livak, K.J., Mullah, B., Graham, R.J., Vinayak, R.S., and Woudenberg, T.M. 1999. Seven‐color, homogeneous detection of six PCR products. Biotechniques 27:342‐349.
   Livak, K.J., Flood, S.J., Marmaro, J., Giusti, W., and Deetz, K. 1995. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl. 4:357‐362.
   Mein, C.A., Barratt, B.J., Dunn, M.G., Siegmund, T., Smith, A.N., Esposito, L., Nutland, S., Stevens, H.E., Wilson, A.J., Phillips, M.S., Jarvis, N., Law, S., de Arruda, M., and Todd, J.A. 2000. Evaluation of single nucleotide polymorphism typing with invader on PCR amplicons and its automation. Genome Res. 10:330‐343.
   Monico, C.G., Rossetti, S., Schwanz, H.A., Olson, J.B., Lundquist, P.A., Dawson, D.B., Harris, P.C., and Milliner, D.S. 2007. Comprehensive mutation screening in 55 probands with type 1 primary hyperoxaluria shows feasibility of a gene‐based diagnosis. J. Am. Soc. Nephrol. 18:1905‐1914.
   Nakagawa, H., Hampel, H., and de la Chapelle, A. 2003. Identification and characterization of genomic rearrangements of MSH2 and MLH1 in Lynch syndrome (HNPCC) by novel techniques. Hum. Mutat. 22:258.
   Nickerson, D.A., Kaiser, R., Lappin, S., Stewart, J., Hood, L., and Landegren, U. 1990. Automated DNA diagnostics using an ELISA‐based oligonucleotide ligation assay. Proc. Natl. Acad. Sci. U.S.A. 87:8923‐8927.
   Olivier, M. 2005. The Invader assay for SNP genotyping. Mutat. Res. 573:103‐110.
   Palomares, M., Delicado, A., Lapunzina, P., Arjona, D., Amiñoso, C., Arcas, J., Martinez, B.A., Fernández, L., and López, P.I. 2006. MLPA vs. multiprobe FISH: Comparison of two methods for the screening of subtelomeric rearrangements in 50 patients with idiopathic mental retardation. Clin. Genet. 69:228‐233.
   Patnaik, M., Dlott, J.S., Fontaine, R.N., Subbiah, M.T., Hessner, M.J., Joyner, K.A., Ledford, M.R., Lau, E.C., Moehlenkamp, C., Amos, J., Zhang, B., and Williams, T.M. 2004. Detection of genomic polymorphisms associated with venous thrombosis using the invader biplex assay. J. Mol. Diagn. 6:137‐144.
   Paynter, R.A., Skibola, D.R., Skibola, C.F., Buffler, P.A., Wiemels, J.L., and Smith, M.T. 2006. Accuracy of multiplexed Illumina platform‐based single‐nucleotide polymorphism genotyping compared between genomic and whole genome amplified DNA collected from multiple sources. Cancer Epidemiol. Biomarkers Prev. 15:2533‐2536.
   Riva, A. and Kohane, I.S. 2002. SNPper: Retrieval and analysis of human SNPs. Bioinformatics 18:1681‐1685.
   Romppanen, E.L. 2001. Oligonucleotide ligation assay: Applications to molecular diagnosis of inherited disorders. Scand. J. Clin. Lab. Invest. 61:123‐129.
   Salisbury, M.W. 2007. Next‐gen sequencing: The waiting game In Genome Technology. pp. 26‐28. Genome Web Intelligence Network, New York.
   Schouten, J.P., McElgunn, C.J., Waaijer, R., Zwijnenburg, D., Diepvens, F., and Pals, G. 2002. Relative quantification of 40 nucleic acid sequences by multiplex ligation‐dependent probe amplification. Nucleic Acids Res. 30:e57.
   Shadrina, M.I., Semenova, E.V., Slominsky, P.A., Bagyeva, G.H., Illarioshkin, S.N., Ivanova‐Smolenskaia, I.I., and Limborska, S.A. 2007. Effective quantitative real‐time polymerase chain reaction analysis of the parkin gene (PARK2) exon 1‐12 dosage. B.M.C. Med. Genet. 8:6.
   Shi, M.M. 2001. Enabling large‐scale pharmacogenetic studies by high‐throughput mutation detection and genotyping technologies. Clin. Chem. 47:164‐172.
   Slater, H., Bruno, D., Ren, H., La, P., Burgess, T., Hills, L., Nouri, S., Schouten, J., and Choo, K.H. 2004. Improved testing for CMT1A and HNPP using multiplex ligation‐dependent probe amplification (MLPA) with rapid DNA preparations: Comparison with the interphase FISH method. Hum. Mutat. 24:164‐171.
   Strachan, T. and Read, A.P. 2004. Human Molecular Genetics 3, 3rd ed., pp. 674. Garland Science, London and New York.
   Strom, C.M., Janeszco, R., Quan, F., Wang, S.B., Buller, A., McGinniss, M., and Sun, W. 2006. Technical validation of a TM Biosciences Luminex‐based multiplex assay for detecting the American College of Medical Genetics recommended cystic fibrosis mutation panel. J. Mol. Diagn. 8:371‐375.
   Taylor, C.F., Charlton, R.S., Burn, J., Sheridan, E., and Taylor, G.R. 2003. Genomic deletions in MSH2 or MLH1 are a frequent cause of hereditary non‐polyposis colorectal cancer: Identification of novel and recurrent deletions by MLPA. Hum. Mutat. 22:428‐33.
   Thiel, C.T., Kraus, C., Rauch, A., Ekici, A.B., Rautenstrauss, B., and Reis, A. 2003. A new quantitative PCR multiplex assay for rapid analysis of chromosome 17p11.2–12 duplications and deletions leading to HMSN/HNPP. Eur. J. Hum. Genet. 11:170‐178.
   Xiao, W. and Oefner, P.J. 2001. Denaturing high‐performance liquid chromatography: A review. Hum. Mutat. 17:439‐474.
   Yobb, T.M., Somerville, M.J., Willatt, L., Firth, H.V., Harrison, K., MacKenzie, J., Gallo, N., Morrow, B.E., Shaffer, L.G., Babcock, M., Chernos, J., Bernier, F., Sprysak, K., Christiansen, J., Haase, S., Elyas, B., Lilley, M., Bamforth, S., and McDermid, H.E. 2005. Microduplication and triplication of 22q11.2: A highly variable syndrome. Am. J. Hum. Genet. 76:865‐876.
   Zoccoli, M.A., Chan, M., Erker, J., Ferreira‐Gonzalez, A., and Lubin, I.M. 2004. Nucleic Acid Sequencing Methods in Diagnostic Laboratory Medicine: Proposed Guideline. Clinical and Laboratory Standards Institute. MM9‐P; 24 No. 18.
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