Nucleic Acids Research

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Nucleic Acids Research, 2002, Vol. 30, No. 12 e57
© 2002 Oxford University Press

Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification

Jan P. Schouten^*, Cathal J. McElgunn, Raymond Waaijer, Danny Zwijnenburg, Filip Diepvens and Gerard Pals¹

MRC-Holland, Hudsonstraat 68, 1057SN Amsterdam, The Netherlands and ¹Department of Clinical Genetics, Free University of Amsterdam, v.d. Boechorststraat 7, 1081BT Amsterdam, The Netherlands

We describe a new method for relative quantification of 40 different DNA sequences in an easy to perform reaction requiring only 20 ng of human DNA. Applications shown of this multiplex ligation-dependent probe amplification (MLPA) technique include the detection of exon deletions and duplications in the human BRCA1, MSH2 and MLH1 genes, detection of trisomies such as Down’s syndrome, characterisation of chromosomal aberrations in cell lines and tumour samples and SNP/mutation detection. Relative quantification of mRNAs by MLPA will be described elsewhere. In MLPA, not sample nucleic acids but probes added to the samples are amplified and quantified. Amplification of probes by PCR depends on the presence of probe target sequences in the sample. Each probe consists of two oligonucleotides, one synthetic and one M13 derived, that hybridise to adjacent sites of the target sequence. Such hybridised probe oligonucleotides are ligated, permitting subsequent amplification. All ligated probes have identical end sequences, permitting simultaneous PCR amplification using only one primer pair. Each probe gives rise to an amplification product of unique size between 130 and 480 bp. Probe target sequences are small (50–70 nt). The prerequisite of a ligation reaction provides the opportunity to discriminate single nucleotide differences.

^* To whom correspondence should be addressed. Tel: +31 20 4447218; Fax: +31 20 6891149; Email: schouten{at}mrc-holland.com

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				R. L. Pollex and R. A. Hegele Copy Number Variation in the Human Genome and Its Implications for Cardiovascular Disease Circulation, June 19, 2007; 115(24): 3130 - 3138. [Full Text] [PDF]

				W. J. Wiersinga, M. C. Dessing, P. A. Kager, A. C. Cheng, D. Limmathurotsakul, N. P. Day, A. M. Dondorp, T. van der Poll, and S. J. Peacock High-Throughput mRNA Profiling Characterizes the Expression of Inflammatory Molecules in Sepsis Caused by Burkholderia pseudomallei Infect. Immun., June 1, 2007; 75(6): 3074 - 3079. [Abstract] [Full Text] [PDF]

				C. G. Monico, S. Rossetti, H. A. Schwanz, J. B. Olson, P. A. Lundquist, D. B. Dawson, P. C. Harris, and D. S. Milliner Comprehensive Mutation Screening in 55 Probands with Type 1 Primary Hyperoxaluria Shows Feasibility of a Gene-Based Diagnosis J. Am. Soc. Nephrol., June 1, 2007; 18(6): 1905 - 1914. [Abstract] [Full Text] [PDF]

				L. J. Mead, M. A. Jenkins, J. Young, S. G. Royce, L. Smith, D. J. B. St. John, F. Macrae, G. G. Giles, J. L. Hopper, and M. C. Southey Microsatellite Instability Markers for Identifying Early-Onset Colorectal Cancers Caused by Germ-Line Mutations in DNA Mismatch Repair Genes Clin. Cancer Res., May 15, 2007; 13(10): 2865 - 2869. [Abstract] [Full Text] [PDF]

				A. L. Gotter, M. A. Nimmakayalu, G. R. Jalali, A. M. Hacker, J. Vorstman, D. Conforto Duffy, L. Medne, and B. S. Emanuel A palindrome-driven complex rearrangement of 22q11.2 and 8q24.1 elucidated using novel technologies Genome Res., April 1, 2007; 17(4): 470 - 481. [Abstract] [Full Text] [PDF]

				E. Riveira-Munoz, Q. Chang, N. Godefroid, J. G. Hoenderop, R. J. Bindels, K. Dahan, O. Devuyst, and for the Belgian Network for the Study of Gitelman Transcriptional and Functional Analyses of SLC12A3 Mutations: New Clues for the Pathogenesis of Gitelman Syndrome J. Am. Soc. Nephrol., April 1, 2007; 18(4): 1271 - 1283. [Abstract] [Full Text] [PDF]

				J. Kanno, T. Hutchin, F. Kamada, A. Narisawa, Y. Aoki, Y. Matsubara, and S. Kure Genomic deletion within GLDC is a major cause of non-ketotic hyperglycinaemia J. Med. Genet., March 1, 2007; 44(3): e69 - e69. [Abstract] [Full Text] [PDF]

				J. A. L. Armour, R. Palla, P. L. J. M. Zeeuwen, M. d. Heijer, J. Schalkwijk, and E. J. Hollox Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats Nucleic Acids Res., February 16, 2007; 35(3): e19 - e19. [Abstract] [Full Text] [PDF]

				L. A. Smit, D. Y.H. Hallaert, R. Spijker, B. de Goeij, A. Jaspers, A. P. Kater, M. H.J. van Oers, C. J.M. van Noesel, and E. Eldering Differential Noxa/Mcl-1 balance in peripheral versus lymph node chronic lymphocytic leukemia cells correlates with survival capacity Blood, February 15, 2007; 109(4): 1660 - 1668. [Abstract] [Full Text] [PDF]

				F. P M Cremers, W. J Kimberling, M. Kulm, A. P de Brouwer, E. van Wijk, H. te Brinke, C. W R J Cremers, L. H Hoefsloot, S. Banfi, F. Simonelli, et al. Development of a genotyping microarray for Usher syndrome J. Med. Genet., February 1, 2007; 44(2): 153 - 160. [Abstract] [Full Text] [PDF]

				C. Beetz, A.O.H. Nygren, J. Schickel, M. Auer-Grumbach, K. Burk, G. Heide, J. Kassubek, S. Klimpe, T. Klopstock, F. Kreuz, et al. High frequency of partial SPAST deletions in autosomal dominant hereditary spastic paraplegia Neurology, December 12, 2006; 67(11): 1926 - 1930. [Abstract] [Full Text] [PDF]

				M. J. Friez, J. R. Jones, K. Clarkson, H. Lubs, D. Abuelo, J.-A. B. Bier, S. Pai, R. Simensen, C. Williams, P. F. Giampietro, et al. Recurrent Infections, Hypotonia, and Mental Retardation Caused by Duplication of MECP2 and Adjacent Region in Xq28 Pediatrics, December 1, 2006; 118(6): e1687 - e1695. [Abstract] [Full Text] [PDF]

				M. Schneider, F. Joncourt, J. Sanz, T. von Kanel, and S. Gallati Detection of Exon Deletions within an Entire Gene (CFTR) by Relative Quantification on the LightCycler Clin. Chem., November 1, 2006; 52(11): 2005 - 2012. [Abstract] [Full Text] [PDF]

				J. C. Mulley, P. Nelson, S. Guerrero, L. Dibbens, X. Iona, J. M. McMahon, L. Harkin, J. Schouten, S. Yu, S. F. Berkovic, et al. A new molecular mechanism for severe myoclonic epilepsy of infancy: Exonic deletions in SCN1A. Neurology, September 26, 2006; 67(6): 1094 - 1095. [Abstract] [Full Text] [PDF]

				T. Pejovic, J. E. Yates, H. Y. Liu, L. E. Hays, Y. Akkari, Y. Torimaru, W. Keeble, R. K. Rathbun, W. H. Rodgers, A. E. Bale, et al. Cytogenetic instability in ovarian epithelial cells from women at risk of ovarian cancer. Cancer Res., September 15, 2006; 66(18): 9017 - 9025. [Abstract] [Full Text] [PDF]

				J. Jeuken, S. Cornelissen, S. Boots-Sprenger, S. Gijsen, and P. Wesseling Multiplex Ligation-Dependent Probe Amplification: A Diagnostic Tool for Simultaneous Identification of Different Genetic Markers in Glial Tumors J. Mol. Diagn., September 1, 2006; 8(4): 433 - 443. [Abstract] [Full Text] [PDF]

				J. D. Cogan, M. W. Pauciulo, A. P. Batchman, M. A. Prince, I. M. Robbins, L. K. Hedges, K. C. Stanton, L. A. Wheeler, J. A. Phillips III, J. E. Loyd, et al. High Frequency of BMPR2 Exonic Deletions/Duplications in Familial Pulmonary Arterial Hypertension Am. J. Respir. Crit. Care Med., September 1, 2006; 174(5): 590 - 598. [Abstract] [Full Text] [PDF]

				H. Hampel, W. Frankel, J. Panescu, J. Lockman, K. Sotamaa, D. Fix, I. Comeras, J. La Jeunesse, H. Nakagawa, J. A. Westman, et al. Screening for Lynch Syndrome (Hereditary Nonpolyposis Colorectal Cancer) among Endometrial Cancer Patients. Cancer Res., August 1, 2006; 66(15): 7810 - 7817. [Abstract] [Full Text] [PDF]

				E. J. Chung, C.-S. Ki, W. Y. Lee, I.-S. Kim, and J.-Y. Kim Clinical Features and Gene Analysis in Korean Patients With Early-Onset Parkinson Disease. Arch Neurol, August 1, 2006; 63(8): 1170 - 1174. [Abstract] [Full Text] [PDF]

				I. Warshawsky, O. B. Chernova, C. A. Hubner, R. Stindl, M. Henneke, A. Gal, and M. R. Natowicz Multiplex Ligation-Dependent Probe Amplification for Rapid Detection of Proteolipid Protein 1 Gene Duplications and Deletions in Affected Males and Carrier Females with Pelizaeus-Merzbacher Disease Clin. Chem., July 1, 2006; 52(7): 1267 - 1275. [Abstract] [Full Text] [PDF]

				M. Procter, L.-S. Chou, W. Tang, M. Jama, and R. Mao Molecular Diagnosis of Prader-Willi and Angelman Syndromes by Methylation-Specific Melting Analysis and Methylation-Specific Multiplex Ligation-Dependent Probe Amplification Clin. Chem., July 1, 2006; 52(7): 1276 - 1283. [Abstract] [Full Text] [PDF]

				M. J. Worsham, K. M. Chen, V. Meduri, A. O. H. Nygren, A. Errami, J. P. Schouten, and M. S. Benninger Epigenetic events of disease progression in head and neck squamous cell carcinoma. Arch Otolaryngol Head Neck Surg, June 1, 2006; 132(6): 668 - 677. [Abstract] [Full Text] [PDF]

				M. Canel, P. Secades, J.-P. Rodrigo, R. Cabanillas, A. Herrero, C. Suarez, and M.-D. Chiara Overexpression of Focal Adhesion Kinase in Head and Neck Squamous Cell Carcinoma Is Independent of fak Gene Copy Number. Clin. Cancer Res., June 1, 2006; 12(11): 3272 - 3279. [Abstract] [Full Text] [PDF]

				M. Crepin, P. Pigny, F. Escande, C. C. Bauters, A. Calender, S. Lefevre, M.-P. Buisine, N. Porchet, and M.-F. Odou Evaluation of denaturing high performance liquid chromatography for the mutational analysis of the MEN1 gene. J. Mol. Endocrinol., April 1, 2006; 36(2): 369 - 376. [Abstract] [Full Text] [PDF]

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