MLPAinter for MLPA interpretation: An integrated approach for the analysis, visualisation and data management of Multiplex Ligation-dependent Probe Amplification

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  van Eijk, Ronald ^a   Eilers, Paul H C ^b   Natté, Remco ^a   Cleton Jansen, Anne Marie ^a   Morreau, Hans ^a   van Wezel, Tom ^a   Oosting, Jan ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED HANDLING; CHROMOSOMAL ABERRATION; CONTROL SAMPLES; DATA MANAGEMENT SYSTEM; GENOMIC SEQUENCE; INTEGRATED APPROACH; PROBE AMPLIFICATION; STATISTICAL APPROACH;

EXPERIMENTS; GAIN CONTROL; INTEGRATED CONTROL; MULTIPLEXING; VISUALIZATION;

INFORMATION MANAGEMENT;

ALGORITHM; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; CHROMOSOME ABERRATION; CHROMOSOME MAP; CHROMOSOME PAINTING; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA BASE; GENETIC DATABASE; METHODOLOGY; SYSTEM ANALYSIS;

ALGORITHMS; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; CHROMOSOME ABERRATIONS; CHROMOSOME MAPPING; CHROMOSOME PAINTING; COMPUTER GRAPHICS; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; SOFTWARE; SYSTEMS INTEGRATION; USER-COMPUTER INTERFACE;

EID: 77949558532     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-67     Document Type: Article

References (18)

1. Petrij-Bosch A, Peelen T, van Vliet M, van Eijk R, Olmer R, Drusedau M, Hogervorst FB, Hageman S, Arts PJ, Ligtenberg MJ, et al. BRCA1 genomic deletions are major founder mutations in Dutch breast cancer patients. Nat Genet 1997, 17:341-345. 10.1038/ng1197-341, 9354803.
2. Klinger K, Landes G, Shook D, Harvey R, Lopez L, Locke P, Lerner T, Osathanondh R, Leverone B, Houseal T, et al. Rapid detection of chromosome aneuploidies in uncultured amniocytes by using fluorescence in situ hybridization (FISH). Am J Hum Genet 1992, 51:55-65. 1682861, 1609805.
3. Devilee P, Cleton-Jansen AM, Cornelisse CJ. Ever since Knudson. Trends Genet 2001, 17:569-573. 10.1016/S0168-9525(01)02416-7, 11585662.
4. Nigro JM, Takahashi MA, Ginzinger DG, Law M, Passe S, Jenkins RB, Aldape K. Detection of 1p and 19q loss in oligodendroglioma by quantitative microsatellite analysis a real-time quantitative polymerase chain reaction assay. Am J Pathol 2001, 158:1253-1262. 1891922, 11290543.
5. Douglas EJ, Fiegler H, Rowan A, Halford S, Bicknell DC, Bodmer W, Tomlinson IP, Carter NP. Array comparative genomic hybridization analysis of colorectal cancer cell lines and primary carcinomas. Cancer Res 2004, 64:4817-4825. 10.1158/0008-5472.CAN-04-0328, 15256451.
6. Lips EH, Dierssen JW, van Eijk R, Oosting J, Eilers PH, Tollenaar RA, de Graaf EJ, van't Slot R, Wijmenga C, Morreau H, et al. Reliable high-throughput genotyping and loss-of-heterozygosity detection in formalin-fixed, paraffin-embedded tumors using single nucleotide polymorphism arrays. Cancer Res 2005, 65:10188-10191. 10.1158/0008-5472.CAN-05-2486, 16288005.
7. Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 2002, 30(e57). 117299, 12060695.
8. Erlandson A, Samuelsson L, Hagberg B, Kyllerman M, Vujic M, Wahlstrom J. Multiplex ligation-dependent probe amplification (MLPA) detects large deletions in the MECP2 gene of Swedish Rett syndrome patients. Genet Test 2003, 7:329-332. 10.1089/109065703322783707, 15000811.
9. Natte R, van Eijk R, Eilers P, Cleton-Jansen AM, Oosting J, Kouwenhove M, Kros JM, van Duinen S. Multiplex ligation-dependent probe amplification for the detection of 1p and 19q chromosomal loss in oligodendroglial tumors. Brain Pathol 2005, 15:192-197.
10. van Dijk MC, Rombout PD, Boots-Sprenger SH, Straatman H, Bernsen MR, Ruiter DJ, Jeuken JW. Multiplex ligation-dependent probe amplification for the detection of chromosomal gains and losses in formalin-fixed tissue. Diagn Mol Pathol 2005, 14:9-16. 10.1097/01.pas.0000146701.98954.47, 15714058.
11. Hameetman L, Szuhai K, Yavas A, Knijnenburg J, van Duin M, van Dekken H, Taminiau AH, Cleton-Jansen AM, Bovee JV, Hogendoorn PC. The role of EXT1 in nonhereditary osteochondroma: identification of homozygous deletions. J Natl Cancer Inst 2007, 99:396-406. 10.1093/jnci/djk067, 17341731.
12. Kantarci S, Donahoe PK. Congenital diaphragmatic hernia (CDH) etiology as revealed by pathway genetics. Am J Med Genet C Semin Med Genet 2007, 145:217-226.
13. Kozlowski P, Jasinska AJ, Kwiatkowski DJ. New applications and developments in the use of multiplex ligation-dependent probe amplification. Electrophoresis 2008, 29:4627-4636. 10.1002/elps.200800126, 19053154.
14. Gerdes T, Kirchhoff M, Bryndorf T. Automatic analysis of multiplex ligation-dependent probe amplification products (exemplified by a commercial kit for prenatal aneuploidy detection). Electrophoresis 2005, 26:4327-4332. 10.1002/elps.200500390, 16240299.
15. Ahn JW, Ogilvie CM, Welch A, Thomas H, Madula R, Hills A, Donaghue C, Mann K. Detection of subtelomere imbalance using MLPA: validation, development of an analysis protocol and application in a diagnostic centre. BMC Med Genet 2007, 8:9. 10.1186/1471-2350-8-9, 1831468, 17338807.
16. Coffa J, Wiel MA, Diosdado B, Carvalho B, Schouten J, Meijer GA. MLPAnalyzer: data analysis tool for reliable automated normalization of MLPA fragment data. Cell Oncol 2008, 30:323-335.
17. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002, 3:RESEARCH0034. 10.1186/gb-2002-3-7-research0034, 126239, 12184808.
18. Corver WE, Middeldorp A, ter Haar NT, Jordanova ES, van Puijenbroek M, van Eijk R, Cornelisse CJ, Fleuren GJ, Morreau H, Oosting J, van Wezel T. Genome-wide allelic state analysis on flow-sorted tumor fractions provides an accurate measure of chromosomal aberrations. Cancer Res 2008, 68:10333-10340. 10.1158/0008-5472.CAN-08-2665, 19074902.