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Published in: BMC Medical Genetics 1/2005

Open Access 01-12-2005 | Technical advance

Detection of large deletions in the LDL receptor gene with quantitative PCR methods

Authors: Dorte Damgaard, Peter H Nissen, Lillian G Jensen, Gitte G Nielsen, Anette Stenderup, Mogens L Larsen, Ole Faergeman

Published in: BMC Medical Genetics | Issue 1/2005

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Abstract

Background

Familial Hypercholesterolemia (FH) is a common genetic disease and at the molecular level most often due to mutations in the LDL receptor gene. In genetically heterogeneous populations, major structural rearrangements account for about 5% of patients with LDL receptor gene mutations.

Methods

In this study we tested the ability of two different quantitative PCR methods, i.e. Real-Time PCR and Multiplex Ligation-Dependent Probe Amplification (MLPA), to detect deletions in the LDL receptor gene. We also reassessed the contribution of major structural rearrangements to the mutational spectrum of the LDL receptor gene in Denmark.

Results

With both methods it was possible to discriminate between one and two copies of the LDL receptor gene exon 5, but the MLPA method was cheaper, and it was far more accurate and precise than Real-Time PCR. In five of 318 patients with an FH phenotype, MLPA analysis revealed five different deletions in the LDL receptor gene.

Conclusion

The MLPA method was accurate, precise and at the same time effective in screening a large number of FH patients for large deletions in the LDL receptor gene.
Appendix
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Literature
1.
go back to reference Goldstein JL, Hobbs HH, Brown MS: Familial Hypercholesterolemia. The metabolic and molecular basis of inherited disease. Edited by: Scriver CR, Beaudet A, Sly WS, Vale D. 2001, New York: McGraw Hill Goldstein JL, Hobbs HH, Brown MS: Familial Hypercholesterolemia. The metabolic and molecular basis of inherited disease. Edited by: Scriver CR, Beaudet A, Sly WS, Vale D. 2001, New York: McGraw Hill
2.
go back to reference Heath KE, Gahan M, Whittall RA, Humphries SE: Low-density lipoprotein receptor gene (LDLR) world-wide website in familial hypercholesterolaemia: update, new features and mutation analysis. Atherosclerosis. 2001, 154: 243-246. 10.1016/S0021-9150(00)00647-X.CrossRefPubMed Heath KE, Gahan M, Whittall RA, Humphries SE: Low-density lipoprotein receptor gene (LDLR) world-wide website in familial hypercholesterolaemia: update, new features and mutation analysis. Atherosclerosis. 2001, 154: 243-246. 10.1016/S0021-9150(00)00647-X.CrossRefPubMed
3.
go back to reference Villeger L, Abifadel M, Allard D, Rabes JP, Thiart R, Kotze MJ, Beroud C, Junien C, Boileau C, Varret M: The UMD-LDLR database: additions to the software and 490 new entries to the database. Hum Mutat. 2002, 20: 81-87. 10.1002/humu.10102.CrossRefPubMed Villeger L, Abifadel M, Allard D, Rabes JP, Thiart R, Kotze MJ, Beroud C, Junien C, Boileau C, Varret M: The UMD-LDLR database: additions to the software and 490 new entries to the database. Hum Mutat. 2002, 20: 81-87. 10.1002/humu.10102.CrossRefPubMed
4.
go back to reference Sun XM, Webb JC, Gudnason V, Humphries S, Seed M, Thompson GR, Knight BL, Soutar AK: Characterization of deletions in the LDL receptor gene in patients with familial hypercholesterolemia in the United Kingdom. Arterioscler Thromb. 1992, 12: 762-770.CrossRefPubMed Sun XM, Webb JC, Gudnason V, Humphries S, Seed M, Thompson GR, Knight BL, Soutar AK: Characterization of deletions in the LDL receptor gene in patients with familial hypercholesterolemia in the United Kingdom. Arterioscler Thromb. 1992, 12: 762-770.CrossRefPubMed
5.
go back to reference Fouchier SW, Defesche JC, Umans-Eckenhausen MW, Kastelein JP: The molecular basis of familial hypercholesterolemia in The Netherlands. Hum Genet. 2001, 109: 602-615. 10.1007/s00439-001-0628-8.CrossRefPubMed Fouchier SW, Defesche JC, Umans-Eckenhausen MW, Kastelein JP: The molecular basis of familial hypercholesterolemia in The Netherlands. Hum Genet. 2001, 109: 602-615. 10.1007/s00439-001-0628-8.CrossRefPubMed
6.
go back to reference Rudiger NS, Heinsvig EM, Hansen FA, Faergeman O, Bolund L, Gregersen N: DNA deletions in the low density lipoprotein (LDL) receptor gene in Danish families with familial hypercholesterolemia. Clin Genet. 1991, 39: 451-462.CrossRefPubMed Rudiger NS, Heinsvig EM, Hansen FA, Faergeman O, Bolund L, Gregersen N: DNA deletions in the low density lipoprotein (LDL) receptor gene in Danish families with familial hypercholesterolemia. Clin Genet. 1991, 39: 451-462.CrossRefPubMed
7.
go back to reference Nissen H, Hansen AB, Guldberg P, Hansen TS, Petersen NE, Horder M: Evaluation of a clinically applicable mutation screening technique for genetic diagnosis of familial hypercholesterolemia and familial defective apolipoprotein B. Clin Genet. 1998, 53: 433-439.CrossRefPubMed Nissen H, Hansen AB, Guldberg P, Hansen TS, Petersen NE, Horder M: Evaluation of a clinically applicable mutation screening technique for genetic diagnosis of familial hypercholesterolemia and familial defective apolipoprotein B. Clin Genet. 1998, 53: 433-439.CrossRefPubMed
8.
go back to reference Jensen HK, Jensen LG, Meinertz H, Hansen PS, Gregersen N, Faergeman O: Spectrum of LDL receptor gene mutations in Denmark: implications for molecular diagnostic strategy in heterozygous familial hypercholesterolemia. Atherosclerosis. 1999, 146: 337-344. 10.1016/S0021-9150(99)00158-6.CrossRefPubMed Jensen HK, Jensen LG, Meinertz H, Hansen PS, Gregersen N, Faergeman O: Spectrum of LDL receptor gene mutations in Denmark: implications for molecular diagnostic strategy in heterozygous familial hypercholesterolemia. Atherosclerosis. 1999, 146: 337-344. 10.1016/S0021-9150(99)00158-6.CrossRefPubMed
9.
go back to reference Rodningen OK, Leren TP: Application of long polymerase chain reaction in the study of the LDL receptor gene. Scand J Clin Lab Invest. 1996, 56: 93-96.CrossRefPubMed Rodningen OK, Leren TP: Application of long polymerase chain reaction in the study of the LDL receptor gene. Scand J Clin Lab Invest. 1996, 56: 93-96.CrossRefPubMed
10.
go back to reference Kim SH, Bae JH, Chae JJ, Kim UK, Choe SJ, Namkoong Y, Kim HS, Park YB, Lee CC: Long-distance PCR-based screening for large rearrangements of the LDL receptor gene in Korean patients with familial hypercholesterolemia. Clin Chem. 1999, 45: 1424-1430.PubMed Kim SH, Bae JH, Chae JJ, Kim UK, Choe SJ, Namkoong Y, Kim HS, Park YB, Lee CC: Long-distance PCR-based screening for large rearrangements of the LDL receptor gene in Korean patients with familial hypercholesterolemia. Clin Chem. 1999, 45: 1424-1430.PubMed
11.
go back to reference Wilhelm J, Pingoud A: Real-time polymerase chain reaction. Chembiochem. 2003, 4: 1120-1128. 10.1002/cbic.200300662.CrossRefPubMed Wilhelm J, Pingoud A: Real-time polymerase chain reaction. Chembiochem. 2003, 4: 1120-1128. 10.1002/cbic.200300662.CrossRefPubMed
12.
go back to reference Wittwer CT, Herrmann MG, Moss AA, Rasmussen RP: Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotechniques. 1997, 22: 130-138.PubMed Wittwer CT, Herrmann MG, Moss AA, Rasmussen RP: Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotechniques. 1997, 22: 130-138.PubMed
13.
go back to reference Freeman WM, Walker SJ, Vrana KE: Quantitative RT-PCR: pitfalls and potential. Biotechniques. 1999, 26: 112-115.PubMed Freeman WM, Walker SJ, Vrana KE: Quantitative RT-PCR: pitfalls and potential. Biotechniques. 1999, 26: 112-115.PubMed
14.
go back to reference 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: e57-10.1093/nar/gnf056.CrossRefPubMedPubMedCentral 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: e57-10.1093/nar/gnf056.CrossRefPubMedPubMedCentral
15.
go back to reference Gille JJ, Hogervorst FB, Pals G, Wijnen JT, van Schooten RJ, Dommering CJ, Meijer GA, Craanen ME, Nederlof PM, de Jong D, McElgunn CJ, Schouten JP, Menko FH: Genomic deletions of MSH2 and MLH1 in colorectal cancer families detected by a novel mutation detection approach. Br J Cancer. 2002, 87: 892-897. 10.1038/sj.bjc.6600565.CrossRefPubMedPubMedCentral Gille JJ, Hogervorst FB, Pals G, Wijnen JT, van Schooten RJ, Dommering CJ, Meijer GA, Craanen ME, Nederlof PM, de Jong D, McElgunn CJ, Schouten JP, Menko FH: Genomic deletions of MSH2 and MLH1 in colorectal cancer families detected by a novel mutation detection approach. Br J Cancer. 2002, 87: 892-897. 10.1038/sj.bjc.6600565.CrossRefPubMedPubMedCentral
16.
go back to reference Damgaard D, Larsen ML, Nissen PH, Jensen JM, Jensen HK, Soerensen VR, Jensen LG, Faergeman O: The relationship of molecular genetic to clinical diagnosis of Familial Hypercholesterolemia in a Danish population. Atherosclerosis. 2005, 180: 155-160. 10.1016/j.atherosclerosis.2004.12.001.CrossRefPubMed Damgaard D, Larsen ML, Nissen PH, Jensen JM, Jensen HK, Soerensen VR, Jensen LG, Faergeman O: The relationship of molecular genetic to clinical diagnosis of Familial Hypercholesterolemia in a Danish population. Atherosclerosis. 2005, 180: 155-160. 10.1016/j.atherosclerosis.2004.12.001.CrossRefPubMed
17.
go back to reference Hobbs HH, Brown MS, Goldstein JL: Molecular genetics of the LDL receptor gene in familial hypercholesterolemia. Hum Mutat. 1992, 1: 445-466.CrossRefPubMed Hobbs HH, Brown MS, Goldstein JL: Molecular genetics of the LDL receptor gene in familial hypercholesterolemia. Hum Mutat. 1992, 1: 445-466.CrossRefPubMed
18.
go back to reference De Preter K, Speleman F, Combaret V, Lunec J, Laureys G, Eussen BH, Francotte N, Board J, Pearson AD, De Paepe A, Van Roy N, Vandesompele J: Quantification of MYCN, DDX1, and NAG gene copy number in neuroblastoma using a real-time quantitative PCR assay. Mod Pathol. 2002, 15: 159-166. 10.1038/modpathol.3880508.CrossRefPubMed De Preter K, Speleman F, Combaret V, Lunec J, Laureys G, Eussen BH, Francotte N, Board J, Pearson AD, De Paepe A, Van Roy N, Vandesompele J: Quantification of MYCN, DDX1, and NAG gene copy number in neuroblastoma using a real-time quantitative PCR assay. Mod Pathol. 2002, 15: 159-166. 10.1038/modpathol.3880508.CrossRefPubMed
19.
go back to reference Joncourt F, Neuhaus B, Jostarndt-Foegen K, Kleinle S, Steiner B, Gallati S: Rapid identification of female carriers of DMD/BMD by quantitative real-time PCR. Hum Mutat. 2004, 23: 385-391. 10.1002/humu.20007.CrossRefPubMed Joncourt F, Neuhaus B, Jostarndt-Foegen K, Kleinle S, Steiner B, Gallati S: Rapid identification of female carriers of DMD/BMD by quantitative real-time PCR. Hum Mutat. 2004, 23: 385-391. 10.1002/humu.20007.CrossRefPubMed
20.
go back to reference Laurendeau I, Bahuau M, Vodovar N, Larramendy C, Olivi M, Bieche I, Vidaud M, Vidaud D: TaqMan PCR-based gene dosage assay for predictive testing in individuals from a cancer family with INK4 locus haploinsufficiency. Clin Chem. 1999, 45: 982-986.PubMed Laurendeau I, Bahuau M, Vodovar N, Larramendy C, Olivi M, Bieche I, Vidaud M, Vidaud D: TaqMan PCR-based gene dosage assay for predictive testing in individuals from a cancer family with INK4 locus haploinsufficiency. Clin Chem. 1999, 45: 982-986.PubMed
21.
go back to reference Wilke K, Duman B, Horst J: Diagnosis of haploidy and triploidy based on measurement of gene copy number by real-time PCR. Hum Mutat. 2000, 16: 431-436. 10.1002/1098-1004(200011)16:5<431::AID-HUMU8>3.0.CO;2-Z.CrossRefPubMed Wilke K, Duman B, Horst J: Diagnosis of haploidy and triploidy based on measurement of gene copy number by real-time PCR. Hum Mutat. 2000, 16: 431-436. 10.1002/1098-1004(200011)16:5<431::AID-HUMU8>3.0.CO;2-Z.CrossRefPubMed
22.
go back to reference Wang J, Ban MR, Hegele RA: Multiplex ligation-dependent probe amplification of LDLR enhances molecular diagnosis of familial hypercholesterolemia. J Lipid Res. 2005, 46: 366-372. 10.1194/jlr.D400030-JLR200.CrossRefPubMed Wang J, Ban MR, Hegele RA: Multiplex ligation-dependent probe amplification of LDLR enhances molecular diagnosis of familial hypercholesterolemia. J Lipid Res. 2005, 46: 366-372. 10.1194/jlr.D400030-JLR200.CrossRefPubMed
Metadata
Title
Detection of large deletions in the LDL receptor gene with quantitative PCR methods
Authors
Dorte Damgaard
Peter H Nissen
Lillian G Jensen
Gitte G Nielsen
Anette Stenderup
Mogens L Larsen
Ole Faergeman
Publication date
01-12-2005
Publisher
BioMed Central
Published in
BMC Medical Genetics / Issue 1/2005
Electronic ISSN: 1471-2350
DOI
https://doi.org/10.1186/1471-2350-6-15

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