Sensitivity and Specificity of Single-Nucleotide Polymorphism Scanning by High-Resolution Melting Analysis

Clinical Chemistry - Tập 50 Số 10 - Trang 1748-1754 - 2004
G. H. Reed1, Carl T. Wittwer1
1Department of Pathology, University of Utah Medical Center, 5B418, 50 N. Medical Dr., Salt Lake City, UT 84132

Tóm tắt

Abstract Background: Screening for heterozygous sequence changes in PCR products, also known as “mutation scanning”, is an important tool for genetic research and clinical applications. Conventional methods require a separation step. Methods: We evaluated the sensitivity and specificity of homogeneous scanning, using a saturating DNA dye and high-resolution melting. Heterozygous single-nucleotide polymorphism (SNP) detection was studied in three different sequence backgrounds of 40%, 50%, and 60% GC content. PCR products of 50–1000 bp were generated in the presence of LCGreen™ I. After fluorescence normalization and temperature overlay, melting curve shape was used to judge the presence or absence of heterozygotes among 1632 cases. Results: For PCR products of 300 bp or less, all 280 heterozygous and 296 wild-type cases were correctly called without error. In 672 cases between 400 and 1000 bp with the mutation centered, the sensitivity and specificity were 96.1% and 99.4%, respectively. When the sequence background and product size with the greatest error rate were used, the sensitivity of off-center SNPs (384 cases) was 95.6% with a specificity of 99.4%. Most false negatives occurred with SNPs that were compared with an A or T wild type sequence. Conclusions: High-resolution melting analysis with the dye LCGreen I identifies heterozygous single-base changes in PCR products with a sensitivity and specificity comparable or superior to nonhomogeneous techniques. The error rate of scanning depends on the PCR product size and the type of base change, but not on the position of the SNP. The technique requires only PCR reagents, the dye LCGreen I, and 1–2 min of closed-tube, post-PCR analysis.

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Tài liệu tham khảo

1997, Clin Chem, 43, 2262, 10.1093/clinchem/43.12.2262

2001, Anal Biochem, 290, 89, 10.1006/abio.2000.4957

2004, Clin Chem, 50, 1328, 10.1373/clinchem.2004.034322

Tietz textbook of clinical chemistry and molecular diagnostics, 4th ed

1989, Proc Natl Acad Sci U S A, 86, 2766, 10.1073/pnas.86.8.2766

1987, Methods Enzymol, 155, 482, 10.1016/0076-6879(87)55032-7

1999, Electrophoresis, 20, 1186, 10.1002/(SICI)1522-2683(19990101)20:6<1186::AID-ELPS1186>3.0.CO;2-6

2001, Hum Mutat, 17, 439, 10.1002/humu.1130

2002, Electrophoresis, 23, 1499, 10.1002/1522-2683(200205)23:10<1499::AID-ELPS1499>3.0.CO;2-X

2003, Clin Chem, 49, 853, 10.1373/49.6.853

2004, Clin Chem, 50, 1156, 10.1373/clinchem.2004.032136

2004, Tissue Antigens, 64, 156, 10.1111/j.1399-0039.2004.00248.x

2004, Mol Genet Metab, 82, 112, 10.1016/j.ymgme.2004.04.004

2004, Am J Clin Pathol, 122, 206, 10.1309/4E6UYBY62N2FCA6N

2004, Molecular microbiology: diagnostic principles and practice, 71

2003, Clin Chem, 49, 396, 10.1373/49.3.396

1999, Electrophoresis, 20, 1195, 10.1002/(SICI)1522-2683(19990101)20:6<1195::AID-ELPS1195>3.0.CO;2-A

1998, Genome Res, 8, 175, 10.1101/gr.8.3.175

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Clinical Chemistry

Tập 50 Số 10

1748-1754

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