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Denaturing temperature selection may underestimate keratin mutation detection by DHPLC
Author(s) -
Strnad Pavel,
Lienau Tim Christian,
Tao GuoZhong,
Ku NamOn,
Magin Thomas M.,
Omary M. Bishr
Publication year - 2006
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.20311
Subject(s) - biology , genetics , selection (genetic algorithm) , mutation , denaturing high performance liquid chromatography , keratin , computational biology , gene , artificial intelligence , computer science
Abstract Keratins 8 and 18 ( KRT8 and KRT18 genes; K8 and K18 proteins) variants are risk factors for developing end‐stage liver disease and may be associated with inflammatory bowel disease and chronic pancreatitis. The frequency of K8/K18 variants in American, British, German, and Italian populations differs. For example, one study showed no amino acid–altering K8/K18 mutations in 256 German patients with liver disorders, while another found 58 out of 467 American liver disease patients with K8/K18 mutations. Both studies used the WaveSystem™, which utilizes DHPLC. We hypothesized that experimental conditions contribute to the discrepancy, and we tested this hypothesis using previously described K8/K18 variants and a novel KRT18 c.1057C>G variant (K18 p.R353G) to optimize the DHPLC conditions in 10 examined exons under a range of denaturing temperatures. Six of 16 tested variants in three of the 10 exons, including the frequent KRT8 c.184G>T (K8 p.G62C), KRT8 c.187A>G (K8 p.I63V), and KRT8 c.1022G>A (K8 p.R341H), could not be reliably detected when using temperatures suggested by the prediction software, but all these variants were readily detectable at 2°C higher denaturing temperatures. Using optimized temperatures, we then tested available genomic DNA from 151 out of the 256 German liver disease patients for the presence of K8 variants in exons 1 and 6, where most of the American cohort K8 variants occur. We identified 12 exonic and two intronic K8 variants: one KRT8 c.184G>T (K8 p.G62C), two KRT8 c.187A>G (K8 p.I63V), seven KRT8 c.1022G>A (K8 p.R341H), one KRT8 c.1128G>A (K8 p.E376E), two intronic KRT8 c.1202+46 A>T, and one hitherto undescribed KRT8 c.1138G>A (K8 p.V380I). Therefore, although DHPLC offers a robust and high throughput means for mutation analysis, assessment of denaturing temperature ranges, and possible inclusion of control mutants should be considered. Hum Mutat 27(5), 444–452, 2006. Published 2006 Wiley‐Liss, Inc.