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Publication Date:
October 2011
ISSN:
1437-4331
DOI:
10.1515/cclm.2011.758

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Clinical Chemistry and Laboratory Medicine (CCLM)

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Alternative methods to a TaqMan assay to detect a tri-allelic single nucleotide polymorphism rs757210 in the HNF1β gene

Jesse J. Swen1 / Renee F. Baak-Pablo1 / Henk-Jan Guchelaar1 / 1

1Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands

Corresponding author: Dr. Tahar van der Straaten, Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, PO Box 9600, 2300 RA Leiden, The Netherlands Phone: +31 71 526 2790, Fax: +31 71 524 8101

Citation Information: Clinical Chemistry and Laboratory Medicine. Volume 50, Issue 2, Pages 279–284, ISSN (Online) 1437-4331, ISSN (Print) 1434-6621, DOI: 10.1515/cclm.2011.758, October 2011

Publication History:
Received:
2011-06-27
Accepted:
2011-10-03
Published Online:
2011-10-21

Abstract

Background: Several studies report difficulties in genotyping HNF1β rs757210 using TaqMan probes. This is possibly due to the tri-allelic nature of this single nucleotide polymorphism (SNP). The aim of the present research was to develop alternative methods for genotyping rs757210.

Methods: Pyrosequencing and high resolution melting analysis of small amplicons (HRM) were developed and tested in panels of type 2 diabetes mellitus patients (n=258) and healthy blood donors (n=183). Results were confirmed by Sanger sequencing.

Results: With pyrosequencing, allele frequencies for the A, G and C allele of 0.42, 0.56, 0.02 and 0.37, 0.62, 0.01 were established in the panel of type 2 diabetes mellitus patients and healthy blood donors, respectively. Similar results were found using the more routinely available HRM method. Results for pyrosequencing and HRM were in 99.6% concordance.

Conclusions: Pyrosequencing and HRM can be used to genotype the tri-allelic SNP rs757210 in the HNF1β gene and have the advantage over the commercially available TaqMan analysis that they can determine the rare C-allele variant.

Keywords: high-resolution melting; HNF1β; pyrosequencing; rs757210; type 2 diabetes mellitus

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