Genotyping β-globin gene mutations on copolymer-coated glass slides with the ligation detection reaction

Stefania Battistella, Francesco Damin, Marcella Chiari, Kathleen Delgrosso, Saul Surrey, Paolo Fortina, Maurizio Ferrari, Laura Cremonesi

Research output: Contribution to journalArticle

Abstract

BACKGROUND: Methods are needed to analyze small amounts of samples for variation in disease-causing genes. One means is to couple the sensitivity and multiplexing capability of the ligation detection reaction (LDR) with the use of simple glass slides specifically functionalized with a novel polymer coating to enhance sensitivity. METHODS: We developed an array-based genotyping assay based on glass slides coated with copolymer (N,N-dimethylacrylamide, N,N-acryloyloxysuccinimide, and 3-(trimethoxysilyl)propyl methacrylate). The assay consists of an LDR with genomic DNA followed by a universal PCR (U-PCR) of genomic DNA-templated LDR product. The LDR occurs in the presence of 3 primers for each sequence variant under investigation: 2 distinguishing primers (allele specific and perfectly complementary to wild-type and mutant alleles) and 1 common locus-specific primer. The 2 allele-specific primers have different capture sequences for binding different complementary probes on a tag array. The LDR product templated from genomic DNA is made fluorescent during the U-PCR via incorporation of a Cy5-labeled universal primer into all LDR products; detection occurs on the coated glass slides. RESULTS: The assay was designed to detect 7 prevalent mutations in the β-globin gene (HBB, hemoglobin, beta) in amultiplex format, and signals for the different alleles are detected by their fluorescence. The assay was applied to 40 genomic DNA samples from both control individuals and patients with known β-thalassemia mutations. Results show good correspondence between the patients' genotypes as assessed by DNA sequence analysis and those generated from the LDR assays. CONCLUSIONS: The developed technology allows accurate identification of sequence variants in a simple, cost-effective way and offers good flexibility for scaling to other applications with different numbers of single-nucleotide polymorphisms or mutations to be detected.

Original languageEnglish
Pages (from-to)1657-1663
Number of pages7
JournalClinical Chemistry
Volume54
Issue number10
DOIs
Publication statusPublished - Oct 1 2008

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, medical

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    Battistella, S., Damin, F., Chiari, M., Delgrosso, K., Surrey, S., Fortina, P., Ferrari, M., & Cremonesi, L. (2008). Genotyping β-globin gene mutations on copolymer-coated glass slides with the ligation detection reaction. Clinical Chemistry, 54(10), 1657-1663. https://doi.org/10.1373/clinchem.2008.107870