Microtransponder-based multiplex assay for genotyping cystic fibrosis

Xin Lin, James A. Flint, Marco Azaro, Thomas Coradetti, Wesley M. Kopacka, Deanna L. Streck, Zhuying Wang, James Dermody, Wlodek Mandecki

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Background: We developed and evaluated a genotyping assay for detection of 50 cystic fibrosis (CF) mutations. The assay is based on small (500 μm) electronic chips, radio frequency (RF) microtransponders (MTPs). The chips are analyzed on a unique fluorescence and RF readout instrument. Methods: We divided the CF assay into 4 panels: core, Hispanic, African-American, and Caucasian. We amplified 18 CF transmembrane regulator (CFTR) DNA fragments covering 50 mutations by use of multiplex PCR using 18 CFTR gene-specific primer pairs. PCR was followed by multiplex allele-specific primer extension (ASPE) reactions and hybridization to capture probes synthesized on MTPs. We used 100 ASPE primers and 100 capture probes. We performed fluorescence measurements of hybridized MTP kits and assay analysis using a custom automated bench-top flow instrument. Results: We validated the system by performing the assay on 23 commercial DNA samples in an internal study and 32 DNA samples in an external study. For internal and external studies, correct calls were 98.8% and 95.7%, false-positive calls 1.1% and 3.9%, and false-negative calls 0.12% and 0.36%, respectively. Conclusions: The MTP-based multiplex assay and analysis platform can be used for CF genotyping.

Original languageEnglish (US)
Pages (from-to)1372-1376
Number of pages5
JournalClinical Chemistry
Volume53
Issue number7
DOIs
StatePublished - Jul 1 2007

Fingerprint

Cystic Fibrosis
Assays
Radio
DNA
Fluorescence
Alleles
Mutation
Multiplex Polymerase Chain Reaction
Regulator Genes
Hispanic Americans
African Americans
Readout systems
Polymerase Chain Reaction
Genes

All Science Journal Classification (ASJC) codes

  • Clinical Biochemistry
  • Biochemistry, medical

Cite this

Lin, X., Flint, J. A., Azaro, M., Coradetti, T., Kopacka, W. M., Streck, D. L., ... Mandecki, W. (2007). Microtransponder-based multiplex assay for genotyping cystic fibrosis. Clinical Chemistry, 53(7), 1372-1376. https://doi.org/10.1373/clinchem.2006.081810
Lin, Xin ; Flint, James A. ; Azaro, Marco ; Coradetti, Thomas ; Kopacka, Wesley M. ; Streck, Deanna L. ; Wang, Zhuying ; Dermody, James ; Mandecki, Wlodek. / Microtransponder-based multiplex assay for genotyping cystic fibrosis. In: Clinical Chemistry. 2007 ; Vol. 53, No. 7. pp. 1372-1376.
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abstract = "Background: We developed and evaluated a genotyping assay for detection of 50 cystic fibrosis (CF) mutations. The assay is based on small (500 μm) electronic chips, radio frequency (RF) microtransponders (MTPs). The chips are analyzed on a unique fluorescence and RF readout instrument. Methods: We divided the CF assay into 4 panels: core, Hispanic, African-American, and Caucasian. We amplified 18 CF transmembrane regulator (CFTR) DNA fragments covering 50 mutations by use of multiplex PCR using 18 CFTR gene-specific primer pairs. PCR was followed by multiplex allele-specific primer extension (ASPE) reactions and hybridization to capture probes synthesized on MTPs. We used 100 ASPE primers and 100 capture probes. We performed fluorescence measurements of hybridized MTP kits and assay analysis using a custom automated bench-top flow instrument. Results: We validated the system by performing the assay on 23 commercial DNA samples in an internal study and 32 DNA samples in an external study. For internal and external studies, correct calls were 98.8{\%} and 95.7{\%}, false-positive calls 1.1{\%} and 3.9{\%}, and false-negative calls 0.12{\%} and 0.36{\%}, respectively. Conclusions: The MTP-based multiplex assay and analysis platform can be used for CF genotyping.",
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Lin, X, Flint, JA, Azaro, M, Coradetti, T, Kopacka, WM, Streck, DL, Wang, Z, Dermody, J & Mandecki, W 2007, 'Microtransponder-based multiplex assay for genotyping cystic fibrosis', Clinical Chemistry, vol. 53, no. 7, pp. 1372-1376. https://doi.org/10.1373/clinchem.2006.081810

Microtransponder-based multiplex assay for genotyping cystic fibrosis. / Lin, Xin; Flint, James A.; Azaro, Marco; Coradetti, Thomas; Kopacka, Wesley M.; Streck, Deanna L.; Wang, Zhuying; Dermody, James; Mandecki, Wlodek.

In: Clinical Chemistry, Vol. 53, No. 7, 01.07.2007, p. 1372-1376.

Research output: Contribution to journalArticle

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AU - Lin, Xin

AU - Flint, James A.

AU - Azaro, Marco

AU - Coradetti, Thomas

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AU - Streck, Deanna L.

AU - Wang, Zhuying

AU - Dermody, James

AU - Mandecki, Wlodek

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AB - Background: We developed and evaluated a genotyping assay for detection of 50 cystic fibrosis (CF) mutations. The assay is based on small (500 μm) electronic chips, radio frequency (RF) microtransponders (MTPs). The chips are analyzed on a unique fluorescence and RF readout instrument. Methods: We divided the CF assay into 4 panels: core, Hispanic, African-American, and Caucasian. We amplified 18 CF transmembrane regulator (CFTR) DNA fragments covering 50 mutations by use of multiplex PCR using 18 CFTR gene-specific primer pairs. PCR was followed by multiplex allele-specific primer extension (ASPE) reactions and hybridization to capture probes synthesized on MTPs. We used 100 ASPE primers and 100 capture probes. We performed fluorescence measurements of hybridized MTP kits and assay analysis using a custom automated bench-top flow instrument. Results: We validated the system by performing the assay on 23 commercial DNA samples in an internal study and 32 DNA samples in an external study. For internal and external studies, correct calls were 98.8% and 95.7%, false-positive calls 1.1% and 3.9%, and false-negative calls 0.12% and 0.36%, respectively. Conclusions: The MTP-based multiplex assay and analysis platform can be used for CF genotyping.

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Lin X, Flint JA, Azaro M, Coradetti T, Kopacka WM, Streck DL et al. Microtransponder-based multiplex assay for genotyping cystic fibrosis. Clinical Chemistry. 2007 Jul 1;53(7):1372-1376. https://doi.org/10.1373/clinchem.2006.081810