Rapid microfluidic solid-phase extraction system for hyper-methylated DNA enrichment and epigenetic analysis

Arpita De, Wouter Sparreboom, Albert van den Berg, Edwin Carlen

Research output: Contribution to journalArticleAcademicpeer-review

12 Citations (Scopus)
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Abstract

Genetic sequence and hyper-methylation profile information from the promoter regions of tumor suppressor genes are important for cancer disease investigation. Since hyper-methylated DNA (hm-DNA) is typically present in ultra-low concentrations in biological samples, such as stool, urine, and saliva, sample enrichment and amplification is typically required before detection. We present a rapid microfluidic solid phase extraction (mu SPE) system for the capture and elution of low concentrations of hm-DNA (<= 1 ng ml(-1)), based on a protein-DNA capture surface, into small volumes using a passive microfluidic lab-on-a-chip platform. All assay steps have been qualitatively characterized using a real-time surface plasmon resonance (SPR) biosensor, and quantitatively characterized using fluorescence spectroscopy. The hm-DNA capture/elution process requires less than 5 min with an efficiency of 71% using a 25 mu l elution volume and 92% efficiency using a 100 mu l elution volume. (C) 2014 AIP Publishing LLC.
Original languageUndefined
Pages (from-to)054119
Number of pages11
JournalBiomicrofluidics
Volume8
Issue number5
DOIs
Publication statusPublished - Sep 2014

Keywords

  • EWI-25471
  • IR-93312
  • METIS-309756

Cite this

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title = "Rapid microfluidic solid-phase extraction system for hyper-methylated DNA enrichment and epigenetic analysis",
abstract = "Genetic sequence and hyper-methylation profile information from the promoter regions of tumor suppressor genes are important for cancer disease investigation. Since hyper-methylated DNA (hm-DNA) is typically present in ultra-low concentrations in biological samples, such as stool, urine, and saliva, sample enrichment and amplification is typically required before detection. We present a rapid microfluidic solid phase extraction (mu SPE) system for the capture and elution of low concentrations of hm-DNA (<= 1 ng ml(-1)), based on a protein-DNA capture surface, into small volumes using a passive microfluidic lab-on-a-chip platform. All assay steps have been qualitatively characterized using a real-time surface plasmon resonance (SPR) biosensor, and quantitatively characterized using fluorescence spectroscopy. The hm-DNA capture/elution process requires less than 5 min with an efficiency of 71{\%} using a 25 mu l elution volume and 92{\%} efficiency using a 100 mu l elution volume. (C) 2014 AIP Publishing LLC.",
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doi = "10.1063/1.4899059",
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Rapid microfluidic solid-phase extraction system for hyper-methylated DNA enrichment and epigenetic analysis. / De, Arpita; Sparreboom, Wouter; van den Berg, Albert; Carlen, Edwin.

In: Biomicrofluidics, Vol. 8, No. 5, 09.2014, p. 054119.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Rapid microfluidic solid-phase extraction system for hyper-methylated DNA enrichment and epigenetic analysis

AU - De, Arpita

AU - Sparreboom, Wouter

AU - van den Berg, Albert

AU - Carlen, Edwin

N1 - eemcs-eprint-25471

PY - 2014/9

Y1 - 2014/9

N2 - Genetic sequence and hyper-methylation profile information from the promoter regions of tumor suppressor genes are important for cancer disease investigation. Since hyper-methylated DNA (hm-DNA) is typically present in ultra-low concentrations in biological samples, such as stool, urine, and saliva, sample enrichment and amplification is typically required before detection. We present a rapid microfluidic solid phase extraction (mu SPE) system for the capture and elution of low concentrations of hm-DNA (<= 1 ng ml(-1)), based on a protein-DNA capture surface, into small volumes using a passive microfluidic lab-on-a-chip platform. All assay steps have been qualitatively characterized using a real-time surface plasmon resonance (SPR) biosensor, and quantitatively characterized using fluorescence spectroscopy. The hm-DNA capture/elution process requires less than 5 min with an efficiency of 71% using a 25 mu l elution volume and 92% efficiency using a 100 mu l elution volume. (C) 2014 AIP Publishing LLC.

AB - Genetic sequence and hyper-methylation profile information from the promoter regions of tumor suppressor genes are important for cancer disease investigation. Since hyper-methylated DNA (hm-DNA) is typically present in ultra-low concentrations in biological samples, such as stool, urine, and saliva, sample enrichment and amplification is typically required before detection. We present a rapid microfluidic solid phase extraction (mu SPE) system for the capture and elution of low concentrations of hm-DNA (<= 1 ng ml(-1)), based on a protein-DNA capture surface, into small volumes using a passive microfluidic lab-on-a-chip platform. All assay steps have been qualitatively characterized using a real-time surface plasmon resonance (SPR) biosensor, and quantitatively characterized using fluorescence spectroscopy. The hm-DNA capture/elution process requires less than 5 min with an efficiency of 71% using a 25 mu l elution volume and 92% efficiency using a 100 mu l elution volume. (C) 2014 AIP Publishing LLC.

KW - EWI-25471

KW - IR-93312

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SP - 054119

JO - Biomicrofluidics

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SN - 1932-1058

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