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What electrophoresis devices can I use for MLPA fragment analysis? - Help Centre / MLPA & Coffalyser.Net / Experimental Setup / Electrophoresis - MRC Holland Support

What electrophoresis devices can I use for MLPA fragment analysis?

The MLPA procedure includes the separation of MLPA fragments on a capillary electrophoresis device. The table below lists some of the more common capillary electrophoresis devices supported by Coffalyser.Net.

Supplier Device(s)
Applied Biosystems SeqStudio Genetic Analyzer
SeqStudio Flex Series Genetic Analyzer
3500 Series Genetic Analyzer
3730 Series Genetic Analyzer
3130 Series Genetic Analyzer
Hitachi Compact CE Sequencer DS3000
Promega Spectrum Compact CE System
SCIEX/Beckman Coulter GenomeLab GeXP
CEQ 8800 Genetic Analysis System
CEQ 8000 Genetic Analysis System

A capillary electrophoresis device suitable for MLPA must:

  • Be supported by Coffalyser.Net; see the Reference Manual for a full list of supported devices.
  • Use denaturing conditions.
  • Be compatible with 6-FAM or Cy5.0 labels used for our primers, and have a second channel suitable for a size marker.
  • Be capable of separating fragments in the 50–500 nt range with sufficiently high resolution to separate MLPA fragments.
  • Have a linear relationship between peak height and fragment concentration (within a certain signal range).
  • Provide clean and reproducible peak patterns (e.g. no excess noise, extra peaks or inconsistent signal heights).

Unsuitable capillary electrophoresis devices

Capillary electrophoresis devices that use non-denaturing conditions are not suitable. Secondary structures will alter the relative mobility of MLPA reaction products, which can lead to different apparent sizes or even to position swaps of fragments in the electropherogram. Devices that this applies to, which are not suitable for MLPA, include the Agilent (formerly Advanced Analytical/AATI) Fragment Analyzer, the Agilent 2100 Bioanalyzer, the Agilent TapeStation systems, the Caliper LabChip GX/GXII and the QIAGEN QIAxcel.

Note
This article is about conventional MLPA. For information about digitalMLPA, see this article.
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Disclaimer

The information provided in this material is correct for the majority of our products. For certain applications, the instructions for use may differ. In the event of conflicting information, the relevant instructions for use take precedence.