Sensitive detection of genetic mutations: Combination of

multiplex PCR and capillary gel electrophoresis

Daniel Lehmann, Margareta Knig, Nicole Lokmer, Friederike Wilmer, and Holger Engel
QIAGEN GmbH, QIAGEN Strasse 1, 40724 Hilden, Germany

Introduction Optimized workflows: Multiplex mutation detection with the

Mutation analysis is performed in several areas of research, including detection and analysis of genetic differences Type-it Mutation Detect PCR Kit and the QIAxcel System
such as identifying mutations for diagnostics, typing of disease loci, and investigating relationship and paternity patterns.
Reliable multiplex PCR assays are essential for such experiments. This includes specific and sensitive co-amplification,
gDNA storage PCR-based
even of low abundant targets or targets with high GC content and secondary structures. However, establishment of Sample collection & gDNA
and whole genome genotyping Detection
sensitive multiplex PCR assays can be challenging, often requiring lengthy optimization of experimental parameters stabilization purification
amplification analysis
and yielding irreproducible results. The analysis of the multiplex PCR fragments is typically performed on an agarose
gel or a capillary electrophoresis-based DNA sequencer, which is time consuming. In the case of the agarose gel,
handling is difficult and not standardized for routine applications.
Here, data are presented that show that the combination of the Type-it Mutation Detect PCR Kit and the capillary
gel electrophoresis QIAxcel System provides a rapid and straightforward standardized procedure for multiplex
analysis of mutations.

TissueLyser QIAamp QIAsafe Type-it PCR Kits QIAxcel

TissueRupter DNeasy Kits REPLI-g Kits Extensive PCR
QIAcard FTA MagAttract and Service portfolio
PAXgene Blood QIAcube
DNA System QIAsymphony

All applications presented herein are for research use only. Not for use in diagnostic procedures.

Size determination of PCR products with the QIAxcel Sensitive mutation detection using multiplex PCR
Detection of multiplex PCR products was performed with 3 bp Resolution with the QIAxcel DNA High Resolution Kit The Type-it Mutation Detect PCR Kit is designed to enable fast and reliable detection of mutations, such as deletions,
the QIAxcel System, a capillary gel electrophoresis insertions, and translocations (see Table). The Type-it Mutation Detect PCR Kit is based on proven QIAGEN Multiplex
instrument with digital data analysis software. Analysis Technology (patent pending).
of 12 samples takes under 10 minutes, compared with Due to its unique components, the dedicated application-directed development, and the optimized protocols, the
over 60 minutes for an agarose gel. Analysis of up to Type-it Mutation Detect PCR Kit provides results without the need for optimization. Reliable results are ensured even
96 samples without manual intervention is possible with when performing sensitive applications such as the detection of minute amounts of tumor DNA in the background of
the ready-to-use gel cartridges. With a resolution down normal DNA.
to 35 bp in the 500 bp range, we were able to
The Type-it Mutation Detect PCR Kit ensures comparable amplification efficiency for all amplicons in a multiplex
conveniently and precisely analyze the multiplex data. Data
experiment allowing reliable detection of minute amounts of a mutation target in the background of DNA from a
analysis was performed using the Biocalculator software.
healthy donor. The next panel shows detection of 25 pg (corresponding to 4 copies) of the mutated target was
PCR products were generated using the HotStarTaq PCR possible in a background of 25 ng human leukocyte DNA without the loss of amplification efficiency. Using a non-
kit according to the kit protocol and run on the DNA multiplex PCR chemistry, poor co-amplification of the two controls and even no detection of the mutation was
High Resolution gel cartridge. Data were collected observed even after optimization of the experimental conditions (see next panel).
digitally.
The gel clearly shows two separated bands with size
Application of Type-it PCR kits
differences of 3 bp. The system is highly suited for the
specific analysis of PCR products. Small size differences Kit Dedicated application Field of research
Alignment marker 15 bp/1,000 bp
can be detected. This characteristic is required when Method OM500 Type-it Mutation Detect Deletions Typing of desease loci
analyzing multiplex PCR reaction, e.g. for mutation Lanes: PCR Kit Insertions Typing of transgenic plants or animals
A01 pUC18/HaeIII in PCR buffer 10 ng/l A08 PCR fragment 332 bp
A02 PCR fragment 96 bp A09 PCR fragment 334 bp Duplications GMO analysis
detection, etc. A03 PCR fragment 99 bp A10 PCR fragments; sizes 332,334 bp
A04 PCR fragments 96 and 99 bp B01 pUC18/HaeIII in PCR buffer 10 ng/l Translocations
A05 PCR fragment 222 bp B02 PCR fragment 441 bp
A06 PCR fragment 225 bp B03 PCR fragment 444 bp SNP preamplification
A07 PCR fragments; sizes 222 and 225 bp B04 PCR fragments 441 and 444 bp

Mutation detection with Type-It Mutation Detect PCR Kit and Summary
the QIAxcel System The Type-it Mutation Detect PCR Kit in combination with the QIAxcel System allows fast and reliable analysis of
multiplex PCR of genetic mutations.

A B
The Type-it Mutation Detect PCR Kit provides:
Type-it MM Supplier I Type-it MM Supplier I Multiplex PCR without optimization requirements
Fast and easy development of new genotyping assays
ng

ng

ng

ng
pg
pg

ng
ng

pg

pg
ng

ng
25

25

25

25
25

M M M M M M
Highly sensitive amplification of low amount of tumor material.
25
25
25

25

25
25

25
0.

0.

0.

0.
0

The QIAxcel DNA High Resolution Kit provides:

Fast and easy analysis of multiple PCR fragments in less than 10 minutes
357 357 High resolution of multiplex PCR fragments
bp bp
Digital data storage and analysis with the Biocalculator software.

Sensitive detection of a mutated cancer-related gene. The indicated amounts of DNA extracted from a lymphoma-related cell line (Ramos) were spiked into human leukocyte
DNA and the mutated Ramos target was detected together with 2 internal controls. Using the Type-it Mutation Detect PCR Kit, the mutated gene was detected even when only
25 pg of tumor DNA (corresponding to approximately 4 target copies) was present. A Electrophoresis was performed on a 1.3% agarose gel. B Electrophoresis was
performed on the QIAxcel System using the QIAxcel High Resolution cartridge. Marker: 100 bp ladder.
04/2009
The PAXgene Blood DNA System is for research use only and not for use in diagnostic procedures.
QIAGEN REPLI-g Kits are for use only as licensed by Amersham Biosciences Corp (part of GE Healthcare
Bio-Sciences) and QIAGEN GmbH. The Phi 29 DNA polymerase may not be re-sold or used except in conjunction
with the other components of this kit. See U.S. Patent Nos. 5,854,033, 6,124,120, 6,143,495, 5,001,050,
5,198,543, 5,576,204, and related U.S. and foreign patents. The REPLI-g Kit is developed, designed, and sold for
research purpose only.

Trademarks: QIAGEN, QIAamp, QIAcard FTA, QIAcube, QIAxcel, DNeasy, HotStarTaq, MagAttract, TissueRupter, REPLI-g, Type-it (QIAGEN Grouo); PAXgene (PreAnalytiX).
1057410

2009 QIAGEN, all rights reserved.

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