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Cat. No. / ID: 150243
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✓ Knowledgeable and professional Product & Technical Support
✓ Fast and reliable (re)-ordering
A lack of sufficient quantities of genomic DNA for genomic analysis can be overcome by global amplification of all DNA within a sample (whole genome amplification). The REPLI-g FFPE Kit consists of DNA Polymerase, novel buffers, and reagents that enable efficient whole genome amplification from formalin-fixed and paraffin embedded (FFPE) tissue without the requirement for prior DNA purification. After lysis of the tissue section, the DNA is processed so that fragmented DNA is ligated. The long DNA strands created are amplified using proven REPLI-g technology.
For the two protocols with different amplification times, typical yields per 50 µl reaction with standard quality templates are up to 10 µg after 2-hour amplification (standard reaction) and up to 40 µg after 8-hour amplification (high-yield reaction).
The availability of sufficient quantities of genomic DNA for genomic analysis is often lacking. Whole genome amplification (WGA) overcomes this limitation by global amplification of all DNA within a sample, providing sufficient quantities to perform all analyses on the same DNA sample.
Genotyping of formalin-fixed, paraffin-embedded (FFPE) tissue samples enables morphological tissue changes to be directly linked to specific genome mutations. However, formalin fixation causes irreversible damage to the DNA, resulting in fragmented DNA that is cross-linked to other biomolecules within the sample. In addition, the limited amount of DNA that can be extracted from FFPE tissue samples is only sufficient for a few analyses.
The REPLI-g FFPE Kit overcomes these problems through a procedure involving a novel DNA processing reaction that prepares and ligates fragmented DNA (see figure " REPLI-g FFPE principle"). Whole genome amplification of this randomly ligated DNA is then performed using proven REPLI-g technology. REPLI-g products combine multiple displacement amplification (MDA) with a uniquely processive DNA polymerase. Due to the high processivity and strand displacement activity, REPLI-g DNA Polymerase minimizes unequal sequence and locus representation. This provides much more reliable results when compared to PCR-based WGA methods. The novel DNA processing reaction allows the advantages of MDA to be extended to highly degraded DNA samples derived from FFPE tissue. Precious sample material can be amplified whilst maintaining locus representation, enabling unlimited downstream analyses to be performed.
The REPLI-g FFPE protocol allows the amplification of purified DNA from FFPE tissue samples or DNA direct from FFPE tissue samples without prior DNA purification. After lysis of the tissue section, the DNA is processed using novel buffers and enzymes that ligate fragmented DNA (see flowchart " REPLI-g FFPE procedure"and figure " High-molecular-weight ligated DNA"). The long DNA strands created by the ligation reaction are amplified using proven REPLI-g technology. Once amplified, the DNA is suitable for immediate use in most downstream genotyping assays without further purification.
DNA amplified using the REPLI-g FFPE procedure is highly suited for use in real-time PCR (e.g., using QuantiFast Kits) and end-point PCR (e.g., using the QIAGEN Fast Cycling PCR Kit), with a PCR amplicon preferably smaller than the average fragment size of the starting template. Further applications are microsatellite analysis (see figure " Reliable microsatellite analysis") and SNP genotyping (REPLI-g FFPE amplified DNA may not be suited for genotyping methods that require restriction digestion for DNA labeling).
DNA amplified using the REPLI-g FFPE procedure is highly suited for use in:
|Yield||10 µg (2h reaction)-40 µg (8h reaction)|
|Starting material||FFPE tissue sections or purified genomic DNA|
|Maximum input volume||1 tissue section (10-40 µm thickness)|
|Reaction time||2-8h (2h: standard; 8h: high-yield reaction)|
|Reaction volume||50 µl|
|Starting amount of DNA||100-300 ng*|
|Applications||Genotyping, PCR, Real-time PCR|
|Samples per run (throughput)||medium|
|Amplification||Whole genomic DNA|
The REPLI-g amplified products can be used directly for downstream analysis such as PCR, PCR-based applications, restriction enzyme digestion, cycle sequencing, and more, after appropriate dilution to adjust to work concentrations.
However, to determine DNA concentration by absorbance, the MDA product should be run through a spin column to eliminate the random hexamers, as they will contribute to the absorbance reading and give an artificially high concentration. For this reason, we recommend determining DNA concentration by PicoGreen analysis, which preferentially binds double-stranded DNA. As a result, single-stranded random hexamers will not contribute to the apparent DNA concentration in the quantitation assay. When using this method, the concentration of the MDA product can be determined directly, without any purification.
A Protocol for the use of PicoGreen to quantitate REPLI-g WGA product can be found in the REPLI-g Mini/Midi Handbook. Please follow this link .
Yes. Chromosomes are equally amplified. We and our customers use amplified DNA for SNP genotyping on a regular basis, using Illumina, TaqMan®, Sequenom, PCR, gel-based sequencing, and other techniques. Tzvetkov et al. (2005) used Affymetrix’ GeneChip Human Mapping 10K Arrays to investigate the accuracy and allele amplification bias in DNA samples subjected to MD-WGA with REPLI-g. They observed an excellent concordance (99.95%) between single-nucleotide polymorphisms (SNPs) called both in the nonamplified and the corresponding amplified DNA. Genomic DNA for this study was extracted from blood samples of four unrelated donors using the QIAamp DNA Blood Kit. High-throughput microarray genotyping of 11 555 different SNPs was performed using GeneChip Human Mapping 10K Arrays version Xba131 (Affymetrix).
For additional references, please visit our continuously expanding Citation Data Base online.
Low yields with REPLI-g Kits for whole genome amplification (WGA) can result from a number of factors:
Note! When using a thermocycler model that does not allow adjusting the temperature of the heated lid, REPLI-g incubation temperature has to be reduced to 25-28°C to ensure optimal reaction conditions and amplification efficiency!
Standard REPLI-g Kits, such as the REPLI-g Mini and Midi, UltraFast Mini-, Screening-, and Mitochondrial DNA Kits are not recommended for the amplification of gDNA extracted from paraffin embedded tissues. DNA recovered from paraffin embedded samples is typically strongly fragmented due to the fixation process, resulting in fragments only a few hundred base pairs long. Phi29 DNA polymerase however works most efficiently on DNA longer than 2 kb in length (ideally, at least a few fragments >10 kb should be present in the gDNA sample). If WGA product from strongly fragmented starting samples is utilized in genotyping assays, significant allele drop out and mis-genotyping can occur.
However, our new REPLI-g FFPE Kit overcomes these limitations by pre-processing of DNA directly derived from paraffin embedded tissue samples. The pre-processing reaction ligates fragments to generate suitable templates for subsequent amplification with REPLI-g Midi DNA Polymerase.
Paez et al. 2004 have shown in direct sequencing experiments sampling 500 000 bp, that the estimated error rate (9.5 x 10-6) was the same in WGA generated samples as in paired unamplified samples.
When using PicoGreen for quantification of REPLI-g FFPE amplifiied DNA, perform the assay after step 15 of the REPLI-g FFPE protocol, prior to the heating step at 95°C.
PicoGreen detects double-stranded DNA with high sensitivity. If the DNA was quantified after denaturation at 95°C using PicoGreen, multiply the yield by a factor of 2 to compensate for the use of single-stranded DNA.
Our WGA tutorial provides further information about Whole Genome Amplification and discusses the various techniques that are used. Additional detailed information is provided about REPLI-g Multiple Displacement Amplification technology (MDA), and recommendations are given on how to achieve the best results.
MDA-amplified product has an average length of 10-12 kb, enabling Southern Blots, RFLP, and other downstream analyses that require large DNA fragments.
Note that the ligation procedure employed in the REPLI-g FFPE Kit results in the formation of very high-molecular-weight DNA and enables uniform whole genome amplification from formalin-fixed, paraffin-embedded (FFPE) tissue.
Phi29 DNA Polymerase has an extremely high processivity and will extend primer-dimers that may be present in the reaction, leading to unspecific amplification products. Furthermore, the REPLI-g reaction is highly sensitive to any traces of DNA. Even minute quantities of contaminating DNA from other sources are eventually amplified over the long duration of the reaction (6-16h). However, these non-specific products will not generate specific results in downstream genetic analysis.
Formalin-fixed, ethanol-preserved samples that are not embedded in paraffin can be processed with the REPLI-g FFPE Kit by leaving out step 4 and 5 of the REPLI-g FFPE protocol. A mix containing FFPE Lysis Solution* and 2 µl Proteinase K can be added to the tissue section at step 3, after the section has been removed from its preservative solution. Proceed with the protocol at step 7: Incubate for 60 min at 60°C and then for a further 10 min at 95°C.
*Typically, 100 µl FFPE Lysis Solution are used. However, a smaller volume can be used for trimmed tissue sections (see protocol step 3 in the REPLI-g FFPE Handbook for more information).
The novel REPLI-g FFPE technology allows whole genome amplification of fragmented DNA directly from formalin-fixed, paraffin-embedded (FFPE) tissue samples.
The REPLI-g FFPE Kit contains reagents for two different reactions: a processing reaction preparing fragmented DNA from paraffin-embedded tissue for whole genome amplification (WGA) and an amplification reaction. Please refer to the REPLI-g FFPE Handbook for details of the procedure.
No, the REPLI-g FFPE Kit cannot restore DNA derived from FFPE tissue samples in its original order. The sample fixation process results in fragmentation of the DNA, and the original order of fragments is lost.
In the REPLI-g FFPE procedure, fragments are eluted from the tissue section and are ligated randomly during the processing reaction of the protocol. However, this does not effect the detection of nucleic acid sequences, such as polymorhisms, in downstream applications.
Phi29 DNA polymerase is a high fidelity proofreading enzyme and assures a very low replication error rate. It has an error rate of 1 x 10-6 - 10-7 nucleotides both in its intrinsic enzymatic activity and during the amplification reaction.
In contrast, Taq DNA polymerase has an intrinsic error rate of approximately 2 x 10-5 nucleotides, with an accumulation of about one mutation per 900 bases after 20 PCR cycles.
Affymetrix GeneChip Mapping assays require restriction sites for the digestion with enzymes. Due to the procedure of random DNA ligation when using the REPLI-g FFPE Kit, original restriction sites may be lost. Therefore, we do not recommend this kit in combination with the Affymetrix GeneChip procedure.
Affymetrix Targeted Genotyping assays on the other hand use a primer extension protocol and should be compatible with the REPLI-g FFPE procedure as they are not affected by the random ligation process.
Highly degraded samples tend not to be amplified evenly across the genome. In general, an average fragment size of 2 kb in a DNA sample is the lower limit, assuming no portions of the genome are degraded to the point where information will be missing. Often, when the largest fragment in a gDNA sample is 2 kb, other fragments are much smaller and some regions of the genome may have been lost due to degradation. At least a small portion of 10 kb fragments or larger need to be present in the gDNA sample for even amplification of the entire genome.
Note: If you are interested in amplifying DNA from paraffin-embedded samples we recommend to use the REPLI-g FFPE Kit.
DOP (Degenerate Oligonucleotide-primed PCR) and PEP (Primer Extension Preamplification) are PCR-based whole genome amplification (WGA) methods. REPLI-g amplification uses MDA (Multiple Displacement Amplification) which is not a PCR-based method. MDA is scalable with yields adjustable from ug to mg quantities, whereas DOP typically yields 2-3 ug of DNA per reaction. DOP also generates a shorter product which is not suitable for certain downstream applications (e.g. Southern blot and sub-cloning).
DOP and PEP products are different from REPLI-g MDA products for a number of reasons. First, after amplification is complete, PEP products have active thermostable polymerase that will degrade the amplification product over time, because the polymerase cannot be inactivated. Second, PEP reactions consist of PCR amplicons which have the potential to contaminate other reactions as 'runaway amplicons' (e.g., amplicons in the aerosol that may be co-amplified if they accidentally get into other reactions).
REPLI-g product has neither of these issues. The polymerase is heat-inactivated after the REPLI-g reaction is complete, so it cannot digest the amplified product. There are no issues with 'runaway amplicons', because the reaction is performed at constant temperature by a hyper-branching amplification mechanism, amplifying the genome randomly without generating specific amplicons.