Wild-type Blocking PCR Combined with Direct Sequencing as a Highly Sensitive Method for Detection of Low-Frequency Somatic Mutations

The overall goal of this procedure is to detect low frequency somatic mutations in a variety of sample types. This methodology can help answer key questions in somatic mutation testing by facilitating the detection of very low frequency mutations. Here we will look for mutations in the myd88 gene in bone marrow samples.

The main advantage of this technique is that it provides highly accurate and sensitive information about the presence of somatic mutations, even with very few neoplastic cells. This wild type blocking PCR based sequencing assay was developed to amplify part of exon five in the myd88 gene, ensuring coverage of the L265 hotspot. The forward and reverse primers were designed with a five prime M13 sequence to allow for a kneeling of complimentary sequencing primers.

Design the blocking oligonucleotide to be approximately 10 to 15 bases in length and complimentary to the wild type template where mutant enrichment is desired. A shorter oligo will improve mismatch discrimination. To achieve high target specificity it's important not to use too much of the blocking nucleotides, as this will result in very sticky oligonucleotides.

To design the blocking oligonucleotide begin by navigating to the Oligo Tools website. Select the Oligo TM prediction tool. A new window will open up.

Paste the sequence of the wild type template to be blocked into the oligo sequence box. Add a plus sign in front of the blocker bases to mark them. Click on the calculate button to determine the approximate TM of the DNA blocker hybrid.

The calculated melting temperatures will appear in the boxes below. Design the blocking oligo to have a melting temperature 10 to 15 degrees Celsius above the extension temperature during thermocycling. Here, the extension temperature is 72 degrees Celsius.

To adjust the melting temperature, add, remove, or substitute blocking bases. Avoid long stretches of three to four blocking C or G bases. Next, to avoid secondary structure formation or self dimerization go back to the Oligo Tools website home screen and select the Oligo Optimizer tool.

A new window will open. Paste the sequence of the wild type template to be blocked into the box. Add a plus sign to indicate blocking bases.

Select the two boxes for secondary structure and self only and press the analyze button to see the scores for hybridization and secondary structure. These scores represent very rough estimates of the melting temperatures of the self dimers and secondary structures respectively. Lower scores are optimal and can be achieved by limiting blocker blocker pairing.

Remove or reposition blocking nucleotides in order to achieve lower scores. The optimized blocking oligo nucleotide for myd88 shown here strikes a balance between the DNA blocker hybrid melting temperature and low enough hybridization and secondary structure scores. It was designed to cover amino acids Q262 to I266, and features a three prime inverted DT to inhibit both extension by DNA polymerase and degradation by three prime exonuclease.

Once the primers have been designed set up the wild type blocking PCR and perform thermocycling as described in the accompanying document. Remove magnetic beads from storage at four degrees Celsius and bring them to room temperature. Transfer 10 microliters of the PCR product to a new PCR plate.

Vortex the magnetic beads vigorously to fully resuspend the magnetic particles and then add 18 microliters of magnetic beads to each well on the new plate. Pipette up and down 10 times to mix. Then incubate the plate at room temperature for five minutes.

Following the incubation, place the PCR plate onto the side skirted magnet plate for two minutes to separate the beads from the solution. Use a multi channel pipette to aspirate the supernatant. Take care to avoid the bead pellet.

Next, dispense 150 microliters of 70%ethanol into each well and incubate the plate at room temperature for at least 30 seconds. Then aspirate the ethanol with a multichannel pipette and discard the tips. Repeat this wash procedure once more.

Using a 20 microliter multichannel pipette aspirate the remaining ethanol from each well and discard the tips. After allowing about 10 minutes for the wells of the plate to dry remove it from the magnet and add 40 microliters of nuclease free water to each well. Pipette up and down 15 times to mix.

Then incubate at room temperature for two minutes. After incubating, place the PCR plate back onto the magnet plate for one minute to separate the beads from solution. Transfer 35 microliters of purified product to a new PCR plate, and perform bidirectional sequencing as described in the accompanying document.

Once bidirectional sequencing has been performed to purify the sequencing products prepare a fresh one in 25 solution of three molar sodium acetate at PH 5.2 and 100%ethanol. Also prepare a fresh solution of 70%ethanol. To each well of both the forward and reverse sequencing plates add 30 microliters of sodium acetate in 100%ethanol and pipette up and down five times to mix.

Then reseal the plate, and incubate in the dark at room temperature for 20 minutes. After 20 minutes have passed, centrifuge the plate at 2, 250 times G for 15 minutes. After the spin, remove the plate sealer, and invert the plate once over a waste container.

If the plate is inverted multiple times the pellets may loosen from the well bottoms. Place the inverted plate on a clean paper towel, and centrifuge at 150 times G for one minute. Next, add 150 microliters of 70%ethanol to each well and reseal the plate.

Spin at 2, 250 times G for five minutes. Then repeat the process of removing the plate sealer and inverting the plate. If the wells are not completely dry, allow them to air dry at room temperature.

Make sure the samples are protected from light. Once the wells are completely dry add 10 microliters of formamide to each well and pipette up and down 10 times to mix. Reseal the plate.

Denature using a thermo cycler at 95 degrees Celsius for three minutes followed by four degrees Celsius for five minutes. After denaturing, replace the plate sealer with a septa and sequence on a sequencing platform according to the manufacturer's instructions. Using sequence analysis software, visualize the traces, and align the sequences to the appropriate reference sequences.

Align myd88 to NCBI reference sequence NM002468. Genomic DNA from patients with and without mutations underwent both conventional and wild type blocking PCR and the resulting PCR products were then sequenced. As can be seen here, the mutant allele was enriched when wild type blocking PCR was performed, and false positives were not seen in wild type DNA.

A characteristic drop off in signal intensity as shown here is often seen if too high a concentration of blocker is used, or if post PCR purification failed to remove blocker prior to bidirectional sequencing. This occurs when enzymatic purification is performed in place of magnetic bead purification. Any PCR based assay that enriches for mutant alleles will detect low frequency artifacts.

These traces show an increase in CG sequencing artifacts, relative to TA artifacts in FFPE tissue when cytosine or methylated cytosine are deaminated via formal infixation to uracil or thiamine respectively. Uracil DNA glycosylase or UDG can excise uracil prior to wild type blocking PCR, helping to reduce sequencing artifacts. However, thiamine resulting from deaminated five methyl cytosine which frequently occurs at CPG islands cannot be excised by UDG.

Decreasing the concentration of blocker used in wild type blocking PCR may help to reduce the occurrence of sequencing artifacts that are not remedied by UDG treatment. After watching this video, you should have a good understanding of how to test somatic mutations with a high degree of accuracy and sensitivity, using the wild type blocking technique. The principle of this technology can be applied to the detection of mutations in small sub populations of cells.

Therefore, it has utility in detecting minimal residual disease, monitoring patients, and predicting early relapse in patients with various neoplasms.