CleanPlex® OncoZoom™ Panel contains a single pool of 601 primer pairs, multiplex PCR reagent, digestion reagent and other reagent components necessary for amplifying target regions of human DNA and constructing amplicon libraries for Next-Generation Sequencing on Illumina Sequencers. The panel targets more than 2900 commonly observed mutational positions (“hot spots”) from 65 oncogenes and tumor suppressor genes.
CleanPlex® OncoZoom® Cancer HotSpot Panel
$936.00 – $7,872.00
In stock (can be backordered)
CleanPlex® OncoZoom® Cancer HotSpot Panel contains a single pool of 601 primer pairs, multiplex PCR reagent, digestion reagent and other reagent components necessary for amplifying target regions of human DNA and constructing amplicon libraries for Next-Generation Sequencing on Illumina Sequencers. The panel targets more than 2900 commonly observed mutational positions (“hot spots”) from 65 oncogenes and tumor suppressor genes.
- Extremely uniform amplification of target regions. 100% observed uniformity at ≥ 0.2x mean depth and 97% observed uniformity at ≥ 0.5x mean depth.
- Compatibility with a variety of sample types. The panel is compatible with genomic DNA, FFPE, frozen tissue, fine needle aspirate, and blood.
- Low DNA input and high sensitivity. only 100 pg of input DNA is needed for germline genotype calling and 10 ng of DNA for somatic mutation detection (down to 1% low frequency allele).
|Sequencing Platform||Illumina Sequencers (MiniSeq, MiSeq, NextSeq, Hiseq)|
|Enrichment Method||Multiplex PCR|
|# of Primer Pools||1|
|# of Primer Pairs||601|
|# of Target Genes||65|
|Target Region Size (bp)||55199|
|Amplicon Size||Average 146 bp (from 125-175 bp)|
|Recommended DNA Input (Amount)||For germline genotype calling: minimum 100 pg;|
For somatic mutation calling with an LOD of 1%: minimum 10 ng
|Sample Type||Genomic DNA, FFPE DNA, cfDNA, and DNA from Blood, Tissue, Cell Culture, and Fine Needle Aspirate (FNA)|
(at ~2000x mean coverage)
|Miseq 2×150 Read Length: ~25 samples|
NextSeq Series Mid Output 2×150 Read Length: ~200
NextSeq Series High Output @ 2×150 Read Length: ~600
|Coverage Uniformity (at ≥ 0.2x mean coverage)||>95%|
|On-target Reads % (% reads aligned to target regions out of total aligned reads)||>95%|
Panel Data Files
|Dimensions||30 x 50 x 20 cm|
|Pack Size (Reactions)|
- Using incompatible index primers.
- DNA quantification was inaccurate, especially if using spectrophotometric methods such as nanodrop, OR DNA quality is extremely poor.
- 30% ethanol instead of 70% ethanol OR using TE/H2O instead of 70% ethanol was used in DNA purification.
- Forgetting to add magnetic beads for any of the purification steps.
- Forgetting to add one or both index primers in the 2nd PCR step.
- Over-digestion, forgetting to add Stop Buffer after digestion, or pausing after digestion step.
- Weak or incompatible magnetic rack. Do not use racks designed for 1.5 ml tube.
Concentrations higher or lower than the typical range of yields may lead to lower uniformity due to uneven amplification of target regions. Concentrations much lower in concentration can prove to be difficult to satisfy Illumina’s loading criteria. Please refer to Illumina’s suggestions for minimum loading concentration and volume.
What are the peaks around 70 – 90 bp in addition to the main library peak on a fragment analyzer trace?
What is peak around 150 -190 bp in addition to the main library peak on the fragment analyzer trace?
They come from incomplete removal of small-molecular-weight materials during magnetic bead purification after digestion. The digestion reagent cuts non-specific amplification products into small pieces, which are then removed during magnetic bead purification. Peaks from 150 – 190 bp are usually caused by the following: