Purigen Biosystems, Inc.

Ionic® FFPE to Pure DNA

Reliable Results from FFPE Samples

Automated extraction of DNA with higher yield and quality

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Overcome the Limitations of Current Technologies

Purification of nucleic acids from FFPE scrolls or slides requires less than 3 minutes of hands-on time per sample (lysis included). Nucleic acids remain in their native form, not denatured or dehydrated


  • Simplify Lysis – Deparaffinize, lyse, and de-crosslink in a single reaction without using harsh chemicals
  • Eliminate Bias – Extract targeted nucleic acid regardless of fragment length or GC content
  • Minimize User Involvement – Extract and purify 8 samples in one hour with just 3 minutes of hands-on time per sample
  • Improve Reliability – Minimize user-to-user variability, cross-contamination, and sample loss

Ionic® Purification System for FFPE Samples

The Ionic Purification System from Purigen Biosystems uses isotachophoresis (ITP) to extract, purify, and concentrate genomic DNA and RNA from cells and and FFPE. Since nucleic acids remain in their native form, not denatured or dehydrated, the Ionic system is ideal for challenging samples with limited starting material or low-quality material.

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Simplified FFPE Purification Workflow

Get pure and native nucleic acid from FFPE samples with higher yield and quality
in less than 3 minutes of total hands-on time per FFPE sample.

Purification in just 3 minutes of hands-on time per sample

Extract More DNA with Higher Quality

3.5X More DNA from FFPE Samples

 

FIGURE 1: Comparison of nucleic acid yields from replicate sections of 32 FFPE samples purified by either the Ionic system or a commercially available column-based kit (32 sections per extraction method). The concentration of amplifiable DNA purified from each sample was determined with the Qiagen MRef Multicopy Reference Assay. For optimal performance from the columns, sections purified by this method were mounted onto slides prior to lysis. Sections purified by Ionic system were processed as unmounted scrolls to demonstrate improved performance using a simpler workflow. The Ionic system yield exceeds that of column-based extraction kit for 31 of 32 samples. Error bars indicate the 95% confidence interval for each data point.

 

Higher Quality DNA vs. Column-based Kits

 

FIGURE 2: Replicate sections from 32 FFPE samples processed by either the Ionic system or a column-based kit (32 each) were assessed with the Agilent QC Plex assay and the resulting amplicons were analyzed on the Agilent Technologies 4200 TapeStation. The resulting traces were scored using the DQC algorithm. Error bars indicate the 95% confidence interval for each data point.

 


Improve NGS Coverage Uniformity with Less Sample Bias

 

 

FIGURE 3: Libraries were prepared and enriched for the SureMASTR Tumor Hotspot Panel (Agilent) and sequenced on the Illumina MiSeq sequencer. Coverage was assessed against control libraries constructed from a high-quality reference sample, Coriell Institute NA12878 DNA (GM12879 cell line). Coverage was compared to the reference as a fraction of total hits. The log ratio of the coverage fraction by target is plotted.

 

 

FIGURE 4: Data from the sequencing of the SureMASTR Tumor Hotspot libraries is plotted here as a coverage ratio versus the amplicon size. The higher intensity of color at each data point indicates overlapping data points. The underrepresented targets in the libraries made from column-purified DNA occur most often in the longer targets.

 

 

FIGURE 5: Sequencing libraries were prepared from DNA extracted using either the Ionic system or a column-based kit. Samples were sequenced on an Illumina MiSeq sequencer using the Agilent Technologies SureSelect XTHS Cancer All-In-Ones Solid Tumor Assay. Coverage was compared to that of a high-quality reference sample (Coriell GM24385 DNA) to determine a coverage ratio for each sample. Results were segregated by purification technology and percentage of GC content in the target sequence. Samples purified by Ionic system show uniform coverage across all targets regardless of GC content.

 

 

FIGURE 6: Sequencing libraries were prepared from DNA extracted using either the Ionic system or a column-based kit. Each set contained samples composed of 1, 2, or 4 FFPE tissue sections of 5 µm thickness. Each set also contained replicate 2-section and 4-section samples. Libraries were prepared using the SureMASTR Tumor Hotspot Panel (Agilent) and sequenced on the Illumina MiSeq sequencer. Library coverage was normalized to the lowest number of reads after sequencing. Coverage was assessed against control libraries constructed from a high-quality reference sample, Coriell Institute NA12878 DNA (GM12879 cell line). Coverage was compared to the reference as a fraction of total hits. The log ratio of the coverage fraction by target is plotted. After sequencing, 26 variants were detected in samples prepared by both the Ionic system and using a column-based kit. 100% of the 26 expected variants were detected in 4 out of 5 samples purified on the Ionic system with no difference between replicates.

 

 

 

Purigen Isotachophoresis Technology

Isotachophoresis separates and concentrates charged molecules in solution solely based on their electrophoretic mobility. Biological samples are gently lysed and added to the Purigen Ionic® Fluidic Chip which applies an electric field to isolate nucleic acid in its natural, native form.