SLIMamp Overview

Streamlined

  • • Single-well amplification with minimal hands-on time
  • • DNA to Sequencer in <8 hours without time-consuming ligation steps
  • • Germline, Somatic and Circulating Tumor DNA Panels
  • • Automation compatible

Robust

  • • Use as little as 2.5 ng FFPE DNA sample (solid tumor assays) or 20 ng circulating tumor DNA (liquid biopsy)
  • • Even sequencing coverage of target regions with industry-leading mapping and on-target rates
  • • Eliminate need for re-running samples with high reproducibility

Economical

  • • High mapping and on-target rates efficiently utilizes sequencing capacity
  • • Labor-saving workflow saves valuable technician time
  • • Eliminate sample failure and need to re-run due to insufficient DNA quantity
  • • Attractive pricing

SLIMamp Process Workflow

Sample-to-sequencer in less than 1 day
Minimal hands-on time with no complex ligation steps






SLIMamp Overlapping Multiplex PCR Technology

Stem-Loop Inhibition-Mediated amplification





Pillar Biosciences’ patented SLIMamp (Stem-Loop Inhibition-Mediated amplification) technology enables specific priming of overlapping target segments. The DNA template (top) has two sets of overlapping primers designed to the region of interest, labeled F1/R1 and F2/R2. Contiguous to the gene-specific primer sequences are tag sequences labeled t1, t2 and t3. Due to tag t1 and partial F2 sequence (labeled F2*) in primers t1-F2 and t1-F2*-R1, each individual strand of the amplified overlap product contains complementary sequences, thus forming a stem-loop. Short products from t1-F2 and t1-F2*-R1 primers are inhibited from amplification due to the stem-loop structure.


For further details, see the reference “Amplification of overlapping DNA amplicons in a single-tube multiplex PCR for targeted next-generation sequencing of BRCA1 and BRCA2” by Schenk D, Song G, Ke Y, Wang Z. PLoS One. 2017 Jul 12;12(7):e0181062. doi:10.1371/journal.pone.0181062. eCollection 2017. PMID: 28704513 for both technical details as well as performance data on BRCA1 and BRCA2 with known mutation status.

ONCO/Reveal BRCA Variant Statistics

A
Unique Variants
Type Count Notes
Insertion 4 1 bp
Deletion 4 1-4 bp, 11 bp, and 40 bp
SNV 47  
Total 66  
B
Variant Detection from 34 unique samples with full ROI region
validated by at least one independent method
Variant Detected Variant not Detected
True Positive (TP) 409 SNV_HET 234 False Negative (FN) 0
SNV_HOM 153
Indels_HET (1-40 bp) 22
False Positive (TP) 0   True Negative (TN)* 603737
*TN= Size of ROI (17769 bp) x Total Samples (34) - Total True positives in all samples
C
Analytical sensitivity and specificity
Statistic Formula Value 95% Cl
Sensitivity TP/(TP+FN) 100.00% 99.10% to 100.00%
Specificity TN/(TN+FP) 100.00% 100.00% to 100.00%
A
Unique Variants
Type Count Notes
Insertion 4 1 bp
Delection 4 1-4 bp, 11 bp, and 40 bp
SNV 47  
Total 66  
B
Variant Detection from 34 unique samples with full ROI region
validated by at least one independent method
Variant Detected Variant not Detected
True Positive (TP) 409 SNV_HET 234 False Negative (FN) 0
SNV_HOM 153
Indels_HET (1-40 bp) 22
False Positive (TP) 0   True Negative (TN)* 603737
*TN= Size of ROI (17769 bp) x Total Samples (34) - Total True positives in all samples
C
Analytical sensitivity and specificity
Statistic Formula Value 95% Cl
Sensitivity TP/(TP+FN) 100.00% 99.10% to 100.00%
Specificity TN/(TN+FP) 100.00% 100.00% to 100.00%


For further details on the samples and methods used to generate this dataset, refer to this PLoS publication.



ONCO/Reveal BRCA1 & BRCA2 Panel Performance






Varying amounts of a BRCA reference standard were used to generate sequencing libraries (5 ng, 10 ng and 20 ng of Horizon Diagnostics HD793 and HD795 reference standards) and sequenced in triplicate. A total of 12 samples were sequenced at a mean coverage of 4800x, and the average coverage of the target at >20% of the mean was 99.67%