QuantideX® qPCR DNA QC Assay

  • Measures the DNA that matters: PCR-amplifiable DNA
  • Provides actionable guidance that rescues low-quality DNA and helps assure the accuracy of next-generation sequencing calls
  • A 2-in-1 assay: Distinguishes low-quality, unamplifiable DNA from DNA with sample-derived PCR inhibition
  • Simple, high-throughput workflow using a convenient multiplexed design
  • Ideal for quantifying challenging sample types like FFPE and FNA

Product Description

The QuantideX qPCR DNA QC Assay* is a multiplexed quantitative PCR assay that measures the absolute copy number of PCR-amplifiable DNA in a sample and reports PCR inhibition.

The QuantideX qPCR DNA QC Assay determines the functional quality of sample DNA using the QFI™ Score, which is the fraction of total genomic DNA copies that can be amplified. The QFI™ Score and copy number of amplifiable DNA provide actionable guidance that informs the input into NGS target enrichment and helps assure high analytical sensitivity and specificity. In addition, the Assay flags PCR inhibitors in the sample and provides an opportunity to salvage such samples through a subsequent clean-up step prior to further processing.

QuantideX DNA Assay Prod Description Fig1 (1)
Figure 1. Correlation between the QFI™ Score and Qubit® DNA concentration for 128 residual clinical samples. FFPE tumors with low levels of functional DNA are identified by the QuantideX® qPCR DNA QC Assay, but not by the Qubit® assay (Sah et al., 2013).

Analytic Characteristics

The functional concentration of FFPE DNA samples revealed by the QuantideX qPCR DNA QC Assay is associated with the accuracy of downstream NGS data.Figure-2_Analytical-Characteristics_Quantidex
Figure 2. Impact of functional DNA quality (indicated by the QFI™ Score) on the number of variants called using a commercial NGS enrichment panel. The number of variants detected increases by more than an order of magnitude as the QFI™ Score decreases below about 6%. More than 90% of these variants are false positives. (Sah et al., 2013)

The absolute copy number of amplifiable DNA can guide inputs into library prep and improve the accuracy of NGS variant calls.

QuantideX qPCR DNA Assay Fig3
Figure 3. The specificity of NGS mutation detection can be dramatically improved by increasing the input of amplifiable DNA from a low-quality FFPE tumor biopsy (QFI™ Score=2.6%). Although the expected BRAF V600E mutation is detected at all inputs, the number of false positives is significantly increased at lower copy number inputs. The QuantideX® Assay informs an input of 200 amplifiable copies, which is associated with detection of a single variant, the expected BRAF V600E mutation. The mass inputs at the top of each bar were measured using spectrophotometry.

Ordering

Product Name Number of Reactions Catalog Number
QuantideX qPCR DNA QC Assay 100 49539

T 877-777-1874 or 512-681-5200
F 512-681-5202
E orders@asuragen.com

*For Research Use Only. Not for use in Diagnostic procedures.

QuantideX® qPCR DNA QC Assay

  • Measures the DNA that matters: PCR-amplifiable DNA
  • Provides actionable guidance that rescues low-quality DNA and helps assure the accuracy of next-generation sequencing calls
  • A 2-in-1 assay: Distinguishes low-quality, unamplifiable DNA from DNA with sample-derived PCR inhibition
  • Simple, high-throughput workflow using a convenient multiplexed design
  • Ideal for quantifying challenging sample types like FFPE and FNA

Product Description

The QuantideX qPCR DNA QC Assay* is a multiplexed quantitative PCR assay that measures the absolute copy number of PCR-amplifiable DNA in a sample and reports PCR inhibition.

The QuantideX qPCR DNA QC Assay determines the functional quality of sample DNA using the QFI™ Score, which is the fraction of total genomic DNA copies that can be amplified. The QFI™ Score and copy number of amplifiable DNA provide actionable guidance that informs the input into NGS target enrichment and helps assure high analytical sensitivity and specificity. In addition, the Assay flags PCR inhibitors in the sample and provides an opportunity to salvage such samples through a subsequent clean-up step prior to further processing.

QuantideX DNA Assay Prod Description Fig1 (1)
Figure 1. Correlation between the QFI™ Score and Qubit® DNA concentration for 128 residual clinical samples. FFPE tumors with low levels of functional DNA are identified by the QuantideX® qPCR DNA QC Assay, but not by the Qubit® assay (Sah et al., 2013).

Analytic Characteristics

The functional concentration of FFPE DNA samples revealed by the QuantideX qPCR DNA QC Assay is associated with the accuracy of downstream NGS data.Figure-2_Analytical-Characteristics_Quantidex
Figure 2. Impact of functional DNA quality (indicated by the QFI™ Score) on the number of variants called using a commercial NGS enrichment panel. The number of variants detected increases by more than an order of magnitude as the QFI™ Score decreases below about 6%. More than 90% of these variants are false positives. (Sah et al., 2013)

The absolute copy number of amplifiable DNA can guide inputs into library prep and improve the accuracy of NGS variant calls.

QuantideX qPCR DNA Assay Fig3
Figure 3. The specificity of NGS mutation detection can be dramatically improved by increasing the input of amplifiable DNA from a low-quality FFPE tumor biopsy (QFI™ Score=2.6%). Although the expected BRAF V600E mutation is detected at all inputs, the number of false positives is significantly increased at lower copy number inputs. The QuantideX® Assay informs an input of 200 amplifiable copies, which is associated with detection of a single variant, the expected BRAF V600E mutation. The mass inputs at the top of each bar were measured using spectrophotometry.

Ordering

Product Name Number of Reactions Catalog Number
QuantideX qPCR DNA QC Assay 100 49539

T 877-777-1874 or 512-681-5200
F 512-681-5202
E orders@asuragen.com

*For Research Use Only. Not for use in Diagnostic procedures.

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