Key Features

Ultrasensitive

Detect mutations at 0.2% VAF and deletions at 1.94 ploidy

Quantitative

Quantitate mutation VAF of samples down to 0.2% VAF

Quick turnaround time

6-hour DNA-to-Library workflow

Versatile

Compatible with several sample types

User-friendly

Easy workflow and data analysis

Benefits

  • CNV and Hotspots: covers 84 mutation hotspots in 14 genes and detect Copy Number Variations (CNVs) in 18 genes including ERBB2 (HER2)
  • Ultrasensitive: SNV and Indels detected and quantitated down to 0.2% VAF; CNVs (amplifications and deletions) detected and quantitated at ≥2.04 and ≤1.97 copies (amplifications and deletions)
  • Sample Flexibility: compatible with several sample types, including cfDNA, tumor section (FFPE or Fresh Frozen), and PBMC DNA. Need as little as 10 ng of DNA
  • Calibration-free quantitation: high quantitation accuracy of variants down to 0.2% VAF
  • Dedicated data analysis pipeline: fastq-to-variant report with a user-friendly cloud or locally-run analysis program

Hotspot Mutations

AKT1ARBRAFBRCA1BRCA2
EGFRERBB2ERBB3ERBB4ESR1
KRASPIK3CAPTENTP53

CNVs

AKT3BRCA1BRCA2BRIP1EGFRERBB2
ERBB3ERBB4ESR1FGFR1MYCNBN
NCSTNPIK3CAPTENPTGS2RAD51CTP53

Sample Data

CNV calls from clinical FFPE samples

  • CNV calls for FFPE DNA samples.
  • Heterozygous deletions were detected at down to 5%  from FFPE samples.

  • The DNA input was between 4.4 ng and 8.3 ng for each sample.

  • Mutation calls for FFPE DNA samples.

  •  Mutation calls for 19 formalin-fixed, paraffin-embedded (FFPE) tissue samples from cancer patients. Mutations were detected down to 0.2% VAF.

Workflow

Step 1: DNA Extraction

DNA is extracted from clinical samples including fresh/frozen tissue, FFPE, or plasma with commercial extraction kits.

Step 2: QASeq NGS library preparation

Highly multiplexed amplicon-based library preparation with molecular barcoding is performed on clinical DNA samples.

6 hours (1.5 hours hands-on)
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Step 3: Sequencing

Indexed samples undergo quality control, pooling, and sequencing on an Illumina sequencing instrument.

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Step 4: Data Analysis

QASeq bioinformatics pipeline analyzes demultiplexed FASRQ files to generate CNV and mutation calls.

CNV+ Breast Cancer NGS Panel workflow is simple and does not require any special equipment. The total turnaround time from DNA to an indexed library is approximately 6 hours, with only 1.5 hours of hands-on time. Sample-to-variant report can be achieved in less than 48 hours in 24/7 mode.

Indexed libraries are compatible with Illumina MiniSeq, MiSeq, NextSeq, and HiSeq platforms. 

Compatible Instruments

Illumina NovaSeq


Illumina HiSeq

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For research use only. Not for use in diagnostic procedures.

CNV+ Breast Cancer NGS Panel

The CNV+ Breast Cancer NGS Panel covers 84 frequently mutated cancer hotspots in 14 genes and CNVs of 18 genes including HER2, amplified in 10-20% of breast cancers and guide treatment with trastuzumab (HERCEPTIN).

The CNV+ Breast Cancer NGS Panel utilizes unique molecular identifiers (UMI) and PCR to accurately quantify SNVs and Indels down to 0.2% VAF as well as detect CNVs in HER2 above 2.04 copies and below 1.97 copies from cfDNA.

Unlike FISH, the CNV+ Breast Cancer NGS Panel can detect hotspot mutations in 14 genes and HER2 CNVs simultaneously in the same reaction. Amplicons all along HER2 allow for ultrafine CNV mapping with sub-gene level identification of CNVs.

The CNV+ Breast Cancer NGS Panel has a high conversion yield (median >60%), allowing sensitive detection from small sample inputs (30ng FFPE DNA, 8ng fresh/frozen DNA, 10ng cfDNA).

Jinny Zhang, Research Scientist II at NuProbe, Ph.D. in Systems, Synthetic and Physical Biology from Rice University, Houston.

Fill out the form below to contact Jinny for questions about the CNV+ products.



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