Key Features

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Ultrasensitive

Detect mutations at 0.2% VAF and deletions at 1.94 ploidy

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Quantitative

Quantitate mutation VAF of samples down to 0.2% VAF

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Quick turnaround time

6-hour DNA-to-Library workflow

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Versatile

Compatible with several sample types

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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
  • Ultrasensitive: SNV and Indels detected and quantitated down to 0.2% VAF; CNVs (deletions and amplifications) detected and quantitated at ≥2.04 and ≤1.97 copies (deletions and amplifications)
  • 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 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

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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 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).

Peng Dai, Ph.D., serves as a senior scientist at Nuprobe. He obtained his Doctorate degree from MIT and has over 7 years of research experience in biotechnology, genomics and sequencing.

Fill in the form below to contact Peng for questions about the CNV+ products.

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