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Comprehensive Cancer Genomic Profiling

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NovoPM™ Cancer Panel Overview

Novogene - NovoPMThe NovoPM™ Cancer Panel is a comprehensive NGS cancer panel that analyzes the complete coding regions of 548 genes and the introns of 21 genes. These genes are known to be relevant for the diagnosis and/or treatment of solid tumors according to National Comprehensive Cancer Network (NCCN) guidelines and medical literature. This panel detects all four types of genomic abnormalities: SNV, InDel, fusion, and copy number variation (CNV). Flexible as well as comprehensive, the NovoPM™ Cancer Panel can be applied to both FFPE tumor samples and liquid biopsies.

The NovoPM Advantage

  • Focus: NovoPM uses hybrid capture technologies to achieve ultra-deep sequencing coverage of clinically relevant genes.
  • Flexibility: ctDNA from plasma or whole blood and DNA from fresh-frozen or FFPE tissue samples are all acceptable.
  • Experience: As of October 2017, NovoPM has been used to analyze 6,492 tumor tissue samples and 5,267 liquid biopsy samples.
  • Bioinformatics: Variant calling in NovoPM is done using Novogene’s state-of-the-art bioinformatics pipeline; clinical significance of the variants is determined according to well-recognized databases including COSMIC, dbSNP, 1000 Genomes, ExAC, OncoKB, ClinVar, PharmGKB, SIFT, and Polyphen2.
  • Value: In addition to identifying abnormalities in individual genes, NovoPM also determines Tumor Mutation Burden (TMB), blood Tumor Mutation Burden (bTMB), and microsatellite instability (MSI) status.
  • Price: With the world’s largest sequencing capacity and superior process efficiency, Novogene provides highly competitive prices for all our services.

Project Overview


Novogene - NovoPM

Sequencing Strategy

  • HiSeq X or NovaSeq 6000 platforms, paired-end 150bp

Data Quality Guarantee

  • We guarantee that ≥ 80% of bases have a sequencing quality score ≥ Q30, which exceeds Illumina’s official guarantee of ≥ 75%

Sample Requirements

  • For FFPE tissue: Approximately ten 4-µm sections, each with tissue area ≥ 25 mm2, tumor content ≥ 20%
  • For extracted tissue DNA: Total DNA≥500 ng; DNA concentration (quantified by Qubit)≥20 ng/μL, total volume≥10 μL; Purity: OD260/280=1.8-2.0 without degradation or RNA contamination
  • For plasma: 4 mL (for ctDNA extraction)
  • For extracted ctDNA: Total ctDNA≥60 ng; DNA concentration (quantified by Qubit)≥3 ng/μL, total volume≥10 μL; Purity: without genomic DNA contamination
  • For whole blood: 10 mL (for ctDNA and white blood cell DNA extraction)
  • For extracted white blood cell DNA: Total DNA≥1 μg; DNA concentration (quantified by Qubit)≥20 ng/μL, total volume≥10 μL; Purity: OD260/280=1.8-2.0 without degradation or RNA contamination

Turnaround Time

  • 13 calendar days for FFPE samples from sample receipt in our laboratory to reporting; 12 calendar days from sample receipt to the delivery of raw sequencing data.
  • 10 calendar days for ctDNA samples from sample receipt in our laboratory to reporting; 9 calendar days from sample receipt to delivery of raw sequencing data.

Recommended Sequencing Depth

  • For tissue samples: 8Gb raw data with at least 1000X effective average sequencing depth
  • For plasma or whole-blood samples: 17Gb raw data with at least 2000X effective average sequencing depth
  • Sensitivity for SNV: 1.0% for tissue DNA and 0.5% for ctDNA

Analysis Pipeline




Interested in learning more about our NovoPM™ comprehensive genomic profiling test? Click on the link below to read our informational brochure.

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Project Example

Seeking potential therapeutic options, a 48-year-old female patient of metastatic breast cancer with multiple lymph node metastases in China underwent a biopsy which was then sent to our lab for analysis with NovoPM. A rare somatic mutation was discovered for which there was a CFDA-approved targeted therapy. The patient responded well to this treatment with significantly extended survival and higher life quality (see details in “Clinical Outcomes” below). This case demonstrated the tremendous clinical value of comprehensive genomic analysis with a large panel like NovoPM, especially in cancer patients who have exhausted other treatment options.

Patient information

AgeCancer TypeSample Type
48Non small cell lung cancer (NSCLC)Tissue Biopsy

Diagnostic Details

Diagnostic Result
Novel ROS1 fusion (SLC34A2-ROS1, chr6:117653720 - chr4:25678781)
Variant Summary
The SLC34A2-ROS1 fusion variant is a common ROS1 fusion in NSCLC accounting for the second highest ROS1 fusion prevalence in NSCLC 1, 2. It is likely generated from an intra-chromosomal deletion and fusion. The novel SLC34A2-ROS1 fusion variant (chr6:117653720 - chr4:25678781, 3′UTR of SLC34A2 in exon 13 was disrupted and inverted to connect a position of intronic_e32_e31 of ROS1) had never been reported before.

References:

  1. Awad MM, Katayama R, Mctigue M, et al. Acquired resistance to crizotinib from a mutation in CD74–ROS1. N Engl J Med. 2013; 368(25):2395–2401.
  2. Rimkunas VM, Crosby KE, Li D, et al. Analysis of receptor tyrosine kinase ROS1-positive tumors in non-small cell lung cancer: identifcation of a FIG-ROS1 fusion. Clin Cancer Res. 2012;18(16):4449–4457.
Relevant Therapy
Crizotinib
Drug Detail
Crizotinib has been approved by FDA for the treatment of advanced metastatic NSCLC with ROS1 or ALK rearrangements. In the Phase I clinical trial of crizotinib, 50 NSCLC patients with ROS1 fusion were enrolled, including 49 cases detected by FISH and 1 by reverse transcriptase-polymerase chain reaction (RT-PCR). The overall response rate (ORR) was 72%, with a median duration of response (DOR) of 17.6 months and a median progression-free survival (PFS) of 19.2 months.

Clinical Outcomes


Figure. Computed tomography and positron emission tomography images of the right lower lobe of the patient. A: mediastinum, upper and lower bilateral clavicle area, left armpit, and lung lymph node metastases at treatment initiation (March 2016). B: most lesions had shrunk significantly 2 months after Crizotinib treatment (May 2016). C: the metastatic lymph nodes had disappeared, with the metabolism returning to normal 11 months after Crizotinib treatment (February 2017).