The Novogene Precision Medicine 2.0 (NovoPM™ 2.0) comprehensive genomic profiling test for solid tumors is a next-generation sequencing (NGS)-based assay that analyzes 484 genes for clinically important alterations at the DNA level. These genes are known to be relevant for the diagnosis and/or treatment of various solid tumors according to National Comprehensive Cancer Network (NCCN) guidelines and the medical literature.
NovoPM™ 2.0 is developed based on NovoPM™ 1.0 with an updated gene list and enhanced analytical performance. Several powerful analyses are also included with the panel: Tumor Mutation Burden (TMB) analysis, blood Tumor Mutation Burden (bTMB) analysis and Microsatellite Instability (MSI) analysis.
The NovoPM™ Advantage
- Comprehensive Results: NovoPM™ 2.0 interrogates the complete coding regions of 468 genes and the introns of 43 genes. It can detect all four types of genomic abnormalities (SNV, InDel, CNV and Fusion) and also generate results (TMB, bTMB and MSI) that can help guide cancer immunotherapies.
- Reliable Performance: Comprehensive analytical validation has been completed and the test includes rigorous quality control measures.
- Competitive Price: With one of the world’s largest sequencing capacity and superior process efficiency, Novogene offers highly competitive prices for all our services.
NovoPM™ 2.0 Test Content
Figure 1. Genomic profiling results generated by NovoPM™ 2.0
NovoPM™ 2.0 interrogates the complete coding regions of 468 genes and the introns of 43 genes for all four types of genomic abnormalities: SNV, InDel, CNV and Fusion. A comparison of the gene lists between NovoPM™ 2.0 and the FDA-approved FoundationOne CDx is shown in Figure 2. The mutation status of some of these genes can guide the potential application of multiple FDA-approved targeted and/or immunotherapies as shown in Table 1. The other genes are also analyzed for their relevance to the diagnosis and/or treatment of various solid tumors according to the medical literature. The clinical interpretation of detected mutations in those genes is done according to Novogene’s in-house oncology knowledgebase constructed on the basis of public resources such as OncoKB.
Figure 2. NovoPM™ 2.0 vs. FoundationOne CDx
Table 1. Gene targets in NovoPM™ 2.0 that are associated with FDA-approved therapies
|Non-Small Cell Lung Cancer||EGFR 19Del and L858R||Gilotrif® (afatinib), Iressa® (gefitinib) or Tarceva® (erlotinib)|
|EGFR T790M||Tagrisso® (osimertinib)|
|ALK re-arrangement||Alecensa® (alectinib), Xalkori® (crizotinib) or Zykadia® (ceritinib)|
|BRAF V600E||Tafinlar® (dabrafenib) in combination with Mekinist® (trametinib)|
|ROS1 fusion||Xalkori® (crizotinib)|
|TMB and bTMB||Opdivo® (nivolumab) and Yervoy® (ipilimumab)|
|Melanoma||BRAF V600E||Tafinlar® (dabrafenib) or Zelboraf® (vemurafenib)|
|Breast Cancer||ERBB2 (HER2) amplification||Herceptin® (trastuzumab)|
|Colorectal Cancer||KRAS wild-type||Erbitux® (cetuximab)|
|Ovarian, Breast and Prostate Cancer||BRCA1 and BRCA2 alterations||Lynparza® (olaparib)|
|Solid Tumors||MSI||Opdivo® (nivolumab) or Keytruda® (pembrolizumab)|
|Solid Tumors||NTRK1/2/3 fusions||Vitrakvi® (larotrectinib)|
NovoPM™ 2.0 Test Specifications
|Sample Type||Sample Requirement|
|Extracted DNA✲||Total DNA ≥ 100 ng; DNA concentration (quantified by Qubit): ≥ 3 ng/μL; Purity: OD260/280 = 1.8-2.0 without degradation or RNA contamination.|
|FFPE||Approximately ten 4-µm sections, each with tissue area ≥ 25 mm² and tumor content ≥ 20%.|
|Whole blood||10 mL (for ctDNA and white blood cell DNA extraction)|
|Blood Plasma||4 mL (for ctDNA extraction)|
|Extracted ctDNA✲||Total ctDNA ≥ 30 ng; DNA concentration (quantified by Qubit) ≥ 1 ng/μL; Purity: without genomic DNA contamination.|
*：The amount of DNA/ctDNA shown is the loading amount for library construction. We ask our clients to send us 20% more for quality control measurements.
- NovaSeq 6000, PE 150
Recommended Sequencing Depth
- To achieve the limit of detection (1.0% and 0.5% for SNV in tissue DNA and ctDNA, respectively), we recommend at least 1,400× and 2,000× effective average sequencing depth for these two types of samples, respectively.
- 12 calendar days from sample receipt to testing report delivery
Data Quality Guarantee
- We guarantee that ≥ 80% of bases have a sequencing quality score ≥ Q30, which exceeds Illumina’s official guarantee of ≥ 75%.
Bioinformatics and Result Interpretation
- Variant calling in NovoPM™ 2.0 is done using Novogene’s state-of-the-art bioinformatics pipeline and well-recognized public databases, including COSMIC, dbSNP, 1000 Genomes, ExAC, OncoKB, ClinVar, PharmGKB, SIFT and Polyphen2.
Interested in learning more about our NovoPM™2.0 comprehensive genomic profiling test? Click on the link below to fill out a short form and download our informational brochure.View brochure & validation reports
NovoPM™ 1.0 and NovoPM™ 2.0 were tested on four types of samples including class B FFPE, class C FFPE, cell line and white blood cell. Both assays detected all the priori mutations successfully, and there was no significant difference in their coverage of the target regions, but NovoPMTM 2.0 performed better on the fraction of clean data, sequencing uniformity and the probe capture ratio (Table 1).
|Sample||Coverage of target region (%)||Probe capture ratio (%)||Uniformity (%)||Data effective ratio (%)|
|White blood cell||99.91||99.96||64.41||69.24||92.38||99.77||43.42||50.29|
Validation with reference standards
- The accuracy of SNV and InDel detection was 99.5% and 93.7%, respectively, for variants with MAF ≥ 1%.
- The accuracy was 100% for 21 hot-spot SNVs/InDels detection in FFPE samples.
- The accuracy of ERBB2 CNV and ALK fusion detection was 100% when tumor cell content ≥ 20%.
- The accuracy of ROS1 and ALK fusion detection was 100% when tumor cell content ≥ 20%.
Reproducibility and specificity
- The detection of SNVs/InDels, CNVs and fusions was highly reproducible.
- When mixed with human DNA, Staphylococcus aureus DNA and Escherichia coli DNA had negligible coverage by the NovoPM™ 2.0 panel. Their presence did not affect the test results.
Validation with clinical FFPE reference samples
- NovoPM™ 2.0 was validated with 41 clinical FFPE reference samples, including 13 with no priori mutations, 21 with priori hot-spot SNVs/InDels, and 7 with priori hot-spot fusions. All the mutations were detected correctly.
Seeking potential therapeutic options, a 48-year-old female patient of non-small cell lung 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.
|Age||Cancer Type||Sample Type|
|48||Non small cell lung cancer (NSCLC)||Tissue Biopsy|
|Novel ROS1 fusion (SLC34A2-ROS1, chr6:117653720 – chr4:25678781)|
|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.
|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.|
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).