APPLICATIONS

Fixed Panels

Oncoscreen /Oncocompass IO

a. General Description - Our most comprehensive assay panel, screening for 520 clinically relevant genes as determined and recommended by the National Comprehensive Cancer Network. This gene panel screens for the majority of all actionable genetic mutations of interest within the oncology therapeutic development space.

Compatible with both tissue (Oncoscreen IO) and blood-based (Oncocompass IO) samples, the breadth of this diagnostic test allows for evaluation of complex biomarkers such as Tumor Mutational Burden (TMB), Microsatellite Instability (MSI), and Homologous Recombination Deficiency (HRD) as well as detection of specific rare mutations such as NTRK1-3 rearrangements, ALK fusions, and KRAS point mutations for treatment guidance of both targeted therapies and immunotherapies.

TMB (FDA approved June 2020) as a biomarker measures the total number of mutations found in DNA in cancer cells, and thus, gives predictive and prognostic value for determining cancer therapy. As this is our most comprehensive panel, Oncoscreen IO has applications for almost all cancer types. It can provide accurate genomic profiling for both clinical trial patient selection as well as therapy response monitoring.

Cancer types and genetic biomarkers

Pan Cancer
  • FGFR

Studies

case studies External links

Colorectal
  • Somatic pole exonuclease domain mutations
  • BRAF
  • MLH1
  • MSH2
  • MSH6
  • APC
  • PMS2
  • MUTYH
Prostate
  • EGFR T790M mutations (the most prevalent mechanism for acquiring EGFR TKI resistance)
  • c-Met Exon 14 Skipping mutations
  • MET amplifications
  • ERBB2 amplifications
  • ALK fusions
  • KRAS point mutations
  • PIKC3A
Breast
  • BRCA1/2
  • PARP1/2
  • ATM
  • PALB2
  • TP53
  • CHEK2
  • STK11
Lung
  • EGFR T790M mutations (the most prevalent mechanism for acquiring EGFR TKI resistance)
  • C-Met Exon 14 Skipping mutations
  • MET amplifications
  • ERBB2 amplifications
  • ALK fusions
  • KRAS point mutations
  • PIKC3A
Gallbladder Cancer
  • ALK fusion
  • KRAS
  • TP53
  • PTEN
  • PIK3CA
  • BRAF
  • APC
  • NRAS
  • IDH1
  • AKT1
  • CTNNB1
Liver
  • TP53
  • CTNNB1
  • AXIN1
  • RB1
  • FGF19
Melanoma
  • BRAF V600
  • GNAQ
  • GNA11
  • NRAS
  • KIT
  • BAP1
  • SF3B1
  • EIF1AX

List of genes

Oncoscreen/Oncocompass Target

General description- A more focused panel, Oncoscreen Target screens for an array of 168 clinically actionable predictive biomarkers. It has the capability to assess the complex biomarker MSI, as well as genetic mutations including those of EGFR, ATM, and MET, as well as genetic rearrangements including those of NTRK1-3, ROS1, and RET. It is available for diagnosis of both tissue (Oncoscreen Target) and blood-based (Oncocompass Target) samples. This panel has applications for a large variety of cancer types including melanoma, lung, breast, prostate, and liver cancer. It can provide comprehensive genomic profiling for clinical trial patient selection as well as therapy response monitoring, and is currently being used for biomarker detection for Tagrisso® (osimertinib) and Afatinib.

Cancer types

Lung
  • EGFR T790M mutations (the most prevalent mechanism for acquiring EGFR TKI resistance)
  • c-Met Exon 14 Skipping mutations
  • MET amplifications
  • ERBB2 amplifications
  • ALK fusions
  • KRAS point mutations
  • PIKC3A
Breast
  • BRCA1
  • BRCA2
  • PARP1
  • ATM
  • PALB2
  • TP53
  • CHEK2
  • STK11
Liver
  • TP53
  • CTNNB1
  • RB1
  • FGF19
Prostate
  • BRCA1
  • BRCA2
  • ATM
  • CHEK2
Melanoma
  • BRAF V600
  • NRAS
  • KIT

List of genes

Oncoscreen Focus

a. General Description -Our OncoScreen Focus panel is used primarily in Lung Cancer applications as a test to screen prospective patients for clinical trials, help guide therapy selection, and also for studies around the world for lung cancer researchers. It screens for 13 of the most actionable genes highly involved in lung cancers including EGFR, MET, and ROS1. It is available for diagnosis for tissue-based samples.

Cancer types

Lung
  • EGFR T790M mutations (the most prevalent mechanism for acquiring EGFR TKI resistance)
  • c-Met Exon 14 Skipping mutations
  • MET amplifications
  • ERBB2 amplifications
  • ALK fusions
  • KRAS point mutations
  • PIKC3A
List of genes
  • EGFR
  • MET
  • ERBB2
  • HRAS
  • KIT
  • ALK
  • BRAF
  • KRAS
  • PDGFRA
  • ROS1
  • RET
  • NRAS
  • PIK3CA

HRD

OncoscreenParpmatch- Our OncoscreenParpmatch is used primarily for indications involving deficiencies in the Homologous Recombination Repair (HRR) pathway. It covers 72 genes associated with the HRR pathway, including BRCA1/2, PALB2, RAD, and ERCC2-4. Specifically designed for PARP inhibitors, this panel is available for the diagnosis of both tissue and blood-based samples. As it focuses on genes relating to the HRR pathway, its applications extend primarily to ovarian,lung, breast, and prostate cancer. The FDA approved the first PARP inhibitor, Olaparib in 2014 for patients with germline BRCA1/2 mutations who have pretreated ovarian cancer, and the agency has since broadened indications for PARP inhibitors in terms of disease settings. Assays that measure HRD status caused by different mechanisms are now the central focus. In May 2020, the FDA also approved Olaparib for patients with metastatic castration-resistant prostate cancer with somatic or germline HRR mutations. Currently, it is being used for biomarker detection in the clinical trials of LYNPARZA® (olaparib), L-MOCA, and Profound.

In addition, Burning Rock has licensed the exclusive rights to Myriad’s MyChoice+ assay for usage in China. Myriad’s MyChoice+ is an assay analyzing loss of heterozygosity, telomeric allelic imbalance, and large scale state transitions to produce a comprehensive assessment of one’s HRD status, otherwise known as HRD score.

The HRD panel comes in 2 versions, The 72 gene or comprehensive 520 gene panel. The benefit with the larger panel is additional complex biomarkers such as TMB and MSI, in addition to other biomarkers. Our 520 panel shows outstanding performance in AZ’s L-MOCA study.

9

1. BRCA1

2. BRCA2

3. ATM

4. BRIP1

9

5. BARD1

6. CDK12

7. CHEK1

8. CHEK2

9

9. FANCL

10. PALB2

11. PPP2R2A

12. RAD51B

9

13. RAD51C

14. RAD51

15. RAD54L

Ovarian, breast, prostate, lung, colorectal, liver

MRD Panel-

combination of tissue testing (patient mutation profiling) with ultra-sensitive ctDNA assay (based on baseline and tissue testing), can be used for minimum residual disease monitoring. The ctDNA assay provides 0.2%LoD and validated performance and high concordance with tissue results.

MRD assay can detect following mutations with input of 20ng DNA, SNV, Indels of EGFR/ALK/KRAS/NRAS/BRAF/ERBB2/MET/PIK3CA

ALK/ROS 1/ NTRK1/RET arrangements
Copy number variation in MET and ERBB2

MSI-H in sample
We combine CtDNA assay with 520 Oncoscreen IO panel to identify mutations of interest for tracking.

Hematological malignancies, lung, solid tumors
Studies -
1. colorectal liver metastasis ctDNA

Early Detection-ELSA Seq methylation based multi-cancer early detection assay
Lung, colorectal, liver, ovarian, pancreatic, esophageal, gastric, cholangio, head and neck
3->6->9 cancer
~80% sensitivity @ 98% specificity
Performance comparable to Grail’s assay (outperformed on lung and colorectal)
Can be used to supplement at risk screening (For example: colonoscopy)
Improve early detection and improve patient outcomes
*Tom
Import info and figures from ESMO article.

RNA Seq

Our RNA sequencing assay has the potential to provide a more comprehensive understanding of a patient’s genetic landscape by identifying gene fusions, assessing post-transcriptional gene expression, and measuring genetic mutations. RNA Seq has applications for measuring expression of actionable oncogenic fusions such as ALK fusions and BCR-ABL fusions, verifying and monitoring insertion of CAR-T cells for CAR-T therapy, as well as accompanying epigenetic assays.