Somatic cancers are caused by mutations that occur in the DNA after conception. Somatic mutations can occur in any of the cells of the body except the germ cells (sperm and egg) and therefore are not passed on to children. They occur in the genomes of all dividing cells, both normal and neoplastic. They may occur as a result of misincorporation during DNA replication or through exposure to exogenous or endogenous mutagens. These alterations can (but do not always) cause cancer or other diseases.
Lung Cancer
Breast Cancer
Colorectal Cancer
Single Gene Test
Other Cancers
Lung Cancer
There are two main classifications of lung cancer: small cell lung cancer and non-small cell lung cancer (NSCLC). Both types of cancers are treated differently. NSCLC begins in the epithelial cells. Adenocarcinoma starts in cells that produce mucus. Squamous cell carcinoma begins in the cells that line the airways. Large cell carcinoma begins in cells other than the two types described above.
There are multiple genes that may be altered, called mutations, in a lung tumor, that drive the cancer. These mutations are not inherited or passed down to children; instead they are restricted only to the patient. Mutations that are known to drive lung cancer may occur in one or more of several genes, including EGFR, ALK, KRAS, BRAF, HER2, ROS1, and RET. Testing the tumor for all these genes can be done by OncoCEPT-Solid NGS assay.
Agent | Target(s) | FDA-approved Indication(s) | Agent |
Afatinib (Gilotrif) | EGFR (HER1/ERBB1), HER2 (ERBB2/neu) | Non-small cell lung cancer (with EGFR exon 19 deletions or exon 21 substitution (L858R) mutations) | Afatinib (Gilotrif) |
Alectinib (Alecensa) | ALK | Non-small cell lung cancer (with ALK fusion) | Alectinib (Alecensa) |
Atezolizumab (Tecentriq) | PD-L1 | Urothelial carcinoma Non-small cell lung cancer | Atezolizumab (Tecentriq) |
Brigatinib (Alunbrig) | ALK | Non-small cell lung cancer (ALK+) | Brigatinib (Alunbrig) |
Certinib (Zykadia) | ALK | Non-small cell lung cancer (with ALK fusion) | Ceritinib (Zykadia) |
Crizotinib (Xalkori) | ALK, MET, ROS1 | Non-small cell lung cancer (with ALK fusion or ROS1 gene alteration) | Crizotinib (Xalkori) |
Dabrafenib (Tafinlar) | BRAF | Non-small cell lung cancer (with BRAF V600E Mutations) | Dabrafenib (Tafinlar) |
Erlotinib (Tarceva) | EGFR (HER1/ERBB1) | Non-small cell lung cancer (with EGFR exon 19 deletions or exon 21 substitution (L858R) mutation) | Erlotinib (Tarceva) |
Gefitinib (Iressa) | EGFR (HER1/ERBB1) | Non-small cell lung cancer (with EGFR exon 19 deletions or Geftinib (Iressa) exon 21 substitution (L858R) mutations) | Geftinib (Iressa) |
Necitumumab | EGFR (HER1/ERBB1) | Squamous non-small cell lung cancer | Necitumumab (Portrazza) |
Osimertinib (Tagrisso) | EGFR | Non-small cell lung cancer (with EGFR T790M mutation) | Osimertinib (Tagrisso) |
Trametinib (Mekinist) | MEK | Non-small cell lung cancer (with BRAF V600E mutation) | Trametinib (Mekinist) |
Tests Offered
2. PDL-1
Immunotherapy companion diagnostic FDA approved Biomarker-PDL1 (22C3 – DAKO) by IHC
Our body’s immune system detects Infected cells and tumour cells and eliminates them with the aid of cytotoxic T lymphocytes. Normal cells differentiate themselves from the tumor cells by expressing a protein signal called PD-L1 (programmed death ligand 1)to limit harm to the surrounding tissue. This PD-L1 signal is a stop sign meant to prevent cytotoxic T cells from destroying normal cells. T cells use a receptor called PD-1 (programmed death receptor 1)to identify the PD-L1 signal. Some tumours can also express the PD-L1 signal in order to deceive the immune system and avoid being detected. Anti-PD-1 therapy works by preventing the interaction between PD-1 and PD-L1 ontumour cells. Patient response from anti-PD-1 therapy (immunotherapy) is associated with PD-L1 expression. Different clones of PDL1 are validated against different targeted immunotherapies and hence a specific PDL1 clone has to be requested for IHC testing, based on targeted immunotherapeutic drugs.eg. PDL1 22C3 for Pembrolizumab.
3. Alk by IHC
ALK (D5F3), companion diagnostic, Ventana- FDA approved molecular biomarker test by IHC
Screening for anaplastic lymphoma kinase (ALK) rearrangements is a very important process in treatment decision making for advanced non-small-cell lung cancer (NSCLC). This particular clone has high sensitivity and specificity than other detection methods. The clone D5F3 recognizes the carboxyl terminus of human ALK protein.
Breast Cancer
Breast cancer can be invasive or noninvasive. Invasive breast cancer spreads into surrounding tissues. Non-invasive breast cancer does not go beyond the milk ducts or lobules in the breast. Most breast cancers start in the ducts or lobes and are called ductal carcinoma or lobular carcinoma respectively. Breast cancers can also be divided into three large subtypes based on the biomarkers they express. These are Hormone receptor-positive, Her2 positive and triple negative breast cancer.
Hormone receptor-positive: Breast cancers expressing estrogen receptors (ER) and/or progesterone receptors (PR) are called “hormone receptor-positive.About 60 to 75% of breast cancers express estrogen and/or progesterone receptors.
Her2 positive: About 1% to 20% of breast cancers depend on the gene called human epidermal growth factor receptor 2 (HER2) to grow.HER2-positive breast cancers grow more quickly. They can also be either hormone receptor-positive or hormone receptor-negative.
Triple negative: Tumor that does not express ER, PR, or HER2 is called triple-negative.Triple-negative cancer is also more common in women withmutations in the BRCA1 or BRCA2 genes. Guidelines require triple-negative breast cancer patients younger than 60 yrs to be tested for BRCA gene mutations.
Below is the list of genes that have clinical significance in management of breast cancer patients. These genes are analyzed using OncoCEPT-Solid NGS assay.
Tests Offered
2. ER – PR – Her2 – (NBC)
OncoCEPT Solid Comprehensive panel
Genes analyzed: BRCA1, BRCA2, PALBL, RAD51 &otherBRCAness Genes
4. PDL1
Immunotherapy companion diagnostic FDA approved Biomarker-PDL1 (22C3 – DAKO) by IHC
Our body’s immune system detects Infected cells and tumour cells and eliminated by cytotoxic T lymphocytes. Normal cells differentiate themselves by expressing a protein signal called PD-L1 to limit harm to surrounding tissue (programmed death ligand 1). This PD-L1 signal is a stop sign meant to prevent cytotoxic T cells from destroying normal cells. T cells use a receptor called PD-1 to identify the PD-L1 signal (programmed death receptor 1). Some tumours can also express the PD-L1 signal in order to deceive the immune system and avoid being detected. Anti-PD-1 therapy works by preventing the interaction between PD-1 and PD-L1 of tumour cells. Patient response from anti-PD-1 therapy (immunotherapy) is associated with PD-L1 expression. Different clones of PDL1 are validated against different targeted immunotherapies and hence specific PDL1 clone is to be requested for IHC test based on Targeted immunotherapeutic drugs for eg. PDL1 22C3 for Pembrolizumab.
Colorectal Cancer
Colorectal cancer begins in healthy cells lining the colon or rectum.ltmay grow into a large mass called a tumor. A tumor can be cancerous or benign. A cancerous tumor is Metastatic when it goes to other parts of the body. These changes usually take years to develop. Both genetic and environmental factors can cause the above changes.
Multiple techniques are used to diagnose colorectal cancers. Molecular tests are performed to identify specific genes, proteins, and other factors which drive the tumor. Metastatic or recurrent colorectal cancer is preferred for molecular testing.
Results of these tests will help decide whether the treatment options include a type of treatment called targeted therapy.Below is the list of genes that have clinical significance in management of colorectal cancer patients. These genes are analyzed using OncoCEPT- Solid NGS assay.
Agent | Target(s) | FDA-approved Indication(s) | Agent |
Cetuximab (Erbitux) | EGFR (HER1/ERBB1) | Colorectal cancer(KRAS, NRAS, BRAF wild type) | Cetuximab (Erbitux) |
Nivolumab (Opdivo) | PD-1 | Colorectal cancer (MSI-H) | Nivolumab (Opdivo) |
Panitumumab (Vectibix) | EGFR (HER1/ERBB1) | Colorectal cancer (KRAS, NRAS, BRAF wild type) | Panitumumab (Vectibix) |
Pembrolizumab (Keytruda) | PD-1 | Colorectal cancer (MSI-H) | Pembrolizumab (Keytruda) |
Tests Offered
1. Colo-comprehensive
Genes analyzed :NRAS,KRAS, BRAF, Her2, PIK3CA, NRTK 1-3.
2. PDL1
Immunotherapy companion diagnostic FDA approved Biomarker-PDL1 (22C3 – DAKO) by IHC
3. MSI by IHC/PCR
Defects in the mismatch repair (MMR) pathway define a well-defined subtype of colorectal cancer (CRC). The presence of MMR impacts the prognosis and benefit of adjuvant treatment in low stage colorectal cancers. MLH1, MSH2, MSH6, and PMS2 protein expression (as determined by IHC) as well as microsatellite instability analysis (MSI) as determined by PCR are well-established methods for detecting Lynch syndrome (LS), and such testing is advised for all new colorectal cancer diagnosis.
MMR IHC and molecular MSI testing are also used as companion diagnostic tests in the selection of specific immuno-oncology therapy in a variety of solid malignancies.
Single Gene Test
Testing of Genes by NGS, EGFR, ALK, ROS1, BRAF, KRAS, NRAS, PIK3CA, ERBB2(Her2)
Other Cancers
OncoCEPT Solid
(CEPT: Comprehensive Evaluation for Personalized Treatment)
Cancer leads to formation of tumor. However, obtaining a tissue sample could be challenging. This leads to limiting amounts of tumor tissue being collected which is expected to be used for multiple and different types of investigations.
Often the investigations can’t be done due to the lack of sample. This test is noninvasive and cost-effective alternative to traditional biopsy samples, especially in lung and breast cancers.
Cancer also evolves Over time. Cancer may relapse after treatment of primary tumor. This relapse occurs due to change its genome. OncoCEPT Liquid can give snapshots of evolving cancer genome when the test is performed at period intervals. This information can help the oncologist pre-empt and modify treatment regimen.
Prominent technical features of OncoCEPT Liquid:
- Detection of somatic mutations in plasma, down to a level of o.1% in genes relevant to solid tumors.
- The assay allows concurrent analysis of DNA and RNA.
- Simultaneously detect multiple types of variants, including hotspots, single nucleotide variants (SNVs), indels, CNVs, and gene fusions, in a single workflow.
- Uses formalin-fixed, paraffin embedded (FFPE) tissues, fine-needle aspirates, fresh tissues as starting sample.
OncoCEPT Solid Comprehensive:
(CEPT: Comprehensive Evaluation for Personalized Treatment)
Tumorigenesis in humans is a multistep process and these steps reflect genetic alterations that drive the progressive transformation of normal human cells into highly malignant derivatives. Cancer treatment decisions are increasingly made on the basis of genomic information contained in the genes. OncoCEPT Solid Comprehensive test detects various multiple relevant biomarkers in a single next-generation sequencing (NGS) test by focusing on precision oncology.
OncocEPT Solid identifies these driver mutations and helps in identifying targeted therapies, prognosis and clinical trials applicable to the patient.
Prominent technical features of OncoCEPT Solid Comprehensive are:
- Enables the detection of variants in 161 key solid tumor genes. These genes are well characterized in the published literature and associated with oncology drugs that are FDA approved, part of NCCN (National Comprehensive Cancer Network) guidelines, or in clinical trials.
- They allow detection of single nucleotide variants (SNVs), copy number variations (CNVs), gene fusions, and Indels in a single workflow.
- Uses formalin fixed, paraffin embedded – FFPE tissuesand fresh tissues as starting sample.
- This test is well characterized with molecular standards and controls necessary for validation.
OncoCEPT Liquid:
(CEPT: Comprehensive Evaluation for Personalized Treatment)
Cancer leads to formation of a tumor. However, obtaining a tissue sample could be challenging. This leads to limited amount of tumor tissue for evaluation, which is expected to be used for multiple and different types of investigations.Often the investigations can’t be done due tolack of tissue sample. This NGS based test is noninvasive and a cost-effective alternative to traditional biopsy samples, especially in lung and breast cancers.
Cancer also evolves over time. Cancer may relapse after treatment of the primary tumor. This relapse occurs due to changes in its genome. OncoCEPT Liquid can give snapshots of evolving cancer genome, when the test is performed at periodic intervals. This information can help the oncologist pre-empt and modify treatment regimen.
Prominent technical features of OncoCEPT Liquid:
- Detection of somatic mutations in plasma, down to a level of 0.1% in genes relevant to solid tumors.
- The assay allows concurrent analysis of DNA and RNA.
- Simultaneously detects multiple variants, including hotspots, single nucleotide variants (SNVs), indels, CNVs, and gene fusions, in a single workflow.
- 150 hotspots in 11 genes focused on solid tumors, are analyzed.
- Sample type: whole blood.
Five microsatellite regions are analyzed.
In normal cells, the DNA mismatch repair (MMR) system recognizes and repairs genetic mismatches generated during DNA replication. A deficient MMR (dMMR) system results in the persistence of DNA mismatches in microsatellites that may then be incorporated into the genetic code as mutations which is sporadic in nature. Tumors that are deficient of DNA mismatch repair (MMR) system are designated as MSI-high and the once with intact MMR are called MSI-stable. Pembrolizumab is indicated for the treatment of adult and pediatric patients with unresectable or metastatic microsatellite instability-high (MSI-H). These tumors are (1) Solid tumors that have progressed following prior treatment and who have no satisfactony alternative treatment options, or (2) colorectal cancer that has progressed following treatment with fluoropyrimidine, oxaliplatin, and irinotecan.
Prominent technical features of MSl test:
- Five microsatellite regions are analyzed.