MOLECULAR ONCOLOGY
Cancer is a disease caused by uncontrolled divison and propagation to nearby/far tissues of cells with damaged or mutated DNA. These cells can’t execute apoptosis (planned death of cells) process because of DNA damage. The cells which divide and increase in number in an uncontrolled way become masses and form the tissue called tumor.
Cancer originates from DNA damage or mutation that is why it is considered as a genetic disease. But if these masses (formed of uncontrollably increasing cells) do not spread to other tissues or organs, the mass is called a benign tumor. But if it is spread into nearby tissues or into different area/s of the body, this is called malignant tumor; in other words cancer.
There are 2 main factors causing cancer; hereditary factors and environmental factors. A genetic change is a necessary component for cancer and these genetic changes usually caused by environmental factors. As it is mentioned in the web-site of Genomic Tumor Council, in limited number of cases (approximately 10%), cancer may be inherited from the mother or father.
Scannings, definitive diagnosis tests, tumor profiling tests, liquid biopsy, hereditary cancer tests are widely used to diagnose cancer.
Advanced improvements devoted to a more acurate cancer understanding at molecular levels are recorded. Information obtained from these improvements are converted into more reliable diagnosis and prognostic biomarkers and several brand-new treatment tools are developped in the last 10 years.
Last 20 years, our knowledge about cancer’s pathogenesis has steadily improved and it has been accepted that tumor formation is a multi-step, complex process that is provided by gains of a chapter of characteristics that underlies the malignities of the cells. Most of these characteristics that are explained by genetic or epigenetic incidents can happen due to subject cells gaining, amplifying or extreme expression of oncogenous and/or function loss, deletion or silence of oncosuppressor genes.
Nowadays Tissue Biopsy and Liquid Biopsy methods are used to obtain tumor for definition of genetic changes somatically: for hereditary cancer types EDTA-Blood Sample is obtained.
In the treatment process of cancer, alongside surgical intervention, chemotherapy and radiotherapy, new generation cures namely: “target-driven treatments” (can be determined by genetic and genomic tests) and “imminotheraphy” (aims to strengthen the patient’s immune system) are used.
In the light of current scientific improvements, precision medicine is becoming more important. Tumor Councils (consisting of MDs from different diciplines) assemble to determine the method of cancer treatment in rare and progressed cases.
Precision medicine in cancer aims to develop treatments not based to the type of cancer but the individual’s genetic factors and exposure to environmental factors. This way, personal treatment principle is adopted and side effects of the process can be reduced.
Tissue Biopsy
Cancer’s mutation data is obtained through biopsies of tumor tissues with in-vasive methods. Biopsy needles are standard medical equipments used to take out biological tissues to diagnose a specific abnormality like masses with cancer.
Molecular genetic methods and FISH are used for genetic analysis of the samples obtained through tissue biopsy.
NESİLLER GENETİK TISSUE BIOPSY TESTS
| TEST NAME | ANALYSED AREA | RESULT RETURN |
|---|---|---|
| Nesiller Tissue - 15 genes | AKT1, BRAF, EGFR, ERBB2, FOXL2, GNA11, GNAQ, KIT, KRAS, MET, NRAS, PDGFRA, PIK3CA, RET, TP53 | 20 days |
| Nesiller Tissue-15 genes+Cyto-histological | AKT1, BRAF, EGFR, ERBB2, FOXL2, GNA11, GNAQ, KIT, KRAS, MET, NRAS, PDGFRA, PIK3CA, RET, TP53 | 20 days |
| Nesiller Tissue - 23 genes | AKT1, ALK, AR, BRAF, CTNNB, EGFR, ERBB2, ESR1, FOXL2, GNA11, GNAQ, KIT, KRAS, MEK1 (MAP2K1), MET, NRAS, PDGFRA, PIK3CA, PTEN, RET, ROS1, SMAD4, TP53 | 20 days |
| Nesiller Tissue-23 genes +Cyto-histological | AKT1, ALK, AR, BRAF, CTNNB, EGFR, ERBB2, ESR1, FOXL2, GNA11, GNAQ, KIT, KRAS, MEK1 (MAP2K1), MET, NRAS, PDGFRA, PIK3CA, PTEN, RET, ROS1, SMAD4, TP53 | 20 days |
| Nesiller Tissue - 50 genes | AKT1, ALK, APC, AR, ATM, BRAF, CDH1, CDKN2A, CTNNB1, EGFR, ERBB2, ERBB3, ERBB4, ESR1, EZH2, FBXW7, FGFR1, FGFR2, FGFR3, FOXL2, GNA11, GNAQ, GNAS, HNF1A,HRAS, IDH1, KDR, KIT, KRAS, MEK1 (MAP2K1), MET, MLH1, MPL, NOTCH1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RB1, RET, ROS1, SF3B1, SMAD4, SMARCB1, SMO, SRC, STK11, TP53, VHL | 20 days |
| Nesiller Tissue-50 genes +Cyto-histological | AKT1, ALK, APC, AR, ATM, BRAF, CDH1, CDKN2A, CTNNB1, EGFR, ERBB2, ERBB3, ERBB4, ESR1, EZH2, FBXW7, FGFR1, FGFR2, FGFR3, FOXL2, GNA11, GNAQ, GNAS, HNF1A,HRAS, IDH1, KDR, KIT, KRAS, MEK1 (MAP2K1), MET, MLH1, MPL, NOTCH1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RB1, RET, ROS1, SF3B1, SMAD4, SMARCB1, SMO, SRC, STK11, TP53, VHL | 20 days |
| IMMUNOTHERAPY TEST | PD-L1 | 10 days |
| IMMUNOTHERAPY TEST | MSI | 10 days |
| COBAS TISSUE | BRAF DNA analysis – exon 11 ve 15 | 10 days |
| COBAS TISSUE | BRAF DNA analysis – exon 11 ve 15- Rapid diagnosis in 24 hours | 1 day |
| COBAS TISSUE | EGFR DNA analysis - exon 18, 19, 20, 21 | 10 days |
| COBAS TISSUE | EGFR DNA analysis - exon 18, 19, 20, 21- Rapid diagnosis in 24 hours | 1 day |
| COBAS TISSUE | KRAS mutation analysis - codon 12&13,61 | 10 days |
| COBAS TISSUE | KRAS mutation analysis - codon 12&13,61- Rapid diagnosis in 24 hours | 1 day |
| COBAS TISSUE | NRAS mutation analysis - codon 12&13, 61, 146 | 10 days |
| COBAS TISSUE | NRAS mutation analysis - codon 12&13, 61, 146- Rapid diagnosis in 24 hours | 1 day |
| NESİLLER LUNG CANCER LARGE PANEL | BRAF DNA analysis – exon 11 ve 15 EGFR DNA analysis – exon 18, 19, 20, 21 KRAS mutation analysis - codon 12&13,61 NRAS mutation analysis - codon 12&13, 61, 146 ALK ROS-1 PD-L1 MSI | 10 days |
| NESİLLER LUNG CANCER LARGE PANEL –RAPID DIAGNOSIS-24 hours | BRAF DNA analysis – exon 11 ve 15 EGFR DNA analysis - exon 18, 19, 20, 21 KRAS mutation analysis - codon 12&13,61 NRAS mutation analysis - codon 12&13, 61, 146 ALK ROS-1 PD-L1 MSI | 1 day |
| NESİLLER LUNG CANCER SMALL PANEL | EGFR DNA analysis - exon 18, 19, 20, 21 ALK ROS-1 PD-L1 | 10 days |
| NESİLLER LUNG CANCER SMALL PANEL - RAPID DIAGNOSIS-24 hours | EGFR DNA analysis - exon 18, 19, 20, 21 ALK ROS-1 PD-L1 | 1 day |
| NESİLLER TISSUE FISH | EML4/ALK | 5 days |
| NESİLLER TISSUE FISH | 1p36&19q13 | |
| NESİLLER TISSUE FISH | 15q26 (IGF1R) | |
| NESİLLER TISSUE FISH | 20q13 (AURKA) | |
| NESİLLER TISSUE FISH | 8q24 (C-myc) [t(2;8), t(8;22), t(8;14)] | |
| NESİLLER TISSUE FISH | C-MET (7q31.2) | |
| NESİLLER TISSUE FISH | EGFR (7p12) | |
| NESİLLER TISSUE FISH | Her2/neu (17q11.2-12) | |
| NESİLLER TISSUE FISH | N-MYC (2p24.3) | |
| NESİLLER TISSUE FISH | t(?;22q12) (EWSR1) t(11;22), t(21;22), t(7;22), t(12;22) | |
| NESİLLER TISSUE FISH | Top2A (17q21-22) | |
| NESİLLER TISSUE FISH | ROS1 (6q22.1) |
Liquid Biopsy
Liquid biopsy is a method used to detect somatic mutations in circulating cell-free tumor DNA. Molecular genetic methods are used for genetic analysis in samples obtained by liquid biopsy. Cell-free DNA which is isolated from patient’s blood is analysed, defined and these changes are applied to treatments and clinical trials.
Liquid Biopsy Practices
Liquid biopsy tests may be used for diagnosis and scanning of:
1) The patients who are diagnosed with cancer;
a) Patients undergoing cancer treatment,
- Medicine determination according to tumor profile,
- Observing the success of the treatment and resistence to it,
- Observing the course of the disease and spread of tumor,
- Clinical trial matching
b) The patients who have completed cancer treatment process,
- Residual disease follow-up,
- Double sickening follow-up,
- The opportunity to consider new treatment options for doctors in case patients’ bodies resist to applied treatments.
2) Scanning targeted Liquid Biopsy is used for:
a) The patients who are suspected of having cancer
- The determination of somatic mutations in genes which may cause cancer
- The verification of disease risk.
b) The individuals in high-risk group (no diagnosis for cancer)
- the determination of somatic mutations in genes which may cause cancer
- Early diagnosis of disease
THE BELOW LISTED PEOPLE ARE WITH HIGH RISKS:
- Cancer history in family,
- Long-time exposure to UV and radiation
- Smoking,
- Subjected to hormone use in the past,
- Exposure to carcinogens.
NESİLLER GENETİK LIQUID BIOPSY TESTS
| TEST NAME | ANALYSED AREA | RESULT RETURN |
|---|---|---|
| NESİLLER LIQUIDTM Monitor-15 Genes | AKT1, BRAF, EGFR, ERBB2, FOXL2, GNA11, GNAQ, KIT, KRAS, MET, NRAS, PDGFRA, PIK3CA, RET, TP53 | 20 days |
| NESİLLER LIQUIDTM Monitor-23 Genes | AKT1, ALK, AR, BRAF, CTNNB, EGFR, ERBB2, ESR1, FOXL2, GNA11, GNAQ, KIT, KRAS, MEK1 (MAP2K1), MET, NRAS, PDGFRA, PIK3CA, PTEN, RET, ROS1, SMAD4, TP53 | 20 days |
| NESİLLER LIQUIDTM Monitor-50 Genes | AKT1, ALK, APC, AR, ATM, BRAF, CDH1, CDKN2A, CTNNB1, EGFR, ERBB2, ERBB3, ERBB4, ESR1, EZH2, FBXW7, FGFR1, FGFR2, FGFR3, FOXL2, GNA11, GNAQ, GNAS, HNF1A,HRAS, IDH1, KDR, KIT, KRAS, MEK1 (MAP2K1), MET, MLH1, MPL, NOTCH1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RB1, RET, ROS1, SF3B1, SMAD4, SMARCB1, SMO, SRC, STK11, TP53, VHL | 20 days |
| NESİLLER LIQUIDTM Monitor-BREAST | AKT1, EGFR, ERBB2, ERBB3, ESR1, FBXW7, KRAS, PIK3CA, SF3B1, TP53 | 20 days |
| NESİLLER LIQUIDTM Monitor-LUNG | ALK, BRAF, EGFR, ERBB2, KRAS, MAP2K1, MET, NRAS, PIK3CA, ROS1, TP53 | 20 days |
| NESİLLER LIQUIDTM Monitor-COLON | AKT1, APC, BRAF, CTNNB1, EGFR, ERBB2, FBXW7, GNAS, KRAS, MAP2K1, NRAS, PIK3CA, SMAD4, TP53 | 20 days |
| NESİLLER LIQUIDTM Scan-15 Genes | AKT1, BRAF, EGFR, ERBB2, FOXL2, GNA11, GNAQ, KIT, KRAS, MET, NRAS, PDGFRA, PIK3CA, RET, TP53 | 20 days |
| NESİLLER LIQUIDTM Scan-23 Genes | AKT1, ALK, AR, BRAF, CTNNB, EGFR, ERBB2, ESR1, FOXL2, GNA11, GNAQ, KIT, KRAS, MEK1 (MAP2K1), MET, NRAS, PDGFRA, PIK3CA, PTEN, RET, ROS1, SMAD4, TP53 | 20 days |
| NESİLLER LIQUIDTM Scan-50 Genes | AKT1, ALK, APC, AR, ATM, BRAF, CDH1, CDKN2A, CTNNB1, EGFR, ERBB2, ERBB3, ERBB4, ESR1, EZH2, FBXW7, FGFR1, FGFR2, FGFR3, FOXL2, GNA11, GNAQ, GNAS, HNF1A,HRAS, IDH1, KDR, KIT, KRAS, MEK1 (MAP2K1), MET, MLH1, MPL, NOTCH1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RB1, RET, ROS1, SF3B1, SMAD4, SMARCB1, SMO, SRC, STK11, TP53, VHL | 20 days |
| COBAS LIQUID | BRAF DNA analysis – exon 11 ve 15 | 10 days |
| COBAS LIQUID | BRAF DNA analysis – exon 11 ve 15- Rapid diagnosis in 24 hours | 1 day |
| COBAS LIQUID | EGFR DNA analysis – exon 18, 19, 20, 21 | 10 days |
| COBAS LIQUID | EGFR DNA analysis – exon 18, 19, 20, 21- Rapid diagnosis in 24 hours | 1 day |
| COBAS LIQUID | KRAS mutation analysis - codon 12&13,61 | 10 days |
| COBAS LIQUID | KRAS mutation analysis - codon 12&13,61- Rapid diagnosis in 24 hours | 1 day |
| COBAS LIQUID | NRAS mutation analysis - codon 12&13, 61, 146 | 10 days |
| COBAS LIQUID | NRAS mutation analysis - codon 12&13, 61, 146- Rapid diagnosis in 24 hours | 1 day |
| NESİLLER LUNG CANCER LARGE-PANEL LIQUID | BRAF DNA analysis – exon 11 and 15 EGFR DNA analysis – exon 18, 19, 20, 21 KRAS mutation analysis - codon 12&13,61 NRAS mutation analysis - codon 12&13, 61, 146 ALK ROS-1 PD-L1 MSI | 10 days |
| NESİLLER LUNG CANCER LARGE-PANEL LIQUID –RAPID DIAGNOSIS-24 Hours | BRAF DNA analysis – exon 11 and 15 EGFR DNA analysis – exon 18, 19, 20, 21 KRAS mutation analysis - codon 12&13,61 NRAS mutation analysis - codon 12&13, 61, 146 ALK ROS-1 PD-L1 MSI | 1 day |
| NESİLLER LUNG CANCER SMALL-PANEL LIQUID | EGFR DNA analysis – exon 18, 19, 20, 21 ALK ROS-1 PD-L1 | 10 days |
| NESİLLER LUNG CANCER SMALL-PANEL LIQUID –RAPID DIAGNOSIS-24 Hours | EGFR DNA analysis – exon 18, 19, 20, 21 ALK ROS-1 PD-L1 | 1 day |
Hereditary Cancer Genetics
Cases of thyroid cancer, breast cancer and colon cancer in the family history are instances of hereditary cancer types. Latest developments contribute both to diagnosis of the cancer and personalization of treatments.
In our laboratory we regularly perform molecular and FISH analysis.
NESİLLER GENETİK HEREDITARY CANCER TESTS
| TEST NAME | ANALYSED AREA | RESULT RETURN |
|---|---|---|
| Nesiller RISK - Breast | ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MRE11A, MUTYH, NBN, NF1, PALB2, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53 | 20 days |
| Nesiller RISK - Ovarian | BRCA1, BRCA2, BRIP1, EPCAM, MLH1, MSH2, MSH6, PALB2, PMS2, PTEN, RAD51C, RAD51D, STK11, TP53 | 20 days |
| Nesiller RISK - Colon | APC, BMPR1A, CDH1, CHEK2, EPCAM, GREM1, MLH1, MSH2, MSH6, MUTYH, PMS2, POLD1, PTEN, SMAD4, STK11, TP53 | 20 days |
| Nesiller RISK - Cerebral | AIP, ALK, APC, CDKN1B, CDKN2A, DICER1, MEN1, MLH1, MSH2, MSH6, NBN, NF1, NF2, PHOX2B, PMS2, PRKAR1A, PTCH1, PTEN, SMARCA4, SMARCB1, SMARCE1, SUFU, TP53, TSC1, TSC2, VHL | 20 days |
| Nesiller RISK - Prostate | ATM, BRCA1, BRCA2, CHEK2, EPCAM, HOXB13, MLH1, MSH2, MSH6, NBN, PALB2, PMS2, RAD51D, TP53 | 20 days |
| Nesiller RISK - Melanoma | BAP1, BRCA2, CDK4, CDKN2A, MITF, PTEN, RB1, TP53 | 20 days |
| Nesiller RISK - Renal | BAP1, EPCAM, FH, FLCN, MET, MITF, MLH1, MSH2, MSH6, PMS2, PTEN, SDHA, SDHB, SDHC, SDHD, TP53, TSC1, TSC2, VHL. | 20 days |
| Nesiller RISK - Gastric | APC, BMPR1A, CDH1, EPCAM, MLH1, MSH2, MSH6, PMS2, STK11, SMAD4, TP53 | 20 days |
| Nesiller RISK -Feocromocitoma | FH, MAX, MEN1, NF1, RET, SDHA, SDHAF2, SDHB, SDHC, SDHD, TMEM127, VHL. | 20 days |
| Nesiller RISK - Pancreas | APC, ATM, BMPR1A, BRCA1, BRCA2, CDKN2A, EPCAM, MLH1, MSH2, MSH6, PALB2, PMS2, STK11, TP53 | 20 days |
| Nesiller Oncoscreening Complete | AIP, ALK, APC, ATM, BAP1, BARD1, BMPR1A, BRCA1, BRCA2, BRIP1, BMPR1A, BUB1B, CDC73, CDH1, CDK4, CDKN1B, CDKN2A, CEBPA, CHEK2, DICER1, EGFR, EPCAM, EXT1, EXT2, FH, FLCN, GALNT12, GATA2, GPC3, GREM1, HNF1A, HOXB13, HRAS, KIT, MAX, MEN1, MET, MITF, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, NF1, NF2, NSD1, PALB2, PHOX2B, PMS1, PMS2, POLD1, PRF1, PRKAR1A, PTCH1, PTEN, RAD50, RAD51C, RAF51D, RB1, RET, RHBDF2, RUNX1, SBDS, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, STK11, SUFU, TMEM127, TP53, TSC1, TSC2, VHL, WT1 | 20 days |
| NESİLLER RISK | APC Gene Mutation Analysis (Familial Adenomatous Polyposis - FAP) | 20 days |
| NESİLLER RISK | BRCA1 Gene Sequence Analysis (predisposition, breast neoplasm / over) | 20 days |
| NESİLLER RISK | BRCA2 Gene Sequence Analysis (predisposition, breast neoplasm / over) | 20 days |
| NESİLLER RISK | BRCA1 + BRCA2 Sequence Analysis (breast neoplasm / over) | 20 days |
| NESİLLER RISK | BRCA1 analysis with MLPA | 20 days |
| NESİLLER RISK | BRCA2 analysis with MLPA | 20 days |
| NESİLLER RISK | BRCA1 and BRCA2 analysis with MLPA | 20 days |
| NESİLLER RISK | MEN1 Gene Sequence Analysis (multiple endocrin neoplasia of type 1) | 20 days |
| NESİLLER RISK | MLH1 Gene Sequence Analysis (Susceptibility to colon cancer) | 20 days |
| NESİLLER RISK | MSH2 Gene Sequence Analysis (Susceptibility to colon cancer) | 20 days |
| NESİLLER RISK | P16 Gene Sequence Analysis (Hereditary Melanoma) | 20 days |
| NESİLLER RISK | p53 Gene Sequence Analysis | 20 days |
| NESİLLER RISK | RET Proto oncogene Gene Sequence Analysis (Medullary Thyriod Carcinoma-MTC) | 20 days |
| NESİLLER RISK | CHEK2 DNA analysis - exon 9 and 10, Breast Cancer, Li-Fraumeni Syndrome Type II | 20 days |
