Molecular Pathology

• Abstract
• What is molecular pathology?
• What are Molecular Pathology Techniques?
• What is next-generation sequencing and what role does it play in cancer diagnosis and treatment?
• Molecular Pathology Test Result Turnaround Times
• What are the tests studied in our institution?
• Panels That Can Be Used In Solid Tumors
• Panels Used In Hematological Cancers
• Liquid Biopsy (Working With Circulating Tumor DNA in Blood) Panels
• İletişim ve Detaylı Bilgi

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What is molecular pathology?

Molecular pathology is a branch of medicine that examines molecular-level changes in cells and seeks to understand how these changes contribute to the formation of diseases. These alterations typically involve changes in DNA, RNA, proteins, and metabolites.

Molecular pathology is primarily used in the diagnosis of cancer and other diseases, employing molecular techniques to investigate various mutations, particularly in cancers. Among these techniques are molecular biology methods such as Polymerase Chain Reaction (PCR), Next Generation Sequencing (NGS), gene expression analysis, microarray technology, and genotype analysis.

Molecular pathology focuses on the causes and treatments of diseases. For example, understanding the molecular genetic mechanisms of cancer can aid in better diagnosing the disease, developing more effective treatments, and preventing the illness

 

 

What are Molecular Pathology Techniques?

Molecular pathology is used to understand the molecular-level causes and mechanisms of diseases, as well as for staging tumors and detecting genetic abnormalities (mutations) in tumors. Some commonly used techniques in molecular pathology include:

1. Polymerase Chain Reaction (PCR): It is a molecular biology technique that allows the amplification of a specific DNA segment to obtain billions of copies.

2. DNA Sequencing: It is a technology that reads the sequence of nucleotides (Adenine, Guanine, Cytosine, Thymine) that make up DNA. This technology is used for identifying mutations in genes. Pyrosequencing, Sanger sequencing, and Next Generation Sequencing (NGS) are methods used for this purpose.

3. FISH/CISH (Fluorescent/Chromogenic In Situ Hybridization): It is a technique that allows the identification of numerous genetic changes, especially chromosomal anomalies in cancer cells, using probes that adhere to the desired region in the genetic material (genome).

4. Comparative Genomic Hybridization (CGH)): This technique is used to detect genomic changes in cancer cells.

5. Immunohistochemistry: This technique allows the detection of the presence or level of sought-after proteins in cancer cells.

6. RNA Sequencing: It is a technology that enables the determination of gene expression.

7. Microsatellite Instability (MSI): This test is used to detect specific DNA damage in cancer cells.

8. Methylation Tests: This test enables the determination of DNA methylation levels, which is one of the epigenetic changes in cancer cells.

9. Liquid biopsy (ctDNA / circulating tumor cell): ctDNA (circulating tumor DNA) is formed as a result of DNA fragments released from cancer cells entering the bloodstream. ctDNA is a molecular biomarker used to determine the presence or progression of cancer. ctDNA analysis can be combined with Next Generation Sequencing (NGS) technology to comprehensively characterize the genetic structure of cancer and monitor the response to treatment.

All of these investigative methods play a crucial role in cancer diagnosis and treatment. For example, the PCR technique can be used to detect the presence of specific genetic mutations. FISH can be utilized to identify genomic changes in cancer cells. Immunohistochemistry is used for identifying proteins in cancer cells. The coordination between Medical Oncology specialists and pathology experts in Molecular Pathology determines which test or priority should be given based on the patient's needs. The use of these tests enables a more precise and personalized approach to cancer diagnosis, prognosis, and treatment.

 

What is next-generation sequencing and what role does it play in cancer diagnosis and treatment?

In today's context, Next Generation Sequencing (NGS) has become a significant tool in cancer diagnosis and treatment. Cancer is a disease that arises from the accumulation of various types of mutations in DNA. These mutations can not only be the cause of cancer but can also be used to determine which treatment may be more effective for a particular cancer. NGS technology is used to identify genetic mutations in cancer cells.

NGS has become a crucial tool in cancer diagnosis, determining the characteristics of cancer, and predicting the course of the disease. Determining the genomic profile of cancer cells provides more detailed information about the type, stage, and genetic structure of cancer. This, in turn, assists in developing a more targeted approach to cancer treatment.

For example, certain types of cancer are associated with specific gene mutations. NGS allows for a rapid and simultaneous examination of numerous gene mutations in cancer cells, helping to detect the presence of specific mutations. This information can aid in determining whether the disease will respond to a particular treatment or if a more aggressive approach is necessary. This knowledge can contribute to the development of a more personalized approach to cancer treatment.

Additionally, the analysis of the genomic profile of cancer cells can be used to predict the progression of cancer. This also helps in predicting the course of the disease in advance, facilitating the planning of a more appropriate treatment.

NGS can also assist in identifying significant issues such as drug resistance in cancer cells. This information may contribute to the development of more effective drug combinations or new treatment strategies in cancer treatment.

In conclusion, NGS is an effective tool used in cancer diagnosis and treatment. The analysis of the genomic profile of cancer cells helps to determine the characteristics of the disease in more detail, aiding in the development of a more personalized and effective treatment approach.

 

Molecular Pathology Test Result Turnaround Times

The turnaround times for molecular pathology tests can vary depending on the type of test, the laboratory workload, the number of samples to be tested, and the patient's condition. Some molecular pathology tests are rapid tests that allow results to be obtained within a few hours. However, certain tests, due to their complex and multi-step workflow, may take a longer time. The completion of these tests can sometimes take several weeks, but during this period, you can contact our department to inquire about the progress of the testing processes. Our technical team and physicians are available for consultation, providing information on the status of the test procedures.

The results of molecular pathology tests should be interpreted by a pathologist or a molecular pathologist. This interpretation demonstrates how the test results are correlated with the patient's condition and how they can be used in planning treatment. The results can play a crucial role in making decisions regarding the patient's treatment. Therefore, even if the results of molecular pathology tests are obtained quickly, careful attention is required for the accurate interpretation of the results.

What are the tests studied in our institution?

Real-time PCR-Based Tests

• KRAS and NRAS mutation analyses
  • These are conducted in some cancer types, particularly colorectal cancers. Results can be obtained within 1-3 days.
• EGFR mutation analysis
  • These are conducted in some cancer types, primarily lung cancer. Results can be obtained within 1-3 days.
• BRAF mutation analysis
  • This study is performed in numerous cancer types, with a focus on malignant melanoma. Results can be obtained within 1-3 days.
• High-risk HPV genotyping
  • It can assess the presence of Human Papillomavirus (HPV) in cervical smear samples, anal smear samples, or tissue samples that could lead to cancer. This test evaluates the presence of 14 different HPV types simultaneously (16, 18, 45, 31, 51, 52, 33/58, 56/59/66, 35/39/68).

Immunohistochemistry-Based Tests

• ALK immunohistochemistry
  • This is a rapid and practical test to assess ALK gene fusion in lung cancers. Results can be obtained within 1-3 days.
• ROS immunohistochemistry
  • This is a rapid and practical test to assess ROS1 gene fusion in lung cancers. Results can be obtained within 1-3 days.
• BRAF V600E immunohistochemistry
  • This is a rapid and practical test to assess BRAF V600E mutation in many different cancer types. Results can be obtained within 1-3 days.
• Pan- TRK immunohistochemistry
  • This is a rapid and practical test to assess NTRK1-2-3 fusion in many different cancer types. Results can be obtained within 1-3 days.
• PDL1 immunohistochemistry (Ventana SP142, Ventana SP263, DAKO 22C3)
  • It is used to assess PDL1 expression in many different types of cancer. Based on the test results, a decision can be made regarding the patient's suitability for immunotherapy. In our department, three different PDL1 antibodies associated with immunotherapy (Ventana SP142, Ventana SP263, DAKO 22C3) are utilized. Results can be obtained within 1-3 days.

FISH/CISH-Based Tests

• HER2/c-erbB2
  • It is a rapid and practical test to assess HER2 gene amplification in various cancer types, including breast cancer and gastroesophageal cancer. Results can be obtained within 1-3 days.
• EBER (EBV Test)
  • It is a rapid and practical test conducted to assess the presence of Epstein-Barr Virus (EBV) in many types of lymphomas. Results can be obtained within 1-3 days.

NGS / Next Generation Sequencing-Based Tests

There are three main categories: panels used in mass-forming cancers, panels used in hematologic tumors, and liquid biopsies.

Panels That Can Be Used In Solid Tumors

-          Lung Cancer Panel

Over 70 genes, including EGFR, ALK, ROS1, KRAS, MET, RET, HER2, BRAF, and STK11 recommended for evaluation in lung cancers, are assessed. Both RNA and DNA are isolated from tumor tissue, and the study progresses in parallel through two channels.

Genes assessed in the test include:

i.        Fusion-evaluated genes: ALK, AXL, BRAF, CCND1, EGFR, FGFR1, FGFR2, FGFR3, MET, NRG1, NTRK1, NTRK2, NTRK3, PPARG, RAF1, RET, ROS1, THADA

ii.       Genes evaluated for SNV and InDel: ABL1, AKT1, ALK, APC, ATM, AURKA, BRAF, CCND1, CCNE1, CDH1, CDK4, CDKN2A, CSF1R, CTNNB1, DDR2, EGFR, ERBB2, ERBB3, ERBB4, ESR1, EZH2, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, FOXL2, GNA11, GNAQ, GNAS, H3F3A, HNF1A, HRAS, IDH1, IDH2, JAK2, JAK3, KDR, KIT, KRAS, MAP2K1, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PIK3R1, PTEN, PTPN11, RB1, RET, RHOA, ROS1, SMAD4, SMARCB1, SMO, SRC, STK11, TERT, TP53, VHL

iii.     Genes evaluated for copy number changes: ABL1, ALK, APC, ATM, AURKA, CCND1, CCNE1, CDH1, CDK4, CDKN2A, DDR2, EGFR, ERBB2, ERBB3, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNAS, JAK2, JAK3, KDR, KIT, KRAS, MDM2, MET, MYC, MYCN, MLH1, MPL, NOTCH1, NRAS, PDGFRA, PIK3CA, PIK3R1, PTEN, RB1, RET, SMAD4, SMARCB1, SMO, STK11, TP53, VHL

iv.     Genes evaluated for expression: ALK, AXL, BRAF, CALCA, CCND1, EGFR, FGFR1, FGFR2, FGFR3, KRT20, KRT7, MET, NTRK1, NTRK2, NTRK3, PTH, RET, ROS1, SLC5A5, THADA, TTF1


-          Colorectal Cancer Panel

For colon and rectum cancers, over 60 genes, including KRAS, NRAS, HER2, BRAF, are recommended for evaluation. The study is conducted using DNA isolated from tumor tissue.

Genes assessed in the test include:

i.       Genes evaluated for SNV and InDel: ABL1, AKT1, ALK, APC, ATM, AURKA, BRAF, CCND1, CCNE1, CDH1, CDK4, CDKN2A, CSF1R, CTNNB1, DDR2, EGFR, ERBB2, ERBB3, ERBB4, ESR1, EZH2, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, FOXL2, GNA11, GNAQ, GNAS, H3F3A, HNF1A, HRAS, IDH1, IDH2, JAK2, JAK3, KDR, KIT, KRAS, MAP2K1, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PIK3R1, PTEN, PTPN11, RB1, RET, RHOA, ROS1, SMAD4, SMARCB1, SMO, SRC, STK11, TERT, TP53, VHL

ii.       Genes evaluated for copy number changes: ABL1, ALK, APC, ATM, AURKA, CCND1, CCNE1, CDH1, CDK4, CDKN2A, DDR2, EGFR, ERBB2, ERBB3, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNAS, JAK2, JAK3, KDR, KIT, KRAS, MDM2, MET, MYC, MYCN, MLH1, MPL, NOTCH1, NRAS, PDGFRA, PIK3CA, PIK3R1, PTEN, RB1, RET, SMAD4, SMARCB1, SMO, STK11, TP53, VHL

 
-          Breast Cancer Panel

For breast cancers, over 60 genes, including PIK3CA, ESR1, HER2, are recommended for evaluation. The study is conducted using DNA isolated from tumor tissue.

Genes assessed in the test include:

-          Genes evaluated for SNV and InDel: ABL1, AKT1, ALK, APC, ATM, AURKA, BRAF, CCND1, CCNE1, CDH1, CDK4, CDKN2A, CSF1R, CTNNB1, DDR2, EGFR, ERBB2, ERBB3, ERBB4, ESR1, EZH2, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, FOXL2, GNA11, GNAQ, GNAS, H3F3A, HNF1A, HRAS, IDH1, IDH2, JAK2, JAK3, KDR, KIT, KRAS, MAP2K1, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PIK3R1, PTEN, PTPN11, RB1, RET, RHOA, ROS1, SMAD4, SMARCB1, SMO, SRC, STK11, TERT, TP53, VHL

-          Genes evaluated for copy number changes: ABL1, ALK, APC, ATM, AURKA, CCND1, CCNE1, CDH1, CDK4, CDKN2A, DDR2, EGFR, ERBB2, ERBB3, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNAS, JAK2, JAK3, KDR, KIT, KRAS, MDM2, MET, MYC, MYCN, MLH1, MPL, NOTCH1, NRAS, PDGFRA, PIK3CA, PIK3R1, PTEN, RB1, RET, SMAD4, SMARCB1, SMO, STK11, TP53, VHL

-          Thyroid Cancer Panel

For thyroid cancers, over 70 genes, including BRAF, RET, KRAS, NRAS, TERT, and RET, are recommended for evaluation. Both gene fusions and other mutations can be detected. Both RNA and DNA are isolated from tumor tissue, and the study progresses in parallel through two channels.

Genes assessed in the test include:

-          Fusion-evaluated genes: ALK, AXL, BRAF, CCND1, EGFR, FGFR1, FGFR2, FGFR3, MET, NRG1, NTRK1, NTRK2, NTRK3, PPARG, RAF1, RET, ROS1, THADA

-          Genes evaluated for SNV and InDel: ABL1, AKT1, ALK, APC, ATM, AURKA, BRAF, CCND1, CCNE1, CDH1, CDK4, CDKN2A, CSF1R, CTNNB1, DDR2, EGFR, ERBB2, ERBB3, ERBB4, ESR1, EZH2, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, FOXL2, GNA11, GNAQ, GNAS, H3F3A, HNF1A, HRAS, IDH1, IDH2, JAK2, JAK3, KDR, KIT, KRAS, MAP2K1, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PIK3R1, PTEN, PTPN11, RB1, RET, RHOA, ROS1, SMAD4, SMARCB1, SMO, SRC, STK11, TERT, TP53, VHL

-          Genes evaluated for copy number changes: ABL1, ALK, APC, ATM, AURKA, CCND1, CCNE1, CDH1, CDK4, CDKN2A, DDR2, EGFR, ERBB2, ERBB3, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNAS, JAK2, JAK3, KDR, KIT, KRAS, MDM2, MET, MYC, MYCN, MLH1, MPL, NOTCH1, NRAS, PDGFRA, PIK3CA, PIK3R1, PTEN, RB1, RET, SMAD4, SMARCB1, SMO, STK11, TP53, VHL

-          Genes evaluated for expression: ALK, AXL, BRAF, CALCA, CCND1, EGFR, FGFR1, FGFR2, FGFR3, KRT20, KRT7, MET, NTRK1, NTRK2, NTRK3, PTH, RET, ROS1, SLC5A5, THADA, TTF1

-          Sarcoma Panel

This panel allows for the detection of diagnostic, known, or previously unidentified new fusions in sarcomas.  It can simultaneously assess over 60 genes, including EWSR1, FOXO1, NTRK1/2/3. Test results identify specific gene mutations in the tumor, providing crucial information not only for specific diagnostic approaches but also for treatment options tailored to the patient's cancer.

Genes assessed in the test include:

-          Fusion-evaluated genes: ALK, BCOR, BRAF, CAMTA1, CIC, CSF1, EGFR, EPC1, ERG, ESR1, EWSR1, FGFR1, FGFR2, FGFR3, FOS, FOSB, FOXO1, FUS, GLI1, HMGA2, JAZF1, MDM2, MEAF6, MET, MGEA5, MKL2, NCOA1, NCOA2, NR4A3, NTRK1, NTRK2, NTRK3, NUTM1, PAX3, PDGFB, PHF1, PLAG1, PRKCA, PRKCB, PRKCD, RET, ROS1, SS18, STAT6, TAF15, TCF12, TFE3, TFG, USP6, YAP1, YWHAE

-          Other Solid Tumors Panel (Excluding tumors listed above)

It is a panel that can be used in many types of solid tumors. The panel assesses nearly 100 genes, including almost all known genes associated with targeted therapies. Both RNA and DNA are isolated from tumor tissue, and the study progresses in parallel through two channels.
 

-          Homologous Recombination Repair Genes Panel

This panel is a DNA-based test that can simultaneously assess mutations in 16 genes involved in DNA repair mechanisms. Test results identify specific gene mutations in the tumor, providing crucial information, especially regarding whether the patient would benefit from specific cancer treatment options, such as PARP inhibitors (PARPi).

Genes assessed in the test include:

i.     ATM, BARD1, BRCA1, BRCA2, BRIP1, CDK12, CHEK1, CHEK2, FANCL, PALB2, PPP2R2A, RAD51B, RAD51C, RAD51D, RAD54L VE TP53

-          Comprehensive Genomic Profiling Version 1

This panel is a DNA-based test that can simultaneously assess mutations in 324 genes. Test results identify specific gene mutations in the tumor, providing crucial information about personalized treatment options for the patient's cancer. This test evaluates mutations in 324 genes and also assesses:

• Microsatellite instability (MSI, one of the parameters used to predict immunotherapy response),
• Genomic heterozygous loss (gLOH, one of the parameters used to determine PARP inhibitor response),
• Tumor Mutation Burden (TMB, one of the parameters used to predict immunotherapy response).

Genes assessed in the test include:

 

 

- Comprehensive Genomic Profiling Version 2

 

This panel is an RNA and DNA-based test that can simultaneously assess mutations in 523 genes. Test results identify specific gene mutations in the tumor, providing crucial information about personalized treatment options for the patient's cancer. This test evaluates mutations in 523 genes and also assesses:

• Microsatellite instability (MSI, one of the parameters used to predict immunotherapy response),
• Tumor Mutation Burden (TMB, one of the parameters used to predict immunotherapy response).

 

  Genes assessed in the test include:

  

Panels Used In Hematological Cancers

-          Lymphoma Panel

1. This panel, with the starting material being RNA isolated from the tumor, covers the majority of fusions and other mutations observed in lymphomas. It can also be used to acquire RNA expression information for many genes. A total of 125 genes are evaluated. Blood, bone marrow aspirate, or biopsy material can be used.
   Genes assessed in the test include:
   i.          Fusion-evaluated genes: ALK, BCL2, BCL6, BCR, BIRC3, CBFB, CCND1, CCND3, CDK6, CHIC2, CIITA, CREBBP, DEK, DUSP22, EIF4A1, ETV6, FGFR1, JAK2, KMT2A, MALT1, MKL1, MLF1, MLLT10, MYC, NFKB2, NOTCH1, NOTCH1, P2RY8, PDCD1LG2, PDGFRA, PRDM16, STIL, TCF3, TP63
   ii.         Genes evaluated for SNV, InDel, and exon skipping mutations: AKT3, ALK, BAX, BCL2, BIRC3, BRAF, BTK, CARD11, CCND1, CD79B, CREBBP, DNMT3A, ETV6, EZH2, FBXW7, IDH1, IDH2, JAK1, JAK2, JAK3, KRAS, MYD88, NOTCH1, NOTCH1, NOTCH2, NRAS, PDGFRA, PLCG1, PLCG2, RHOA, SF3B1, STAT3, STAT5B, STAT6, WT1, XPO1
   iii.        Genes evaluated for expression: AICDA, ASB13, BATF3, BCL2, BCL2A1, BCL3, BCL6, BLNK, BMF, BMP7, CCDC50, CCND1, CCND2, CCND3, CD274, CD44, CDC25A, CDKN2A, CDKN2B, CEBPD, CEBPE, CEBPG, CREB3L2, CTLA4, CYB5R2, DENND3, DLEU1, DNMT3B, DNTT, E2F2, ENTPD1, EXOC2, FAM216A, FOXP1, FUT8, IL16, IRF4, IRF8, ITPKB, KIAA0101, LIMD1, LMO2, LRMP, LZTS1, MAL, MAML3, MME, MUC1, MYBL1, MYC, NEK6, NFKB1, NME1, PAICS, PDCD1, PDCD1LG2, PIM1, PIM2, PPAT, PRKAR2B, PTPN1, PYCR1, RAB29, RAG1, RAG2, RANBP1, S1PR2, SERPINA9, SH3BP5, STRBP, TNFRSF13B, TNFSF4, WT1
    

   
   -          Myeloid Leukemia Panel

   Fusions and mutations observed in myeloid neoplasms, including chronic myeloid leukemia (CML), are evaluated. Both RNA and DNA are isolated from the tumor, and the study progresses in parallel through two channels. Blood, bone marrow aspirate, or biopsy material can be used.

   i.       Fusion-evaluated genes: ABL1, BCR, CBFB, CHD1, CHIC2, CREBBP, CSF1R, ERG, ETV6, FGFR1, GLIS2, IKZF1, IKZF3, JAK2, KAT6A, KMT2A, MECOM, MKL1, MLLT10, MLLT4, MYC, MYH11, NF1, NOTCH1, NUP214, NUP98, PDCD1LG2, PDGFRA, PDGFRB, PICALM, PML, RBM15, ROS1, RUNX1, RUNX1T1, SETD2, TCF3, TFG

   ii.       Genes evaluated for SNV and InDel: ABL1, ANKRD26, AKT3, ASXL1, BCOR, BRAF, CALR, CBL, CEBPA, CREBBP, CSF3R, DCK, DDX41, DNM2, DNMT3A, ETNK1, ETV6, EZH2, FBXW7, FGFR2, FGFR3, FLT3, GATA1, GATA2, GNAS, IDH1, IDH2, IKZF3, JAK1, JAK2, JAK3, KDM6A, KIT, KRAS, MPL, MYD88, NOTCH1, NPM1, NRAS, PDGFRA, PHF6, PML, PTPN11, RARA, RUNX1, SETBP1, SF3B1, SLC29A1, SRSF2, STAG2, TET2, TP53, U2AF1, WT1, XPO1, ZRSR2

   iii.       Genes evaluated for expression: ABL1, CEBPA, CTLA4, FLT3, ID4, IRF4, IRF8, MECOM, MUC1, MYC, MYH11, PDCD1, PDCD1LG2, RARA, ROS1, RUNX1, RUNX1T1, WT1

    

   
   -          Acute Lymphoblastic Leukemia (ALL) Panel

   This panel, with the starting material being RNA, covers the majority of fusions and other mutations observed in acute lymphoblastic leukemias. It can also be used to acquire RNA expression information for many genes. A total of 81 genes can be evaluated. Blood, bone marrow aspirate, or biopsy material can be used.

   i.      Fusion-evaluated genes: ABL1, ABL2, BCL11B, BCL2, BCL6, BCR, EBF1, EPOR, ETV6, FGFR1, IKZF1, IKZF2, IKZF3, JAK2, KLF2, KMT2A, MLLT4, MYC, NF1, NOTCH1, NTRK3, NUP214, NUP98, P2RY8, PAG1, PAX5, PBX1, PDCD1LG2, PDGRFA, PDGFRB, PICALM, PTK2B, RUNX1, SEMA6A, SETD2, STIL, TAL1, TCF3, TYK2, ZCCHC7, CHD1, CREBBP, CRLF2, CSF1R

   ii.       Genes evaluated for SNV and InDel: ABL1, BCL2, ETV6, EZH2, FBXW7, FLT3, IDH1, IDH2, IKZF3, IL7R, JAK1, JAK2, JAK3, KDM6A, KRAS, MLP, NOTCH1, NRAS, NT5C2, PAX5, PDGFRA, PTPN11, SH2B3, STAT3, STAT5B, TYK2, WT1, CREBBP, CRLF2, CSF1R, DNM2

   iii.     Genes evaluated for expression: ABL1, AICDA, BCL2, BCL6, BLNK, DNTT, FLT3, HOXA10, HOXA9, IRF4, IRF8, LMO1, LYL1, MYC, NTRK3, PDCD1, PDCD1LG2, RAG1, RAG2, RUNX1, SOX11, TAL1, TLX1, TLX3, WT1CD274, CRLF2, CSF1R, CTLA4

   
   
   -          Comprehensive Hematology Panel

   This panel, with the starting material being RNA, covers a significant portion of fusions and other mutations observed in all hematopoietic neoplasms (leukemias and lymphomas). It can also be used to acquire RNA expression information for many genes. A total of 199 genes are evaluated. Blood, bone marrow aspirate, or biopsy material can be used.

   Genes assessed in the test include:

   i.      Fusion-evaluated genes: ABL1, ABL2, ALK, BCL11B, BCL2, BCL6, BCR, BIRC3, CBFB, CCND1, CCND3, CDK6, CHD1, CHIC2, CIITA, CREBBP, CRLF2, CSF1R, DEK, DUSP22, EBF1, EIF4A1, EPOR, ERG, ETV6, FGFR1, GLIS2, IKZF2, IKZF3, JAK2, KAT6A, KLF2, KMT2A, MALT1, MECOM, MKL1, MLF1, MLLT10, MLLT4, MYC, MYH11, NF1, NFKB2, NOTCH1, NTRK3, NUP214, NUP98, P2RY8, PAG1, PAX5, PBX1, PDCD1L, PDGFRA, PDGFRB, PICALM, PML, PRDM16, PTK2B, RARA, RBM15, ROS1, RUNX1, RUNX1T1, SEMA6A, SETD2, STIL, TAL1, TCF3, TFG, TP63, TYK2, ZCCHC7.

   ii.     Genes evaluated for SNV and InDel: ABL1, AKT3, ALK, ASXL1, BAX, BCL2, BIRC3, BRAF, BTK, CALR, CARD11, CBL, CCND1, CD79B, CEBPA, CREBBP, CRLF2, CSF3R, DCK, DNM2, DNMT3A, ETV6, EZH2, FBXW7, FGFR2, FGFR3, FLT3, GATA1, GATA2, GNAS, IDH1, IDH2, IKZF1, IKZF3, IL7R, JAK1, JAK2, JAK3, KDM6A, KIT, KRAS, MPL, MYD88, NOTCH1, NOTCH2, NPM1, NRAS, NT5C2, PAX5, PDGFRA, PHF6, PLCG1, PLCG2, PML, PTPN11, RARA, RHOA, SETBP1, SF3B1, SH2B3, SLC29A1, SRSF2, STAT3, STAT5B, STAT6, TYK2, U2AF1, WT1, XPO1

   iii.      Genes evaluated for expression: AICDA, ASB13, BATF3, BCL2, BCL2A1, BCL3, BCL6, BLNK, BMF, BMP7, CCDC50, CCND1, CCND2, CCND3, CD274, CD44, CDC25A, CDKN2A, CDKN2B, CEBPA, CEBPD, CEBPE, CEBPG, CREB3L2, CRLF2, CTLA4, CYB5R2, DENND3, DLEU1, DNMT3B, DNTT, E2F2, ENTPD1, EXOC2, FAM216A, FLT3, FOXP1, FUT8, HOXA10, HOXA10, HOXA9, ID4, IL16, IRF4, IRF8, ITPKB, KIAA0101, LIMD1, LMO1, LMO2, LRMP, LYL1, LZTS1, MAL, MAML3, MECOM, MME, MUC1, MYBL1, MYC, MYH11, NEK6, NFKB1, NME1, NTRK3, PAICS, PDCD1, PDCD1L G2, PIM1, PIM2, PPAT, PRKAR2 B, PTPN1, PYCR1, RAB29, RAG1, RAG2, RANBP1, RUNX1, S1PR2, SERPINA, SH3BP5, SOX11, STRBP, TAL1, TLX1, TLX3, TNFRSF1, TNFSF4, WT1

Liquid Biopsy (Working With Circulating Tumor DNA in Blood) Panels

-          Liquid Biopsy Panel

This panel, with the starting material being circulating free DNA molecules isolated from blood, covers mutations observed in many types of solid tumors (lung, colon, breast, melanoma, etc.). A total of 28 genes are evaluated in this panel.
 
Genes assessed in the test include:  
   

-          Comprehensive Liquid Biopsy Panel

This panel, with the starting material being circulating free DNA molecules isolated from blood, covers mutations observed in many types of solid tumors (lung, colorectal, breast, melanoma, etc.). It also includes fusions and copy number changes in certain genes (ALK, ROS1, NTRK1, FGFR2, FGFR3). A total of 77 genes are evaluated in this panel.

Genes assessed in the test include:

 

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